1714P - Detection and monitoring of translocation renal cell carcinoma via epigenomic profiling of cell-free DNA

Background

Translocation renal cell carcinoma (tRCC) is an aggressive subtype of kidney cancer usually driven by a fusion involving the TFE3 gene. Due to histologic overlap with other subtypes of RCC, tRCC is frequently misclassified. Methods for accurate diagnosis of this molecularly distinct entity are therefore a pressing need. Epigenomic profiling of ctDNA via plasma chromatin immunoprecipitation and sequencing (ChIP-seq) has recently emerged as a powerful tool to detect and molecularly subtype cancers and may offer a more sensitive and specific detection of molecular fusions. We aimed to detect tRCC in plasma and to discriminate tRCC from ccRCC based on epigenomic profiling of cfDNA.

Methods

We first identified differentially expressed gene, methylated regions and regulatory elements (REs) specific to tRCC vs. ccRCC via RNA-seq, methylated DNA immunoprecipitation sequencing (MeDIP-seq) and ChIP-Seq, of 4 tRCC and 5 ccRCC cell lines. We collected 16 plasma samples from metastatic patients with tRCC, 12 with ccRCC and 9 healthy patients. Ultra low pass whole genome sequencing (ulpWGS) was performed to infer ctDNA fraction (TF), and cfMeDIP-seq, H3K4me3/H3K27ac cfChIP-seq for epigenomic profiling. Signal at tRCC-specific regions derived from cell lines profiling was aggregated for each mark. Classification performance was evaluated using the area under the receiver operating characteristic (AUROC) curve.

Results

Overall 8/16 tRCC and 5/12 ccRCC samples had >3% TF by ulpWGS. H3K4me3 and H3K27ac cfChIP-seq signal was significantly higher in all tRCC samples compared to healthy (p<10^-6, AUROC =1), at tRCC-specific promoters and tRCC-specific REs respectively. Furthermore, H3K27ac signal in plasma was also significantly higher at tRCC-specific REs in tRCC samples compared to ccRCC (p<10^-4, AUROC=0.95). MeDIP-seq could not discriminate between tRCC and ccRCC.

Conclusions

Although a majority of tRCC plasma samples profiled had TF < 3%, all could be distinguished from healthy samples on the basis of cfChIP. H3K27ac cfChIP-Seq was also discriminatory for tRCC vs. ccRCC. Epigenomic profiling of cfDNA appears as a powerful tool for both detection of tRCC and discrimination from ccRCC/healthy plasma, with potential implications for diagnosis and guiding therapy.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.

Funding

The V Foundation (V Scholar Award grant number V2022-018).

Disclosure

J.E. Berchuck: Financial Interests, Personal, Invited Speaker, Speaker honoraria: Guardant Health; Financial Interests, Personal, Advisory Board, Consulting fees: Genome Medical, Oncotect, Precede Biosciences, TracerDx; Financial Interests, Personal, Writing Engagement, Scientific Writer: Digital Science Press; Financial Interests, Personal, Advisory Board, Consulting Fees: Guardant Health; Financial Interests, Personal, Stocks/Shares, Company Equity: Cityblock Health, Genome Medical, Oncotect, Precede Biosciences, TracerDx; Financial Interests, Institutional, Advisory Board, Institutional patent filed on methods to detect neuroendocrine prostate cancer through tissue-informed cell-free DNA methylation analysis and licensed by Precede Biosciences: Precede Biosciences; Financial Interests, Personal, Coordinating PI: Precede Biosciences. M. Freedman: Financial Interests, Personal, Other, I am a co-founder, shareholder, and consultant of Precede Biosciences. Precede Biosciences is a liquid biopsy company that seeks to deliver tumor-derived epigenomic information from a blood draw: Precede Biosciences; Financial Interests, Personal, Other, I was a moderator for the The Third Transatlantic Exchange in Oncology: Liquid Biopsy as an Emerging Approach in Precision Cancer Medicine: L'Institut Servier; Financial Interests, