Multimodal Single-Cell Transcriptomic and Proteomic Correlatives of Patients Outcomes Following Anti-BCMA Cellular Therapy with Ciltacabtagene Autoleucel (Cilta-cel) in Relapsed Multiple Myeloma
Introduction Multimodal single cell technologies allow us to dissect the mechanisms of therapeutic resistance by integrating transcriptomics and proteomics through the combination of antibody labeling and next-generation sequencing. Using CITE-seq, mass cytometry (CyTOF) and quantitative multiplexed...
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| Veröffentlicht in: | Blood 2023-11, Vol.142 (Supplement 1), p.93-93 |
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| creator | Vieira dos Santos, Junia Melnekoff, David Aleman, Adolfo Bhalla, Sherry Mouhieddine, Tarek H. Van Oekelen, Oliver Rajeeve, Sridevi Upadhyaya, Bhaskar Ghodke-Puranik, Yogita Leshchenko, Violetta Rahman, Adeeb Afik, Shaked Lewinsky, Hadas Thibaud, Santiago Cho, Hearn Jay Richter, Joshua Rodriguez, Cesar Sanchez, Larysa Rossi, Adriana C Richard, Shambavi Chari, Ajai Jagannath, Sundar Parekh, Samir Lagana, Alessandro |
| description | Introduction
Multimodal single cell technologies allow us to dissect the mechanisms of therapeutic resistance by integrating transcriptomics and proteomics through the combination of antibody labeling and next-generation sequencing. Using CITE-seq, mass cytometry (CyTOF) and quantitative multiplexed proteomics (Olink), we sought to understand the determinants of chimeric antigen receptor (CAR) T cell response and the overall survival of patients with relapsed or refractory multiple myeloma (RRMM) receiving ciltacabtagene autoleucel (Cilta-Cel) cellular therapy.
Methods
Twenty five patients received Cilta-Cel and had bone marrow (BM) and peripheral blood (PB) samples collected at baseline and after CAR T infusion. We isolated 262,520 BM cells and 241,657 PB cells, which were later sequenced using CITE-seq. Additionally, we submitted PB samples for CyTOF analysis and acquired 10,162,426 cells used for downstream analysis. We analyzed 92 cytokines using Olink immuno-oncology panel in PB samples. Downstream analysis was performed using the R packages Seurat, CATALYST, FlowSOM and Olink Analyze.
Results
Our cohort had a median progression-free survival (PFS) of 732 days. To focus our correlative analyses on patients experiencing early relapse, the initial cohort was divided into 2 groups: PFS 18 months (n = 15). CAR-T cell expansion was observed in week 2 post-infusion and continued up to week 4. The percentage of CD4 and CD8 CAR-T cells significantly increased between weeks 1-3 and weeks 4-6 weeks (p |
| doi_str_mv | 10.1182/blood-2023-186395 |
| format | Article |
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Multimodal single cell technologies allow us to dissect the mechanisms of therapeutic resistance by integrating transcriptomics and proteomics through the combination of antibody labeling and next-generation sequencing. Using CITE-seq, mass cytometry (CyTOF) and quantitative multiplexed proteomics (Olink), we sought to understand the determinants of chimeric antigen receptor (CAR) T cell response and the overall survival of patients with relapsed or refractory multiple myeloma (RRMM) receiving ciltacabtagene autoleucel (Cilta-Cel) cellular therapy.
Methods
Twenty five patients received Cilta-Cel and had bone marrow (BM) and peripheral blood (PB) samples collected at baseline and after CAR T infusion. We isolated 262,520 BM cells and 241,657 PB cells, which were later sequenced using CITE-seq. Additionally, we submitted PB samples for CyTOF analysis and acquired 10,162,426 cells used for downstream analysis. We analyzed 92 cytokines using Olink immuno-oncology panel in PB samples. Downstream analysis was performed using the R packages Seurat, CATALYST, FlowSOM and Olink Analyze.
