Introduction: multiple myeloma definition
Multiple myeloma (MM) is a clonal plasma cell malignancy characterized by overproduction of monoclonal immunoglobulins (M-proteins) [ 1 ]. This expansion is accompanied by suppression of normal immunoglobulin synthesis and progressive marrow infiltration, which underlies disease pathophysiology.
MM represents the second most common hematological malignancy and accounts for 15% of newly diagnosed hematologic cancers and nearly 20% of related mortality. Incidence in Western populations is 5–7 cases per 100,000 persons per year, with a median diagnostic age near 70 years, underscoring its strong age association [ 2 ]. Incidence rises steeply with age [ 3 ].
Clinically, MM is defined by bone marrow infiltration and end-organ damage. Key features include clonal plasma cell proliferation, monoclonal protein production, and organ dysfunction, most frequently involving bone, hematopoiesis, and renal function. Typical manifestations include osteolytic lesions, anemia, hypercalcemia, and renal dysfunction. Diagnostic criteria require ≥10% clonal plasma cells in the bone marrow or biopsy-proven plasmacytoma plus monoclonal protein and myeloma-defining events [ 4 ].
The etiological basis of MM remains incompletely defined, but accumulating evidence indicates a substantial genetic component. Epidemiological studies have demonstrated a 2- to 4-fold increased risk among first-degree relatives of MM patients [ 5 ], supporting inherited susceptibility and motivating investigation into somatic and germline genetic determinants.
Over the past two decades, therapeutic advances have transformed MM management. Proteasome inhibitors (PIs) and immunomodulatory drugs (IMiDs) have improved overall survival (OS) across successive therapeutic eras [ 6 ]. Current treatment paradigms favor combination regimens integrating PIs and IMiDs for newly diagnosed disease. MM is therefore increasingly managed as a chronic, although still incurable, malignancy. Despite this progress, MM remains largely incurable, mainly due to intrinsic and acquired drug resistance. Clinical and molecular studies show that relapse in nearly universal. Therapeutic refractoriness drives progression and mortality [ 7 ].
At the biological level, resistance arises from multiple mechanisms, including genomic instability, epigenetic alterations, defective apoptotic signaling, immune system dysregulation, and protective interactions between malignant plasma cells and the bone marrow microenvironment [ 8 ]. High-throughput molecular profiling has improved the characterization of resistance mechanisms and strengthened risk stratification, supporting biologically informed treatment selection and the development of mechanism-based therapeutic strategies [ 9 ].
Altogether, these advances support biomarker-driven, risk-adapted therapeutic strategies [ 10 ].
While previous reviews have typically addressed germline susceptibility and somatic evolution in MM as separate domains, or have focused on static descriptions of genomic alterations, this work advances an integrated evolutionary genomics framework that conceptualizes disease initiation and progression as a continuous, multilayered process shaped by inherited genetic background, early clonal selection, and therapy-driven dynamics. By moving beyond a binary germline-versus-somatic perspective, this apporach captures the temporal and biological continuity underlying progression from precursor states to symptomatic disease. Importantly, it provides a clinically oriented scaffold for integrating emerging approaches, such as polygenic risk scores and subclonal reconstruction, into unified models for risk stratification, longitudinal disease monitoring, and treatment adaptation. In this way, the proposed framework not only synthesizes existing knowledge but also offers a conceptual basis for translating genomic complexity into actionable precision oncology strategies.
In this review, we synthesize current evidence supporting this model and discuss its implications for precision oncology in MM.
Risk factors and genetic predisposition
Building on the biological and clinical approach outlined above, MM is recognized as a multifactorial disease arising from the combined effects of aging, environmental exposures, precursor disease states, and inherited genetic susceptibility. These factors interact to shape disease initiation, clonal evolution, and clinical heterogeneity. Epidemiological and molecular studies have identified several determinants that modulate individual risk of disease initiation, progression, and clinical presentation. Together, these determinants inform risk stratification and screening strategies.
Environmental and clinical risk factors
Demographic and population-level determinants
Age represents the strongest independent risk factor for MM. Incidence rises sharply after age 50, peaking around 65, consistent with cumulative mutational burden and immune aging. Forecast models project a marked rise in incident cases over the coming decades. Age is therefore a fundamental component of risk stratification, particularly for screening and early intervention in precursor conditions. Notably, although age is strongly associated with disease incidence, evidence regarding its relationship with specific genomic subtypes remains conflicting. Some studies have reported a higher frequency of IgH translocations, particularly t(4;14), in older patients [ 11 ], whereas others have observed lower rates of these high-risk events in elderly-onset disease, together with distinct mutational profiles and fewer MYC rearrangements [ 12 ]. These discrepancies likely reflect differences in cohort composition, sample size, and analytical approaches, and suggest that age-related differences in genomic architecture and evolutionary trajectories remain incompletely defined.
Consistent sex-related differences in MM incidence have been reported across population registries, with a modest but reproducible male predominance observed worldwide [ 13 ]. Male-to-female incidence ratios range between 1.2:1 and 1.5:1 across diverse geographic regions [ 14 ]. Large population-based datasets confirm that approximately 55–57% of cases occur in men [ 15 ].
MM exhibits significant racial disparities, with African Americans experiencing approximately twice the incidence observed in white populations [ 16 ]. Greenberg et al. proposed that this disparity reflects a higher prevalence of monoclonal gammopathy of undetermined significance (MGUS) rather than increased malignant progression [ 17 ]. This interpretation is supported by more recent large-scale analyses, which show no evidence of differences in progression rates from MGUS to MM across racial groups, indicating that disparities are primarily driven by differences in disease initiation [ 18 ]. These findings reinforce a model in which population-level differences in MGUS prevalence, rather than accelerated progression, account for the higher incidence observed in individuals of African ancestry. Population-level differences have also been described in Chinese cohorts, where patients are diagnosed at a younger median age (∼59 years) and often present with higher disease burden [ 19 ]. Genomic analyses suggest partially distinct mutational landscapes compared with Western cohorts, including differences in NF-κB pathway alterations [ 19 ]. The biological basis of these demographic disparities remains incompletely defined.
Age also modifies prognosis. Increasing age is associated with inferior progression-free survival (PFS) and OS [ 20 ]. Age-stratified genomic analyses indicate shifts in lesion frequency, including distribution of high-risk IgH translocations and gain(1q) across age groups [ 21 ], supporting partially distinct evolutionary trajectories in elderly-onset disease.
Taken together, age, sex, and ancestry define a foundational demographic risk framework in MM. These variables inform population-level risk estimation and screening strategies.
Precursor conditions
Virtually all cases of MM are preceded by asymptomatic precursor conditions, primarily MGUS or smoldering MM (SMM). Epidemiological evidence indicates that MGUS affects approximately 3.2% of individuals older than 50 years, with an average annual progression rate to MM of about 1% [ 22 ]. Progression risk is strongly influenced by monoclonal protein burden, bone marrow infiltration, and genetic background [ 23 ].
SMM is associated with a substantially elevated risk of progression to overt MM, particularly during the first five years following diagnosis [ 24 ]. Solitary plasmacytoma also carries a significant risk of progression to systemic disease. These precursor states define biologically and clinically identifiable high-risk populations.
Environmental, occupational, lifestyle and clinical modifiers
Environmental and occupational exposures are associated with MM susceptibility in multiple epidemiological studies. Meta-analyses report elevated risk in selected occupational groups, including firefighters, who exhibit nearly a 50% increased risk, and hairdressers, with approximately a 40% higher risk [ 25 ]. Farming populations likewise show elevated incidence, particularly in contexts involving pesticide exposure [ 26 ].
At the exposure level, pesticides, herbicides, organic solvents, and petroleum-derived products have been associated with increased MM risk [ 27 ]. Proposed mechanisms include genotoxic stress, chronic inflammation, and DNA damage.
Lifestyle-related factors
Lifestyle factors influence MM risk largely through effects on precursor plasma cell disorders, with obesity emerging as the most consistent modifiable contributor. Obesity has been strongly associated with increased MGUS and MM risk, with reported odds ratios in the range of approximately 1.7–2.0 [ 28 , 29 ]. This association likely reflects chronic inflammatory and metabolic dysregulation.
Large prospective cohort analyses demonstrate a clear dose-dependent association between body mass index (BMI) and MM incidence, with a 17% increase in risk per 5 kg/m² increment in cumulative average adult BMI and a 28% increase per 5 kg/m² rise in young adult BMI [ 29 ]. Obesity has also been associated with inferior clinical outcomes [ 30 ]. Proposed mechanisms include IGF-1 pathway activation, adipokine imbalance, inflammatory cytokine signaling, and adipocyte-stromal interactions. In contrast, tobacco smoking shows no consistent association with MM incidence in large meta-analyses [ 31 ]. However, heavy exposure has been associated with a 2.26-fold increased likelihood of MGUS [ 28 ].
Physical activity appears to exert a modest protective effect, although associations attenuate after adjustment for BMI [ 32 , 33 ].
Dietary patterns may further modulate susceptibility, with plant-based diets associated with lower MM risk [ 34 ]. Vitamin D deficiency has been linked to poorer clinical outcomes rather than disease initiation [ 35 ].
Clinical and immune-related comorbidities as modifying risk factors
Clinical comorbidities and immune-mediated conditions have been investigated as MM risk modifiers, with generally modest and heterogeneous associations. More recent meta-analyses suggest an increased risk, particularly for chronic HCV infection [ 36 , 37 ]. Clinical data further support a biologically relevant interaction between chronic viral infection and plasma cell dyscrasia, including potential modulation of disease progression following antiviral therapy [ 38 ]. Type 2 diabetes mellitus (T2D) shows inconsistent associations [ 39 ].
Emerging evidence implicates gut microbiota composition as a biological modifier of MM susceptibility and progression. Mendelian randomization analyses have identified taxa-specific causal associations, and mechanistic studies suggest that dysbiosis may promote disease progression through immune modulation, nitrogen-recycling pathways, and metabolic crosstalk within the bone marrow microenvironment [ 40 ]. Microbiota composition has been associated with treatment response and minimal residual disease (MRD) status [ 38 ].
Autoimmune diseases have been associated with increased susceptibility to MGUS and MM [ 41 ], supporting a role for chronic immune activation. However, large epidemiological analyses show heterogeneous and generally weak associations. Null or weak associations have been reported for primary Sjögren syndrome [ 42 ], ankylosing spondylitis [ 43 ], and rheumatoid arthritis [ 44 ], while findings in systemic lupus erythematosus are inconsistent. Pernicious anemia and ankylosing spondylitis show the most consistent associations with increased MM risk [ [41] , [43] ]. Interestingly, periodontitis, a chronic oral inflammatory disease, has also been linked to MM risk [ 45 ], suggesting a potential role for systemic inflammatory burden in oncogenesis ( Table 1 ). Table 1 Established and proposed risk factors and susceptibility modifiers in MM. Table 1 dummy alt text Risk factor Association with MM Quantitative estimate Disease stage affected Proposed mechanisms References Advanced age Strong increase in incidence with age Incidence rises exponentially after age 50; peak after 65 MM Accumulated somatic mutations, immune senescence, chronic inflammation [ 46 ] Male sex Higher incidence vs females Male:female ratio ∼1.2–1.5 MM Hormonal and immune modulation; cytogenetic subtype differences [ [13] , [47] ] African / African-American or Asian ancestry Higher incidence vs White populations Different mutational landscape and ∼2-fold higher incidence MGUS/MM Higher MGUS prevalence; genetic susceptibility contribution [ [16] , [17] , [19] , [48] , [49] , [50] ] MGUS Obligatory precursor condition Prevalence ∼3.2% (>50 yrs); progression ∼1%/year MGUS→MM Pre-malignant clonal plasma cell expansion [ [22] , [23] ] SMM High progression risk Highest risk within first 5 years SMM→MM Increased clonal burden and genomic instability [ 51 ] Family history (first-degree relatives) Increased risk ∼2–4-fold increased risk MGUS/MM Germline susceptibility variants; shared familial factors [ 52 , 53 ] Obesity / high BMI Increased MGUS and MM risk OR ∼1.7–2.0; +17% risk per 5 kg/m² adult BMI MGUS/MM Chronic inflammation, IGF-1 signaling, adipokine dysregulation [ 28 , 29 ] Occupational exposure Elevated risk Firefighters ∼+50%; hairdressers ∼+40% MM Chemical and combustion-related exposures [ 25 ] Pesticides / solvents / petroleum products Increased risk Association reported (no pooled estimate) MM Genotoxic stress, inflammatory signaling [ 27 ] Smoking No clear MM association Ever smoking RR/OR ∼0.92 MM No consistent effect observed [ 31 ] Heavy smoking Increased MGUS risk ∼2.26-fold increased likelihood MGUS Genotoxic and oxidative stress [ 28 ] T2D (clinical and genetic evidence) Modest/inconsistent epidemiological associations; genetic variants associated with MM risk Clinical OR ∼1.1–1.6 (observational); genetic variant OR up to ∼2.13 MM/MGUS Metabolic/inflammatory dysregulation; shared genetic susceptibility (Ríos et al., 2015; [ 39 ]) Chronic viral infections (HCV, HBV, HIV) Increased risk (stronger for HCV; modest for HBV); heterogeneity across studies HCV: RR 1.84; OR 2.67. HBV: RR 1.25 (borderline) MGUS/MM Chronic antigenic stimulation; sustained immune activation; B-cell proliferation; inflammatory microenvironment; potential modulation by antiviral therapy [ [37] , [54] , [55] , [56] ] Microbiome and dysbiosis Significant association with MM risk, progression, and treatment response; supported by genetic and mechanistic data MR: taxa-specific effects (e.g., OR ∼1.7 risk-increasing; protective taxa identified); MRD-negativity associated with higher Eubacterium hallii abundance MGUS/MM; disease progression; treatment response (MRD) Chronic immune modulation; nitrogen-recycling bacteria and glutamine metabolism; inflammatory signaling; tumor-microbiome metabolic crosstalk [ [38] , [40] , [57] , 58 ] Autoimmune disease Increased risk for specific disorders Significant associations for pernicious anemia and ankylosing spondylitis MM Chronic immune activation [ [43] , [59] ] Physical activity Possible protective effect Modest association after BMI adjustment MM Immune and inflammatory regulation [ 32 ] Plant-based dietary patterns Lower MM risk association Association reported MM Anti-inflammatory and metabolic effects [ [34] , [60] , 61 ] Vitamin D deficiency Associated with poorer outcomes Association reported MM outcomes Immune and bone metabolism pathways [ 35 ] Abbreviations: MM, multiple myeloma; MGUS, monoclonal gammopathy of undetermined significance; SMM, smoldering multiple myeloma; OR, odds ratio; BMI, body mass index; T2D, type 2 diabetes. Summary of epidemiological, clinical, lifestyle, and host-related factors associated with increased or modified risk of MGUS and MM. Effect sizes are approximate and derived from representative large cohort studies and meta-analyses cited in the main text. Evidence strength reflects overall consistency across studies rather than individual reports. Reported associations for some factors are heterogeneous across populations and study designs.
