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3258 Integrated Coding and Non-Coding Transcriptional Single-Cell Atlas of Multiple Myeloma: Unraveling the Effects of Myeloma Genotype on the Bone Marrow Microenvironment

Program: Oral and Poster Abstracts
Session: 651. Multiple Myeloma and Plasma Cell Dyscrasias: Basic and Translational: Poster II
Hematology Disease Topics & Pathways:
Research, Fundamental Science, Adult, Genomics, Bioinformatics, Immunology, Biological Processes, Technology and Procedures, Study Population, Human
Sunday, December 8, 2024, 6:00 PM-8:00 PM

Marina E Michaud1, Sarthak Satpathy, MSc2*, William Pilcher3*, Edgar Gonzalez-Kozlova, PhD4*, Dimitra Karagkouni, PhD5*, Lijun Yao, PhD6*, Yered Pita-Juarez, PhD7*, Chaitanya Acharya, PhD8*, Mark Hamilton, MD8, Shivani Nanda9*, Yizhe Song10, Julia T Wang11*, Mojtaba Bakhtiari, MD1*, David Avigan, MD12, Taxiarchis Kourelis, MD13, Madhav V. Dhodapkar, MD PhD14, Sagar Lonial, MD15*, Swati Bhasin, PhD16, Immune Network17*, Li Ding, PhD18*, Sacha Gnjatic, PhD19*, Ioannis S Vlachos, PhD20*, George Mulligan, PhD8 and Manoj Bhasin, PhD1

1Department of Pediatrics, Emory University, Atlanta, GA
2Department of Biomedical Informatics, Emory University, Atlanta, GA
3Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA
4Icahn School of Medicine At Mount Sinai, New York, NY
5Department of Pathology, Cancer Research Institute, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA
6WUSTL, Saint Louis
7Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
8Multiple Myeloma Research Foundation, Norwalk, CT
9Broad Institute of Harvard and MIT, Cambridge, MA
10WUSTL, St Louis, MO
11McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO
12Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
13Division of Hematology, Mayo Clinic, Rochester, MN
14Winship Cancer Institute of Emory University, Atlanta, GA
15Winship Cancer Institute, Atlanta, GA
16Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA
17Immune Network, Multiple Myeloma Research Foundation, Norwalk, CT
18Washington University, St. Louis, MO
19Icahn School of Medicine at Mount Sinai, New York, NY
20Beth Israel Deaconess Medical Center, Boston, MA

Introduction: In recent years, multiple myeloma (MM) research has increasingly focused on unraveling the complex interactions between malignant plasma cells and their surrounding bone marrow microenvironment (BMME). To further elucidate these interactions, we developed a comprehensive single-cell atlas of the MM BMME, integrating both coding and noncoding (ncRNA) transcriptional profiles. By correlating these profiles with specific cytogenetic abnormalities in myeloma cells, we aim to uncover how ncRNAs regulate the phenotypic and functional states of myeloma cells and, consequently, shape the cellular landscape of the BMME. A detailed understanding of how the noncoding transcriptome affects the cellular components and immune landscape of the BMME is essential for advancing our knowledge of MM pathogenesis and identifying novel biomarkers and therapeutic targets.

Methods: Our atlas was constructed using single-cell RNA sequencing data from 481 samples of CD138neg cells sorted from bone marrow aspirates of MM patients enrolled in the MMRF CoMMpass study. This dataset includes accompanying whole-genome sequencing and survival data, enabling correlative analysis between transcriptional profiles, cytogenetic abnormalities, and patient outcomes. To generate a combined coding and non-coding transcriptome, we developed an expanded human reference genome by systematically merging mRNA and ncRNA transcripts from the LncBook2.0 and GENECODEv42 reference genomes. The sequencing data was aligned to this expanded genome, followed by quality control processing, batch correction, clustering, and supervised analysis.