Results
Our cohort had a median progression-free survival (PFS) of 732 days. To focus our correlative analyses on patients experiencing early relapse, the initial cohort was divided into 2 groups: PFS <18 months (n = 10) and PFS >18 months (n = 15). CAR-T cell expansion was observed in week 2 post-infusion and continued up to week 4. The percentage of CD4 and CD8 CAR-T cells significantly increased between weeks 1-3 and weeks 4-6 weeks (p<0.001) and significantly decreased after week seven (p<0.05). We detected novel and significant differences among four cell populations associated with PFS longer than 18 months. These patients had a higher percentage of activated CD4 Central Memory (CM) and CD4 cytotoxic cells (p<0.05) relative to the total percentage of CAR-T cells in weeks 4-6, suggesting a key role for CD4 cells in cross priming or direct cytotoxicity in this context. In patients with a PFS longer than 18 months, the CD8 CM CART cell population had a significantly higher percentage in weeks 1-3 and 4-6 (p<0.05) when compared to their counterparts, suggesting that these were the cardinal effector population in these patients.
Myeloid-derived suppressor cells (MDSCs) have been shown to be a central component of the tumor microenvironment in myeloma, with subsets being capable to mount potent suppressive activity at the tumor site. In the BM CITE-seq myeloid compartment, MDSCs were significantly increased in month 1 (p<0.05) in patients with a shorter PFS. Our PB CyTOF data confirmed this finding as the percentage of MDSCs was significantly higher in weeks 1-3 (p<0.05) in the shorter PFS group when compared to their counterparts.
Using a mixed linear regression model on Olink data, we detected 26 cytokines significantly different (p<0.05) between the shorter and longer PFS groups. A pseudobulk analysis of the BM CITE-seq samples for differentially expressed genes encoding the 26 cytokines revealed 22 genes differentially expressed (p<0.05) between patients with a PFS shorter than 18 months and patients with a PFS longer than 18 months in CAR-T, T-cell, NK cell and myeloid cell populations. In the shorter PFS group, VEGFA was significantly higher in CD8 TEMRA CAR-T cells when compared to their counterparts. In the longer PFS group, we observed significantly higher levels of genes involved in T cell activation, such as CD27 and CD28, and pro-inflammatory cytokines such as TNF and IL-15 in the T cell and Myeloid cell compartments. This pattern suggests that higher production of cytotoxic and pro-inflammatory cytokines, combined with enhanced T cell activation, plays an important role in prolonging the response to CAR-T therapy.
Conclusions
Single cell immune profiling and transcriptomic sequencing identified subpopulations of CD4 and CD8 cells which in concert may influence long term CAR-T outcomes. Our findings demonstrate an early expansion of CART, with very few CART cells surviving after 3 months, suggesting that the efficacy of this therapy is related to early dynamics of these populations. We also provide additional evidence associating immunosuppressive MDSC populations in BM and PB patients with a shorter PFS. Ongoing studies will further analyze the role of the immune microenvironment and clonal T cell dynamics in relation to patient outcomes.
Mouhieddine:Legend Biotech: Consultancy. Rahman:ImmunAI: Current Employment. Afik:ImmunAI: Current Employment. Lewinsky:ImmunAI: Current Employment. Cho:Takeda, Inc.: Research Funding; Bristol Myers-Squibb: Research Funding. Richter:Bristol-Meyers-Squibb: Membership on an entity's Board of Directors or advisory committees; Abbvie: Consultancy; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Genentech: Consultancy; Adaptive Biotechnologies: Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy; Sanofi: Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees; Astra Zeneca: Membership on an entity's Board of Directors or advisory committees. Rodriguez:Janssen, Takeda, Bristol Myers Squibb, Amgen, Karyopharm Therapeutics: Membership on an entity's Board of Directors or advisory committees. Sanchez:Janssen Pharmaceuticals: Consultancy, Honoraria. Rossi:JNJ: Membership on an entity's Board of Directors or advisory