24 research outputs found
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675 Genomic drivers of large B-cell lymphoma resistance to CD19 CAR-T therapy
Background
CD19-directed chimeric antigen receptor-reprogrammed autologous T cells are breakthrough immunotherapies for heavily pretreated patients with diffuse large B-cell lymphoma (DLBCL), but across CAR-19 products, ~60% of patients fail to respond or relapse. Inflammatory markers and clinical factors associate with impaired responses, but tumor-intrinsic resistance drivers are largely undefined.
Methods
To characterize the genomic mechanisms involved resistance to CAR-19, we interrogated whole genome sequencing (WGS) from 28 relapsed/refractory (r/r) aggressive lymphoma patients uniformly treated with axicabtagene ciloleucel (axi-cel).
Results
Because prognostic factors defined in the frontline treatment setting are largely inapplicable to CAR-19, we leveraged the WGS data, including comparative analyses with untreated DLBCL cases in the Pan-Cancer Analysis of Whole Genomes (PCAWG) (figure 1). In analyses of individual mutated genes, TP53 was significantly enriched (p=0.002) in CAR-19 patients, but did not predict outcome. However, mutations in either NFKBIA or MYC associated with worse PFS after CAR-19 (p=0.04, p=0.025 respectively). We next identified 12 single base substitution (SBS) mutational signatures in our cohort and found presence of APOBEC (SBS2 and SBS13) signatures associated with worse PFS, with 4/5 patients progressing (p=0.03). Copy number analysis by GISTIC2.0 revealed focal deletions of RHOA and RB1 to be significantly enriched in our cohort and independently predicted poor outcome (p=0.0007, p=0.05 respectively). WGS identifies structural variants and complex events. We found chromothripsis, a catastrophic shattering and reassembly of chromosomes, in 39.3% of r/r DLBCL, which was strongly associated with poor CAR-19 outcome, with 9/11 affected cases progressing (p=0.041). Finally, reduced expression (n=3) or genomic alteration (n=3) of CD19 did not associate with poor outcome. One case with durable response contained a sub-clonal CD19 mutation (L174V) previously reported as associated with CAR-19 resistance. These findings demonstrate predominance of CD19-independent resistance and indicate antigen-mediated tumor killing is not the only mechanism of tumor eradication. Genomic complexity appears to promote an immunosuppressive tumor microenvironment (TME), limiting CAR-19 efficacy.
Conclusions
Leveraging the resolution of WGS, we observed that markers of genomic complexity (chromothripsis and APOBEC) and specific genomic alterations (RHOA and RB1 deletions) associate with resistance to CAR-19 immunotherapy for aggressive B-cell lymphomas (figure 1). 93.8% of CAR-19 relapsed patients contained at least one or these genomic alterations. Recent patient data demonstrate that an immunosuppressed TME leads to CAR-19 failure. Combining these findings with our genomics findings, successful CAR-19 therapy must overcome the immune-exhausted TME to mobilize the host immune system and eliminate the tumor.