Results: The resulting coding and non-coding atlas comprises over 1.9 million cells, spanning immune, plasma, and stromal compartments. Remarkably, ncRNAs constituted 46% of the associated genes, including 22,102 long ncRNAs (lncRNAs) and 3,112 small ncRNAs. Subclustering analysis of the major immune compartments (B lymphoid, myeloid, and NK and T lymphoid) yielded 70 subclusters, with ncRNAs representing 24-38% of the top 100 differentially expressed genes within each compartment. This underscores the significant role of ncRNAs in distinguishing immune subpopulations. Moreover, examining the association between specific cytogenetic abnormalities and the immune composition of the BMME, 30 subclusters were found to be differentially abundant (P < 0.05) between cytogenetic abnormalities, supporting our hypothesis that myeloma cell genotypes significantly shape the immune microenvironment. For instance, patients with CCND1 amplification displayed an increase CD4+ central memory T cells with a decrease in CD8+ cytotoxic T cells. Similarly, patients with 1q21 gain exhibited an increase in TGFβ-stimulated monocytes, while a decrease in cytotoxic CD8+ T and CD56dim NK cells was observed in patients with 17p13 deletion.

Next, examining which ncRNAs are associated with specific cytogenetic abnormalities, we identified 14 ncRNAs significantly differentially expressed across cytogenetic abnormalities. Increased expression of six of these ncRNAs were associated with poor overall survival both independently and in combination (P < 0.05, HR = 3.7). Notably, three of these ncRNAs have documented roles in cancer progression but have not been previously studied in the context of MM. Subsequently stratifying patients based on their enrichment of these outcome-associated ncRNAs revealed even stronger associations with immune composition, including an increase in CD4+ regulatory T cells (P < 0.05). This further supports our hypothesis that myeloma cell genotypes shape the BMME. Lastly, by constructing a gene regulatory network to predict the interactions between coding and noncoding RNAs, we illustrate the regulatory networks of ncRNAs modulating the phenotypes of myeloma and immune cell subpopulations.

Conclusion: In summary, we present the first high-resolution transcriptomic atlas of the MM BMME, integrating both coding and noncoding RNAs. This study reveals distinct immune subpopulations associated with specific myeloma cell genotypes and highlights the central role of ncRNAs in modulating the phenotypic and functional states of both malignant and non-malignant cells in the MM BMME. Our findings emphasize the potential of ncRNAs as therapeutic targets and prognostic markers for MM, offering new avenues for research and clinical intervention.

Disclosures: Hamilton: Kite Pharma-Gilead: Membership on an entity's Board of Directors or advisory committees. Avigan: Kowa Pharmaceutical: Consultancy, Other: Advisory Board; Sanofi: Consultancy, Other: Advisory Board; Janssen: Consultancy, Other: Advisory Board; Partners Therapeutics: Consultancy, Other: Advisory Board; Aviv Med Tech: Consultancy, Other: Advisory Board; Bristol Myers Squibb: Consultancy, Other: Advisory Board; Takeda: Consultancy, Other: Advisory Role; Legend Biotech: Consultancy, Other: Advisory Role; Juno Therapeutics: Consultancy, Other: Advisory Role; Karyopharm Therapeutics: Consultancy, Other: Advisory Role; Chugai Pharma: Consultancy, Other: Advisory Role; Kite/Gilead: Consultancy, Other: Advisory Role, Research Funding; Celgene: Consultancy, Other: Advisory Role, Research Funding; Paraxel: Current Employment; Pharmacyclics: Research Funding; Kite, a Gilead Company: Research Funding. Kourelis: Pfizer: Research Funding; Novartis: Research Funding. Dhodapkar: Janssen: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; Lava Therapeutics: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Kite: Membership on an entity's Board of Directors or advisory committees. Lonial: Bristol Myers Squibb, Janssen Biotech Inc, Novartis, Takeda: Research Funding; TG Therapeutics Inc (no cancer agents currently): Membership on an entity's Board of Directors or advisory committees; AbbVie Inc, Amgen Inc, Bristol Myers Squibb, Celgene Corporation, Genentech, a member of the Roche Group, GSK, Janssen Biotech Inc, Novartis, Pfizer Inc, Regeneron Pharmaceuticals Inc, Takeda Pharmaceuticals USA Inc: Membership on an entity's Board of Directors or advisory committees. Bhasin: Anxomics: Current Employment, Current equity holder in private company. Vlachos: NIDDK: Research Funding; NHLBI: Research Funding; NCI: Research Funding; Mosaic: Consultancy; Guidepoint Global: Consultancy; Harvard Stem Cell Institute: Research Funding.

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