Table 1
Established and proposed risk factors and susceptibility modifiers in MM.
Abbreviations: MM, multiple myeloma; MGUS, monoclonal gammopathy of undetermined significance; SMM, smoldering multiple myeloma; OR, odds ratio; BMI, body mass index; T2D, type 2 diabetes. Summary of epidemiological, clinical, lifestyle, and host-related factors associated with increased or modified risk of MGUS and MM. Effect sizes are approximate and derived from representative large cohort studies and meta-analyses cited in the main text. Evidence strength reflects overall consistency across studies rather than individual reports. Reported associations for some factors are heterogeneous across populations and study designs.
| Risk factor | Association with MM | Quantitative estimate | Disease stage affected | Proposed mechanisms | References |
| Advanced age | Strong increase in incidence with age | Incidence rises exponentially after age 50; peak after 65 | MM | Accumulated somatic mutations, immune senescence, chronic inflammation | [ 46 ] |
| Male sex | Higher incidence vs females | Male:female ratio ∼1.2–1.5 | MM | Hormonal and immune modulation; cytogenetic subtype differences | [ [13] , [47] ] |
| African / African-American or Asian ancestry | Higher incidence vs White populations | Different mutational landscape and ∼2-fold higher incidence | MGUS/MM | Higher MGUS prevalence; genetic susceptibility contribution | [ [16] , [17] , [19] , [48] , [49] , [50] ] |
| MGUS | Obligatory precursor condition | Prevalence ∼3.2% (>50 yrs); progression ∼1%/year | MGUS→MM | Pre-malignant clonal plasma cell expansion | [ [22] , [23] ] |
| SMM | High progression risk | Highest risk within first 5 years | SMM→MM | Increased clonal burden and genomic instability | [ 51 ] |
| Family history (first-degree relatives) | Increased risk | ∼2–4-fold increased risk | MGUS/MM | Germline susceptibility variants; shared familial factors | [ 52 , 53 ] |
| Obesity / high BMI | Increased MGUS and MM risk | OR ∼1.7–2.0; +17% risk per 5 kg/m² adult BMI | MGUS/MM | Chronic inflammation, IGF-1 signaling, adipokine dysregulation | [ 28 , 29 ] |
| Occupational exposure | Elevated risk | Firefighters ∼+50%; hairdressers ∼+40% | MM | Chemical and combustion-related exposures | [ 25 ] |
| Pesticides / solvents / petroleum products | Increased risk | Association reported (no pooled estimate) | MM | Genotoxic stress, inflammatory signaling | [ 27 ] |
| Smoking | No clear MM association | Ever smoking RR/OR ∼0.92 | MM | No consistent effect observed | [ 31 ] |
| Heavy smoking | Increased MGUS risk | ∼2.26-fold increased likelihood | MGUS | Genotoxic and oxidative stress | [ 28 ] |
| T2D (clinical and genetic evidence) | Modest/inconsistent epidemiological associations; genetic variants associated with MM risk | Clinical OR ∼1.1–1.6 (observational); genetic variant OR up to ∼2.13 | MM/MGUS | Metabolic/inflammatory dysregulation; shared genetic susceptibility | (Ríos et al., 2015; [ 39 ]) |
| Chronic viral infections (HCV, HBV, HIV) | Increased risk (stronger for HCV; modest for HBV); heterogeneity across studies | HCV: RR 1.84; OR 2.67. HBV: RR 1.25 (borderline) | MGUS/MM | Chronic antigenic stimulation; sustained immune activation; B-cell proliferation; inflammatory microenvironment; potential modulation by antiviral therapy | [ [37] , [54] , [55] , [56] ] |
| Microbiome and dysbiosis | Significant association with MM risk, progression, and treatment response; supported by genetic and mechanistic data | MR: taxa-specific effects (e.g., OR ∼1.7 risk-increasing; protective taxa identified); MRD-negativity associated with higher Eubacterium hallii abundance | MGUS/MM; disease progression; treatment response (MRD) | Chronic immune modulation; nitrogen-recycling bacteria and glutamine metabolism; inflammatory signaling; tumor-microbiome metabolic crosstalk | [ [38] , [40] , [57] , 58 ] |
| Autoimmune disease | Increased risk for specific disorders | Significant associations for pernicious anemia and ankylosing spondylitis | MM | Chronic immune activation | [ [43] , [59] ] |
| Physical activity | Possible protective effect | Modest association after BMI adjustment | MM | Immune and inflammatory regulation | [ 32 ] |
| Plant-based dietary patterns | Lower MM risk association | Association reported | MM | Anti-inflammatory and metabolic effects | [ [34] , [60] , 61 ] |
| Vitamin D deficiency | Associated with poorer outcomes | Association reported | MM outcomes | Immune and bone metabolism pathways | [ 35 ] |
Familial aggregation and inherited susceptibility
Besides environmental and clinical determinants, inherited genetic susceptibility contributes substantially to MM risk. Evidence from familial aggregation studies, rare germline variant analyses, and large-scale GWAS indicates that both high-impact pathogenic variants and polygenic risk architectures contribute to disease predisposition [ 62 , 63 ]. These data support a complex inherited susceptibility landscape.
Familial clustering and epidemiological inheritance
A substantial heritable component underlies disease susceptibility, as evidenced by consistent familial clustering patterns and the two- to four-fold increased risk observed among first-degree relatives of affected individuals [ 5 , 64 ].
Germline alterations in DNA repair and genome maintenance pathways, including genes such as TP53 and BRCA1/2 , together with immune regulatory and telomere-associated genes ( DIS3, TNFRSF13B, TREX1, POT1 , and TERT ), have been implicated in familial cases [ 65 , 66 ]. Large cohort studies further demonstrate that pathogenic germline variants in DNA repair pathways are present in approximately 9.1% of sporadic MM cases and up to 18% of familial cases [ 67 ].
Rare pathogenic germline variants
Rare pathogenic germline variants (PGVs) are detected in approximately 5–30% of patients with MM, with a higher prevalence in familial and early-onset cases, predominantly affecting genes involved in DDR, telomere maintenance, and immune regulation [ [68] , [69] , [70] ].
High- and moderate-penetrance DDR genes, including TP53 (∼2–3%), PALB2, ATM, CHEK2 , and BRCA1/2 , are identified in 4–7% of unselected cohorts and promote defective homologous recombination and impaired p53-mediated apoptosis [ 70 ], thereby accelerating genomic instability. Recurrent alterations in telomere-related genes such as POT1 and TERT , observed in approximately 2–5% of familial MM cases, promote chromosomal fragility and clonal evolution, mirroring mechanisms described in other malignancies [ 65 ]. Variants in immune and B-cell regulatory genes, including TNFRSF13B / TACI and DIS3 , occur in approximately 3–15% of patients and disrupt plasma cell maturation and immune surveillance [ [66] , [67] , [71] ] ( Table 2 ). Table 2 Germline predisposition genes and pathways associated with MM susceptibility. Table 2 dummy alt text FUNCTIONAL CATEGORY GENE(S) BIOLOGICAL FUNCTION REPORTED ASSOCIATION IN MM CLINICAL / BIOLOGICAL RELEVANCE KEY REFERENCES DDR TP53 Genome surveillance, apoptosis control Rare pathogenic germline variants reported High-impact tumor suppressor pathway [ 64 , 70 ] DDR BRCA1, BRCA2 Homologous recombination repair Pathogenic germline variants detected in MM cohorts Homologous recombination deficiency context [ 67 , 70 ] DDR ATM DNA damage signaling kinase Recurrent germline variants reported Genome stability regulation [ 70 ] DDR CHEK2 Checkpoint kinase Germline variants reported Cell-cycle checkpoint control [ 70 ] DNA REPAIR / HR SUPPORT PALB2 HR repair partner of BRCA2 Germline variants reported HR pathway integrity [ 70 ] TELOMERE MAINTENANCE POT1 Telomere protection complex Recurrent familial MM variants Telomere dysfunction, chromosomal instability [ 65 ] TELOMERE MAINTENANCE TERT Telomerase catalytic subunit Familial predisposition variants reported Replicative immortality pathways [ 65 ] IMMUNE REGULATION / B-CELL SIGNALING TNFRSF13B (TACI) B-cell survival and NF-κB signaling Germline risk variants and GWAS signals Plasma cell survival signaling [ 71 , 72 ] IMMUNE REGULATION TREX1 DNA exonuclease, immune tolerance Predisposition variants reported Immune dysregulation context [ 65 ] RNA PROCESSING / EXOSOME DIS3 RNA exonuclease Germline and somatic variants reported Plasma cell regulatory pathways [ [66] , [71] ] EPIGENETIC REGULATION EP300 Histone acetyltransferase Rare germline susceptibility variants proposed IRF4/B-cell transcriptional control [ 73 ] KINASE SIGNALING PDPK1 PI3K pathway kinase Rare splice variants reported B-cell differentiation signaling [ 73 ] GWAS RISK LOCI CDCA7L MYC-related regulatory network Reproducible GWAS locus Transcriptional regulation [ 72 , 74 ] GWAS RISK LOCI CBX7 Chromatin regulation GWAS locus at 22q13.1 Tumor suppressor regulatory context [ 72 ] GWAS RISK LOCI ULK4 Autophagy-related signaling GWAS association region Regulatory variant cluster [ 72 ] GWAS RISK LOCI RFWD3 DNA repair / replication stress GWAS locus DDR pathway linkage [ 75 ] GWAS RISK LOCI CDKN2A Cell-cycle control GWAS locus Tumor suppressor pathway [ 75 ] Abbreviations: DDR, DNA damage response; HR, homologous recombination; GWAS, genome-wide association study. Representative genes and loci implicated through familial aggregation studies, pathogenic germline variant analyses, and genome-wide association studies. Listed genes map to recurrently implicated functional pathways including DNA damage response, telomere maintenance, immune regulation, RNA processing, epigenetic control, and cell-cycle regulation. The table summarizes representative loci.
Table 2
Germline predisposition genes and pathways associated with MM susceptibility.
Abbreviations: DDR, DNA damage response; HR, homologous recombination; GWAS, genome-wide association study. Representative genes and loci implicated through familial aggregation studies, pathogenic germline variant analyses, and genome-wide association studies. Listed genes map to recurrently implicated functional pathways including DNA damage response, telomere maintenance, immune regulation, RNA processing, epigenetic control, and cell-cycle regulation. The table summarizes representative loci.
| FUNCTIONAL CATEGORY | GENE(S) | BIOLOGICAL FUNCTION | REPORTED ASSOCIATION IN MM | CLINICAL / BIOLOGICAL RELEVANCE | KEY REFERENCES |
| DDR | TP53 | Genome surveillance, apoptosis control | Rare pathogenic germline variants reported | High-impact tumor suppressor pathway | [ 64 , 70 ] |
| DDR | BRCA1, BRCA2 | Homologous recombination repair | Pathogenic germline variants detected in MM cohorts | Homologous recombination deficiency context | [ 67 , 70 ] |
| DDR | ATM | DNA damage signaling kinase | Recurrent germline variants reported | Genome stability regulation | [ 70 ] |
| DDR | CHEK2 | Checkpoint kinase | Germline variants reported | Cell-cycle checkpoint control | [ 70 ] |
| DNA REPAIR / HR SUPPORT | PALB2 | HR repair partner of BRCA2 | Germline variants reported | HR pathway integrity | [ 70 ] |
| TELOMERE MAINTENANCE | POT1 | Telomere protection complex | Recurrent familial MM variants | Telomere dysfunction, chromosomal instability | [ 65 ] |
| TELOMERE MAINTENANCE | TERT | Telomerase catalytic subunit | Familial predisposition variants reported | Replicative immortality pathways | [ 65 ] |
| IMMUNE REGULATION / B-CELL SIGNALING | TNFRSF13B (TACI) | B-cell survival and NF-κB signaling | Germline risk variants and GWAS signals | Plasma cell survival signaling | [ 71 , 72 ] |
| IMMUNE REGULATION | TREX1 | DNA exonuclease, immune tolerance | Predisposition variants reported | Immune dysregulation context | [ 65 ] |
| RNA PROCESSING / EXOSOME | DIS3 | RNA exonuclease | Germline and somatic variants reported | Plasma cell regulatory pathways | [ [66] , [71] ] |
| EPIGENETIC REGULATION | EP300 | Histone acetyltransferase | Rare germline susceptibility variants proposed | IRF4/B-cell transcriptional control | [ 73 ] |
| KINASE SIGNALING | PDPK1 | PI3K pathway kinase | Rare splice variants reported | B-cell differentiation signaling | [ 73 ] |
| GWAS RISK LOCI | CDCA7L | MYC-related regulatory network | Reproducible GWAS locus | Transcriptional regulation | [ 72 , 74 ] |
| GWAS RISK LOCI | CBX7 | Chromatin regulation | GWAS locus at 22q13.1 | Tumor suppressor regulatory context | [ 72 ] |
| GWAS RISK LOCI | ULK4 | Autophagy-related signaling | GWAS association region | Regulatory variant cluster | [ 72 ] |
| GWAS RISK LOCI | RFWD3 | DNA repair / replication stress | GWAS locus | DDR pathway linkage | [ 75 ] |
| GWAS RISK LOCI | CDKN2A | Cell-cycle control | GWAS locus | Tumor suppressor pathway | [ 75 ] |
Clinically, PGVs are associated with younger age at diagnosis, increased familial cancer burden, and differential therapeutic responses, with drug-response associations reported for selected DDR alterations. Targeted enrichment strategies report higher PGV detection rates, supporting risk-adapted screening algorithms [ 68 ].
