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DiPersio, John F.

https://orcid.org/0000-0002-0429-3133

Mayo Clinic

Washington University in St. Louis

Citations 43

NT-I7, a Long-Acting Interleukin 7, Increases Lymphocyte Counts and Induces CD8+ T-cell Clonotype Expansion in Patients with Newly Diagnosed High-Grade Gliomas
Butt, Omar H. , Singhal, Kartik , Luo, Jingqin , Rettig, Michael P. , Foltz, Jennifer A. , Huang, Jiayi , Zhou, Alice Y. , Tao, Yu , Griffith, Obi L., Griffith, Malachi, Johanns, Tanner M. , Ansstas, George , Zhang, Chaocai , Tang, Justin , Christ, Stephanie , Ferrando-Martinez, Sara , Lee, Byung Ha , Chheda, Milan G., Fehniger, Todd A. , Campian, Jian L., Griffith, Malachi , Griffith, Obi L. , Huang, Jiayi , Griffith, Obi L , Griffith, Malachi , DiPersio, John F , Chheda, Milan G , Fehniger, Todd A , Campian, Jian L , Luo, Jingqin , Ansstas, George , DiPersio, John F. , Chheda, Milan G. , Campian, Jian

Clinical Cancer Research | March 25, 2026 | Volume: 32 | Issue: 13 | Pages: 2581-2592

10.1158/1078-0432.ccr-25-2953 Get It

Abstract Purpose: Standard care for high-grade gliomas (HGG) involves maximal surgical resection followed by radiation and temozolomide. Postoperative adjuvant therapy frequently causes lymphopenia, which is associated with poor prognosis. Interleukin 7 (IL7) is essential for lymphocyte development, homeostasis, and survival. NT-I7 (efineptakin alfa), a long-acting recombinant IL7, reverses lymphopenia and improves survival in murine glioma models. However, the safety, maximum tolerated dose (MTD), and impact of NT-I7 on immune cells in patients with HGG remain unknown. Patients and Methods: We conducted a phase I trial (NCT03687957) examining the MTD and effect of NT-I7 on lymphocytes in patients with newly diagnosed HGG. The primary endpoint was dose-limiting toxicity; secondary endpoints included absolute lymphocyte count (ALC) changes over time, overall response, progression-free survival, and overall survival. Exploratory endpoints included immune profiling at different time points using single-cell RNA sequencing (scRNA-seq) in a subset of patients. Results: NT-I7 was well tolerated with a MTD of 720 µg/kg. Moreover, NT-I7 significantly increased ALCs for more than 12 weeks in duration. Early elevations in CD4+, CD8+ T cells and NK cells further coincided with increased TNF and CXCL9 cytokine levels. Comprehensive immune profiling of peripheral blood T cells revealed selective clonotype expansion within CD8+, but not CD4+, T cells following NT-I7 administration. Finally, a subset of our patients with MGMT promoter–unmethylated glioblastoma, which are typically associated with a poorer prognosis, demonstrated promising clinical responses. Conclusions: NT-I7 has the potential to maintain and increase lymphocyte counts in patients with HGG and warrants further investigation, particularly in combination with immune-based therapies.
Robust HbF induction and improvement of anemia and hemolysis with base editing in sickle cell disease: Safety and efficacy findings from the ongoing BEACON study
Sharma, Akshay , Frangoul, Haydar , Mapara, Markus Y. , Dalal, Jignesh , Alavi, Asif, Jaroscak, Jennifer, Ayala, Ernesto , Ziga, Edward, Rifkin-Zenenberg, Stacey , Ambati, Srikanth, Chen, Yinzhong , Chesler, Sarah, Joseney-Antoine, Marcelyne, Ianniello, Leanne, Habtemariam, Bahru, Lin, Ling , Goyal, Sunita , Simon, Amy, Gupta, Ashish V , Kanter, Julie , DiPersio, John F. , Eapen, Mary , Chockalingam, Priya , Goyal, Sunita, Thompson, Alexis A. , Heeney, Matthew M.

