Parekh, Samir

Abstract Although the human genome encodes a vast repertoire of noncoding RNAs that regulate gene expression, the noncoding genome remains underexplored due to technical challenges. Specifically, during transcriptomic sequencing data alignment, the overlap between noncoding and coding loci can create ambiguous read alignments that are subsequently discarded from downstream analysis. For this reason, most of the noncoding genome is excluded from standard genomic annotations used for sequencing alignment. To address this challenge and enable concurrent profiling of the coding and noncoding transcriptome, we systematically integrated standard coding (GENCODE) and noncoding (LncBook) genome annotations, preserving coding gene annotations and removing overlapping noncoding regions. The resulting integrated genome annotation expanded the number of annotated noncoding genes from 40,785 to 138,296 while preserving all coding genes and reducing ambiguous read assignment. To evaluate the utility of our integrated genome annotation for uncovering novel, biologically relevant noncoding RNAs (ncRNAs), we realigned CD138-positive bulk RNA-seq (N = 942) and CD138-negative single-cell RNA-seq (N = 478) data from the MMRF CoMMpass study, generating a comprehensive coding-noncoding atlas of the myeloma bone marrow microenvironment with noncoding genes representing 51% of highly variable genes and displaying significant cell type specificity. Tumor expression profiling based on this integrated profiling identified 15 clusters, including two enriched for amp(1q21) or t(4;14) and associated with shorter progression-free survival (PFS). Differential expression and systematic filtering yielded 19 candidate high-risk ncRNAs, including previously uncharacterized ENSG00000310209 , which was associated with poor PFS (HR = 1.141, P = 0.0025), increased IRF4 activity, Wnt pathway activation, CCL5 signaling, and the accumulation of anergic-like CD8+ T cells. These findings establish integrated coding-noncoding analysis as a strategic approach for discovering functional ncRNAs from transcriptomic sequencing data.

Abstract The CoMMpass study (NCT01454297) is a prospective, longitudinal observational study involving 1,141 newly diagnosed multiple myeloma (NDMM) patients. Bone marrow aspirates from the study participants were collected for comprehensive molecular characterization of tumor (using bulk RNA sequencing and whole genome sequencing) and tumor immune microenvironment using 3’ single-cell RNA sequencing (scRNA-seq). To support exploration of this rich multi-omic dataset, we developed CoMMpass Explorer (CE), an intuitive interactive platform that enables real-time analysis of clinical and genomic data from CoMMpass. A central feature of CE is cohort building, where users can filter and stratify patients by clinical, genomic, and survival data elements to create custom cohorts for analysis. CE provides five main views: Overall Summary for clinical feature distribution, Kaplan-Meier curves, and multivariate Cox proportional hazards models; Mutational Profile for visualizing and comparing somatic mutations; Tumor Profile for bulk differential expression and gene set enrichment; Immune Microenvironment for comparing cell type abundance and cell cycle dynamics between cohorts using scRNA-seq data; and Pseudo-Bulk, which aggregates single-cell expression by cell type to enable cohort-level comparisons of transcriptional programs using DEseq2. CE reproduces prior CoMMpass studies, including WEE1 expression being associated with poorer progression-free survival (Simhal, et al.) and different mutation frequencies between African American and European American patients (Manojlovic, et al.). We further demonstrate CE’s utility by interrogating the 2025 Consensus Genomic Staging (CGS) risk classification system (Avet-Loiseau, et al). We compared CGS high-risk (HR, n=249) vs. CGS standard-risk (SR, n=573) patients. HR patients have significantly worse progression-free survival, overall survival, and time to second-line therapy compared with SR patients. Univariate models recapitulated expected differences in the clinical features that define CGS risk. Bulk tumor RNA-seq and ssGSEA highlighted a more proliferative and genomically unstable transcriptional program in HR group, with upregulation of angiogenesis and cell-cycle-related pathways. In the immune microenvironment, monocytes were more abundant in the SR group. Pseudo-bulk RNA-seq of plasma cells showed overexpression of ANXA1, NSD2, IGF1R, MAF and related genes in HR. CE democratizes access to the CoMMpass multi-omic resource, allowing researchers to interrogate clinical and molecular heterogeneity. By enabling hypothesis generation and replication of published results, CE serves as a valuable tool for identifying prognostic biomarkers and meaningful patterns in gene expression, mutation profiles, and the immune microenvironment. Citation Format: Wanxing Zhang, Chaitanya R. Acharya, Steven M. Foltz, David E. Avigan, Samir Parekh, Ravi Vij, Shaji Kunnathu Kumar, Taxiarchis Kourelis, Sagar Lonial, Hearn Cho, Ioannis S. Vlachos, Sacha Gnjatic, Li Ding, Manoj Bhasin, George Mulligan. CoMMpass Explorer: An interactive platform to explore clinical and genomic data from newly diagnosed multiple myeloma patients from the landmark CoMMpass observational study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 5504.