committees; Adaptive: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees. Richard:Heidelberg Pharma: Research Funding; Bristol Myers Squibb: Honoraria; C4 Therapeutics: Research Funding; Janssen: Honoraria. Chari:Secura Bio: Consultancy, Other: Advisory Board; Karyopharm: Other: Advisory Board; AbbVie: Other: Advisory Board; BMS: Consultancy, Other: Advisory Board, Research Funding; Antengene: Consultancy; Shattuck Labs: Other: Advisory Board; Amgen: Consultancy, Other: Advisory Board, Research Funding; Sanofi: Other: Advisory Board; Glaxo Smith Kline: Other: Advisory Board; Millenium/Takeda: Consultancy, Research Funding; Seattle Genetics: Other: Advisory Board, Research Funding; Genentech: Other: Advisory Board; Janssen: Consultancy, Other: Advisory Board, Research Funding. Jagannath:Regeneron: Consultancy; Takeda: Consultancy; Caribou Biosciences: Consultancy; Sanofi: Consultancy, Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy, Honoraria; Bristol Myers Squibb: Consultancy, Honoraria; DMC: Membership on an entity's Board of Directors or advisory committees; Genmab: Membership on an entity's Board of Directors or advisory committees; Karyopharm: Consultancy; IMS: Membership on an entity's Board of Directors or advisory committees, Other: Support for attending meetings and/or travel; ASH: Membership on an entity's Board of Directors or advisory committees; SOHO: Membership on an entity's Board of Directors or advisory committees; Mount Sinai Hospital: Current Employment. Parekh:Caribou Biosciences: Research Funding; Amgen: Research Funding; Celgene/BMS Corporation: Research Funding; Karyopharm Therapeutics: Research Funding; Grail, LLC: Membership on an entity's Board of Directors or advisory committees.]]></description><identifier>ISSN: 0006-4971</identifier><identifier>EISSN: 1528-0020</identifier><identifier>DOI: 10.1182/blood-2023-186395</identifier><language>eng</language><publisher>Elsevier Inc</publisher><ispartof>Blood, 2023-11, Vol.142 (Supplement 1), p.93-93</ispartof><rights>2023 The American Society of Hematology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c1855-1f3c2d074f93ed7c9c8d2b3f74e291cbfba0ef89482dc4f3d06855cfe014e3d53</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids></links><search><creatorcontrib>Vieira dos Santos, Junia</creatorcontrib><creatorcontrib>Melnekoff, David</creatorcontrib><creatorcontrib>Aleman, Adolfo</creatorcontrib><creatorcontrib>Bhalla, Sherry</creatorcontrib><creatorcontrib>Mouhieddine, Tarek H.</creatorcontrib><creatorcontrib>Van Oekelen, Oliver</creatorcontrib><creatorcontrib>Rajeeve, Sridevi</creatorcontrib><creatorcontrib>Upadhyaya, Bhaskar</creatorcontrib><creatorcontrib>Ghodke-Puranik, Yogita</creatorcontrib><creatorcontrib>Leshchenko, Violetta</creatorcontrib><creatorcontrib>Rahman, Adeeb</creatorcontrib><creatorcontrib>Afik, Shaked</creatorcontrib><creatorcontrib>Lewinsky, Hadas</creatorcontrib><creatorcontrib>Thibaud, Santiago</creatorcontrib><creatorcontrib>Cho, Hearn Jay</creatorcontrib><creatorcontrib>Richter, Joshua</creatorcontrib><creatorcontrib>Rodriguez, Cesar</creatorcontrib><creatorcontrib>Sanchez, Larysa</creatorcontrib><creatorcontrib>Rossi, Adriana C</creatorcontrib><creatorcontrib>Richard, Shambavi</creatorcontrib><creatorcontrib>Chari, Ajai</creatorcontrib><creatorcontrib>Jagannath, Sundar</creatorcontrib><creatorcontrib>Parekh, Samir</creatorcontrib><creatorcontrib>Lagana, Alessandro</creatorcontrib><title>Multimodal Single-Cell Transcriptomic and Proteomic Correlatives of Patients Outcomes Following Anti-BCMA Cellular Therapy with Ciltacabtagene Autoleucel (Cilta-cel) in Relapsed Multiple Myeloma</title><title>Blood</title><description><![CDATA[Introduction
Multimodal single cell technologies allow us to dissect the mechanisms of therapeutic resistance by integrating transcriptomics and proteomics through the combination of antibody labeling and next-generation sequencing. Using CITE-seq, mass cytometry (CyTOF) and quantitative multiplexed proteomics (Olink), we sought to understand the determinants of chimeric antigen receptor (CAR) T cell response and the overall survival of patients with relapsed or refractory multiple myeloma (RRMM) receiving ciltacabtagene autoleucel (Cilta-Cel) cellular therapy.