Blood | December 4, 2025 | Volume: 146 | Issue: Supplement 1 | Pages: 2532-2532

10.1182/blood-2025-2532 Get It

Abstract Introduction Elevated levels of fetal hemoglobin (HbF) ameliorate sickle cell disease (SCD) manifestations. BEAM-101 is an investigational cell therapy comprising ex vivo base-edited autologous CD34+ hematopoietic stem and progenitor cells (HSPCs) that directly target the HBG1/2 promoters to disrupt BCL11A binding, switching production from sickle (HbS) to majority anti-sickling HbF. We present ongoing data from the BEACON study (NCT05456880), a Phase 1/2, single-arm, open-label study evaluating a single dose of BEAM-101 in individuals with SCD and severe vaso-occlusive crises (sVOCs). Methods Eligible patients were aged 12–35 years with SCD and ≥4 sVOCs in the 2-year period prior to informed consent. After mobilization with weight-based or tiered fixed-dose plerixafor, autologous CD34+ HSPCs were collected by leukapheresis and genetically modified with an adenine base editor. Following conditioning with pharmacokinetically adjusted myeloablative busulfan (target cumulative AUC 80 hr*mg/L), patients received a single dose of BEAM-101 (≥3.0×106 viable CD34+ cells/kg). Patients were then monitored for neutrophil and platelet engraftment, adverse events (AEs), total Hb, Hb fractions, % F-cells, hemolysis markers, sVOCs, and additional protocol endpoints for up to 24 months. Results As of June 16, 2025, enrollment has been completed and 46 patients have initiated mobilization. Of the 26 patients who have received BEAM-101, mean duration of follow-up was 6.2 (range 1.0–18.7) months. Baseline demographics were: age 18–34 years, 24 βS/βS genotype, 21 self-reported Black/African American, and 11 female. One patient, who successfully engrafted and obtained stable HbF levels >60%, withdrew consent 5 months post-infusion. For the 26 treated patients, the median number of stem cell collection cycles was 1 (range 1–4); 18 (69.2%) required a single cycle, 4 required 2 cycles, and 4 required >2 cycles. Target cell dose was achieved with a median of 3 (1–12) collection days. Patients received a mean BEAM-101 dose of 8.4 (range 3.2–23.4) ×106 viable CD34+ cells/kg. By the data cut, patients achieved neutrophil (n=26) and platelet (n=24) engraftment at a median of 18 (12–30) days and 19 (11–50) days, respectively, with a median duration of 7 (4–17) days of neutropenia. Of the 24 evaluable patients, 9 (37.5%) achieved platelet engraftment without requiring platelet transfusion through the transplant process. No patients had ≥Grade 3 AEs or serious AEs related to BEAM-101. One patient died due to respiratory failure, assessed as likely related to busulfan conditioning, 4 months post-infusion as previously reported. Mean total Hb increased to 12.1 (range 9.0–14.7) g/dL by Month (M) 1 (n=24), 15.6 (11.9–18.6) g/dL by M6 (n=11), and was sustained through follow-up. Four patients had total Hb levels above the normal range beyond M6 without any associated clinical manifestations or need for therapeutic intervention. Erythropoietin levels trended towards normal in all patients, including those with elevated total Hb. Mean endogenous HbF (HbF/[HbF+HbS]) was >60% and HbS was <40% by M1, which was sustained through last follow-up. At M6, mean % F-cells were 99.2% (97.0–99.9; n=10) and mean HbF/F-cell was 20.8 (18.0–23.9; n=9) pg, exceeding the protective threshold of 10 pg against sickling. Peripheral blood editing was at a mean of 68.5% by M3 (n=16), 69.6% by M6 (n=10), and 72.8% by M12 (n=5). Hemolysis markers and sickling parameters normalized or improved for all patients. No patients experienced any investigator-reported sVOCs post-engraftment. Conclusions The BEAM-101 treatment process is characterized by a low number of mobilization and collection cycles and high editing efficiency, resulting in rapid neutrophil and platelet engraftment and robust pancellular HbF expression, with durability observed up to 18 months. Additionally, there is a corresponding reduction in HbS levels to <40%, and improvements or resolution of hemolysis parameters and anemia, along with resolution of investigator-reported sVOCs post-engraftment. The safety profile of the BEAM-101 treatment regimen is consistent with busulfan conditioning, autologous HSCT, and underlying SCD. These results demonstrate the potential for base editing of the HBG1/2 promoters as a safe and effective therapeutic modality for the treatment of SCD that also has the potential to minimize hospitalization and treatment process burden for patients, families, and sites.
Phase I study of NT-I7, a long-acting interleukin-7, in severe treatment-related lymphopenia following standard radiation and temozolomide for high-grade glioma
Campian, Jian , Grossman, Stuart A. , Kask, Angela Shaulov , Kosydar, Samuel , Piotrowski, Anna F. , Tang, Justin , Chheda, Milan G. , Schullery, Dan, Desideri, Serena , Danda, Neeraja , Ferrando-Martinez, Sara , Lee, Byung Ha , Fling, Steven P. , Ye, Xiaobu , Grossman, Stuart A , Kosydar, Samuel R , Strowd, Roy E. , DiPersio, John F. , Schullery, Dan, D’Amico, Leonard