Abstract Introduction Understanding the tumor immune microenvironment (TIME) in multiple myeloma (MM) is critical for identifying prognostic biomarkers and therapeutic targets. We hypothesized that specific immune cell populations within the bone marrow TIME are associated with clinical outcomes and could enhance patient stratification. To this end, we conducted the largest CyTOF-based immune profiling study to date in MM, profiling >300 million bone marrow immune cells from patients enrolled in the CoMMpass study. Methods We analyzed >1,000 bone marrow samples from ~700 newly diagnosed MM patients enrolled in the MMRF CoMMpass study (NCT01454297), using a harmonized protocol and 41-antibody CyTOF panel at five academic centers. The majority were baseline samples (n=671), with additional samples spanning up to 3.5 years post-diagnosis (n>300). Each site contributed ~200 samples on average. The cohort included 40% females, with a median age of 63 years and BMI of 27.8. ISS stages were evenly distributed (I: 36%, II: 36%, III: 29%), and 84% had ECOG 0-1. Autologous stem cell transplant was performed in 58% of patients, and 22% received maintenance therapy. Results We profiled 311 million single cells across the cohort, identifying major immune compartments: Neutrophils (36.0%), CD4 T cells (19.7%), NK cells (9.9%), monocytes (7.6%), B cells (5.7%), and CD8 T cells (5.6%). Less abundant populations included dendritic cells, γδ T cells, plasmablasts, and pDCs. In our preliminary analysis with multivariate cox regression modeling, we identified clinical factors including stem cell transplant, ISS stage, and ECOG status, as independent predictors of overall survival (OS). After adjusting for age and sex, higher proportions of naïve B cells, pDCs, and γδ T cells were independently associated with improved OS, while CD4+ T cell abundance was positively associated with prolonged progression-free survival (PFS). In contrast, elevated neutrophil proportions were significantly linked to inferior OS and demonstrated a trend toward shorter PFS. Longitudinal immune profiling in more than 200 patients identified a gradual accumulation of naïve B cells and a pronounced post-treatment rise in CD45+ plasmablasts, highlighting persistent B cell activity as a candidate mechanism for sustained therapeutic efficacy. Conclusion This study presents the largest immune proteomic atlas in MM to date, linking TIME composition to clinical outcomes. A favorable immune landscape was marked by preserved humoral immunity (naïve B cells, plasmablast expansion), enrichment of pDCs and γδ T cells, and lower neutrophil abundance, collectively associated with improved survival outcomes. These findings lay the groundwork for immune-guided prognostication and highlight new opportunities for therapeutic targeting in MM. Ongoing analyses aim to further resolve baseline and longitudinal immune dynamics in relation to treatment response.