Abstract 675 Figure 1
Genomic alterations associated with disease progression. (a) The heatmap shows the significant genomic alteration present in at least 4 patients associated with progression after CD19 CAR-T cell therapy. (b) Kaplan-Meier curve of progression free survival with the combination of statistically significant genomic anomalie
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Genomic drivers of large B-cell lymphoma resistance to CD19 CAR-T therapy
Abstract Introduction: Anti-CD-19 chimeric antigen receptor-reprogrammed autologous T cells are breakthrough immunotherapies for heavily pretreated patients with aggressive B-cell lymphomas; however, across CAR-19 products, ~60% of patients do not achieve remission or relapse and unfortunately typically progress and rapidly die. Factors associated with impaired response to CAR-19 include inflammatory markers such as interferon signaling and clinical factors such as the need for bridging therapy and high pre-CAR-19 tumor burden, but cell-intrinsic driver of CAR-19 resistance remain largely undefined. Methods: To characterize the genomic mechanisms involved in diffuse large B cell lymphoma (DLBCL) resistance to CAR-19, we interrogated whole genome sequencing (WGS) from 28 relapsed/refractory (r/r) aggressive lymphoma patients treated with axicabtagene ciloleucel (axi-cel). The median coverage was 44.8X. To increase statistical power of analyses, we included also 50 newly diagnosed DLBCL patients from the Pan-Cancer Analysis of Whole Genomes (PCAWG). Results: As reported in other series, neither double hit cytogenetics nor MYC-BCL2 double expression associated with CAR-19 resistance, despite their negative predictive power for newly diagnosed DLBCL patients. Chapuy and LymphGen classification algorithms also demonstrated no prognostic significance. Among known mutated driver genes, only TP53 was significantly enriched in our cohort in comparison to the PCAWG cohort (p=0.002), but it did not predict poor CAR-19 outcome. Among other genes known to be involved in DLBCL pathogenesis, only mutations in NFKBIA or MYC, associated with worse PFS (p=0.04, p=0.025 respectively). Next, we identified 12 single base substitution (SBS) mutational signatures detected in our cohort of r/r lymphomas, four of which are caused by exposure to distinct chemotherapies (Landau et al., 2020, Nat Comm). The melphalan-related signature (SBS-MM1) was identified in 4 out 5 patients who received high dose melphalan followed by autologous stem cell transplant, and 75% of patients exposed to platinum had evidence of one of the three known platinum signatures. Across different SBS signatures, only presence of APOBEC (SBS2 and SBS13) associated with worse PFS with 4/5 patients progressing (p=0.03). We compared newly diagnosed and r/r DLBCL by GISTIC2.0 copy number variation (CNV) analysis, revealing three gene deletions significantly enriched in our r/r cohort: TP53, RHOA and RB1. Interestingly, the deletions involving RHOA and RB1 both independently predicted poor outcome (p=0.0007 and p=0.05 respectively) with 5/5 and 6/8 patients progressing respectively. The third, involving TP53 (46.4% of patients), had no prognostic impact but reflected the high-risk nature of the heavily pretreated tumors. WGS allows detailed identification of structural variants and complex events. Indeed, we found evidence of chromothripsis, a catastrophic event in which one or more chromosomes are shattered and aberrantly reassembles generating multiple aneuploidies, in 39.3% of r/r DLBCL. This strongly associated with poor CAR-19 outcome, with 9/11 affected cases experiencing early progression (p=0.041). Finally, reduced expression (n=3) or genomic alteration (n=3) of CD19 did not associate with poor outcome. We found one case, with durable response, containing a sub-clonal mutation in CD19 (L174V) at baseline, previously reported as associated with CAR-19 resistance. In line with recent evidence, these findings indicate that antigen-mediated tumor killing is not the only mechanism of tumor eradication, and CD19-independent resistance mechanisms predominate. Conclusions: Leveraging the high resolution of WGS, we observed that markers of genomic complexity (chromothripsis and APOBEC) and specific genomic alterations (RHOA and RB1 deletion) associate with resistance to CAR-19 immunotherapy for aggressive B-cell lymphomas. Fifteen out of sixteen patients (93.8%) who relapsed on CAR-19 contained at least one of the described genomic alterations. Recent data demonstrate that an immunosuppressed TME leads to CAR-19 failure in patients, and animal studies show activation of host T cells by CAR-T cells. Combining these findings with these genomics findings, successful CAR-19 therapy must overcome the immune-exhausted tumor microenvironment to mobilize the host immune system and eliminate the tumor. Figure 