Methods
Twenty five patients received Cilta-Cel and had bone marrow (BM) and peripheral blood (PB) samples collected at baseline and after CAR T infusion. We isolated 262,520 BM cells and 241,657 PB cells, which were later sequenced using CITE-seq. Additionally, we submitted PB samples for CyTOF analysis and acquired 10,162,426 cells used for downstream analysis. We analyzed 92 cytokines using Olink immuno-oncology panel in PB samples. Downstream analysis was performed using the R packages Seurat, CATALYST, FlowSOM and Olink Analyze.
Results
Our cohort had a median progression-free survival (PFS) of 732 days. To focus our correlative analyses on patients experiencing early relapse, the initial cohort was divided into 2 groups: PFS <18 months (n = 10) and PFS >18 months (n = 15). CAR-T cell expansion was observed in week 2 post-infusion and continued up to week 4. The percentage of CD4 and CD8 CAR-T cells significantly increased between weeks 1-3 and weeks 4-6 weeks (p<0.001) and significantly decreased after week seven (p<0.05). We detected novel and significant differences among four cell populations associated with PFS longer than 18 months. These patients had a higher percentage of activated CD4 Central Memory (CM) and CD4 cytotoxic cells (p<0.05) relative to the total percentage of CAR-T cells in weeks 4-6, suggesting a key role for CD4 cells in cross priming or direct cytotoxicity in this context. In patients with a PFS longer than 18 months, the CD8 CM CART cell population had a significantly higher percentage in weeks 1-3 and 4-6 (p<0.05) when compared to their counterparts, suggesting that these were the cardinal effector population in these patients.
Myeloid-derived suppressor cells (MDSCs) have been shown to be a central component of the tumor microenvironment in myeloma, with subsets being capable to mount potent suppressive activity at the tumor site. In the BM CITE-seq myeloid compartment, MDSCs were significantly increased in month 1 (p<0.05) in patients with a shorter PFS. Our PB CyTOF data confirmed this finding as the percentage of MDSCs was significantly higher in weeks 1-3 (p<0.05) in the shorter PFS group when compared to their counterparts.
Using a mixed linear regression model on Olink data, we detected 26 cytokines significantly different (p<0.05) between the shorter and longer PFS groups. A pseudobulk analysis of the BM CITE-seq samples for differentially expressed genes encoding the 26 cytokines revealed 22 genes differentially expressed (p<0.05) between patients with a PFS shorter than 18 months and patients with a PFS longer than 18 months in CAR-T, T-cell, NK cell and myeloid cell populations. In the shorter PFS group, VEGFA was significantly higher in CD8 TEMRA CAR-T cells when compared to their counterparts. In the longer PFS group, we observed significantly higher levels of genes involved in T cell activation, such as CD27 and CD28, and pro-inflammatory cytokines such as TNF and IL-15 in the T cell and Myeloid cell compartments. This pattern suggests that higher production of cytotoxic and pro-inflammatory cytokines, combined with enhanced T cell activation, plays an important role in prolonging the response to CAR-T therapy.
Conclusions
Single cell immune profiling and transcriptomic sequencing identified subpopulations of CD4 and CD8 cells which in concert may influence long term CAR-T outcomes. Our findings demonstrate an early expansion of CART, with very few CART cells surviving after 3 months, suggesting that the efficacy of this therapy is related to early dynamics of these populations. We also provide additional evidence associating immunosuppressive MDSC populations in BM and PB patients with a shorter PFS. Ongoing studies will further analyze the role of the immune microenvironment and clonal T cell dynamics in relation to patient outcomes.