Neuro-Oncology Advances | June 7, 2025 | Volume: 7 | Issue: 1 | Pages: No page available

10.1093/noajnl/vdaf117 Get It

Abstract Background High-grade gliomas (HGG) have a poor prognosis despite aggressive treatment. Severe, persistent lymphopenia occurring in HGG patients after concurrent chemoradiation is associated with worse survival. NT-I7, a long-acting interleukin-7 analog, has been shown to increase CD4 and CD8 counts in healthy, septic, and HIV-positive adults. This multi-institutional, NCI-funded dose-escalation trial is the first to evaluate NT-I7 safety and activity in HGG patients with severe treatment-related lymphopenia (TRL) and the effect of co-administered glucocorticoids. Methods Eligible HGG patients had CD4 counts <300 cells/mm3 after 5 weeks of standard chemoradiation and were receiving either ≤0.75 or ≥4 mg/day of dexamethasone. Patients received a single intramuscular dose of NT-I7 (60 or 360 µg/kg) post-chemoradiation, followed by safety evaluation and multi-parameter, longitudinal monitoring of lymphocyte populations and immunologic function. Results NT-I7 was well tolerated in all 12 patients (median age 64; median CD4 count 161 cells/mm³) before the study closed prematurely. Absolute lymphocyte counts doubled in 83% (10/12; 95% CI: 51.6%-97.9%) of patients, and CD4 counts doubled in 42% (5/12; 95% CI: 15.2%-72.3%) of patients. Glucocorticoid use did not significantly affect CD4 or lymphocyte increases. Correlative immune profiling revealed increased Ki67 expression in CD4 (P < .005) and CD8 (P < .05) after one week, along with the expansion of CD4 and CD8 T-cell subsets and CD56 + natural killer cells. Conclusions NT-I7 is well tolerated and effectively increases lymphocyte and CD4 counts in severe TRL patients, regardless of glucocorticoid use, suggesting its potential to mitigate TRL and improve outcomes in HGG.
Initial Results from the BEACON Clinical Study: A Phase 1/2 Study Evaluating the Safety and Efficacy of a Single Dose of Autologous CD34+ Base Edited Hematopoietic Stem Cells (BEAM-101) in Patients with Sickle Cell Disease with Severe Vaso-Occlusive Crises
Gupta, Ashish O. , Sharma, Akshay , Frangoul, Haydar , Dalal, Jignesh , Alavi, Asif, Jaroscak, Jennifer, Ayala, Ernesto, Ziga, Edward, Rifkin-Zenenberg, Stacey , Chen, Guo , Chen, Yinzhong , Lin, Ling , Joseney-Antoine, Marcelyne, Ianniello, Leanne, Gardner, Beth, Hartigan, Adam J., Ciaramella, Giuseppe , Goyal, Sunita , Simon, Amy, Kanter, Julie , Alavi, Asif, DiPersio, John F. , Eapen, Mary , Minella, Alex C. , Chockalingam, Priya , Goyal, Sunita, Thompson, Alexis A. , Heeney, Matthew M.