Abstract Introduction: Multiple Myeloma (MM) is a complex hematologic malignancy, where patients often display one or more potentially high risk cytogenetic alterations associated with poor outcomes. Traditional high risk cytogenetics events in myeloma, such as NSD2 t(4;14) translocations, gain of 1q21, or deletion of 17p13, have often been studied in isolation, but emerging evidence suggests the combination of these high risk alterations has a greater negative prognostic impact than any on their own. This has been recently reflected in risk stratification guidelines from IMS and IMWG, which consider certain events, such as t(4;14), as high risk only in combination with gain of 1q21 or deletion of 1p32. Still, the mechanisms through which multi-hit high risk events disrupt the microenvironment and promote poor outcomes remains unclear. We hypothesize that myelomas with multiple high risk alterations remodel the immune environment to promote tumor progression and immune escape. Methods: To study the role of multi-hit high risk cytogenetics on the immune microenvironment, we analyzed CD138-bone marrow aspirate single-cell RNA sequencing (scRNAseq) data from 337 newly diagnosed MM patients from the MMRF CoMMpass study, generated as part of the Immune Atlas initiative. Cytogenetic alterations for these patients were derived from whole-genome and whole-exome sequencing of CD138+ bone marrow aspirates from the MMRF CoMMpass cohort. Patients were classified as multi-hit high-risk MM if they exhibited either (i) two high-risk cytogenetic events, including NSD2 t(4;14), MAF t(14;16), del(17p13), or (ii) one high-risk event with gain of 1q21. Results: Based on cytogenetic information, 33 patients in the Immune Atlas cohort were classified as 'multi-hit’ high-risk, while 34 patients had only a single high-risk alteration. These multi-hit high risk patents displayed significantly worse progression free survival compared to standard risk patients, adjusting for age, therapy, and ASCT (HR=2.34, p<7.2e-5), while single-hit patients showed a non-significant trend towards worse outcomes (HR=1.51, p=0.071). The most frequent multi-hit risk event in the cohort was NSD2 t(4;14) in combination with 1q21, observed in 23 patients. Compositional analysis of the immune populations in the scRNAseq data revealed that relative to both standard and single-hit high risk patients, multi-hit high risk patients displayed significant reductions in IFN-I stimulated CD4+ and CD8+ T cell populations, marked by decreased expression for antiviral response markers such as ISG15, XAF1, and IFI44L. Enrichment of inflammatory CD16+ non-classical monocytes was also observed. Further analysis of the most frequent multi-hit risk event, NSD2 with 1q21, revealed distinct enrichment of late-activated cytotoxic HLA+ CD8+T cells and cytotoxic CD4+.T cells. Neither alteration was observed in patients with single-hit NSD2 or 1q21. Further analysis on the interactions between high risk events revealed distinct transcriptomic profiles dependent on the high risk events involved, particularly in multi-hit events involving mutations or deletions of TP53 or gain of 1q21. Reduction in IFN-I signaling across various immune populations was primarily restricted to multi-hit risk events involving gain of 1q21. Conversely, patients with biallelic loss of TP53 displayed significant enrichment of these same IFN-I populations. Given this contrast in IFN-I signaling spanning multiple immune subtypes, we hypothesized that the malignant myeloma cells might similarly display altered IFN-I activity. Utilizing CD138+ myeloma bulk RNA sequencing data from CoMMpass, we found that IFN-I response scores strongly correlated between paired scRNA immune and bulk RNAseq tumor datasets (R2: 0.75, p=1.63e-32). Across 660 patients with bulk RNAseq and cytogenetic data, we confirmed significant reductions in IFN-I response scores in tumor cells in multi-hit high risk involving 1q21, and significant enrichment in those with complete loss of TP53 relative to standard-risk MM. Conclusions: Overall, we do observe that MM patients with multiple high risk cytogenetic alterations display distinct immunologic traits relative to standard risk or single-hit high risk patients in addition to significantly worse outcomes. Furthermore, we find variability in the immune alterations observed based on the cytogenetic events involved, further illustrating the heterogeneity in how MM shapes the immune microenvironment.

