Abstract 5141: Macrophage transcriptomic signature validation in scRNA seq and overall survival differences in urothelial carcinoma

Introduction: While the prognostic value of immune system biomarkers has been well explored, role of cancer associated macrophages in bladder cancer(BC) is unclear due to lack of consistent results, coupled with tissue nonspecific transcriptomic signature.

Methodology: Data acquisition from 3,936 patients of The Cancer Genome Atlas (TCGA) in addition to Gene Expression Omninus (GEO) data sets GSE13507, GSE16945, GSE48277, GSE32894, GSE149582, as well as European Genotype Phenotype EGAS000001004507 was obtained. Tumor associated macrophages M1 and M2 were defined utilizing 188 and 159 gene expression profiles via xCell computational algorithm. To obtain bladder tissue residence macrophage signatures, scRNA seq was performed on tissue collected from surgical resection of 5 HG bladder cancer patients and 2 healthy controls. CellRanger software package with default parameters was utilized giving a total of 8,068 cells. FindAllMarkers was utilized for integration of DEG genes (cancer vs control) among the cluster and identification of BC macrophage specific markers. Endpoint of OS were measured in months from the time of cystectomy to follow up.

Results: Surprisingly, presence of M1 infiltration was found to be associated with improved OS in two out of eight cohorts only (GSE32894, GSE70691, p<0.001), while the remainder detected no significant difference. Similarly, no association with OS was detected among all 8 cohorts with M2 infiltration. To improve our understanding of tissue specific markers of macrophage population in bladder, we then analyzed macrophage clusters detected within scRNAseq of BC patients compared to healthy. Gene ontology enrichment analysis of functions within tumor specific macrophages demonstrated an exaggerated expression of mTORC1 signaling, PI3K/AKT/mTOR signaling, TGF beta and EGF receptor pathways compared to non-cancer controls. Reanalysis of 22 tissue specific markers for M1/M2 infiltration showed no difference in any of the 8 cohorts with M1 high vs low infiltration. Similarly, addition of M2 infiltration as predictive marker yielded no further associations with OS in all but one cohort (GSE32894, p=0.00041), where high M2 tumor presence was associated with improved OS.

Conclusion: Our study represents the largest TAMs evaluation of BC across 8 cohorts with additional scRNA seq exploration of tissue specific signatures, demonstrating no association with OS in bladder cancer.

Citation Format: Laura Bukavina, Spencer Bell, Daniel Geynisman, Ilaha Isali, Daniel Ranti, John Sfakianos, Henkel Valentine, Adam Calaway, Alexander Kutikov, Andres Correa, Robert Uzzo, Lee Ponsky, Philip Abbosh. Macrophage transcriptomic signature validation in scRNA seq and overall survival differences in urothelial carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5141.

Role of Gut Microbiome in Neoadjuvant Chemotherapy Response in Urothelial Carcinoma: A Multi-Institutional Prospective Cohort Evaluation

Treatment with neoadjuvant chemotherapy (NAC) in muscle invasive bladder cancer (MIBC) is associated with clinical benefit in urothelial carcinoma. While extensive research evaluating role of tumor mutational expression profiles and clinicopathologic factors into chemoresponse has been published, the role of gut microbiome (GM) in bladder cancer in chemoresponse has not been thoroughly evaluated. A working knowledge of the microbiome and its effect on all forms of cancer therapy in BC is critical. Here we examine gut microbiome of bladder cancer patients undergoing NAC. Overall, there was no significant difference in alpha and beta diversity by responder status. However, analysis of fecal microbiome samples showed that a higher abundance of Bacteroides within both institutional cohorts during NAC was associated with residual disease at the time of radical cystectomy regardless of chemotherapy regimen. Group community analysis revealed presence of favorable microbial subtypes in complete responders. Finally, fecal microbial composition outperformed clinical variables in prediction of complete response (AUC 0.88 vs AUC 0.50), however, no single microbial species could be regarded as a fully consistent biomarker. Microbiome-based community signature as compared to single microbial species is more likely to be associated as the link between bacterial composition and NAC response.

Abstract CT178: Prevalence of PD-L1 expression in 1st-line (1L) locally advanced/unresectable or metastatic urothelial carcinoma (UC)

Background: Treatments for 1L advanced, unresectable, or metastatic UC include platinum-based chemotherapy, immune checkpoint blockade, or clinical trial enrollment. Not all patients benefit from, or are eligible for, specific therapies due to comorbidities and performance status. There is an urgent need for biomarker-directed strategies to enable patient selection and improve outcomes. Currently the only clinically used molecular biomarker is programmed cell death ligand-1 (PD-L1) protein expression in tumor tissue. Although variably defined with different assays, higher PD-L1 expression generally correlates with increased response rates to immune checkpoint blockade. Improved understanding of the prevalence and potential prognostic role of PD-L1 testing can further enhance its clinical utility and guide novel clinical trial designs.