Blood | December 5, 2024 | Volume: 144 | Issue: Supplement 1 | Pages: 513-513

10.1182/blood-2024-204888 Get It

Fetal hemoglobin (HbF) is anti-sickling and elevated HbF ameliorates sickle cell disease (SCD) manifestations. BEAM-101 is an investigational cell therapy comprised of autologous CD34+ hematopoietic stem and progenitor cells (HSPCs) that are base edited ex vivo to introduce naturally occurring A-to-G substitutions into the promoters of the HBG1/2 genes that encode γ-globin to disrupt BCL11A transcriptional repressor binding sites, leading to increased HbF production. We previously demonstrated in pre-clinical studies that base editing potently induced HbF (>60%) and proportionately reduced sickle hemoglobin (HbS) (<40%) without relying on double-stranded DNA breaks. We present initial data from BEACON (NCT05456880), a Phase 1/2, single-arm, open-label study evaluating the safety and efficacy of a single dose of BEAM-101 in patients with SCD with severe vaso-occlusive crises (VOCs). Patients 18-35 years diagnosed with SCD and ≥4 severe VOCs in the 2-year period prior to screening per trial criteria were eligible. After plerixafor mobilization, autologous CD34+ HSPCs were collected by leukapheresis/isolation and genetically modified with an adenine base editor. After myeloablative conditioning with pharmacokinetically adjusted busulfan, patients received a single infusion of BEAM-101 (≥3.0 × 106 viable CD34+ cells/kg) and are monitored for neutrophil and platelet engraftment, adverse events (AEs), total hemoglobin (Hb), Hb fractions, % F-cells, hemolysis markers, peripheral blood editing, and VOCs for 24 months. As of July 2, 2024, >20 patients are enrolled and BEAM-101 has been manufactured for 8 patients, of whom 6 patients have been dosed. One patient not included in this analysis discontinued during the mobilization/collection period prior to BEAM-101 treatment for non-medical reasons. Baseline demographics were as follows: 5/6 patients βS/βS, 1/6 patients βS/β0, all self-reported Black/African American, 50% female, aged 19-27 years. Of the 6 patients, half (n=3) required only a single mobilization cycle and the other half required 2. Patients received a mean BEAM-101 dose of 11.9 × 106 (5.2-23.4) viable CD34+ cells/kg. Excepting safety data that include all patients dosed (n=6), the following data are from patients dosed with ≥1 month of follow up (n=4; 6, 5, 2, and 1 month[s] post-treatment, each). All 4 patients with ≥1 month of follow up achieved neutrophil and platelet engraftment at a median of 17 (15-19) and 20 (11-34) days, respectively. One patient died due to respiratory failure, likely related to busulfan conditioning, 4 months after infusion. In all patients dosed (n=6), there have been no ≥Grade 3 AEs or serious AEs related to BEAM-101. Using the central laboratory data, patients' total Hb increased from baseline (mean 9.3 [7.9-10.9] g/dL) to 17.9, 18.2, 11.0, and 11.8 g/dL at last time point (LTP) available for P1, P2, P3, and P4, respectively. No signs/symptoms or interventions were undertaken for high total Hb. All patients achieved >60% HbF of non-transfused Hb (total Hb − HbA) at Month (M) 1 and sustained this elevation to the LTP available. By M1, HbS% in non-transfused blood dropped to ≤36% in all 4 patients and was sustained through LTP. In total blood, % F-cells were 99.6% in P1 at M6, 94.4% in P2 at M4, 52.0% in P3 at M2, and 13.3% in P4 at M1 with all patients having >19 pg HbF/F-cell at LTP available. Peripheral blood editing in nucleated cells, measured in P1 (at M6) and P2 (at M3), was 69.9% and 76.1%, respectively. Markers of hemolysis (lactate dehydrogenase, indirect bilirubin, haptoglobin, and reticulocyte counts) have normalized or improved for all patients. No VOCs have been reported by investigators following BEAM-101 treatment. These initial data show a safety profile for BEAM-101 consistent with busulfan conditioning and autologous HSCT. Treatment with BEAM-101 resulted in rapid engraftment, improvement in hemolysis markers, and marked improvement of anemia in all 4 dosed patients. We observed rapid and robust HbF induction consistent with pre-clinical data by M1 (>60%) and corresponding HbS reduction (≤36%) in non-transfused blood in all post-treatment assessments. No VOCs were reported by investigators post-treatment. These initial data support base editing of the HBG1/2 promoters as an effective therapeutic modality for the treatment of SCD and will continue to be investigated in the ongoing BEACON study. Updated data to be presented.
CTIM-30. NT-I7, A LONG-ACTING INTERLEUKIN-7, PROMOTES ACTIVATION, CYTOTOXIC FUNCTION, AND SELECTIVE CLONOTYPE EXPANSION OF CD8+ T CELLS IN PATIENTS WITH HIGH GRADE GLIOMAS
Barozinsky, Kaiden, Butt, Omar H. , Etter, Kelsey, Grote, Cierra, Nehring, Leslie, Katumba, Ruth , Ferrando-Martinez, Sara , Stermer, Kristina, Lee, Byung Ha , Johanns, Tanner M. , Huang, Jiayi , Chheda, Milan G. , Campian, Jian , Foltz, Jennifer A. , Zhou, Alice Y. , Singhal, Kartik , Griffith, Obi L. , Griffith, Malachi , Etter, Kelsey, Grote, Cierra, Luo, Jingqin , Huang, Jiayi, DiPersio, John F. , Fehniger, Todd A.