Polygenic susceptibility and GWAS architecture
Large-scale genome-wide association studies (GWAS) meta-analyses have identified >20 susceptibility loci, implicating regulatory networks in immune response, plasma cell differentiation, autophagy, apoptosis, and cell cycle control [ 76 , 77 ]. Inherited risk is predominantly polygenic, driven by cumulative low-penetrance variants [ 75 , 78 ]. Polymorphisms in telomerase-related genes, particularly TERT , further link telomere biology to susceptibility [ 79 ]. Expanded meta-analyses identified additional loci enriched in regulatory regions controlling B-cell differentiation [ 77 ].
Trans-ancestry studies identified shared susceptibility loci at 7p15.3, 17p11.2, and 22q13.1 across African and European ancestry populations, while an additional locus at 3p22.1 showed significant association exclusively in EA cohorts [ 72 ]. Functional annotation indicates enhancer regulation of CDCA7L , missense variation in TNFRSF13B/TACI , and regulatory clustering near CBX7 [ 72 , 74 ].
Polygenic risk score (PRS) models show that individuals in the highest risk quintile have a 3.44-fold increased MM risk compared with the lowest quintile [ 80 ].
Despite these promising findings, PRS are not yet clinically actionable for screening high-risk individuals or relatives in MM, and their implementation in routine practice remains constrained by several key limitations [ 81 , 82 ]. First, PRS models have not been prospectively validated in large, independent cohorts, limiting confidence in their real-world performance and clinical generalizability. In the context of MM, this limitation is particularly relevant given the relatively low disease incidence and the lack of prospective screening approaches in asymptomatic populations. In addition, predictive accuracy is reduced in ancestrally diverse populations, reflecting both the underrepresentation of non-European populations in GWAS and population-specific genetic architectures [ 83 ]. Furthermore, there are no standardized thresholds to define clinically meaningful risk categories, and it remains unclear how PRS-based stratification should be integrated with established MM risk factors such as MGUS status, family history, and cytogenetic markers. As a result, PRS should currently be considered research tools rather than validated instruments for population screening or risk assessment in relatives. Future efforts should focus on prospective validation, cross-population calibration, and integration with somatic genomic features and clinical variables to develop more robust and clinically actionable risk prediction models.
However, several limitations constrain the interpretation and translational impact of GWAS findings. Most studies are heavily biased toward populations of European ancestry, limiting generalizability and potentially exacerbating disparities in risk prediction [ 84 , 85 ]. Moreover, the effect sizes of individual susceptibility variants are modest, and the biological mechanisms linking many loci to MM pathogenesis remain incompletely defined, as many GWAS signals map to regulatory regions with context-dependent functional effects [ 86 ]. Importantly, currently identified susceptibility loci explain only a fraction of the heritable risk of MM, with large-scale interaction analyses estimating that known variants and their interactions account for approximately 17% of heritability, highlighting a substantial component of “missing heritability” [ 76 , 87 ]. Reproducibility across cohorts is also variable, reflecting differences in study design, sample size, statistical power, and phenotype definition. In addition, comparative analyses across studies reveal partial overlap in identified loci, but also inconsistencies in effect sizes and significance levels, highlighting the influence of cohort composition and analytical pipelines. Importantly, GWAS approaches primarily capture common variants and do not adequately account for rare high-impact mutations, structural variation, or epigenetic regulation, thereby providing only a partial view of inherited risk architecture. These limitations are further underscored by sequencing-based studies, which have identified rare pathogenic variants and additional layers of genetic complexity not captured by GWAS approaches [ [63] , [87] ]. Furthermore, conflicting evidence exists regarding the functional relevance of several susceptibility loci, with limited experimental validation and uncertainty about their contribution to disease biology. Although gene–gene interaction analyses have identified a limited number of interacting loci, the overall contribution of epistatic effects remains incompletely resolved, and robust replication across independent cohorts is still lacking. Gene–environment interactions are even less well characterized, representing a major unresolved area in MM susceptibility research. Addressing these challenges will require larger multi-ancestry cohorts, integrative multi-omic approaches, functional validation of candidate loci, and standardized analytical frameworks to improve robustness, biological interpretation, and clinical applicability [ 62 , 85 , 86 ].
Genetic-environment interactions
Genetic-environment interactions constitute another layer of MM etiology, where inherited susceptibility amplifies the biological impact of environmental exposures. Rare germline variants affecting DNA damage response, telomere maintenance, and immune pathways may increase cellular vulnerability to genotoxic stressors [ 67 ].
Occupational exposure to pesticides and solvents has been associated with increased MM risk, and may exert stronger biological effects in individuals carrying germline alterations in DNA repair pathways [ 27 ]. Germline alterations in DNA repair genes and immune regulators increase cellular sensitivity to genotoxic stressors including pesticides, solvents, and benzene, accelerating mutational accumulation, inflammatory signaling, and clonal evolution during progression from MGUS and SMM to MM [ 88 , 64 ]. Obesity may further synergize with polygenic risk through chronic inflammation and metabolic reprogramming of the bone marrow microenvironment [ 89 ]. In genetically predisposed individuals, these inflammatory and metabolic pressures may facilitate earlier clonal expansion and disease progression.
High-resolution longitudinal cohort efforts integrating exposure data, clonal hematopoiesis dynamics, and molecular profiling further support the role of G × E interactions in shaping disease trajectories and provide a foundation for personalized prevention and surveillance strategies in high-risk populations [ 90 ].
Collectively, these findings support a model in which germline susceptibility not only influences overall disease risk but may also shape the evolutionary trajectories of plasma cell neoplasia [ [64] , [91] ]. In particular, inherited alterations affecting DNA repair, telomere maintenance, and immune regulation may create permissive genomic backgrounds that shape the spectrum of primary somatic events, such as IgH translocations or hyperdiploid karyotypes [ 88 ]. Although direct mechanistic evidence in MM remains limited, emerging integrative genomic data suggest that germline-driven differences in genomic stability and mutational processes may influence the timing, type, and selection of early driver events. Future studies integrating germline variation with longitudinal somatic profiling will be essential to define how inherited risk architectures constrain clonal initiation and shape subsequent evolutionary pathways.
Somatic genomic landscape of MM
Primary cytogenetic abnormalities represent early detectable genomic events in MM and define major biological subtypes. These lesions arise during premalignant stages, persist throughout clonal evolution, and shape downstream mutational trajectories, clinical behavior, and therapeutic vulnerability. Two largely mutually exclusive categories account for most cases: recurrent immunoglobulin heavy chain (IgH) chromosomal translocations and hyperdiploidy. Together, these categories define distinct evolutionary routes and underpin cytogenetic risk stratification.
Primary cytogenetic categories
Primary cytogenetic events define early MM subtypes and shape genomic evolution.
IgH-driven translocations
• IgH translocations as early genomic drivers and their clinical detection
Chromosome 14q32 rearrangements involving the IgH locus represent one of the most frequent and relevant primary genomic events in MM [ 92 ]. These alterations arise early during disease progression, are detectable in MGUS, and generally persist during progression, while secondary alterations such as MYC activation and TP53 loss accumulate later [ 93 ].
At the functional level, IgH translocations juxtapose oncogenes to the highly active IgH enhancer region, leading to deregulated expression of genes involved in cell cycle control, epigenetic regulation, transcriptional programs, and survival. IgH rearrangements are detected in approximately 40–50% of NDMM patients using conventional techniques [ 94 , 95 ], and may approach 50–60% with comprehensive genomic profiling. • Dominant IgH translocation subtypes and biological consequences
Four chromosomal partners account for the majority of primary IgH translocations: CCND1 (11q13), CCND3 (6p21), FGFR3/WHSC1 (MMSET) (4p16), and MAF (16q23) [ 96 ].
The t(11;14)(q13;q32), present in approximately 15–20% of patients [ 97 , 98 ], drives CCND1 overexpression [ 99 ] and is associated with a lymphoplasmacytic phenotype, frequent CD20 expression, and relative biological indolence [ 100 ]. This subgroup is generally classified as standard risk [ 101 ]. Tumors with t(11;14) show relative dependence on BCL2-mediated survival pathways, which is associated with increased response rates to venetoclax-based strategies in selected patient subsets [ 102 ].
The t(4;14)(p16.3;q32), observed in approximately 10–15% of cases [ 103 ], results in simultaneous activation of FGFR3 and WHSC1 (MMSET) [ 103 ]. MMSET overexpression alters chromatin methylation and DNA damage response pathways [ 104 ], while FGFR3 contributes oncogenic signaling in a subset of patients harboring activating mutations, detected in approximately 17% of t(4;14)-positive tumors [ 98 ]. This subgroup defines a high-risk entity characterized by aggressive clinical behavior, frequent renal involvement, and inferior survival [ 92 ]. PI-based therapy partially mitigates adverse prognosis, highlighting the therapeutic relevance of molecular stratification [ 105 ].
The t(14;16)(q32;q23), present in approximately 2–3% of patients [ 106 ], induces MAF overexpression and has been associated with inferior survival [ [106] , [107] ]. MAF activation promotes APOBEC3A and APOBEC3B expression, generating a hypermutator phenotype characterized by APOBEC mutational signatures and increased genomic instability [ 108 ].
Less frequent primary events include t(6;14) (1–2%), associated with CCND3 activation and generally neutral prognosis [ 109 ], and t(14;20) (∼1%), associated with MAFB activation and adverse prognosis in overt MM [ 110 ].
Hyperdiploidy
In parallel to IgH-driven disease, hyperdiploidy represents the second major primary cytogenetic category in MM and accounts for approximately 45–50% of NDMM cases in Western populations [ 111 , 112 ]. It is defined by non-random gain of odd-numbered chromosomes, most commonly involving chromosomes 3, 5, 7, 9, 11, 15, 19, and 21. These gains are acquired in structured evolutionary sequences rather than through random aneuploidy, defining a distinct early oncogenic route.
Reported incidence varies across cohorts, likely reflecting technical and population differences [ 111 , 112 ]. Among patients with cytogenetically abnormal karyotypes, hyperdiploidy is the most frequent numerical pattern, occurring in approximately 46–68% of cases, compared with pseudodiploid or hypodiploid configurations.
From a clinical perspective, patients with abnormal metaphase karyotypes exhibit inferior survival outcomes compared with those with normal karyotypes [ 113 ]. Hyperdiploid MM is associated with more favorable survival compared with hypodiploid disease, defined by fewer than 45 chromosomes [ 114 ], indicating that numerical chromosomal patterns differ in impact.
Prognostic impact is heterogeneous. Patients with hyperdiploidy plus high-risk cytogenetic abnormalities, including del(17p13), t(4;14), and gain of 1q21, experience significantly worse survival outcomes than patients with isolated hyperdiploidy [ 115 ]. Chromosome-specific effects further modulate prognosis within the hyperdiploid subgroup. Among hyperdiploid patients, only trisomy 3 and trisomy 5 were independently associated with improved OS, whereas trisomy 21 correlated with adverse clinical outcomes [ 116 , 117 ], indicating that trisomy pattern, not chromosome count alone, influences prognosis.
Secondary genomic events and progression-associated events
Secondary genomic events shape MM progression biology and include chromosome-arm aneuploidy, focal CNVs, and secondary structural alterations that accumulate on primary cytogenetic backgrounds.
Aneuploidy-driven/trigger progression in MM
With the advent of high-resolution molecular cytogenetic techniques, studies show that 95–100% of patients with MM harbor abnormal karyotypes, often characterized by highly complex combinations of structural and numerical alterations.
Early comparative genomic hybridization and FISH-based studies established that these alterations are nonrandom and biologically selected. Reported recurrent chromosome-arm gains involving 19p, 9q, 11q, 12q, 15q, 17q, and 22q, together with deletions affecting 6q and 16q. Subsequent interphase FISH analyses confirmed chromosomal aberrations in up to 86% of NDMM patients, with frequent gains of chromosomes 3, 5, 7, 9, 11, 15, and 21 and losses involving chromosomes 13 and 17, and identified del(13q14) and IGH translocations as major prognostic markers [ 118 ].
gain
At the chromosome-arm level, gain of 1q is the most frequent and clinically relevant numerical event. It occurs in approximately 35–40% of NDMM patients and increases in frequency at relapse, where it strongly correlates with treatment resistance and inferior survival [ [115] , [119] ].
Prognostic impact appears to be copy-number dependent, with ≥4 copies generally associated with inferior outcomes compared with three copies, although this association is influenced by co-existing cytogenetic abnormalities and contemporary treatment strategies [ 120 ]. Notably, the prognostic effect of +1q/1q21 gains is not uniform across studies: in thalidomide-based regimens no significant survival impact has been reported, and in other series the adverse association observed in univariate analyses did not retain independent prognostic value in multivariable models [ 121 ].
deletion
Deletion of chromosome 1p is detected in approximately 27–30% of patients and represents another major adverse lesion [ 122 ]. del(1p) is independently associated with poor prognosis [ 116 , 123 , 124 ]. Of particular biological relevance are deletions involving 1p12 and 1p32.3, regions that harbor critical tumor suppressor candidates.
del(13q)
Deletion of chromosome 13q occurs in approximately 50–60% of patients [ [124] , [125] ]. Its adverse prognostic signal largely reflects co-occurrence with other high-risk lesions.
del(17p)
Deletion of chromosome 17p involving the TP53 represents the most clinically impactful arm-level abnormality. Del(17p) is detected in approximately 8–10% of NDMM patients and is consistently associated with inferior PFS and OS [ 126 , 127 ]. Its prevalence increases dramatically during disease progression, reaching very high frequencies in advanced and relapsed stages [ 128 , 129 ]. TP53 functions as a central regulator of cell-cycle arrest, DNA repair, and apoptosis, and 17p loss is associated with aggressive disease, inferior OS, and increased risk of extramedullary involvement [ [111] , [124] 130 , 131 ].