Mouhieddine:Legend Biotech: Consultancy. Rahman:ImmunAI: Current Employment. Afik:ImmunAI: Current Employment. Lewinsky:ImmunAI: Current Employment. Cho:Takeda, Inc.: Research Funding; Bristol Myers-Squibb: Research Funding. Richter:Bristol-Meyers-Squibb: Membership on an entity's Board of Directors or advisory committees; Abbvie: Consultancy; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Genentech: Consultancy; Adaptive Biotechnologies: Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy; Sanofi: Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees; Astra Zeneca: Membership on an entity's Board of Directors or advisory committees. Rodriguez:Janssen, Takeda, Bristol Myers Squibb, Amgen, Karyopharm Therapeutics: Membership on an entity's Board of Directors or advisory committees. Sanchez:Janssen Pharmaceuticals: Consultancy, Honoraria. Rossi:JNJ: Membership on an entity's Board of Directors or advisory committees; Adaptive: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees. Richard:Heidelberg Pharma: Research Funding; Bristol Myers Squibb: Honoraria; C4 Therapeutics: Research Funding; Janssen: Honoraria. Chari:Secura Bio: Consultancy, Other: Advisory Board; Karyopharm: Other: Advisory Board; AbbVie: Other: Advisory Board; BMS: Consultancy, Other: Advisory Board, Research Funding; Antengene: Consultancy; Shattuck Labs: Other: Advisory Board; Amgen: Consultancy, Other: Advisory Board, Research Funding; Sanofi: Other: Advisory Board; Glaxo Smith Kline: Other: Advisory Board; Millenium/Takeda: Consultancy, Research Funding; Seattle Genetics: Other: Advisory Board, Research Funding; Genentech: Other: Advisory Board; Janssen: Consultancy, Other: Advisory Board, Research Funding. Jagannath:Regeneron: Consultancy; Takeda: Consultancy; Caribou Biosciences: Consultancy; Sanofi: Consultancy, Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy, Honoraria; Bristol Myers Squibb: Consultancy, Honoraria; DMC: Membership on an entity's Board of Directors or advisory committees; Genmab: Membership on an entity's Board of Directors or advisory committees; Karyopharm: Consultancy; IMS: Membership on an entity's Board of Directors or advisory committees, Other: Support for attending meetings and/or travel; ASH: Membership on an entity's Board of Directors or advisory committees; SOHO: Membership on an entity's Board of Directors or advisory committees; Mount Sinai Hospital: Current Employment. Parekh:Caribou Biosciences: Research Funding; Amgen: Research Funding; Celgene/BMS Corporation: Research Funding; Karyopharm Therapeutics: Research Funding; Grail, LLC: Membership on an entity's Board of Directors or advisory committees.]]></description><issn>0006-4971</issn><issn>1528-0020</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNp9UU1v1DAQtRCVWFp-ALc5wsHgj2Q3Eacloi1SV61gOUeOPW6NnDiynVb79_hleHc5c5o3M3pvRu8R8p6zT5w34vPgQzBUMCEpb9ayrV-RFa9FQxkT7DVZMcbWtGo3_A15m9JvxnglRb0if3aLz24MRnn46aZHj7RD72Ef1ZR0dHMOo9OgJgMPMWQ8dV2IEb3K7hkTBAsPBeKUE9wvWYexDK-D9-Gl6MF2yo5-7XZbOOouXkXYP2FU8wFeXH6CzvmstBqyesQJYbvk4HHR6OHDaUUL_Ahugh_l4pzQwOnj2SPsDujDqK7IhVU-4bt_9ZL8uv62727p3f3N9257RzVv6ppyK7UwbFPZVqLZ6FY3RgzSbioULdeDHRRD27RVI4yurDRsXWjaYrEKpanlJeFnXR1DShFtP0c3qnjoOeuPIfSnEPpjCP05hML5cuZgeezZYeyTLlZpNC6izr0J7j_sv6NBlLE</recordid><startdate>20231102</startdate><enddate>20231102</enddate><creator>Vieira dos Santos, Junia</creator><creator>Melnekoff, David</creator><creator>Aleman, Adolfo</creator><creator>Bhalla, Sherry</creator><creator>Mouhieddine, Tarek H.