Neuro-Oncology | November 11, 2024 | Volume: 26 | Issue: Supplement_8 | Pages: viii92-viii92

10.1093/neuonc/noae165.0363 Get It

Abstract Lymphopenia following chemoradiation for high grade gliomas (HGG) is common and is associated with decreased survival. NT-I7 (efineptakin alfa) is a long-acting analog of the lymphocyte pro-survival cytokine, interleukin-7. Our Phase I dose-escalation study of 19 patients with HGG demonstrated early elevations in CD4+ and CD8+ T cells in the first 4 weeks after administration of NT-I7. In this study, we explored the diversity and potential functionality of the NT-I7-expanded T cell population. A subset of 4 subjects with glioblastoma multiforme (GBM) treated at 720 µg/kg of NT-I7 during adjuvant temozolomide in our study (NCT03687957) underwent Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) of peripheral blood. CITE-seq with TCR clonotype sequencing (10x Genomics 5’) permitted simultaneous tracking of the T cell phenotype at the protein level, individual T cell clones, and gene expression dynamics between 4 timepoints: pre-treatment, and post-treatment weeks 1, 2, and 13. Here, we report the results of differential expression analyses between timepoints and patient-specific differences in T cell clonotype expansions. Both CD4+ and CD8+ T cells in our study patients had increased expression of T cell activation markers LTB, CISH, and CD74. CD8+ T cell subsets demonstrated additional elevations in genes important in cytotoxic function (granzymes (GZMA, GZMB) and perforin (PRF1)), MHC Class II expression (HLA-DRA, HLA-DRB1), and AP-1 transcription factor subunits (JUND, JUN, JUNB, FOS, FOSB). After excluding known viral antigen clonotypes, 2 of 4 patients demonstrated TCR clonotype expansion. Notably, nearly all the expanded TCR clonotypes were found within CD8+ T cells, but not CD4+ T cells. NT-I7 promotes activation, cytotoxic function, and selective clonotype expansion of CD8+ T cells in patients with HGG. This, combined with its role in increased CD4+ T cell counts, suggests NT-I7 may be a powerful tool to restore immune function after treatment-associated lymphopenia in HGG.
Outcomes after Transplant in Relapsed/Refractory KMT2Ar (MLLr) and mNPM1 (NPM1c) leukemia Patients Achieving Remissions after Menin Inhibition: SNDX-5613 (revumenib) Ph1 Experience
Issa, Ghayas C., Cuglievan, Branko , Stein, Eytan M. , Arellano, Martha , Khera, Nandita , Stone, Richard M. , Thirman, Michael J. , Karras, Nicole, Gu, Yu , Bagley, Rebecca G., Rosen, Galit, Tamang, David, Dishman, Kimberly, Scalera, Sushama, Meyers, Michael L., Madigan, Kate, McNeer, Nicole, Issa, Ghayas , Žučenka, Andrius , DiPersio, John F. , Madigan, Kate, Aldoss, Ibrahim

Blood | November 28, 2022 | Volume: 140 | Issue: Supplement 1 | Pages: 914-916

10.1182/blood-2022-164600 Get It

Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis
Jayasinghe, Reyka G. , Lee, Brian , Bhasin, Swati S. , Pilcher, William , Dasari, Surendra , Fiala, Mark A. , Pita-Juárez, Yered , Strausbauch, Michael, Kelly, Geoffrey , Thomas, Beena , Kumar, Shaji , Anderson, Emilie, Wendl, Michael C. , Dawson, Travis , D’souza, Darwin , Cheloni, Giulia , Li, Ying , Dhodapkar, Kavita M. , Vij, Ravi , Vlachos, Ioannis S. , Mehr, Shaadi , Hamilton, Mark , Auclair, Daniel , Kourelis, Taxiarchis , Avigan, David , Dhodapkar, Madhav V. , Gnjatic, Sacha , Ding, Li , Jayasinghe, Reyka G , Bhasin, Swati S , Pilcher, William , Dasari, Surendra , Fiala, Mark A , Pita-Juarez, Yered , Kumar, Shaji K , Dawson, Travis , Oh, Stephen T , Li, Ying , Rahman, Adeeb H , Dhodapkar, Kavita M , Hamilton, Mark , Auclair, Daniel , Dhodapkar, Madhav V , Gnjatic, Sacha , Bhasin, Manoj K , Ding, Li , Vlachos, Ioannis S , Yao, Lijun , Doxie, Deon Bryant , Gonzalez‐Kozlova, Edgar , Thomas, Beena E., Cho, Hearn Jay , Oh, Stephen T. , DiPersio, John F. , Kim-Schulze, Seunghee