Other arm-level gains/losses
Additional recurrent arm-level gains include gains of 8q, 9q, and 11q, with 8q gain of particular relevance due to the MYC locus at 8q24 [ [124] , [130] , [132] ]. Recurrent arm-level losses include 1p, 6q, 8p, 9q, 13q, 16q, and 17p, contributing to tumor suppressor gene depletion and genomic imbalance [ [124] , [125] , 133 ]. Several of these losses co-occur with gain(1q), defining broader chromosomal instability patterns.
MYC secondary events
Dysregulation of MYC represents a central secondary genomic event in MM progression [ 134 ]. Unlike primary IgH translocations, MYC rearrangements are rare in premalignant stages (3–4%) [ 135 ], but increase in frequency in NDMM (approximately 15–20%) [ 110 , [135] , [136] ] and become further enriched at relapse, where they are associated with proliferative transcriptional programs and inferior clinical outcomes [ 130 , 136 ].
Recurrent MYC rearrangements, focal gains, and amplifications involving 8q24 constitute multiple structural mechanisms converging on MYC activation [ 130 , 136 ]. These alterations are particularly enriched in tumors with homologous recombination deficiency and show an inverse correlation with t(4;14) [ [135] , [136] ]. Their frequent coexistence with primary IgH translocations supports a multistep evolutionary model of myeloma progression.
Functionally, MYC activation drives proliferative transcriptional programs contributing to clonal diversification, adverse clinical behavior and progression [ [130] , [134] ]. The stepwise increase in MYC alterations from MGUS to symptomatic and relapsed MM reinforces its role as a progression-associated lesion rather than an initiating event.
Driver-focused copy number remodeling
Building on the arm-level architecture described above, focal CNVs modulate oncogenic dosage and functional heterogeneity without defining new cytogenetic categories.
Recurrent amplifications and deletions target gene-dense regions that modulate key oncogenic pathways. Representative events include focal amplification of CKS1B (1q21) and MYC (8q24), deletions involving TP53 (17p13), CDKN2C and FAF1 (1p32), RB1 (13q14), CYLD (16q12), and BIRC2/BIRC3 (11q22), converging on cell-cycle regulation, DNA damage response, and NF-κB signaling [ 130 , 136 ].
Focal CNVs interact with aneuploid backgrounds to promote transcriptional reprogramming, clonal fitness, and therapeutic resistance. Integrated analyses associate specific CNV patterns with aggressive transcriptional states and inferior survival (Gupta et al., 2019).
Longitudinal studies further show CNV remodeling under therapeutic pressure, fostering branched clonal evolution and resistance [ 130 ]. CNV remodeling frequently coexists with complex structural variation, reinforcing genomic instability and hierarchical evolution [ 137 ] ( Fig. 1 ). Fig. 1 Integrated Genomic Architecture and Hierarchical Evolution of MM. Primary IgH translocations and hyperdiploidy define early MM biological subtypes. Secondary cytogenetic changes and CNV remodeling add arm-level and focal gains and deletions affecting key oncogenes and tumor suppressors. Somatic mutations and structural variants further deregulate signaling and genome control pathways. These alterations accumulate through branching clonal evolution from precursor states to relapsed disease under therapeutic pressure. Fig 1 dummy alt text

Genomic detection strategies: from FISH to NGS and optical genome mapping (OGM)
Accurate identification of myeloma genomic abnormalities is central for risk stratification and therapeutic decision-making. Conventional diagnostic workflows rely on fluorescence in situ hybridization (FISH), SNP arrays, targeted sequencing, and OGM, typically requiring plasma cell enrichment for optimal sensitivity.
Conventional cytogenetics and FISH
Conventional metaphase cytogenetics and interphase FISH remain central to MM diagnosis and risk stratification, forming the backbone of current clinical guidelines. FISH, performed on plasma cell-enriched samples, overcomes the low proliferative index that limits metaphase analysis and reliably detects high-risk lesions such as t(4;14), t(14;16), del(17p), 1q gain, and 1p deletion [ 138 ]. Detection rates consistently exceed those of conventional cytogenetics: abnormalities were identified in 49.2% versus 16.9% of cases in one cohort [ 139 ], and up to 97% versus 30% when FISH combined with array-CGH was compared with karyotyping alone [ 140 ].
Beyond detection, FISH allows estimation of lesion burden and subclonal distribution, guiding risk-adapted therapy. Conventional cytogenetics, although less sensitive, retains complementary value by providing a global view of ploidy and chromosomal complexity, including hyperdiploidy and complex karyotypes [ 141 ].
NGS-based structural variant detection
NGS extends structural variant detection beyond predefined probe panels. Whole-genome sequencing (WGS) and targeted sequencing approaches can identify cryptic rearrangements, resolve complex breakpoints, and uncover novel fusion partners [ 135 ]. Panel design remains critical, as limited genomic coverage may underestimate clinically relevant alterations, including certain MYC rearrangements.
Beyond structural rearrangements, NGS enables simultaneous detection of single-nucleotide variants (SNVs) and small insertions/deletions (indels), particularly relevant for TP53 , where focal deletions frequently coexist with inactivating mutations.
NGS sensitivity depends on sequencing depth and variant allele fraction; high-depth sequencing achieves >98% sensitivity for SNVs and indels [ 142 ]. Integrated WES/RNA-seq demonstrate complete concordance with FISH for CNAs while additionally resolving translocation breakpoints and mutations [ 143 ]. High-performance custom panels also show >99% sensitivity for IGH translocations and CNVs [ 144 ].
Collectively, these findings support integrated NGS-cytogenetic strategies, as NGS captures structural variants and sequence mutations, providing gene-level profiling beyond conventional cytogenetics.
Optical genome mapping (OGM)
Optical Genome Mapping (OGM) enables detection of structural variants, CNVs, and aneuploidy in a single experiment, overcoming the locus restriction of targeted FISH panels. Across clinical cohorts, OGM identifies canonical abnormalities detectable by FISH while revealing additional structural variants. One study reported a ∼30% increase in prognostic yield compared with FISH [ 145 ], whereas another detected additional alterations in up to 60% of cases, including chromoanagenesis events [ 146 ]. High concordance with FISH for variants ≥5% with a variant allele frequency supports reliability for major clonal events [ 147 ].
By capturing balanced rearrangements and numerical changes in a single workflow, OGM functions as a high-resolution digital karyotype and may consolidate multiple cytogenetic assays. However, OGM sensitivity decreases for low-level subclones (15–20%) and it cannot reliably resolve centromeric or telomeric rearrangements [ 148 ]. Performance may be reduced in samples with low plasma cell purity or highly subclonal populations. In addition, OGM requires ultra-high molecular weight DNA, which can be challenging to obtain from bone marrow samples. Importantly, OGM does not detect SNVs or small insertions/deletions [ 149 ], and therefore requires integration with sequencing platforms for comprehensive profiling.
Prognostic implications and therapeutic modulation
Cytogenetic abnormalities are the strongest predictors of clinical outcome. Deletion 17p, t(4;14), and 1q21 gain are independent adverse prognostic factors for PFS, with del(17p13) also predicting inferior OS [ 112 ]. Cytogenetic complexity further worsens prognosis.
High-dose therapy followed by autologous stem cell transplantation improves response depth but does not fully offset high-risk cytogenetic features. In contrast, incorporation of PI shows particular benefit in t(4;14) and 1q21 gain disease, supporting molecularly risk-adapted therapy [ 97 , 105 ].
Mutational profiles and clonal evolution
High-resolution chromatin conformation studies show that CNV breakpoints frequently occur at the boundaries of topologically associating domains (TADs), suggesting preferential disruption of regulatory regions. TADs organize the genome into insulated neighborhoods that constrain enhancer-promoter interactions and shape gene expression programs [ 150 ]. TAD disruption alters enhancer-promoter interactions and contributes to oncogenic dysregulation [ 151 ]. Compared with normal B cells, MM shows increased TAD number, reduced average TAD size, and A/B compartment switching in ∼20% of genomic regions, consistent with higher-order genome reorganization [ 152 , 153 ] ( Fig. 2 ). Fig. 2 Cytogenetic evolution and hierarchical acquisition of alterations in MM progression. Abbreviations: MM, multiple myeloma; MGUS, monoclonal gammopathy of undetermined significance; SMM, smoldering multiple myeloma; HRD, homologous recombination deficiency; IgH, immunoglobulin heavy chain; del, chromosomal deletion; amp, amplification; t, chromosomal translocation; NRAS , neuroblastoma RAS viral oncogene homolog; KRAS , Kirsten rat sarcoma viral oncogene homolog; BRAF, B-Raf proto-oncogene serine/threonine kinase; CCND1 , cyclin D1; DIS3 , DIS3 homolog exosome endoribonuclease; IRF4 , interferon regulatory factor 4; FGFR3 , fibroblast growth factor receptor 3; PRDM1 , PR domain zinc finger protein 1 (BLIMP1); MYC, MYC proto-oncogene. In the non-hyperdiploid group, mutation labels are color-coded according to the associated IgH translocation subtype, as indicated in the right-hand color legend. Fig 2 dummy alt text

Comparative genomic studies indicate that MGUS is genetically related to MM but exhibits a lower burden of genomic abnormalities. The frequency of chromosomal gains and losses, including hyperdiploidy, 1q gain, and del(13q), is reduced in MGUS, supporting a stepwise accumulation of genomic instability during progression. MGUS also shows a less complex somatic mutation spectrum that correlates with chromosomal and mutational burden [ 154 ]. MYC translocations and TP53 lesions are typically absent in MGUS, supporting their role as transformation-associated events.
Large sequencing cohorts demonstrate that progression is accompanied by diversification of mutational processes affecting both coding and non-coding regions. Analysis of CoMMpass whole-exome and whole-genome datasets identified recurrent SNVs, structural rearrangements, and characteristic mutational signatures linked to endogenous enzymatic activity and therapy-related mutagenesis [ [91] , [155] ]. Integrated genomic analyses combining sequencing, CNV profiling, and cytogenetics describe linear, branching, and parallel evolutionary trajectories, highlighting dynamic clonal architecture [ [91] , [137] ].
In MM, subclonal architecture can be reconstructed from bulk NGS data using probabilistic frameworks based on Bayesian clustering of variant allele frequencies and copy-number–adjusted cancer cell fractions. These approaches model the contribution of individual mutations to the overall tumor population, accounting for tumor purity and local copy number, and group variants into clusters that reflect distinct clonal populations. In particular, Dirichlet-process-based models enable data-driven inference of the number and composition of subclonal populations without requiring prior specification of cluster number [ 152 , 156 ]. This allows the identification of phylogenetically related clones and the distinction between truncal and branch mutations, providing a basis for reconstructing tumor evolutionary histories. These approaches have been applied in longitudinal and progression settings to track clonal dynamics over time and under therapeutic pressure, revealing that subclonal diversity often precedes clinical transformation and that relapse may arise from pre-existing minor clones [ [152] , [157] , 158 ]. However, despite their relevance, their implementation in routine clinical practice remains limited by the lack of standardized bioinformatic pipelines, methodological variability across tools, and the intrinsic constraints of bulk sequencing data. The development of robust and standardized analytical approaches will be essential to fully integrate subclonal resolution into precision oncology strategies.
An additional layer of complexity arises from allele-specific expression of somatic variants. Transcriptomic profiling shows that mutant alleles are variably expressed, with selective activation or silencing that modulates functional impact beyond DNA sequence alone [ 159 ].
At the pathway level, somatic mutations are enriched in receptor tyrosine kinase signaling and cell adhesion networks. Sequencing of tumors and myeloma cell lines identified recurrent alterations affecting plasma cell adhesion, migration, and microenvironmental interactions [ 160 ].
Germline susceptibility variants may further modulate the risk and molecular progression of plasma cell dyscrasias. Rare inherited EP300 variants have been proposed to contribute through IRF4 pathway dysregulation, increased BCL6 activity, and reduced p53 signaling [ [73] , [74] , [88] , 108 ]. Additional candidate variants include PDPK1 splice-site alterations affecting immunoglobulin recombination and transcription regulators. Several candidate risk variants cluster at 22q13 near APOBEC -family loci and are consistently associated with APOBEC-related mutagenesis in MM evolution [ [74] , [112] ].
At relapse, genomic complexity increases. Integrative analyses show more chromosomal imbalances at relapse than at diagnosis, driven mainly by additional losses, with recurrent relapse-associated gains on 8q and losses of 10q [ 137 , [158] , [161] ].
Large CNVs (>100 Mb) exert stronger transcriptional effects than smaller alterations and preferentially deregulate cytokine-related and integrin signaling pathways. Relapse-associated expression changes include activation of PRAME (22q11) and BOP1 (8q24). Global DNA methylation patterns remain relatively stable between diagnosis and relapse, indicating a dominant role for chromosomal remodeling over epigenetic reprogramming in late-stage progression [ 161 ].
Germline genetic susceptibility
GWAS
As mentioned above, GWAS have established that MM has a substantial inherited component driven by a polygenic architecture. Numerous common low-penetrance variants collectively contribute to disease susceptibility. Large-scale meta-analyses indicate that germline risk loci explain approximately 20–25% of heritable risk, confirming that genetic predisposition arises from the cumulative effect of multiple regulatory variants rather than rare high-penetrance alleles. GWAS therefore provide direct molecular evidence of inherited susceptibility beyond familial aggregation. International collaborations such as IMMEnSE were instrumental to power discovery and cross-cohort validation [ 162 ].