Abstract Introduction: Cilta-cel is approved in the US and the EU for the treatment of patients (pts) with lenalidomide-refractory multiple myeloma (MM) after ≥1 prior line of therapy (pLOT), including a proteasome inhibitor and an immunomodulatory agent based on the CARTITUDE-1 (CART-1, NCT03548207) and CARTITUDE-4 (CART-4, NCT04181827) studies. Cilta-cel led to deep and durable responses and significant survival benefit in pts with relapsed/refractory MM (RRMM) after ≥3 pLOT in CART-1. In CART-4, cilta-cel led to a significant overall survival benefit with a higher proportion of pts achieving deep, sustained minimal residual disease negativity vs standard of care in pts with lenalidomide-refractory MM after 1–3 pLOT. We investigated the mechanism of action of cilta-cel by correlating biomarkers from peripheral blood and the bone marrow TME with progression-free survival (PFS) and number of pLOT in pts with RRMM from CART-1 and CART-4. Methods: Biomarker analyses were performed using peripheral blood and bone marrow aspirates (BMAs) collected in both CART-1 and CART-4 studies. Immunophenotyping by flow cytometry was performed using peripheral blood at baseline/time of apheresis in samples from both studies. Immune fitness at baseline was assessed in pts by pLOT and in association with PFS. Gene set enrichment scores were derived from RNA sequencing data of the TME using BMAs. Mixed-effects models were used to identify signatures/pathways modulated over time (day [D] 28 and at 6 months [mo] post infusion vs screening) and in association with PFS and pLOT. Results: In total, 176 CART-4 and 97 CART-1 pts received cilta-cel as study treatment. Immunophenotyping data were available from 248 peripheral blood samples (1 pLOT, n=56; 2 pLOT, n=61; ≥3 pLOT, n=131). At apheresis, CD4+ naïve T cells (%) were higher in pts with 1 or 2 pLOT, compared with those with ≥3 pLOT, while no difference was found in pts with ≥3 pLOT with further breakdown (i.e., 3–4 vs 5–6 vs ≥7 pLOT). Further, higher baseline levels of CD4+ naïve T cells were associated with longer PFS. These data suggest that the negative impact on peripheral immune fitness with the addition of LOT may plateau when pts have received ≥3 pLOT. TME gene expression data were available from 148 BMA samples (screening, n=50; D28, n=50; 6 mo, n=48) from CART-4. Analyses of gene expression signatures suggest depletion of B cells and antibodies at D28 post cilta-cel infusion, with partial recovery at 6 mo. This was corroborated in parallel by flow cytometry and immunoglobulin quantification. Further, elevated expression of genes associated with myeloid cells, including tumor-associated macrophages (TAM, likely M1), and of genes associated with cytotoxic T cells were also observed at D28. Elevated expression of genes associated with B-cell receptors, T-cell differentiation and activation, and cytokine signaling pathways were found at both D28 and 6 mo. Pts with longer PFS (>18 mo) had higher levels of M1 TAM at D28, while those with shorter PFS had higher levels of regulatory T cells and more suppressed interferon pathway genes at 6 mo, suggesting that relapse may be associated with a more suppressive immune response. In pts with fewer pLOT, more profound B-cell depletion on D28, better recovery at 6 mo, and elevated B-cell receptor signaling were inferred from gene expression data. Pts with 1 pLOT also demonstrated higher elevation of M1 TAM expression on D28 from screening as compared with pts with 3 pLOT, similar to what was observed in pts with longer PFS. Conclusions: Correlative biomarker data suggest that longer PFS is associated with better immune fitness at baseline and stronger immune responses post cilta-cel infusion, as observed in peripheral blood and within the TME of pts with RRMM in CART-1 and CART-4. The peripheral immune fitness was more pronounced in pts with 1 and 2 pLOT vs 3 pLOT and beyond, where deterioration plateaued. This suggests the impact of T-cell immune fitness on PFS may be limited beyond the third LOT. Importantly, other covariates, including factors within the immune TME and tumor burden, may play a significant role in balancing this compromised intrinsic T-cell immune fitness at apheresis, thereby contributing to PFS durability after 3 pLOT. Overall, these results support increased benefits in treating pts with MM with cilta-cel in earlier LOTs.