</creator><creator>Van Oekelen, Oliver</creator><creator>Rajeeve, Sridevi</creator><creator>Upadhyaya, Bhaskar</creator><creator>Ghodke-Puranik, Yogita</creator><creator>Leshchenko, Violetta</creator><creator>Rahman, Adeeb</creator><creator>Afik, Shaked</creator><creator>Lewinsky, Hadas</creator><creator>Thibaud, Santiago</creator><creator>Cho, Hearn Jay</creator><creator>Richter, Joshua</creator><creator>Rodriguez, Cesar</creator><creator>Sanchez, Larysa</creator><creator>Rossi, Adriana C</creator><creator>Richard, Shambavi</creator><creator>Chari, Ajai</creator><creator>Jagannath, Sundar</creator><creator>Parekh, Samir</creator><creator>Lagana, Alessandro</creator><general>Elsevier Inc</general><scope>AAYXX</scope><scope>CITATION</scope></search><sort><creationdate>20231102</creationdate><title>Multimodal Single-Cell Transcriptomic and Proteomic Correlatives of Patients Outcomes Following Anti-BCMA Cellular Therapy with Ciltacabtagene Autoleucel (Cilta-cel) in Relapsed Multiple Myeloma</title><author>Vieira dos Santos, Junia ; Melnekoff, David ; Aleman, Adolfo ; Bhalla, Sherry ; Mouhieddine, Tarek H. ; Van Oekelen, Oliver ; Rajeeve, Sridevi ; Upadhyaya, Bhaskar ; Ghodke-Puranik, Yogita ; Leshchenko, Violetta ; Rahman, Adeeb ; Afik, Shaked ; Lewinsky, Hadas ; Thibaud, Santiago ; Cho, Hearn Jay ; Richter, Joshua ; Rodriguez, Cesar ; Sanchez, Larysa ; Rossi, Adriana C ; Richard, Shambavi ; Chari, Ajai ; Jagannath, Sundar ; Parekh, Samir ; Lagana, Alessandro</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c1855-1f3c2d074f93ed7c9c8d2b3f74e291cbfba0ef89482dc4f3d06855cfe014e3d53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vieira dos Santos, Junia</creatorcontrib><creatorcontrib>Melnekoff, David</creatorcontrib><creatorcontrib>Aleman, Adolfo</creatorcontrib><creatorcontrib>Bhalla, Sherry</creatorcontrib><creatorcontrib>Mouhieddine, Tarek H.</creatorcontrib><creatorcontrib>Van Oekelen, Oliver</creatorcontrib><creatorcontrib>Rajeeve, Sridevi</creatorcontrib><creatorcontrib>Upadhyaya, Bhaskar</creatorcontrib><creatorcontrib>Ghodke-Puranik, Yogita</creatorcontrib><creatorcontrib>Leshchenko, Violetta</creatorcontrib><creatorcontrib>Rahman, Adeeb</creatorcontrib><creatorcontrib>Afik, Shaked</creatorcontrib><creatorcontrib>Lewinsky, Hadas</creatorcontrib><creatorcontrib>Thibaud, Santiago</creatorcontrib><creatorcontrib>Cho, Hearn Jay</creatorcontrib><creatorcontrib>Richter, Joshua</creatorcontrib><creatorcontrib>Rodriguez, Cesar</creatorcontrib><creatorcontrib>Sanchez, Larysa</creatorcontrib><creatorcontrib>Rossi, Adriana C</creatorcontrib><creatorcontrib>Richard, Shambavi</creatorcontrib><creatorcontrib>Chari, Ajai</creatorcontrib><creatorcontrib>Jagannath, Sundar</creatorcontrib><creatorcontrib>Parekh, Samir</creatorcontrib><creatorcontrib>Lagana, Alessandro</creatorcontrib><collection>CrossRef</collection><jtitle>Blood</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vieira dos Santos, Junia</au><au>Melnekoff, David</au><au>Aleman, Adolfo</au><au>Bhalla, Sherry</au><au>Mouhieddine, Tarek H.