Abstract B045: Deep genomic and single cell molecular profiles define immunogenic pancreatic cancer
Authors: Wungki Park, Shigeaki Umeda, Catherine O'Connor, Haochen Zhang, Roshan Sharma, Allison Richards, Yingjie Zhu, Elias-Ramzey Karnoub, Xin Pei, Anna M. Varghese, Kevin Soares, Alejandro Jimenez Sanchez, Hulya Ozkan Sahin, Kenneth Yu, Vinod P. Balachandran, Joanne Chou, Fergus Keane, David Kelsen, Olca Basturk, Chaitanya Bandlamudi, Marinela Capanu, Tal Nawy, Michael Berger, Ronan Chaligne, Ghassan Abou-Alfa, Jorge S. Reis-Filho, Nadeem Riaz, Dana Pe'er, Christine A. Iacobuzio-Donahue, Eileen M. O'Reilly
Journal: Cancer Research (2024)

Abstract Background: Most pancreatic cancers (PC) are resistant to immunotherapy and have a poor prognosis with advanced stage (III/IV, 80%). However, recent cancer vaccine trials have demonstrated that long-term host anti-cancer immunity can improve outcomes of patients (pts) with resectable PC (stage I/II, 20%), harboring high-quality neoantigens or select KRAS alterations. It has been proposed that immunogenic PC is a genetically defined subgroup (5-10%), enriched by hypermutated PC with DNA-damage repair deficiencies including homologous repair (HRD) and mismatch repair (dMMR). Until now, comprehensive molecular studies have been mostly conducted in resected PC. Methods: All tissues were collected following an Institutional Review Board (IRB 21-275) protocol at the Memorial Sloan Kettering. Whole-exome from N=78, exome-captured bulk RNA from N=61, and single-nucleus RNA from N=23 biopsy samples of advanced PC were analyzed. Gene set enrichment and digital cytometry, singe base substitution (SBS) mutational signature, neoantigen, and genomic instability score (GIS) for HRD and immunogenicity were evaluated. Demographics, treatment history, and overall survival (OS) for pts with PC with or without HRD and dMMR were abstracted from the medical record. Results: A total of N=77 WES samples included N=21 core HRD (cHRm: 3 BRCA1, 17 BRCA2, 1 both), N=7 non-core HRD (ncHRm: 3 ATM, 2 CHEK2, 1 RAD50, 1 BARD1), and N=7 dMMR, and N=42 No DDR. N=46 males. Median age 65 years. Median OS (95% confidence interval): 26 months (m) (17-NR) for cHRm, 90m (14-NR) for dMMR, 7.4m (6.8-NR) for ncHRm, and 19m (15-27) for No DDR group. N=49 (63%) pts received first-line platinum chemotherapy. Median tumor mutation burden (TMB-WES): 2 (IQR: 2-3), 35 (30-47), 1 (1-2), and 1, respectively for cHRm, dMMR, ncHRm, and No DDR. TMB-WES significantly higher for dMMR vs. No DDR (95%CI: 35 [30-47] vs 1 [1-2], p=0.001). GIS higher for cHRm vs. No DDR (95%CI: 31 [18-38) vs 14 [9-18], p=0.008). Only two BRCA1m tumors had significant SBS3. N=61 exome captured RNAseq analysis showed cHRm (N=17) vs. No DDR (N=39) had highly enriched gene programs for upregulated immune activity in adaptive immune response (odds ratio [OR]: 0.49, p=1.7e-10), humoral immune response, and T cell activation (OR: 0.44, p=2.7e-8). Digital cytometry showed higher infiltration of gamma delta T cells (p=0.039) and lower regulatory T cells (p=0.001) in cHRm vs. No DDR. 59,771 nuclei were profiled from 23 (16 baseline and 7 follow-ups [5 matched]) biopsy samples from pts with HRD [gBRCA1 (N=3), gBRCA2 (N=14)] and No DDR (N=6). HRD tumors vs. No DDR had higher level of infiltrating CD8+ cytotoxic T cells (p&amp;lt;0.01). Tumors of long-term survivors (&amp;gt; 18m) vs. short-term survivors had significantly lower-level infiltration of macrophages (p&amp;lt;0.01) and Tregs (p=0.05). Conclusions: Our deep genomic and single-cell resolution transcriptomic analyses successfully profiled advanced PC enriched with DDR. HRD and dMMR render PC immunogenic. Further investigations for targeted immunotherapy is warranted. Citation Format: Wungki Park, Shigeaki Umeda, Catherine O'Connor, Haochen Zhang, Roshan Sharma, Allison Richards, Yingjie Zhu, Elias-Ramzey Karnoub, Xin Pei, Anna M. Varghese, Kevin Soares, Alejandro Jimenez Sanchez, Hulya Ozkan Sahin, Kenneth Yu, Vinod P. Balachandran, Joanne Chou, Fergus Keane, David Kelsen, Olca Basturk, Chaitanya Bandlamudi, Marinela Capanu, Tal Nawy, Michael Berger, Ronan Chaligne, Ghassan Abou-Alfa, Jorge S. Reis-Filho, Nadeem Riaz, Dana Pe'er, Christine A. Iacobuzio-Donahue, Eileen M. O'Reilly. Deep genomic and single cell molecular profiles define immunogenic pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B045.