Abstract 6699: Delineating germline, tumor and extrinsic factors driving mucosal melanoma (MM) risk and response to immune checkpoint inhibitor (ICI) treatment
Authors: Florentia Dimitriou, Priyadharsini Nagarajan, Sabitha Prabhakaran, Neus Bota, Mark Knafl, Randy A. Chu, Ashish V. Damania, Pranoti V. Sahasrabhojane, Yasmine Hoballah, Jillian S. Losh, Nadim J. Ajami, Scott E. Woodman, Jennifer A. Wargo, Andrew Futreal, Jennifer L. McQuade
Journal: Cancer Research (2024)

Abstract Introduction MM is a rare melanoma subtype with distinct biology, low immunogenicity and tumor mutational burden, and subsequently lower response rates to ICIs. The biology of MM is poorly understood. We sought to prospectively, uniformly, and comprehensively profile a cohort of MM patients to determine the interplay of molecular variation, germline predisposition, immunity, gut, mucosal and tumor microbiome and modifiable risk factors on ICI response and resistance in advanced MM. Methods Patients (pts) with MM treated with standard-of-care ICI as any treatment line presenting to MD Anderson are being prospectively enrolled for longitudinal collection for molecular, microbiome, and lifestyle factor profiling. Planned analyses include: whole genome sequencing of normal and tumor tissue, RNA sequencing, and T cell receptor sequencing from fresh tumor samples; germline sequencing and genotype analyses; NanoString Digital Spatial Profiling (DSP) from formalin-fixed paraffin embedded (FFPE) specimens; whole genome shotgun, microbiome profiling and 16S rRNA gene sequencing (16S) of fecal specimens and affected mucosal and tumor sites (swabs); participant lifestyle and patient reported outcomes (PROs) assessments. Fresh tissue is collected and used to develop PDX models and cell lines. Results 98 pts have been enrolled to date; 83 (85%) Caucasians, 8 (8%) Hispanic, 4 (4%) Asians. 67 (68%) females. Median age at MM diagnosis is 64 years (range 32-91 years). MM primary sites include 24 (24%) naso-oral, 29 (30%) urogenital, 26 (27%) anorectal, 7 (7%) conjunctival and 12 (12%) other. Clinical somatic mutation testing was performed in 76 (76%) pts and common mutations were KIT (n = 12, 16%), NRAS (n = 8, 11%) and BRAF V600 or non-V600 (n = 9, 12%). At data cut-off (November 2023), 18 (18%) pts deceased. Median follow-up from first diagnosis to last visit/death was 16 months (range 1-178 months). Sample collections at data cut-off include: blood samples (n = 95; 219 samples); fecal specimens (n = 50; 97 samples); mucosal swabs (tumor/tumor adjacent/oral cavity; n = 38; 101 samples); fresh frozen tumor/normal (n = 38; 55 samples), fresh tumor/normal (n = 28; 36 samples) and FFPE tumor (n = 21; 37 samples) tissue. PROs and dietary assessments have been collected from 47 pts. Fresh tissue for PDX model and cell line development has been collected from 11 pts. Conclusion This is an ongoing prospective study that is expected to drive insights into the tumor/microenvironment/host interactions and factors regulating immunogenicity to predict response and resistance to ICIs in a rare and understudied melanoma subtype. Interrogation of the role of the gut microbiome and its modifiable determinants will lead to the investigation of new therapeutic strategies to modulate the microbiome to improve treatment outcomes in MM. Data will be presented from initial cohort analyses. Citation Format: Florentia Dimitriou, Priyadharsini Nagarajan, Sabitha Prabhakaran, Neus Bota, Mark Knafl, Randy A. Chu, Ashish V. Damania, Pranoti V. Sahasrabhojane, Yasmine Hoballah, Jillian S. Losh, Nadim J. Ajami, Scott E. Woodman, Jennifer A. Wargo, Andrew Futreal, Jennifer L. McQuade. Delineating germline, tumor and extrinsic factors driving mucosal melanoma (MM) risk and response to immune checkpoint inhibitor (ICI) treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6699.