</au><au>Van Oekelen, Oliver</au><au>Rajeeve, Sridevi</au><au>Upadhyaya, Bhaskar</au><au>Ghodke-Puranik, Yogita</au><au>Leshchenko, Violetta</au><au>Rahman, Adeeb</au><au>Afik, Shaked</au><au>Lewinsky, Hadas</au><au>Thibaud, Santiago</au><au>Cho, Hearn Jay</au><au>Richter, Joshua</au><au>Rodriguez, Cesar</au><au>Sanchez, Larysa</au><au>Rossi, Adriana C</au><au>Richard, Shambavi</au><au>Chari, Ajai</au><au>Jagannath, Sundar</au><au>Parekh, Samir</au><au>Lagana, Alessandro</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Multimodal Single-Cell Transcriptomic and Proteomic Correlatives of Patients Outcomes Following Anti-BCMA Cellular Therapy with Ciltacabtagene Autoleucel (Cilta-cel) in Relapsed Multiple Myeloma</atitle><jtitle>Blood</jtitle><date>2023-11-02</date><risdate>2023</risdate><volume>142</volume><issue>Supplement 1</issue><spage>93</spage><epage>93</epage><pages>93-93</pages><issn>0006-4971</issn><eissn>1528-0020</eissn><abstract><![CDATA[Introduction
Multimodal single cell technologies allow us to dissect the mechanisms of therapeutic resistance by integrating transcriptomics and proteomics through the combination of antibody labeling and next-generation sequencing. Using CITE-seq, mass cytometry (CyTOF) and quantitative multiplexed proteomics (Olink), we sought to understand the determinants of chimeric antigen receptor (CAR) T cell response and the overall survival of patients with relapsed or refractory multiple myeloma (RRMM) receiving ciltacabtagene autoleucel (Cilta-Cel) cellular therapy.
Methods
Twenty five patients received Cilta-Cel and had bone marrow (BM) and peripheral blood (PB) samples collected at baseline and after CAR T infusion. We isolated 262,520 BM cells and 241,657 PB cells, which were later sequenced using CITE-seq. Additionally, we submitted PB samples for CyTOF analysis and acquired 10,162,426 cells used for downstream analysis. We analyzed 92 cytokines using Olink immuno-oncology panel in PB samples. Downstream analysis was performed using the R packages Seurat, CATALYST, FlowSOM and Olink Analyze.
Results
Our cohort had a median progression-free survival (PFS) of 732 days. To focus our correlative analyses on patients experiencing early relapse, the initial cohort was divided into 2 groups: PFS <18 months (n = 10) and PFS >18 months (n = 15). CAR-T cell expansion was observed in week 2 post-infusion and continued up to week 4. The percentage of CD4 and CD8 CAR-T cells significantly increased between weeks 1-3 and weeks 4-6 weeks (p<0.001) and significantly decreased after week seven (p<0.05). We detected novel and significant differences among four cell populations associated with PFS longer than 18 months. These patients had a higher percentage of activated CD4 Central Memory (CM) and CD4 cytotoxic cells (p<0.05) relative to the total percentage of CAR-T cells in weeks 4-6, suggesting a key role for CD4 cells in cross priming or direct cytotoxicity in this context. In patients with a PFS longer than 18 months, the CD8 CM CART cell population had a significantly higher percentage in weeks 1-3 and 4-6 (p<0.05) when compared to their counterparts, suggesting that these were the cardinal effector population in these patients.
Myeloid-derived suppressor cells (MDSCs) have been shown to be a central component of the tumor microenvironment in myeloma, with subsets being capable to mount potent suppressive activity at the tumor site. In the BM CITE-seq myeloid compartment, MDSCs were significantly increased in month 1 (p<0.05) in patients with a shorter PFS. Our PB CyTOF data confirmed this finding as the percentage of MDSCs was significantly higher in weeks 1-3 (p<0.05) in the shorter PFS group when compared to their counterparts.