1 Figure 1. Disclosures Jain: Takeda: Consultancy, Honoraria; BMS/Celgene: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Kite/Gilead: Consultancy, Honoraria. Faramand: Novartis: Research Funding; Kite/Gilead: Research Funding. Landgren: Amgen: Research Funding; Janssen: Research Funding; Amgen: Honoraria; Celgene: Research Funding; Janssen: Other: IDMC; Janssen: Honoraria; Takeda: Other: IDMC; GSK: Honoraria. Locke: Iovance Biotherapeutics: Consultancy, Other: Scientific Advisory Role; Gerson Lehrman Group: Consultancy; Calibr: Consultancy, Other: Scientific Advisory Role; Janssen: Consultancy, Other: Scientific Advisory Role; Umoja: Consultancy, Other; Novartis: Consultancy, Other, Research Funding; Bluebird Bio: Consultancy, Other: Scientific Advisory Role; Allogene Therapeutics: Consultancy, Other: Scientific Advisory Role, Research Funding; Kite, a Gilead Company: Consultancy, Other: Scientific Advisory Role, Research Funding; Takeda: Consultancy, Other; Emerging Therapy Solutions: Consultancy; EcoR1: Consultancy; Cowen: Consultancy; Wugen: Consultancy, Other; Legend Biotech: Consultancy, Other; GammaDelta Therapeutics: Consultancy, Other: Scientific Advisory Role; Cellular Biomedicine Group: Consultancy, Other: Scientific Advisory Role; BMS/Celgene: Consultancy, Other: Scientific Advisory Role; Amgen: Consultancy, Other: Scientific Advisory Role; Moffitt Cancer Center: Patents & Royalties: field of cellular immunotherapy. Maura: Medscape: Consultancy, Honoraria; OncLive: Honoraria. Davila: Precigen: Research Funding
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Genomic Drivers of Large B-Cell Lymphoma Resistance to CD19 CAR-T Therapy
Abstract
Introduction: Anti-CD-19 chimeric antigen receptor-reprogrammed autologous T cells are breakthrough immunotherapies for heavily pretreated patients with aggressive B-cell lymphomas; however, across CAR-19 products, ~60% of patients do not achieve remission or relapse and unfortunately typically progress and rapidly die. Factors associated with impaired response to CAR-19 include inflammatory markers such as interferon signaling and clinical factors such as the need for bridging therapy and high pre-CAR-19 tumor burden, but cell-intrinsic driver of CAR-19 resistance remain largely undefined.
Methods: To characterize the genomic mechanisms involved in diffuse large B cell lymphoma (DLBCL) resistance to CAR-19, we interrogated whole genome sequencing (WGS) from 28 relapsed/refractory (r/r) aggressive lymphoma patients treated with axicabtagene ciloleucel (axi-cel). The median coverage was 44.8X. To increase statistical power of analyses, we included also 50 newly diagnosed DLBCL patients from the Pan-Cancer Analysis of Whole Genomes (PCAWG).
Results: As reported in other series, neither double hit cytogenetics nor MYC-BCL2 double expression associated with CAR-19 resistance, despite their negative predictive power for newly diagnosed DLBCL patients. Chapuy and LymphGen classification algorithms also demonstrated no prognostic significance. Among known mutated driver genes, only TP53 was significantly enriched in our cohort in comparison to the PCAWG cohort (p=0.002), but it did not predict poor CAR-19 outcome. Among other genes known to be involved in DLBCL pathogenesis, only mutations in NFKBIA or MYC, associated with worse PFS (p=0.04, p=0.025 respectively).
Next, we identified 12 single base substitution (SBS) mutational signatures detected in our cohort of r/r lymphomas, four of which are caused by exposure to distinct chemotherapies (Landau et al., 2020, Nat Comm). The melphalan-related signature (SBS-MM1) was identified in 4 out 5 patients who received high dose melphalan followed by autologous stem cell transplant, and 75% of patients exposed to platinum had evidence of one of the three known platinum signatures. Across different SBS signatures, only presence of APOBEC (SBS2 and SBS13) associated with worse PFS with 4/5 patients progressing (p=0.03).
We compared newly diagnosed and r/r DLBCL by GISTIC2.0 copy number variation (CNV) analysis, revealing three gene deletions significantly enriched in our r/r cohort: TP53, RHOA and RB1. Interestingly, the deletions involving RHOA and RB1 both independently predicted poor outcome (p=0.0007 and p=0.05 respectively) with 5/5 and 6/8 patients progressing respectively. The third, involving TP53 (46.4% of patients), had no prognostic impact but reflected the high-risk nature of the heavily pretreated tumors.
WGS allows detailed identification of structural variants and complex events. Indeed, we found evidence of chromothripsis, a catastrophic event in which one or more chromosomes are shattered and aberrantly reassembles generating multiple aneuploidies, in 39.3% of r/r DLBCL. This strongly associated with poor CAR-19 outcome, with 9/11 affected cases experiencing early progression (p=0.041).