Cancer Research Communications | August 31, 2022 | Volume: 2 | Issue: 10 | Pages: 1255-1265

10.1158/2767-9764.crc-22-0022 Get It

As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared immune cells of multiple myeloma bone marrow samples from 18 patients assessed by single-cell RNA sequencing (scRNA-seq), mass cytometry (CyTOF), and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to understand the concordance of measurements among single-cell techniques. Cell type abundances are relatively consistent across the three approaches, while variations are observed in T cells, macrophages, and monocytes. Concordance and correlation analysis of cell type marker gene expression across different modalities highlighted the importance of choosing cell type marker genes best suited to particular modalities. By integrating data from these three assays, we found International Staging System stage 3 patients exhibited decreased CD4+ T/CD8+ T cells ratio. Moreover, we observed upregulation of RAC2 and PSMB9, in natural killer cells of fast progressors compared with those of nonprogressors, as revealed by both scRNA-seq and CITE-seq RNA measurement. This detailed examination of the immune microenvironment in multiple myeloma using multiple single-cell technologies revealed markers associated with multiple myeloma rapid progression which will be further characterized by the full-scale immune atlas project. Significance: scRNA-seq, CyTOF, and CITE-seq are increasingly used for evaluating cellular heterogeneity. Understanding their concordances is of great interest. To date, this study is the most comprehensive examination of the measurement of the immune microenvironment in multiple myeloma using the three techniques. Moreover, we identified markers predicted to be significantly associated with multiple myeloma rapid progression.
Abstract 1729: Single-cell transcriptome profiling of multiple myeloma bone marrow samples suggests that disease progression interplays with tumor and tumor microenvironment in The MMRF CoMMpass Study
Sato, Kazuhiro , Chiang, I-Ling, D’souza, Darwin , Kourelis, Taxiarchis , Thomas, Beena , Lee, Brian , Upadhyaya, Bhaskar , Fortier, Julie M. , Dawson, Travis , Kumar, Shaji , Cho, Hearn, Raj, Bee, Vij, Ravi , Vlachos, Ionnis, Mehr, Shaadi , Hamilton, Mark , Auclair, Daniel , Dasari, Surendra , Avigan, David , Dhodapkar, Madhav V. , Ding, Li , Yao, Lijun , Wang, Tianjiao , Jayasinghe, Reyka G. , Pilcher, William , Gonzalez‐Kozlova, Edgar , Pita-Juárez, Yered , Doxie, Deon Bryant , Thomas, Beena, Bhasin, Swati S. , Fiala, Mark A. , Leech, John M. , Kim-Schulze, Seunghee , Oh, Stephen T. , DiPersio, John F. , Rahman, Adeeb H , Gnjatic, Sacha , Bhasin, Manoj K

Cancer Research | June 15, 2022 | Volume: 82 | Issue: 12_Supplement | Pages: 1729-1729