Methods: This observational study will enroll 250 patients diagnosed with advanced UC either prior to or during 1L therapy, as initiated at the discretion of participating clinicians from 60 US community sites. The primary endpoint is prevalence (with exact [Clopper-Pearson] 95% CI) of PD-L1 high expression by VENTANA SP263 Assay on pretreatment tumor tissue (classified as PD-L1 high if ≥25% of tumor cells [TCs] exhibit staining; or if immune cells [IC] present >1% and IC with staining ≥25%; or IC present =1% and IC with staining =100%). Secondary endpoints include the association of pretreatment PD-L1 expression with pretreatment tumor tissue mutational burden (tTMB), descriptions of treatment response and outcomes (objective response rate based on RECIST 1.1, progressive-free survival [PFS], and overall survival [OS]) and assessment of their correlations with PD-L1 expression. Exploratory endpoints include the association of pretreatment tumor tissue PD-L1 with pretreatment blood-based tumor mutational burden (bTMB), changes in circulating tumor DNA levels, the correlation between tTMB and bTMB values, and the association of those biomarkers with PFS and OS. Enrollment will take place over 24 months. Patients will be followed for up to 30 months after enrollment. With 250 patients, the 95% CI for 30%, 45%, and 60% observed prevalence of PD-L1 high expression are (24.4%, 36.1%), (38.9%, 51.2%), and (53.6%, 66.1%), respectively; the various secondary and exploratory analyses will be descriptive.

Citation Format: Petros Grivas, Alicia K. Morgans, Yair Lotan, Jeffrey Gregg, Daniel Geynisman, Terence Friedlander, Piyush K. Agarwal, Marija Tesic-Schnell, Andrew Bernstein, Doris Makari, Joshua J. Meeks. Prevalence of PD-L1 expression in 1st-line (1L) locally advanced/unresectable or metastatic urothelial carcinoma (UC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT178.

Abstract 07: Challenges of applying tumor genome analysis to the germline: Examples from GI oncology

Purpose: To describe the spectrum of potential and confirmed germline genomic events identified incidentally during routine medium throughput somatic tumor DNA sequencing, and to provide a framework for pre- and post-test consent and counseling for these patients and families.

Patients and Methods: Targeted next generation sequencing was used to evaluate for possible actionable genomic events in tumor tissue obtained from consecutive new patients seen at the University of Chicago Gastrointestinal Medical Oncology clinic between 9/2012 and 9/2013. Patients had a diagnosis of either metastatic gastroesophageal, hepatobiliary or colorectal cancer. A panel consisting of medical oncologists, an oncology fellow, cancer geneticists and genetic counselors reviewed the results of each case (N=112). Patients were grouped based on their post-test probability of possessing a potentially inherited mutation in a cancer susceptibility gene. The patients within the high-risk group included those with a somatic mutation in one or more of the genes within accepted panels that test for inherited cancer syndromes. Patient age and family history were also taken into account. The high-risk patients were then contacted and formally evaluated and counseled by our cancer risk specialists. When possible and indicated, germline genetic testing was obtained.

Results: One hundred and twelve cases were analyzed. Of these, 23 cases (21%) were identified to have somatic, and potentially germline, mutations in BRCA1, BRCA2, PTEN, CDH1, STK11 or MLH1/MSH6 via routine NGS of tumor samples. Seven patients ultimately underwent germline testing of which three (43%) had confirmed germline mutations - interestingly, all were BRCA2. Most identified cases would not meet current criteria to refer for genetic counseling. Variants of unknown significance in germline BRCA2 posed a challenge with respect to counseling and recommendations. There was one positive control patient with a known clinical diagnosis of Gorlin syndrome, in whom routine NGS of his gastric tumor sample identified a PTCH1 gene mutation (previously unknown).

Conclusions: Next generation sequencing technology offers much promise, as we enter the age of individualized medicine, but also poses many challenges for both germline and somatic DNA testing. We identified, incidentally, several cases (∼20%) with a potentially inherited cancer susceptibility gene via routine somatic tumor DNA sequencing. Of patients available and willing to undergo further testing, several (43%, 3/7) of these cases were confirmed germline events. Many of these patients would not have been referred for counseling without the somatic sequencing information. This report raises awareness of the challenges facing NGS tumor analyses, and provides a framework for pre- and post-test consent and counseling of patients undergoing routine tumor sequencing.

Citation Format: Andrea Amico, Sarah Nielsen, Daniel Geynisman, Brittany Rambo, George Ben Carey, Cassandra Gulden, Jim Fackenthal, Olufunmilayo Olopade, Daniel Catenacci. Challenges of applying tumor genome analysis to the germline: Examples from GI oncology. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 07. doi:10.1158/1538-7445.CANSUSC14-07