Despite significant improvements in survival of patients with multiple myeloma (MM), outcomes remain heterogeneous, and a significant proportion of patients experience suboptimal outcomes. Importantly, traditional prognostic factors based on data from patients treated with older therapies no longer capture prognosis accurately in the contemporary era of novel triplet or quadruplet therapies. Therefore, risk stratification requires refinement in the context of available and investigational treatment options in routine practice and clinical trials, respectively. The current identification of high-risk MM (HRMM) in routine practice is based on the Revised International Staging System, which stratifies patients using a combination of widely available serum biomarkers and chromosomal abnormalities assessed via fluorescence in situ hybridization. In recent years, a substantial body of evidence concerning additional clinical, biological, and molecular/genomic prognostic factors has accumulated, along with new MM risk stratification tools and consensus reports. The International Myeloma Society, along with the International Myeloma Working Group, convened an Expert Panel with the primary aim of revisiting the definition of HRMM and formulating a practical and data-driven consensus definition, based on new evidence from molecular/genomic assays, updated clinical data, and contemporary risk stratification concepts. The Panel proposes the following Consensus Genomic Staging (CGS) of HRMM which relies upon the presence of at least one of these abnormalities: (1) del(17p), with a cutoff of >20% clonal fraction, and/or TP53 mutation; (2) an IgH translocation including t(4;14), t(14;16), or t(14;20) along with 1q+ and/or del(1p32); (3) monoallelic del(1p32) along with 1q+ or biallelic del(1p32); or (4) β2 microglobulin ≥5.5 mg/L with normal creatinine (<1.2 mg/dL).

CARTITUDE-1 evaluated ciltacabtagene autoleucel (cilta-cel) in patients with heavily pretreated relapsed/refractory multiple myeloma (RRMM). We describe overall survival (OS), ≥5-year progression-free outcomes, associated biomarkers, and safety, with a median study follow-up of 61.3 months. For the 97 treated patients, median OS was 60.7 months (95% CI, 41.9 to not estimable). One third (32/97) of patients remain alive and progression-free for ≥5 years after a single cilta-cel infusion, without maintenance treatment. Twelve of these patients treated at a single center underwent serial minimal residual disease (MRD) and positron emission tomography-computed tomography assessments, and all (100%) were MRD-negative (at least 10 −5 threshold) and imaging-negative at year 5 or later after cilta-cel. Baseline characteristics, including the presence of high-risk cytogenetics and extramedullary disease, were generally comparable for the 32 patients who were progression-free for ≥5 years versus patients who had progressive disease by year 5. A trend of lower baseline tumor burden, higher fraction of naïve T-cells in the cilta-cel drug product, higher T cell-to-neutrophil ratio, higher hemoglobin and platelets at baseline, and higher effector-to-target ratio were associated with ≥5-year progression-free status. The safety profile of cilta-cel remained consistent with previous reports. To our knowledge, our data provide the first evidence that cilta-cel is potentially curative in patients with RRMM.