10.1158/1538-7445.am2022-1729 Get It

Abstract Multiple Myeloma (MM) is a hematologic malignancy marked by uncontrolled clonal expansion of plasma cells. Previous research has examined single-cell transcriptome profiles of Monoclonal gammopathy of undetermined significance (MGUS) and MM tumor microenvironment (TME) and found that natural killer (NK) cell abundance is elevated in the early stages and correlated with altered chemokine receptor expression. This study suggested the critical role of immune cells on myeloma progression from asymptomatic MGUS to symptomatic MM. Up to date, however, there are no published studies comprehensively comparing tumor and immune populations differences between MM NON-progressors (NPs) and FAST-progressors (FPs) and investigating how clonal plasma cells affect disease progression in a large cohort. Therefore, understanding how tumor and immune cells influence disease progression within symptomatic MM is of great interest.Here, we subjected CD138-negative Bone Marrow Mononuclear cells (BMMC) samples from 418 MM patients to scRNA-seq. From MMRF CoMMpass study (NCT01454297), we also have whole exome sequencing (WES) and bulk RNA-seq from CD138-positive fraction of BMMC samples. Based on time to progressive disease (TTPD), we classified patients into 2 categories. Patients with TTPD less than 18 months were classified as FAST-progressors (FPs), whereas patients with TTPD more than 5 years were classified as NON-progressors (NPs). By analyzing patient genomic alterations and its association with progression, we found that there was a significant association of slow MM progression with t(11;14) (p = 0.048), consistent with previous study. In our preliminary analysis, we profiled 83 CD138-sorted MM bone marrow samples using scRNA-seq. Interestingly, we found plasma cells from samples with the same genetic alterations tend to cluster together, highlighting the important role of genetic drivers in transcriptome profiles of plasma cells. Moreover, integrated analysis of bone marrow samples from 83 MM patients and 4 healthy donors revealed an atypical naïve-B cell subset with enrichment of cells from fast-progressors and partial expression of MS4A1. Differentially expressed genes for this naïve-B cell subset includes KLF9, BCL2L11, JOSD1, and IRS2, etc. Overall, as part of MMRF immune profiling research, this study will help to interrogate how genetic alterations and disease progression interplay MM tumor and TME and provide a sufficiently broad and valuable dataset for systematically characterizing MM at single-cell resolution. Hopefully, this study could identify novel targets for MM immunotherapies, and ultimately identify patients with high risk of fast progression for early intervention in the clinic. Citation Format: Lijun Yao, Tianjiao Wang, Kazuhiro Sato, Reyka Jayasinghe, I-Ling Chiang, Darwin D'souza, William Pilcher, Edgar Gonzalez-Kozlova, Yered Pita-Juarez, Taxiarchis Kourelis, Deon Bryant Doxie, Beena Thomas, Brian Lee, Swati Sharma Bhasin, Upadhyaya Bhaskar, Mark Fiala, Julie Fortier, Travis Dawson, John Leech, Shaji Kumar, Hearn Cho, Seunghee Kim-Schulze, Bee Raj, Stephen Oh, the MMRF Immune Profiling Research Team, John Dipersio, Ravi Vij, Adeeb Rahman, Ionnis Vlachos, Shaadi Mehr, Mark Hamilton, Daniel Auclair, Surendra Dasari, David Avigan, Madhav Dhodapkar, Sacha Gnjatic, Manoj Bhasin, Li Ding. Single-cell transcriptome profiling of multiple myeloma bone marrow samples suggests that disease progression interplays with tumor and tumor microenvironment in The MMRF CoMMpass Study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1729.
Single-Cell RNA-Seq Analysis of CD138-Depleted Bone Marrow Samples Reveals Genetic Alterations and Disease Progression Correlate with Tumor and Bone Marrow Immune Microenvironment in the Mmrf Commpass Study
Wang, Tianjiao , Sato, Kazuhiro , Kourelis, Taxiarchis , Thomas, Beena , Lee, Brian , Upadhyaya, Bhaskar , Fortier, Julie M. , Dawson, Travis , Kumar, Shaji , Raj, Bee, Vij, Ravi , Vlachos, Ioannis S. , Mehr, Shaadi , Hamilton, Mark , Auclair, Daniel , Dasari, Surendra , Avigan, David , Dhodapkar, Madhav V. , Gnjatic, Sacha , Ding, Li , Gnjatic, Sacha , Vlachos, Ioannis S , Yao, Lijun , Jayasinghe, Reyka G. , Pilcher, William , Gonzalez‐Kozlova, Edgar , Pita-Juárez, Yered , Doxie, Deon Bryant , Thomas, Beena E, Bhasin, Swati S. , Fiala, Mark A. , Leech, John M. , Cho, Hearn Jay , Kim-Schulze, Seunghee , Oh, Stephen T. , DiPersio, John F. , Rahman, Adeeb H , Bhasin, Manoj K