Finally, reduced expression (n=3) or genomic alteration (n=3) of CD19 did not associate with poor outcome. We found one case, with durable response, containing a sub-clonal mutation in CD19 (L174V) at baseline, previously reported as associated with CAR-19 resistance. In line with recent evidence, these findings indicate that antigen-mediated tumor killing is not the only mechanism of tumor eradication, and CD19-independent resistance mechanisms predominate.
Conclusions: Leveraging the high resolution of WGS, we observed that markers of genomic complexity (chromothripsis and APOBEC) and specific genomic alterations (RHOA and RB1 deletion) associate with resistance to CAR-19 immunotherapy for aggressive B-cell lymphomas. Fifteen out of sixteen patients (93.8%) who relapsed on CAR-19 contained at least one of the described genomic alterations. Recent data demonstrate that an immunosuppressed TME leads to CAR-19 failure in patients, and animal studies show activation of host T cells by CAR-T cells. Combining these findings with these genomics findings, successful CAR-19 therapy must overcome the immune-exhausted tumor microenvironment to mobilize the host immune system and eliminate the tumor.
Figure 1 Figure 1.
Disclosures
Jain: Takeda: Consultancy, Honoraria; BMS/Celgene: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Kite/Gilead: Consultancy, Honoraria. Faramand: Novartis: Research Funding; Kite/Gilead: Research Funding. Landgren: Amgen: Research Funding; Janssen: Research Funding; Amgen: Honoraria; Celgene: Research Funding; Janssen: Other: IDMC; Janssen: Honoraria; Takeda: Other: IDMC; GSK: Honoraria. Locke: Iovance Biotherapeutics: Consultancy, Other: Scientific Advisory Role; Gerson Lehrman Group: Consultancy; Calibr: Consultancy, Other: Scientific Advisory Role; Janssen: Consultancy, Other: Scientific Advisory Role; Umoja: Consultancy, Other; Novartis: Consultancy, Other, Research Funding; Bluebird Bio: Consultancy, Other: Scientific Advisory Role; Allogene Therapeutics: Consultancy, Other: Scientific Advisory Role, Research Funding; Kite, a Gilead Company: Consultancy, Other: Scientific Advisory Role, Research Funding; Takeda: Consultancy, Other; Emerging Therapy Solutions: Consultancy; EcoR1: Consultancy; Cowen: Consultancy; Wugen: Consultancy, Other; Legend Biotech: Consultancy, Other; GammaDelta Therapeutics: Consultancy, Other: Scientific Advisory Role; Cellular Biomedicine Group: Consultancy, Other: Scientific Advisory Role; BMS/Celgene: Consultancy, Other: Scientific Advisory Role; Amgen: Consultancy, Other: Scientific Advisory Role; Moffitt Cancer Center: Patents & Royalties: field of cellular immunotherapy. Maura: Medscape: Consultancy, Honoraria; OncLive: Honoraria. Davila: Precigen: Research Funding
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Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma
CD19-directed chimeric antigen receptor (CAR-19)-T cells are groundbreaking immunotherapies approved for use against large B-cell lymphomas. While host inflammatory and tumor microenvironmental markers associate with efficacy and resistance, the tumor-intrinsic alterations underlying these phenomena remain undefined. CD19 mutations associate with resistance but are uncommon, and most patients who relapse retain expression of the wild-type receptor, implicating other genomic mechanisms. We therefore leveraged the comprehensive resolution of whole-genome sequencing to assess 51 tumor samples from 49 CAR-19-treated large B-cell lymphoma patients. We find that pre-treatment presence of complex structural variants, APOBEC mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. In addition, the recurrent 3p21.31 chromosomal deletion containing the RHOA tumor suppressor was strongly enriched in patients failed by CAR-T therapy. Pretreatment reduced expression or mono-allelic loss of CD19 did not affect responses, suggesting CAR-19 therapy success and resistance are due to multiple mechanisms. Our study shows tumor-intrinsic genomic alterations are key among the complex interplay of factors that underly CAR-19 efficacy and resistance for large B-cell lymphomas
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