A landmark meta-analysis conducted by Mitchell et al. analyzed 9866 cases and 239,188 controls. This study validated nine previously reported susceptibility loci and identified eight additional risk regions. Newly implicated loci included JARID2 (6p22.3), ATG5 (6q21), SMARCD3 (7q36.1), CCAT1 (8q24.21), CDKN2A (9p21.3), WAC (10p12.1), RFWD3 (16q23.1), and PREX1 (20q13.13) [ 75 ]. Earlier GWAS also identified additional loci, including a variant at 2q12.3 associated with increased MM risk and replicated across multiple cohorts [ 163 ].
Trans-ethnic GWAS approaches further refined inherited MM risk architecture by leveraging ancestry-specific linkage disequilibrium (LD) structure, which is particularly relevant given higher incidence in individuals of African ancestry. Rand et al. combined European and African ancestry cohorts and replicated several established European risk loci at CDCA7L (7p15.3), TNFRSF13B (17p11.2), and CBX7 (22q13.1). They also improved fine-mapping of shared susceptibility regions using ancestry-specific LD patterns [ 72 ]. The expanded African ancestry meta-analysis by Du et al. showed concordant risk architecture across populations while identifying ancestry-dependent effect sizes [ 164 ]. More recently, Went et al. reported that multi-ancestry PRS identify the highest predicted genetic risk in admixed American populations, partly driven by enrichment of risk alleles at loci such as 3p22.1 near ULK4 [ 165 ].
Beyond single-locus associations, pathway-based and interaction analyses reveal higher-order genetic dependencies. Polygenic interaction modeling of two independent GWAS datasets identified 16 significant interacting variant pairs, supporting a contribution of epistatic effects to inherited MM risk [ 76 ]. Independent replication studies further confirmed additional susceptibility loci, including variants at 8q24, 7p15.3, 3p22.1, and 2p23.3 [ [166] , [167] , [168] ].
Functionally, many GWAS risk variants localize to non-coding regulatory regions and act through expression quantitative trait loci (eQTL) mechanisms in hematopoietic tissues. Risk loci cluster near genes involved in plasma cell differentiation and immune signaling, including TNFRSF13B / TACI and PREX1 . Integration of transcriptome-wide association studies (TWAS) has prioritized >100 candidate susceptibility genes, including APOBEC -family members, linking inherited risk to mutational processes relevant to somatic progression in MM. Importantly, aggregation of GWAS signals into PRS enables population-level susceptibility stratification, with individuals in the highest percentiles exhibiting a significantly increased relative risk. Trans-ethnic modeling improves PRS portability across ancestries and supports more equitable risk prediction strategies.
Candidate gene association studies
Candidate gene association studies have evaluated inherited variants in pathways related to drug transport, DNA repair, autophagy, immune regulation, plasma cell differentiation, microenvironmental signaling and telomere maintenance. Reported associations span susceptibility, clinical features, treatment outcomes and comorbidities [ [79] , [166] , 169 , 170 ] ( Table 3 ). Table 3 Candidate-gene polymorphisms associated with MM susceptibility and treatment outcome. Table 3 dummy alt text Functional domain Gene Variant / haplotype Reported association type Reported effect Key references Xenobiotic transport GSTM1, GSTT1 Gene deletions Treatment outcome No significant association with response or survival after VAD or high-dose melphalan [ 171 ] Xenobiotic metabolism GSTP1 Val/Val genotype Treatment outcome Improved outcome with conventional chemotherapy [ 172 ] Drug transport ABCB1 (MDR1) C1236T, C3435T Treatment outcome T alleles associated with longer PFS; no OS association [ 173 ] Drug transport ABCB1 rs2235013 Survival Associated with survival differences [ 174 ] Drug transport ABCC2 rs4148388 Survival Associated with survival differences [ 174 ] Drug transport ABCB1 rs1045642 Susceptibility No association with MM risk (meta-analysis) [ 175 ] Drug transport ABCB1, ABCG2, ABCC1, ABCC2, ABCC3 Multiple SNPs Susceptibility Association with MM risk in candidate-gene case–control study [ 176 ] IMiD target regulation CRBN rs1714327, rs1705814; rs6768972, rs1672753 (promoter SNPs) Treatment outcome (lenalidomide and thalidomide-based regimens) Minor alleles associated with lower probability of ≥PR and shorter PFS in RRMM; promoter variants independently associated with PFS and OS in CTD-treated patients; additional CRBN polymorphisms associated with differential IMiD response [ [177] , [178] , [179] ] Inflammasome regulation CARD8 rs2043211 (C10X) Susceptibility / clinical features AT genotype associated with increased MM risk and immune-related features [ 180 ] Inflammatory signaling NF-κB rs28362491 (−94 ins/del ATTG) Clinical features Associated with higher tumor burden parameters [ 180 ] Cytokine regulation IL18 rs16944 Clinical features Associated with hematologic and tumor burden parameters [ 180 ] Cytokine network IL6, IL1, IL10 Multiple SNPs Susceptibility Associated with MM risk in meta-analyses [ 181 ] Plasma cell differentiation ELL2 rs6877329 Susceptibility / biology Reduced enhancer activity and ELL2 expression; MM risk locus [ [55] , [182] , 183 ] Telomere maintenance TERT pathway genes Common polymorphisms Susceptibility Associated with MM risk and telomere length variation [ 79 ] Angiogenesis VEGF rs699947 / rs833061 / rs2010963 (ACG haplotype) Treatment outcome Shorter time to thalidomide failure [ 184 ] Angiogenesis VEGF rs1570360 (−1154G>A) Biology / prognosis Associated with higher marrow microvessel density [ 185 ] Angiogenesis VEGF, VEGFR2 Multiple SNPs / haplotypes Treatment outcome Associated with response and time to treatment failure [ 185 ] Class switch recombination (CSR) CSR pathway genes Multiple SNPs Susceptibility and survival Genetic polymorphisms in CSR genes associated with MM risk and survival in IMMEnSE [ 186 ] Antigen presentation HLA-DRB1 DRB1×01:01 tagged allele Susceptibility GWAS risk signal [ 187 ] Antigen presentation HLA-C, HLA-B C07:02 g, B07:02 g Susceptibility Associated with MM risk [ 187 ] NK regulation HLA/KIR combinations C1−/C2+/Bw4+, KIR ligand pairs Susceptibility Associated with MM occurrence and NK licensing patterns [ 188 , 189 ] Transcriptional regulation HNF1B; outcome-related eQTL loci; integrative genomic risk loci Common variants; eQTL SNPs; germline variants incorporated in genomic risk models Survival Associated with overall survival in MM (IMMEnSE); regulatory variants influencing gene expression predict survival differences; integrative analyses confirm germline contribution to clinical outcome heterogeneity [ [170] , [190] , [191] , [192] ] Post-transcriptional regulation (miRNA binding variants) Multiple target genes (miRSNPs) miRNA-binding site polymorphisms Susceptibility miRSNPs associated with altered MM risk in IMMEnSE cohorts [ 193 , 194 ] Abbreviations: PFS, progression-free survival; OS, overall survival; VAD, vincristine-doxorubicin-dexamethasone; HLA, human leukocyte antigen; KIR, killer cell immunoglobulin-like receptor; NK, natural killer. Representative associations reported in candidate-gene and pharmacogenetic studies, grouped by functional pathway. Reported effects include disease susceptibility, clinical features, treatment response, or survival endpoints. Findings are heterogeneous across cohorts and treatments.
Table 3
Candidate-gene polymorphisms associated with MM susceptibility and treatment outcome.
Abbreviations: PFS, progression-free survival; OS, overall survival; VAD, vincristine-doxorubicin-dexamethasone; HLA, human leukocyte antigen; KIR, killer cell immunoglobulin-like receptor; NK, natural killer. Representative associations reported in candidate-gene and pharmacogenetic studies, grouped by functional pathway. Reported effects include disease susceptibility, clinical features, treatment response, or survival endpoints. Findings are heterogeneous across cohorts and treatments.
| Functional domain | Gene | Variant / haplotype | Reported association type | Reported effect | Key references |
| Xenobiotic transport | GSTM1, GSTT1 | Gene deletions | Treatment outcome | No significant association with response or survival after VAD or high-dose melphalan | [ 171 ] |
| Xenobiotic metabolism | GSTP1 | Val/Val genotype | Treatment outcome | Improved outcome with conventional chemotherapy | [ 172 ] |
| Drug transport | ABCB1 (MDR1) | C1236T, C3435T | Treatment outcome | T alleles associated with longer PFS; no OS association | [ 173 ] |
| Drug transport | ABCB1 | rs2235013 | Survival | Associated with survival differences | [ 174 ] |
| Drug transport | ABCC2 | rs4148388 | Survival | Associated with survival differences | [ 174 ] |
| Drug transport | ABCB1 | rs1045642 | Susceptibility | No association with MM risk (meta-analysis) | [ 175 ] |
| Drug transport | ABCB1, ABCG2, ABCC1, ABCC2, ABCC3 | Multiple SNPs | Susceptibility | Association with MM risk in candidate-gene case–control study | [ 176 ] |
| IMiD target regulation | CRBN | rs1714327, rs1705814; rs6768972, rs1672753 (promoter SNPs) | Treatment outcome (lenalidomide and thalidomide-based regimens) | Minor alleles associated with lower probability of ≥PR and shorter PFS in RRMM; promoter variants independently associated with PFS and OS in CTD-treated patients; additional CRBN polymorphisms associated with differential IMiD response | [ [177] , [178] , [179] ] |
| Inflammasome regulation | CARD8 | rs2043211 (C10X) | Susceptibility / clinical features | AT genotype associated with increased MM risk and immune-related features | [ 180 ] |
| Inflammatory signaling | NF-κB | rs28362491 (−94 ins/del ATTG) | Clinical features | Associated with higher tumor burden parameters | [ 180 ] |
| Cytokine regulation | IL18 | rs16944 | Clinical features | Associated with hematologic and tumor burden parameters | [ 180 ] |
| Cytokine network | IL6, IL1, IL10 | Multiple SNPs | Susceptibility | Associated with MM risk in meta-analyses | [ 181 ] |
| Plasma cell differentiation | ELL2 | rs6877329 | Susceptibility / biology | Reduced enhancer activity and ELL2 expression; MM risk locus | [ [55] , [182] , 183 ] |
| Telomere maintenance | TERT pathway genes | Common polymorphisms | Susceptibility | Associated with MM risk and telomere length variation | [ 79 ] |
| Angiogenesis | VEGF | rs699947 / rs833061 / rs2010963 (ACG haplotype) | Treatment outcome | Shorter time to thalidomide failure | [ 184 ] |
| Angiogenesis | VEGF | rs1570360 (−1154G>A) | Biology / prognosis | Associated with higher marrow microvessel density | [ 185 ] |
| Angiogenesis | VEGF, VEGFR2 | Multiple SNPs / haplotypes | Treatment outcome | Associated with response and time to treatment failure | [ 185 ] |
| Class switch recombination (CSR) | CSR pathway genes | Multiple SNPs | Susceptibility and survival | Genetic polymorphisms in CSR genes associated with MM risk and survival in IMMEnSE | [ 186 ] |
| Antigen presentation | HLA-DRB1 | DRB1×01:01 tagged allele | Susceptibility | GWAS risk signal | [ 187 ] |
| Antigen presentation | HLA-C, HLA-B | C07:02 g, B07:02 g | Susceptibility | Associated with MM risk | [ 187 ] |
| NK regulation | HLA/KIR combinations | C1−/C2+/Bw4+, KIR ligand pairs | Susceptibility | Associated with MM occurrence and NK licensing patterns | [ 188 , 189 ] |
| Transcriptional regulation | HNF1B; outcome-related eQTL loci; integrative genomic risk loci | Common variants; eQTL SNPs; germline variants incorporated in genomic risk models | Survival | Associated with overall survival in MM (IMMEnSE); regulatory variants influencing gene expression predict survival differences; integrative analyses confirm germline contribution to clinical outcome heterogeneity | [ [170] , [190] , [191] , [192] ] |
| Post-transcriptional regulation (miRNA binding variants) | Multiple target genes (miRSNPs) | miRNA-binding site polymorphisms | Susceptibility | miRSNPs associated with altered MM risk in IMMEnSE cohorts | [ 193 , 194 ] |
Xenobiotic transport and drug metabolism (ABC, GST)
ATP-binding cassette (ABC) transporters are key xenobiotic efflux pumps that contribute to multidrug resistance in MM. They export chemotherapeutic agents from malignant plasma cells, thereby reducing intracellular drug accumulation. Major transporters implicated include ABCB1 (P-glycoprotein/ MDR1 ), ABCC1 ( MRP1 ), ABCC5 ( MRP5 ), and ABCG2 ( BCRP ), frequently upregulated in relapsed and refractory disease. Increased transporter expression is frequently driven by epigenetic demethylation and microenvironment-derived signaling pathways, including resistin-mediated NF-κB activation. These mechanisms collectively promote cross-resistance.
Polymorphisms in xenobiotic transport and detoxification genes have been investigated as modifiers of treatment response and outcome. Early studies reported that GSTM1 and GSTT1 deletions did not significantly influence response or survival in NDMM patients treated with vincristine, doxorubicin, and dexamethasone (VAD) or high-dose melphalan [ 171 ]. Similarly, Schilthuizen et al. analyzed CYP3A4, CYP3A5, MDR1, GSTM1 , and GSTT1 variants in 209 NDMM patients and found no significant associations with outcome or toxicity [ 195 ]. In contrast, data from the MRC VII trial showed that the GSTP1 Val/Val genotype was associated with improved outcome in patients receiving conventional chemotherapy-based regimens [ 172 ], suggesting context-dependent pharmacogenetic effects.
Genetic variation in MDR1 (ABCB1) has also been associated with differential outcomes. Xiao et al. reported that the T allele at C1236T was associated with longer PFS than CC homozygotes, and the T allele at C3435T was associated with longer PFS than CC, with no significant OS association [ 173 ].
Larger multicenter analyses from the IMMEnSE consortium identified survival associations for ABCB1 and ABCC2 variants [ 174 ], supporting a role of transporter polymorphism in therapy modulation rather than baseline susceptibility [ 176 ]. ABCC2 overexpression has also been linked to increased drug clearance and resistance [ 174 ]. In contrast, a meta-analysis of MDR1 rs1045642 (C > T) across four case-control studies found no association with disease susceptibility, consistent with a predominant role in therapy modulation rather than baseline risk [ 175 ].