7507 Background: CARTITUDE-1 evaluated cilta-cel in pts with heavily pretreated RRMM who historically have an expected median progression-free survival (PFS) of <6 months (mo) and median overall survival (OS) of ~1 year (y). At 33.4 mo median follow-up, median PFS was 34.9 mo, and median OS was not reached (36-mo OS rate, 62.9%; Lin et al, ASCO 2023). We report OS, ≥5 y progression-free outcomes, and safety with a median study follow-up of 60.3 mo. Methods: Pts in CARTITUDE-1 received a single cilta-cel infusion. Correlative analyses were performed utilizing drug product, baseline, and postinfusion samples. Pts are followed for progression, survival, and safety in a 15-y follow-up study, CARTinue (NCT05201781), with pt evaluations per local standard of care (reported annually at a minimum). Results: Of 97 pts treated, 32 (33.0%) remain alive and progression free for ≥5 y after cilta-cel, without further MM treatment. For these 32 pts, prior to enrollment in CARTITUDE-1, median time from start of last line of therapy (LOT) to progression was 4.0 mo (range, 0.7–48.6). Among the 32, median age was 60 y (range, 43–78), median number of prior LOT was 6.5 (range, 3–14), 23.3% had high risk cytogenetics, 12.5% had extramedullary disease (EMD), 90.6% were triple-class refractory, and 46.9% were penta-drug refractory. Baseline characteristics of pts who were progression free for ≥5 y, including those with high-risk cytogenetics and EMD, were comparable to pts with progressive disease (PD) within 5 y. Compared with pts who had PD within 5 y, biomarkers significantly associated with ≥5 y progression free status included a higher fraction of naïve T cells in the drug product, lower neutrophil to T cell ratio, higher hemoglobin and platelets at baseline, and higher effector-to-target ratio (Cmax to sBCMA at baseline). At Cmax, these pts also had significantly higher CD4 central memory CAR+ T cell subsets and CAR+ T cells that were positive for the activation markers CD38, CD25, and PD-1. Data were collected on a subset of pts from a single center where local serial MRD assessments were performed. All 12 pts at this center who were progression free for ≥5 y were MRD negative at 10 –6 and imaging negative by PET/CT yearly for 5 y. Overall, at 60.3 mo median follow-up in CARTITUDE-1 (N=97), median OS was 60.6 mo (95% CI, 41.9–NE). With continued follow-up, 3 additional pts reported a second primary malignancy (1 of which was acute myeloid leukemia; onset, 2.8 y after infusion). No new cases of movement and neurocognitive disorders were reported. Conclusions: The median OS for pts enrolled in CARTITUDE-1 was 5 y, and 33% of pts remain progression free for ≥5 y following a single cilta-cel infusion. These data provide the first evidence that cilta-cel is potentially curative in pts with RRMM. Clinical trial information: NCT03548207 , NCT05201781 .

Abstract Although initial therapy of mantle cell lymphoma (MCL) is not standardized, bendamustine plus rituximab (BR) is commonly used in older patients. Rituximab (R) maintenance after induction is often used. Thus, the open-label, randomized phase 2 ECOG-ACRIN Cancer Research Group E1411 trial was designed to test 2 questions: (1) does addition of bortezomib to BR induction (BVR) and/or (2) addition of lenalidomide to rituximab (LR) maintenance improve progression-free survival (PFS) in patients with treatment-naïve MCL? From 2012 to 2016, 373 previously untreated patients, 87% aged ≥60 years, were enrolled in this trial. At a median follow-up of 7.5 years, there is no difference in the median PFS of BR compared with BVR (5.5 vs 6.4 years; hazard ratio [HR], 0.90; 90% confidence interval [CI], 0.70-1.16). There were no unexpected additional toxicities with BVR treatment compared with BR, with no impact on total dose/duration of treatment received. Independent of the induction treatment, addition of lenalidomide did not significantly improve PFS, with median PFS in R vs LR (5.9 vs 7.2 years; HR, 0.84; 90% CI, 0.62-1.15). Most patients completed the planned 24 cycles of LR at the scheduled dose. In summary, adding bortezomib to BR induction does not prolong PFS in treatment-naïve MCL, and LR maintenance was not associated with longer PFS compared with R alone after BR. Nonetheless, the &gt;5-year median PFS outcomes in this prospective cooperative group trial indicate the efficacy of BR followed by R maintenance as highly effective initial therapy for older patients with MCL. This trial was registered at www.clinicaltrials.gov as #NCT01415752.