Using a mixed linear regression model on Olink data, we detected 26 cytokines significantly different (p<0.05) between the shorter and longer PFS groups. A pseudobulk analysis of the BM CITE-seq samples for differentially expressed genes encoding the 26 cytokines revealed 22 genes differentially expressed (p<0.05) between patients with a PFS shorter than 18 months and patients with a PFS longer than 18 months in CAR-T, T-cell, NK cell and myeloid cell populations. In the shorter PFS group, VEGFA was significantly higher in CD8 TEMRA CAR-T cells when compared to their counterparts. In the longer PFS group, we observed significantly higher levels of genes involved in T cell activation, such as CD27 and CD28, and pro-inflammatory cytokines such as TNF and IL-15 in the T cell and Myeloid cell compartments. This pattern suggests that higher production of cytotoxic and pro-inflammatory cytokines, combined with enhanced T cell activation, plays an important role in prolonging the response to CAR-T therapy.
Conclusions
Single cell immune profiling and transcriptomic sequencing identified subpopulations of CD4 and CD8 cells which in concert may influence long term CAR-T outcomes. Our findings demonstrate an early expansion of CART, with very few CART cells surviving after 3 months, suggesting that the efficacy of this therapy is related to early dynamics of these populations. We also provide additional evidence associating immunosuppressive MDSC populations in BM and PB patients with a shorter PFS. Ongoing studies will further analyze the role of the immune microenvironment and clonal T cell dynamics in relation to patient outcomes.
Mouhieddine:Legend Biotech: Consultancy. Rahman:ImmunAI: Current Employment. Afik:ImmunAI: Current Employment. Lewinsky:ImmunAI: Current Employment. Cho:Takeda, Inc.: Research Funding; Bristol Myers-Squibb: Research Funding. Richter:Bristol-Meyers-Squibb: Membership on an entity's Board of Directors or advisory committees; Abbvie: Consultancy; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Genentech: Consultancy; Adaptive Biotechnologies: Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy; Sanofi: Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees; Astra Zeneca: Membership on an entity's Board of Directors or advisory committees. Rodriguez:Janssen, Takeda, Bristol Myers Squibb, Amgen, Karyopharm Therapeutics: Membership on an entity's Board of Directors or advisory committees. Sanchez:Janssen Pharmaceuticals: Consultancy, Honoraria. Rossi:JNJ: Membership on an entity's Board of Directors or advisory committees; Adaptive: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees. Richard:Heidelberg Pharma: Research Funding; Bristol Myers Squibb: Honoraria; C4 Therapeutics: Research Funding; Janssen: Honoraria. Chari:Secura Bio: Consultancy, Other: Advisory Board; Karyopharm: Other: Advisory Board; AbbVie: Other: Advisory Board; BMS: Consultancy, Other: Advisory Board, Research Funding; Antengene: Consultancy; Shattuck Labs: Other: Advisory Board; Amgen: Consultancy, Other: Advisory Board, Research Funding; Sanofi: Other: Advisory Board; Glaxo Smith Kline: Other: Advisory Board; Millenium/Takeda: Consultancy, Research Funding; Seattle Genetics: Other: Advisory Board, Research Funding; Genentech: Other: Advisory Board; Janssen: Consultancy, Other: Advisory Board, Research Funding. Jagannath:Regeneron: Consultancy; Takeda: Consultancy; Caribou Biosciences: Consultancy; Sanofi: Consultancy, Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy, Honoraria; Bristol Myers Squibb: Consultancy, Honoraria; DMC: Membership on an entity's Board of Directors or advisory committees; Genmab: Membership on an entity's Board of Directors or advisory committees; Karyopharm: Consultancy; IMS: Membership on an entity's Board of Directors or advisory committees, Other: Support for attending meetings and/or travel; ASH: Membership on an entity's Board of Directors or advisory committees; SOHO: Membership on an entity's Board of Directors or advisory committees; Mount Sinai Hospital: Current Employment. Parekh:Caribou Biosciences: Research Funding; Amgen: Research Funding; Celgene/BMS Corporation: Research Funding; Karyopharm Therapeutics: Research Funding; Grail, LLC: Membership on an entity's Board of Directors or advisory committees.]]></abstract><pub>Elsevier Inc</pub><doi>10.1182/blood-2023-186395</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| title | Multimodal Single-Cell Transcriptomic and Proteomic Correlatives of Patients Outcomes Following Anti-BCMA Cellular Therapy with Ciltacabtagene Autoleucel (Cilta-cel) in Relapsed Multiple Myeloma |
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