DNA damage response and genomic stability
Genomic instability is a defining feature of MM and reflects alterations in DDR pathways that promote clonal evolution and therapeutic resistance. Both intrinsic repair defects and microenvironmental modulation contribute to altered DDR dynamics [ 196 , 197 ]. Bone marrow niche-derived signals modulate DDR activation and repair capacity, reinforcing instability and therapy resistance [ 197 ].
DDR signaling is frequently compromised. Alterations in checkpoint regulators such as ATM and TP53 blunt apoptotic responses, allowing unstable clones to persist [ 196 ]. Compensatory activation of specific repair modules may further sustain survival under genotoxic stress [ 196 ]. The microenvironment amplifies instability through hypoxia, oxidative stress, inflammatory cytokines, and stromal-derived factors that increase DNA damage and influence DDR pathway choice [ 198 ]. Epigenetic regulators also modulate DDR control. SIRT6 regulates DNA damage signaling and genome stability, and elevated expression correlates with adverse outcomes and resistance to DNA-damaging agents [ 199 ].
Immune regulation and inflammatory pathways (NLRP3, NF-κB, cytokines)
Dysregulation of the NLRP3 inflammasome pathway has been described in MM, with reduced NLRP3 and caspase-1 in marrow plasma cells accompanied by elevated circulating IL-18 and altered sRANKL/OPG ratios [ 200 ]. Inflammasome activation also extends beyond malignant plasma cells, as β2-microglobulin induces NLRP3 activation in tumor-associated macrophages, increasing IL-1β/IL-18 and promoting progression [ 201 ].
Polymorphisms in inflammasome-related genes, particularly CARD8 - C10X (rs2043211), have been associated with MM susceptibility and immune-related clinical characteristics [ 180 ], while variants in NF-κb1 (rs28362491) and IL-18 (rs16944) correlated with tumor burden parameters [ 180 ]. Meta-analyses further report associations between IL-6, IL-1 , and IL-10 polymorphisms and MM susceptibility [ 181 ]. Although peripheral T helper subsets are implicated in MM biology, associations with inflammasome polymorphisms appear limited [ 180 ], indicating that inflammatory dysregulation may be compartment-restricted.
Plasma cell differentiation and transcriptional regulation (ELL2, IRF4 axis)
Functional characterization of germline susceptibility loci provides mechanistic insight into inherited risk. Li et al. identified rs6877329 as a functional variant at 5q15, showing disruption of a B cell-specific enhancer ∼35 kb upstream of ELL2 that loops to the ELL2 promoter [ 55 ]. The rs6877329-C risk allele reduces enhancer activity and was associated with decreased ELL2 expression in CD138⁺ plasma cells, supported by eQTL analyses, and this effect was lineage-restricted with no detectable effect in non-plasma cell compartments.
Ali et al. confirmed that the 5q15 risk allele lowers ELL2 expression across populations and associates with increased ribosomal gene expression [ 182 ]. ELL2 regulates terminal B-cell differentiation and immunoglobulin production as part of the super-elongation complex. Park et al. showed that ELL2 drives secretory mRNA production and activates the unfolded protein response (UPR) in plasma cells [ 202 ]. Reduced ELL2 expression therefore links regulatory variation to impaired differentiation and risk of transformation. ELL2 interfaces with core plasma-cell transcriptional programs, and its perturbation may favor differentiation states that support clonal persistence [ 202 ].
Angiogenesis and microenvironment modulators (VEGF/VEGFR)
Angiogenesis contributes to MM pathogenesis and prognosis, and increased marrow microvessel density is associated with unfavorable outcomes, supporting the rationale for targeting vascular endothelial growth factor (VEGF) signaling [ 203 ].
Genetic variation within the VEGF signaling axis modulates angiogenic activity and response to thalidomide-based regimens. The ACG haplotype composed of rs699947, rs833061, and rs2010963, associated with increased VEGF production, was linked to shorter time to thalidomide failure in relapsed MM and shorter time to next treatment in thalidomide-treated NDMM cohorts [ 184 ].
At the tissue level, VEGF rs1570360GG carriers showed higher bone marrow microvessel density [ 185 ]. Polymorphisms in VEGF and VEGFR2 have been associated with treatment response and with disease risk and aggressiveness in case-control analyses [ 204 ]. Genotypes associated with higher angiogenic signaling were linked to increased relapse or progression risk independent of ISS or transplant status [ 185 ].
HLA polymorphisms and immune surveillance
Human leukocyte antigen (HLA) molecules mediate immune surveillance by presenting antigenic peptides to T-cell receptors. HLA class I/II polymorphisms shape peptide-binding repertoires and influence immune recognition thresholds [ 205 ]. In MM, inherited HLA variation has been implicated in disease susceptibility and immune control [ 187 ].
GWAS identified HLA-DRB501 as risk allele tagging the classical HLA-DRB101:01 [ 187 ]. In addition, HLA-C07:02 g and HLA-B07:02 g were also reported as independent susceptibility factors, supporting contributions from both class I and class II molecules. HLA class I variation may also influence NK-cell regulation through KIR interactions, thereby influencing immune surveillance [ 189 ].
Beelen et al. reported that a C1-/C2+/Bw4+ epitope combination was associated with MM occurrence, with increased Bw4/KIR3DL1 and C2/KIR2DL1 genotype co-occurrence in MM patients [ 188 ]. Martínez-Sánchez et al. reported that MM risk is associated with less diverse and lower-affinity KIR-HLA-C licensing interactions, a pattern associated with reduced NK responsiveness and potential immune escape [ 189 ].
Therapeutically, inhibitory NK checkpoints restrain anti-myeloma activity, and targeting these pathways may enhance NK cytotoxicity [ 206 ]. Collectively, inherited HLA/KIR variation shapes MM susceptibility and immune control by modulating NK-cell education and effector function.
Genetic determinants of therapeutic response in MM
Genetic determinants of response to PIs
PIs inhibit the proteolytic core of the ubiquitin-proteasome system (UPS), a central regulator of protein turnover and signaling homeostasis. By blocking UPS-dependent degradation, proteins accumulate, inducing proteotoxic stress and activation of terminal UPR. This mechanism is particularly relevant in malignant plasma cells, where high immunoglobulin production and genetically driven secretory load create substantial proteostasis stress and intrinsic vulnerability [ 207 ].
Proteasome blockade induces ER stress, immunoglobulin retention, UPR hyperactivation, and disruption of survival transcriptional programs. Experimental data indicate that the magnitude of UPR activation correlates with PI sensitivity, supporting a transcriptional state-dependent response.
Response to PIs is heterogeneous and reflects tumor-intrinsic programs and inter-individual modifiers. Tumor genomic architecture can increase protein synthesis, secretory burden, and regulatory instability, elevating proteostasis workload and UPS dependence [ 208 , 209 ]. Next-generation inhibitors differ in subunit selectivity and depth of catalytic blockade, modulating stress-network disruption and response patterns [ 208 , 209 ]. Gene expression-based predictors further support a transcriptionally determined component of PI response [ 210 ]. Germline polymorphisms in proteasome-related genes have been reported, although most signals remain candidate modifiers without clinical validation [ 211 ].
Differences between Btz, carfilzomib (Kfz), and ixazomib (Ixa) reflect distinct subunit engagement and depth of catalytic blockade superimposed on shared UPS dependence.
Btz is a reversible β5 subunit inhibitor that perturbs proteostasis and stress-response networks in MM cells. It induces proteotoxic stress, activates the UPR, and modulates NF-κb signaling in a context-dependent manner, targeting genetically constrained survival circuits [ 209 ].
UPR effectors including PERK and ATF4 are rapidly activated. Baseline and inducible expression of UPR regulators such as XBP1, ATF3 , and ATF4 has been associated with differential Btz sensitivity, supporting transcriptional state-dependent response [ 212 , 213 ]. NF-κb effects are context dependent and can include canonical activation, underscoring condition-dependent pathway modulation [ 214 ].
Gene-expression signatures further support drug-class–specific transcriptional determinants of response [ 210 ].
Pharmacogenomic studies suggest that regulatory variation may contribute to response heterogeneity [ 211 ]. Variants in proteasome subunits (e.g., PSMB5, PSMB6, PSMB9) have been associated with differential response in exploratory cohorts, although survival correlations remain inconsistent [ 215 , 211 ].
Resistance emerges through transcriptional and genetic adaptation, including rewiring, UPS dysregulation, and therapy-driven clonal selection [ 216 ]. Refractory disease frequently coexists with broader signaling alterations, including RAS-pathway mutations [ 217 ]. CRISPR-based screens indicate distributed genetic control of PI sensitivity rather than single dominant resistance drivers [ 218 ].
Kfz, through irreversible binding and deeper catalytic blockade, may partially overcome resistance linked to reversible β5 inhibition (Ito, 2020; [ 219 ]). However, resistance ultimately emerges through similar adaptive remodeling mechanisms. Exploratory pharmacogenomic data suggest that germline variation outside proteasome subunits may influence outcomes. However, they remain hypothesis-generating [ 220 ].
Ixa is an oral β5-targeting PI with partially overlapping resistance patterns [ [216] , [221] ]. Preclinical data suggest multiple regulatory determinants of Ixa sensitivity. Wild-type KRAS status has been associated with greater Ixa sensitivity than activating KRAS variants [ 221 ]. In lymphoid malignancies, sensitivity correlates with immunoproteasome activity and can be enhanced by interferon-driven immunoproteasome induction, implicating inducible subunit composition as a regulatory layer [ 222 ]. Additional studies implicate checkpoint kinase- and MYC -associated transcriptional programs in response heterogeneity [ 223 ]. In myeloma-related models, Ixa has been linked to induction of miR-33b with downstream inhibition of PIM1 , and to microenvironmental effects including stronger disruption of NF-κB signaling in stromal compartments than Btz, with reduced cytokine-mediated resistance and effects on osteoclast/osteoblast balance [ 224 ].
Clinically, IRd significantly prolongs PFS in RRMM in a phase III trial, with benefit observed across prespecified subgroups including high-risk cytogenetic categories [ 225 ]. High-risk abnormalities such as del(17p), t(4;14), t(14;16), and 1q21 gain remain associated with inferior PFS overall [ 226 ]. Subgroup analyses suggest that IRd reduces the hazard of progression versus Rd alone in high-risk patients, indicating partial mitigation of cytogenetic risk rather than full risk neutralization. Very high clonal burden of del(17p) remains associated with the poorest outcomes [ 227 ]. Earlier phase I/II studies also supported activity and tolerability [ 226 ].
From a pharmacogenetic perspective, no germline SNPs in proteasome subunits or angiogenesis pathways have been validated as predictors of Ixa efficacy or toxicity. Although preclinical work supports selective subunit inhibition balance, clinical translation remains limited, and biomarker-driven studies are needed to define robust predictors in high-risk and combination-treated populations.
Genetic determinants of response to IMiDs and immunotherapies
IMiDs (thalidomide, lenalidomide, pomalidomide) are central immune-modulating agents in MM, combining tumor-intrinsic transcriptional targeting with immune and microenvironmental effects [ 228 ].
IMiDs bind cereblon (CRBN), the substrate receptor of a cullin-RING E3 ligase complex, inducing degradation of IKZF1 and IKZF3 and defining the CRBN-IKZF-IRF4 axis [ [228] , [229] ]. This leads to IRF4 and MYC downregulation and reprogramming of survival networks, while simultaneously enhancing T- and NK-cell function [ 228 , 230 ]. Alterations affecting CRBN and related pathway components, together with transcriptional rewiring and clonal selection under treatment pressure, are key determinant of resistance [ 231 , 232 ].
Beyond mutations and CNAs, treatment-selected DNA methylation changes also contribute. CRBN flanking/enhancer hypermethylation (up to 64% of IMiD-resistant cases) and PSMD5 promoter hypermethylation (15–24% of PI-refractory cases), both correlating with reduced expression [ 233 ].
Genetic and microenvironmental basis for immune-based therapies in MM
MM is characterized by genetically and transcriptionally driven immune dysregulation and immune escape. Malignant plasma cells reshape the bone marrow niche through cytokine signaling, stromal interactions, and immune checkpoint modulation, generating an immunosuppressive microenvironment that suppresses anti-tumor immune responses [ [215] , [234] , 235 ].
Soluble mediators (IL-6 and TGF-β), adhesion-dependent signaling, and checkpoint pathways (PD-L1 and TIGIT), support this suppressive niche. High-risk lesions, such as del(17p), t(4;14), and 1q gain have been associated with activation of NF-kB/IRF4-centered networks and APRIL/BAFF signaling, potentially favoring expansion of immunosuppressive populations and impair NK and CD8⁺ T-cell cytotoxicity. MYC -rearranged disease has also been linked to reduced antigen-presentation programs, including MHC-I downregulation, further promoting immune evasion.
Microenvironmental circuits involving macrophage polarization, dendritic-cell dysfunction, regulatory T-cell expansion, and impaired NK-cell activity further limit antitumor immunity and contribute to resistance [ 235 ].
These immune alterations provide the biological substrate for immune-based therapies and partly explain synergy between monoclonal antibodies and IMiDs [ 234 ].
IMiDs and cereblon modulators
Genetic and regulatory variation may modulate IMiD response, but is not yet clinically consolidated. Efficacy reflects tumor dependency on CRBN-centered programs plus host immune context, whereas resistance involves CRBN-pathway disruption, transcriptional rewiring, and clonal selection [ 231 , 232 ]. In MM, TLR4 and TIRAP SNPs were associated with lower response rates and shorter PFS/OS in IMiD-containing primary therapy [ 236 ]. SNPs in ADME genes such as ABCB1, ABCG2 and CYP3A4 have been associated with response/toxicity to lenalidomide-based therapy [ 237 ]. Germline variation within the CRBN has also been implicated: minor alleles at rs1714327 and rs1705814 were associated with outcomes in thalidomide-containing regimens (CTD) [ 179 ]. However, reproducible genome-wide significant loci for IMiD-specific response are lacking, and most SNP associations remain suggestive; clinical implementation is premature.