Blood | November 24, 2021 | Volume: 138 | Issue: Supplement 1 | Pages: 2691-2691

10.1182/blood-2021-154081 Get It

Abstract Multiple Myeloma (MM) is the second most common hematologic malignancy, marked by uncontrolled clonal expansion of plasma cells. MM genome is complex and heterogeneous, with a high frequency of structural variants (SVs) and copy-number abnormalities (CNAs). Single-cell sequencing technologies offer advantages over traditional bulk methods in cancer genomics research for evaluating cellular heterogeneity and investigating evolution of cellular subpopulations within the tumor. Thus, there is an impetus to translate the growing understanding of the genomic landscape of MM into dissecting the tumor heterogeneity using scRNA-seq. So far, there are no reported studies systematically comparing tumor and immune populations differences between MM NON-progressors (NPs) and RAPID-progressor (RPs) and investigating how clonal plasma cells contribute to progression in a large cohort. In addition, the bone marrow microenvironment plays an important role in the evolution of premalignant MM and MM progression. A previous study of single-cell transcriptomics analysis of Monoclonal gammopathy of undetermined significance (MGUS) and MM tumor microenvironment (TME) revealed that natural killer (NK) cell abundance is frequently increased in the early stages and associated with altered chemokine receptor expression. This study shed the light on the role of immune cells on disease progression from asymptomatic MGUS to symptomatic MM. However to date, how immune cells influence disease progression within symptomatic MM is still unclear. Here, we subjected 344 CD138-negative Bone Marrow Mononuclear cells (BMMC) samples to scRNA-seq. To control for the first line therapy, 272 patients were treated with RVD and Autologous stem cell transplant (ASCT) and were stratified into 3 groups based on progression: 200 NON-progressors (NPs) (PFS> 5 years), 7 Intermediate Progressors (IPs, PFS 2-4 years) and 38 RAPID-progressors (RPs) (PFS<=18 months). In addition, there are 72 subjects treated with RVD but without ASCT, including 34 NPs, 2 IPs and 36 RPs. From MMRF CoMMpass study (NCT01454297), we also have whole exome sequencing (WES) and bulk RNA-seq from CD138-positive fraction of BMMC samples. Our preliminary analysis of scRNA-seq of 6 samples treated by the same first-line therapies (RVD but without ASCT) revealed that plasma cells (PCs) from two patients (MMRF2550 and MMRF2562) with chromosome 13q deletion clustered together, whereas PCs from a patient (MMRF2187) with t(8;14) Myc translocation formed a distinct cluster. Interestingly, PCs from a patient (MMRF2271) with both chromosome 13q deletion and t(8;14) formed another independent cluster. These observations highlight the important role of genetic drivers in transcriptome profiles of plasma cells. In addition, we further investigated how progression features correlate with the immune microenvironment and identified differentially expressed genes between NK cells from RPs versus those from NPs, which could potentially serve as MM progression markers. Interestingly, several cytotoxicity genes are significantly upregulated in FPs, such as GZMB and KLRB1 (log Fold Change=1.44, and 8.41 respectively). Overall, our preliminary results provide a small glimpse of the interconnected nature of driver genetic alterations and progression features in MM tumor and TME. This study will provide a sufficiently broad, deep, and diverse vast dataset for accurately characterizing MM at single-cell resolution to help interrogate how genetic alterations and disease progression interplay MM tumor and TME. We hope this study could identify novel candidate targets for therapeutic approaches, and ultimately stratify patients by risk of progression for early intervention in the clinic. Disclosures Kumar: Roche-Genentech: Consultancy, Research Funding; Merck: Research Funding; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; KITE: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Consultancy, Research Funding; Novartis: Research Funding; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Beigene: Consultancy; Carsgen: Research Funding; Bluebird Bio: Consultancy; Astra-Zeneca: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncopeptides: Consultancy; Tenebio: Research Funding; BMS: Consultancy, Research Funding; Antengene: Consultancy, Honoraria; Adaptive: Membership on an entity's Board of Directors or advisory committees, Research Funding; Sanofi: Research Funding. Oh: Abbvie: Membership on an entity's Board of Directors or advisory committees; Blueprint Medicines: Membership on an entity's Board of Directors or advisory committees; Celgene Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees; Constellation: Membership on an entity's Board of Directors or advisory committees; CTI Biopharma: Membership on an entity's Board of Directors or advisory committees; Disc Medicine: Membership on an entity's Board of Directors or advisory committees; Geron: Membership on an entity's Board of Directors or advisory committees; Incyte: Membership on an entity's Board of Directors or advisory committees; Kartos Therapeutics: Membership on an entity's Board of Directors or advisory committees; PharamaEssentia: Membership on an entity's Board of Directors or advisory committees; Sierra Oncology: Membership on an entity's Board of Directors or advisory committees. Vij: BMS: Research Funding; Takeda: Honoraria, Research Funding; Sanofi: Honoraria, Research Funding; BMS: Honoraria; GSK: Honoraria; Oncopeptides: Honoraria; Karyopharm: Honoraria; CareDx: Honoraria; Legend: Honoraria; Biegene: Honoraria; Adaptive: Honoraria; Harpoon: Honoraria. Avigan: Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Pharmacyclics: Research Funding; Kite Pharma: Consultancy, Research Funding; Juno: Membership on an entity's Board of Directors or advisory committees; Partner Tx: Membership on an entity's Board of Directors or advisory committees; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Membership on an entity's Board of Directors or advisory committees; Aviv MedTech Ltd: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; Legend Biotech: Membership on an entity's Board of Directors or advisory committees; Chugai: Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy; Parexcel: Consultancy; Takeda: Consultancy; Sanofi: Consultancy.