Antibody-based therapies
Efficacy of antibody-based therapies is determined by antigen locus integrity, transcriptional regulation of target density, and host immunogenetic background [ 238 , 239 ]. Anti-CD38 therapy depletes CD38⁺ immune regulatory populations and reshapes T-cell repertoires, linking antigen expression to immune-mediated clearance [ 240 ]. Inherited antigen sequence variation can weaken epitope recognition and contribute to primary resistance, supported by variant-level analyses showing loss of antibody binding due to germline antigen variation [ 241 ]. Antigen-density heterogeneity and host immunogenetic variation, including Fcγ receptor polymorphisms, further modulate response [ 242 ].
T-cell-redirecting strategies
T-cell-redirecting therapies are tightly coupled to antigen-locus integrity, clonal architecture, and immune transcriptional states. Bispecific antibodies and CAR-T cells bypass MHC restriction but impose strong selective pressure that favors antigen-loss variants and immune-state shifts [ 243 ].
Bispecifics and CAR-T constructs engage CD3 and redirect cytotoxicity toward antigens such as BCMA and GPRC5D [ 244 ]. Activity depends on antigen density/epitope architecture and T-cell activation states, while pre-existing heterogeneity provides a substrate for escape [ 243 ] ( Table 4 ). Table 4 Genetic and transcriptional escape mechanisms in T-cell–redirecting therapies. Table 4 dummy alt text TARGET THERAPY TYPE GENETIC / MOLECULAR ALTERATION REPORTED PATTERN FUNCTIONAL IMPLICATION REFERENCE BCMA (TNFRSF17) BCMA CAR-T Biallelic loss (deletions) Rare but confirmed in post-CAR-T relapse Loss of BCMA expression, absent soluble BCMA, impaired CAR-T expansion [ 245 ] BCMA (TNFRSF17) CAR-T / bispecific antibodies Biallelic deletions and mutations Subset of post-BCMA immunotherapy relapses Target loss–mediated escape [ 246 ] BCMA (TNFRSF17) CAR-T / bispecific antibodies Co-alterations in NF-κB regulators (CYLD, TRAF3) Enriched in resistant/high-risk cases Compensatory survival signaling [ [243] , [246] ] GPRC5D Bispecific antibodies / CAR-T Biallelic deletions, copy-number loss, regulatory loss Recurrent mechanism at relapse after GPRC5D-targeted therapy Reduced or absent antigen density [ 246 ] — BCMA CAR-T Transcriptional reprogramming (SOX4, CD24 ↑; SDC1, XBP1 ↓) Residual post-therapy clones Dedifferentiation and lineage plasticity [ [245] , [246] ] — CAR-T / bispecific antibodies T-cell exhaustion signatures (PDCD1, HAVCR2, LAG3 ↑) Resistance with retained antigen Effector T-cell dysfunction [ 243 ] Genetic and transcriptional mechanisms associated with resistance to T-cell–redirecting therapies in MM include target-antigen loss through biallelic deletions, mutations, and CNVs, as well as non-genetic escape programs such as tumor-cell dedifferentiation and T-cell exhaustion. Reported frequencies vary across studies and platforms and are often derived from small, genomically profiled relapse cohorts using bulk and/or single-cell sequencing approaches. Alterations in NF-κB pathway regulators (e.g., CYLD, TRAF3) are shown when co-occurring with antigen loss or resistance phenotypes.
Table 4
Genetic and transcriptional escape mechanisms in T-cell–redirecting therapies.
Genetic and transcriptional mechanisms associated with resistance to T-cell–redirecting therapies in MM include target-antigen loss through biallelic deletions, mutations, and CNVs, as well as non-genetic escape programs such as tumor-cell dedifferentiation and T-cell exhaustion. Reported frequencies vary across studies and platforms and are often derived from small, genomically profiled relapse cohorts using bulk and/or single-cell sequencing approaches. Alterations in NF-κB pathway regulators (e.g., CYLD, TRAF3) are shown when co-occurring with antigen loss or resistance phenotypes.
| TARGET | THERAPY TYPE | GENETIC / MOLECULAR ALTERATION | REPORTED PATTERN | FUNCTIONAL IMPLICATION | REFERENCE |
| BCMA (TNFRSF17) | BCMA CAR-T | Biallelic loss (deletions) | Rare but confirmed in post-CAR-T relapse | Loss of BCMA expression, absent soluble BCMA, impaired CAR-T expansion | [ 245 ] |
| BCMA (TNFRSF17) | CAR-T / bispecific antibodies | Biallelic deletions and mutations | Subset of post-BCMA immunotherapy relapses | Target loss–mediated escape | [ 246 ] |
| BCMA (TNFRSF17) | CAR-T / bispecific antibodies | Co-alterations in NF-κB regulators (CYLD, TRAF3) | Enriched in resistant/high-risk cases | Compensatory survival signaling | [ [243] , [246] ] |
| GPRC5D | Bispecific antibodies / CAR-T | Biallelic deletions, copy-number loss, regulatory loss | Recurrent mechanism at relapse after GPRC5D-targeted therapy | Reduced or absent antigen density | [ 246 ] |
| — | BCMA CAR-T | Transcriptional reprogramming (SOX4, CD24 ↑; SDC1, XBP1 ↓) | Residual post-therapy clones | Dedifferentiation and lineage plasticity | [ [245] , [246] ] |
| — | CAR-T / bispecific antibodies | T-cell exhaustion signatures (PDCD1, HAVCR2, LAG3 ↑) | Resistance with retained antigen | Effector T-cell dysfunction | [ 243 ] |
Biallelic loss of TNFRSF17 (BCMA) is a demonstrated resistance mechanism to BCMA CAR-T, with absent soluble BCMA and impaired CAR-T expansion [ 245 ]. BCMA loss also occurs after BCMA bispecifics, indicating a shared escape route across platforms; although uncommon (<5% of relapses), acquired biallelic TNFRSF17 loss is a convergent treatment-selected mechanism [ [246] , [247] , [248] , [249] ]. GPRC5D loss is recurrent after GPRC5D -directed therapies [ 246 ], and high-risk features such as 1q gain and NF-κb lesions (e.g., CYLD, TRAF3 ) associate with inferior PFS [ [243] , [246] ].
Therapeutic pressure plays a central role in shaping clonal evolution, with different treatment classes imposing distinct selective bottlenecks, consistent with immunoediting processes [ 250 ]. Conventional agents such as PIs and IMiDs exert broader cytotoxic and microenvironmental effects, contributing to gradual shifts in clonal composition and promoting the outgrowth of resistant subclones. In contrast, modern immunotherapies, including CAR T-cell therapies and bispecific antibodies, impose highly specific antigen-directed selective pressures. A key mechanism of resistance in this context is antigen escape, characterized by downregulation or loss of target antigens such as BCMA, as well as the expansion of antigen-negative tumor populations [ 251 , 252 ]. Emerging evidence in MM supports both the selection of pre-existing antigen-negative subclones and the acquisition of genetic alterations affecting target antigens under immune pressure. These mechanisms enable tumor cells to evade immune-mediated killing and represent a major driver of relapse following immunotherapy. However, while antigen escape is increasingly well characterized in the context of immunotherapy, direct comparative evidence defining how distinct therapeutic classes differentially shape clonal bottlenecks remains limited. Understanding antigen escape and therapy-specific evolutionary bottlenecks will be critical for the development of next-generation strategies aimed at preventing resistance and achieving durable responses.
Post-BCMA CAR-T relapse can show stemness programs (e.g., SOX4, CD24 ) with reduced plasma-cell markers (e.g., SDC1, XBP1 ), consistent with plasticity [ [245] , [246] ]. Dual-targeted BCMA/CD24 CAR-T improves control in models (Sun et al., 2024). These observations motivate combinations aimed at restoring T-cell fitness to improve durability [ 253 , 254 ].
Biomarkers and resistance under immune pressure
Tumor-intrinsic genomic architecture influences response depth and durability, and high-risk lesions such as del(17p), 1q gain, and alterations in NF-κB regulators including CYLD and TRAF3 have been associated with inferior outcomes after T-cell-redirecting therapies [ [243] , [246] ]. Integrity of the therapeutic target locus is a direct determinant of susceptibility, as biallelic loss or focal deletion of TNFRSF17 or GPRC5D can mediate resistance to BCMA- and GPRC5D -directed platforms [ [245] , [246] ]. More broadly, increased genomic complexity and subclonal diversity contribute to response heterogeneity, consistent with models linking intratumoral diversity to therapeutic resistance [ 255 ].
Transcriptomic and immunoregulatory programs provide complementary biomarkers. Post–BCMA CAR-T relapse samples may show enrichment of stemness-associated programs (e.g., SOX4, CD24) together with downregulation of plasma-cell differentiation markers (e.g., SDC1, XBP1), consistent with plasticity and dedifferentiation as escape routes [ [245] , [246] ]. In parallel, expanded T-cell populations at relapse frequently display exhaustion-associated signatures with increased expression of inhibitory receptor genes including PDCD1, HAVCR2 , and LAG3 , linking immune-state profiles with functional resistance and limited persistence of redirected T-cell responses [ 243 ]. Host immunogenetic background and the bone marrow microenvironment further modulate efficacy. Germline variation in immune signaling and antigen-presentation pathways, including TLR-axis and HLA polymorphisms, has been associated with differential response and survival in IMiD-containing regimens [ 236 , 256 ]. At the microenvironmental level, immunosuppressive myeloid populations, regulatory T cells, and dysfunctional antigen-presenting cells can reduce effector activity and limit redirected T-cell effectiveness.
This structural and functional complexity limits the predictive value of single-analyte biomarkers and supports composite models incorporating immune-context variables [ 257 ]. Longitudinal analyses indicate that immune therapies constrain clonal diversity and select resistant populations, consistent with immunoediting [ 258 ]. Overall, available evidence supports composite biomarkers integrating antigen density, tumor genomics, transcriptional states, and microenvironmental features to improve response prediction and inform stratified sequencing and combination strategies.
Genetically stratified targeted therapies
Genetically stratified targeted therapies in MM exploit tumor-specific genetic and epigenetic vulnerabilities identified through cytogenetic and regulatory profiling. Agents such as HDAC and BCL-2 inhibitors exemplify mechanism-based strategies directed at epigenetic dysregulation and apoptotic dependency, illustrating the shift toward molecular selection based on tumor architecture ( Table 5 ). Table 5 Examples of genetically stratified targeted strategies in MM. Table 5 dummy alt text GENETIC FEATURE TARGETED STRATEGY / AGENT BIOLOGICAL RATIONALE KEY REFERENCES T(11;14) Venetoclax BCL-2 dependency and mitochondrial priming profile [ 259 , 260 ] T(4;14) / MMSET HDAC inhibitor–based combinations Epigenetic dysregulation and chromatin-regulatory dependency [ 261 , 262 ] DEL(17P), 1Q GAIN Intensified / targeted combinations Relative MCL-1 or BCL-xL dependence and network instability [ [261] , [263] ] Illustrative examples of genetically stratified targeted approaches in MM. Strategies reflect enrichment of therapeutic sensitivity in biologically defined subgroups and should be interpreted within combination-regimen and clinical-trial contexts.
Table 5
Examples of genetically stratified targeted strategies in MM.
Illustrative examples of genetically stratified targeted approaches in MM. Strategies reflect enrichment of therapeutic sensitivity in biologically defined subgroups and should be interpreted within combination-regimen and clinical-trial contexts.
| GENETIC FEATURE | TARGETED STRATEGY / AGENT | BIOLOGICAL RATIONALE | KEY REFERENCES |
| T(11;14) | Venetoclax | BCL-2 dependency and mitochondrial priming profile | [ 259 , 260 ] |
| T(4;14) / MMSET | HDAC inhibitor–based combinations | Epigenetic dysregulation and chromatin-regulatory dependency | [ 261 , 262 ] |
| DEL(17P), 1Q GAIN | Intensified / targeted combinations | Relative MCL-1 or BCL-xL dependence and network instability | [ [261] , [263] ] |
HDAC inhibitors: epigenetic vulnerability and regulatory network targeting
Epigenetic dysregulation is a recurrent feature of MM and provides a rationale for targeting chromatin and transcriptional control. HDAC inhibitors disrupt gene-expression programs and appear particularly relevant in biologically defined subsets such as t(4;14) disease with MMSET overexpression, where epigenetic dependency may be accentuated. Their synergy with proteasome inhibitors reflects convergence of proteostasis stress and epigenetic deregulation, supporting use in rational combinations rather than as standalone agents [ 261 , 262 ].
BCL-2 inhibitors: genetically defined apoptotic dependency
Targeting apoptotic circuitry is one of the clearest examples of stratified therapy in MM. Venetoclax exploits apoptotic vulnerability most strongly in t(11;14) disease, which typically displays transcriptional and mitochondrial profiles consistent with BCL-2 dependence, partly linked to CCND1 dysregulation. Mechanistically, venetoclax binds BCL-2, displaces pro-apoptotic factors such as BIM, activates BAX/BAK, and induces mitochondrial outer membrane permeabilization and selective apoptosis [ 264 ].
Sensitivity correlates with high BCL2 / BCL2L1 mRNA ratios and mitochondrial priming, whereas dependency on MCL-1 or BCL-xL is more typical outside t(11;14), including in high-risk subgroups. Clinical studies confirm higher response rates in relapsed t(11;14)-positive patients, particularly in combination regimens [ 259 , 260 ].
Stratification using FISH together with expression-based dependency markers can refine selection, while activity outside molecularly selected subgroups is reduced and may be attenuated by lesions such as 1q gain. Emerging extensions include MCL-1 inhibitors and broader BH3-mimetic strategies targeting non-BCL-2-dependent clones.
Other targeted agents and antigen-defined strategies
Beyond epigenetic and apoptotic targeting, additional precision strategies address surface antigens and deregulated signaling networks within a context of antigen heterogeneity and clonal selection. High-risk features such as 1q gain and del(17p), which disrupt cell-cycle and p53-centered programs, increasingly justify intensified regimens and investigational combinations including nuclear export (XPO1) inhibition. Whole-genome features such as chromothripsis and APOBEC mutational activity further refine biological risk and support escalation beyond standard backbones, consistent with network-level, genetically informed combination strategies [ 261 , 262 ].
Germline genetics and clinical outcomes in MM
Disease progression and survival
Interindividual differences in progression and survival in MM are not fully explained by tumor burden, cytogenetics, or treatment response alone [ 265 ]. Real-world analyses show that comorbidity burden influences early mortality, particularly within the first year after diagnosis [ 266 ], yet host germline variation also contributes to heterogeneity in progression dynamics and outcomes [ 267 ]. Inherited factors may modulate plasma-cell biology, immune interactions, and treatment tolerance, shaping both precursor evolution and durability of response [ 88 ].
GWAS have identified survival-associated loci, including variants at 16p13 linked to overall survival independently of conventional risk markers [ 78 ]. A subset of patients carries pathogenic inherited variants in DNA damage–repair genes such as BRCA1, BRCA2, CHEK2 , and ATM , enriched relative to the general population [ 130 , 265 ]. Common germline loci also influence immune regulation and plasma-cell function [ 75 ]. Notably, the clinical impact of DNA repair-deficient variants appears therapy dependent, as carriers may experience comparable or even improved outcomes with intensive DNA-damaging approaches, including high-dose melphalan and autologous transplantation [ 268 , 269 ]. In addition, non-coding variants affecting transcriptional programs, including IRF4 -related pathways, have been associated with survival differences [ 270 ].
Treatment-Related toxicity
Treatment-related toxicity partly reflects inherited differences in drug-metabolizing enzymes, transporters, DNA repair pathways, and stress-response genes [ 271 ].
These germline factors interact with tumor biology, the microenvironment, and treatment characteristics to influence tolerance and complications such as neuropathy, cytopenias, infections, thromboembolism, renal injury, and second malignancies [ [272] , [273] , [274] ]. Toxicities from IMiDs and alkylators further suggest interactions between DNA-damaging exposure, marrow reserve, and DNA-repair capacity, although validated germline predictors remain limited [ 229 , 230 ].
Peripheral neuropathy
Peripheral neuropathy, particularly with Btz and thalidomide, is influenced by host germline variation [ 275 ]. Btz-induced neuropathy involves axonal injury, mitochondrial dysfunction, and stress-response dysregulation, with susceptibility linked to variants at the PKNOX1/CBS locus and to inflammatory or angiogenic profiles such as IL-8 and VEGF [ [276] , [277] ]. Thalidomide-related neuropathy also shows interindividual variability consistent with genetic differences in neuronal resilience and repair [ 278 ].
Bone disease
Myeloma-associated bone disease reflects disrupted bone remodeling driven by malignant plasma cells and the microenvironment, leading to osteolytic lesions and skeletal-related events [ [279] , [280] , [281] , [282] ]. Skeletal complications and altered bone formation markers may appear even in smoldering stages [ 283 ].
Interindividual variability in severity suggests a contribution of host germline variation. Variants in pathways regulating bone remodeling, immune signaling, and Wnt activity may influence susceptibility to osteolytic damage and skeletal involvement at diagnosis [ 284 ]. These data support integrating germline profiling into skeletal-risk models, particularly in MGUS or smoldering disease where bone changes may precede systemic progression [ 285 ].
Gastrointestinal toxicity and mucositis
Susceptibility to gastrointestinal toxicity and mucositis is partly influenced by inherited variation [ 286 ]. These complications can impair quality of life and treatment adherence [ 287 ]. Variation in genes regulating drug metabolism, mucosal repair, inflammatory signaling, and epithelial integrity likely modulates severity, and GWAS in transplant recipients have identified loci associated with chemotherapy-induced oral mucositis [ 288 ].
Thromboembolic complications
Inherited germline variation contributes to thromboembolic risk in MM, which arises from both disease- and treatment-related prothrombotic states [ 289 ]. Variants affecting coagulation and endothelial pathways, including F5, F2, MTHFR , and SERPINE1 , may predispose subsets of patients to venous thromboembolism [ 290 , 291 ]. These genetic differences interact with inflammation and treatment exposure to shape individual susceptibility.
Clinical implications and future directions
Future research in MM should prioritize integrated longitudinal designs that link genomic architecture to functional and clinical phenotypes. Although current cytogenetic and sequencing frameworks define major driver categories, important gaps remain in subclonal reconstruction, evolutionary timing, and functional interpretation. This limitation is particularly relevant in the context of MM as a genetically complex and evolutionarily dynamic disease, characterized by marked clonal heterogeneity and a continuous transition from precursor states to symptomatic disease [ 292 ]. Serial multi-omics profiling combining WGS, transcriptomics, epigenomics, and single-cell approaches will be essential to map clonal dynamics under treatment pressure and distinguish early driver events from adaptive changes. In this context, single-cell profiling technologies represent a key opportunity to resolve intratumoral heterogeneity and refine precision oncology strategies [ 152 ].
From a clinical perspective, the translation of these genomic insights into routine practice remains incomplete. Current risk stratification systems, including the Revised International Staging System (R-ISS), incorporate selected cytogenetic abnormalities such as del(17p), t(4;14), and 1q gain, but largely rely on static genomic features and do not capture clonal heterogeneity, subclonal dynamics, or treatment-driven evolution. Integrating longitudinal genomic data, MRD assessment, and clonal architecture into these frameworks represents a key opportunity to refine prognostic accuracy and enable adaptive risk stratification.
Improving genomic resolution in routine practice is equally important. Broader implementation of high-coverage sequencing, optical mapping, and chromatin-conformation–aware methods may reveal structural variants and regulatory disruptions not captured by standard FISH or targeted panels. Harmonized testing platforms and reporting standards will be required to ensure reproducible and clinically actionable stratification. However, the implementation of advanced genomic approaches, including subclonal inference from bulk sequencing data, remains limited by the lack of standardized bioinformatic pipelines, methodological variability, and restricted accessibility in clinical laboratories.
From the germline perspective, systematic predisposition-testing approaches are needed, as current criteria likely underestimate inherited risk. Integration of germline sequencing, polygenic risk scores, and family-based screening approaches may enable earlier identification of high-risk individuals and inform surveillance strategies in MGUS and SMM, including assessment of gene–environment interactions. Nevertheless, routine germline testing is not yet widely implemented outside selected clinical contexts, as penetrance, clinical utility, and management guidelines remain insufficiently defined. In addition, PRS, despite demonstrating population-level risk stratification, are not currently clinically actionable due to the lack of prospective validation, reduced performance across diverse ancestries, and absence of standardized thresholds or integration frameworks with established clinical risk factors.
Functional validation remains critical, as many GWAS loci and CNVs map to regulatory regions with incompletely defined roles. CRISPR-based perturbation screens and microenvironment-aware models can translate association signals into pathway dependencies and therapeutic targets, guiding rational combination strategies and resistance-prevention approaches. Unresolved questions remain regarding the interaction between germline susceptibility, somatic evolution, and environmental exposures, highlighting the need for integrative studies that connect genetic architecture with functional and clinical phenotypes.
Clinical translation will require embedding genomic data into adaptive trial designs supported by real-time molecular monitoring. Biomarker-driven and genomically stratified trials, complemented by multi-layer data modeling and artificial intelligence approaches, can enable evolution-aware precision management rather than static risk assignment. From a therapeutic standpoint, genomic information is increasingly relevant for treatment selection and monitoring, including the identification of targetable dependencies (e.g., BCL-2 in t(11;14) disease) and the anticipation of resistance mechanisms such as antigen escape in T-cell–redirecting therapies. Integration of genomic, transcriptomic, and immune profiling into treatment algorithms may enable more precise patient selection, inform combination strategies, and improve long-term disease control. Ultimately, bridging the gap between genomic discovery and clinical implementation will be essential to fully realize the potential of precision oncology in MM.
Conclusions
MM is defined by a multilayered genomic architecture in which primary cytogenetic events, secondary structural alterations, copy-number remodeling, somatic mutations, and inherited susceptibility collectively shape disease behavior. IgH translocations and hyperdiploidy establish early biological subtypes, whereas arm-level and focal CNVs, MYC activation, and TP53 loss drive progression, heterogeneity, and therapy-influenced clonal evolution.
Germline predisposition and polygenic susceptibility further modulate interindividual risk and interact with environmental and immune factors, particularly in precursor states, reinforcing the concept of MM as a genomically defined disease spectrum rather than a purely clinicopathologic entity.
Despite these advances, translation into uniformly effective precision care remains incomplete, as detection gaps, subclonal complexity, and limited functional interpretation constrain predictive accuracy. An integrated precision framework linking cytogenetics, comprehensive sequencing, germline risk, immune context, and dynamic clonal assessment provides a realistic path to improve early detection, personalize therapy, delay resistance, and enhance long-term outcomes.
However, several key barriers continue to limit clinical implementation. Emerging tools such as PRSs and subclonal reconstruction methodologies, while conceptually aligned with this framework, are not yet standardized or clinically actionable. Overcoming these limitations will require prospective validation, harmonized analytical pipelines, and integration of genomic data into real-time clinical decision-making. Addressing these challenges will be essential to fully translate the evolutionary genomics approach into effective precision oncology strategies in MM.
CRITICAL VIEW
Most reviews in multiple myeloma (MM) genetics still treat germline risk, primary cytogenetics, and relapse biology as separable layers, often summarized as static “lists” of lesions or biomarkers. This review takes a different stance: MM is best conceptualized as a dynamic evolutionary genomic ecosystem, where germline susceptibility and somatic architecture are not parallel narratives but interacting determinants of clonal initiation, diversification, and therapy-driven selection. Our central contribution is therefore an evolution-aware integrative framework that links (i) inherited predisposition (polygenic burden and rare predisposition variants), (ii) founding genomic events (IgH translocations and hyperdiploidy), (iii) progression-associated remodeling (CNV restructuring, MYC dysregulation, TP53 loss, complex structural variation), and (iv) treatment adaptation (immune pressure, antigen escape, and transcriptional plasticity) into a single coherent model of disease behavior.
How this review distinguishes itself from existing literature. We move beyond “high-risk feature” cataloguing by emphasizing trajectory rather than status: the clinically relevant question is increasingly which evolutionary path a patient’s disease is on, not merely which lesion is present at diagnosis. In practice, this shifts attention toward clonal architecture, timing of events, and the selective pressures imposed by modern therapy. We highlight that the same genomic feature can carry different implications depending on context (co-lesions, subclonal fraction, prior therapies, immune landscape), and we explicitly frame resistance as the predictable outcome of repeated evolutionary bottlenecks. This perspective naturally connects cytogenetics and sequencing outputs to actionable clinical hypotheses: anticipating relapse routes, prioritizing early intensification for unstable evolutionary states, and designing combinations that reduce the probability of convergent escape.
Scope and depth of coverage. The review provides deep coverage of: (1) inherited predisposition (familial clustering, rare pathogenic germline variants, GWAS/PRS and functional interpretation), (2) primary cytogenetic subtypes and how they constrain downstream evolution, (3) CNV and structural-variant remodeling as major engines of progression and relapse, (4) modern genomic detection strategies (from FISH and targeted panels to WGS/WES and optical genome mapping), and (5) therapy-driven adaptation, with emphasis on immunotherapy-era resistance (including antigen loss and immune-state failure). We provide selective, mechanism-focused coverage of the microenvironment and epigenetics only insofar as they modulate genomic instability, immune escape, or treatment selection; an exhaustive review of microenvironmental biology, MRD methodology, or non-genetic pharmacology is intentionally outside our remit.
Why this matters now. MM treatment has entered an era in which deep responses are achievable, yet durable control is still limited by evolutionary inevitability under sequential selective pressures. A static genomic snapshot is no longer enough. We argue that the next practical advance will come from evolution-aware precision myeloma, integrating germline and tumor genomics with longitudinal monitoring to (i) identify patients at risk before symptomatic disease, (ii) detect early divergence toward high-risk trajectories, and (iii) pre-empt convergent resistance pathways—particularly under immune-based therapies where antigen escape and immune dysfunction can rapidly dominate outcomes. In short, our review aims to reposition MM genomics from descriptive stratification to predictive evolutionary management, providing a conceptual and translational bridge between inherited risk, clonal dynamics, and treatment durability.
CRediT authorship contribution statement
María Carretero-Fernández: Writing – review & editing, Writing – original draft, Methodology, Investigation. Antonio José Cabrera-Serrano: Writing – review & editing, Writing – original draft, Methodology, Investigation. Lucía Ruíz Durán: Writing – review & editing, Writing – original draft, Methodology, Investigation. Mariam Ibañez: Writing – review & editing, Investigation. Marco Bonilla: Writing – review & editing, Writing – original draft, Methodology, Investigation. Francisco Mesa: Writing – review & editing, Methodology, Investigation. Juan Francisco Gutiérrez-Bautista: Writing – review & editing, Methodology, Investigation. Rachid Chahboun: Writing – review & editing, Methodology, Investigation. Fernando Jesús Reyes-Zurita: Writing – review & editing, Methodology, Investigation. Joaquín Martínez-Lopez: Writing – review & editing, Methodology, Investigation. Rosa Collado: Writing – review & editing, Methodology, Investigation. Juan Sainz: Writing – review & editing, Writing – original draft, Methodology, Investigation, Funding acquisition, Conceptualization.
Declaration of competing interest
The authors declare no conflict of interest. The funders had no role in the writing of the manuscript, or in the decision to publish the reviewed material.
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Funding
This work was supported by the Instituto de Salud Carlos III (Madrid, Spain; DTS23/00030 , PI17/02256 and PI20/01845 ), and from the Consejería de Salud y Familia de la Junta de Andalucía ( PY20/01282 ).
Abbreviated title: Genetic Architecture and Susceptibility in Multiple Myeloma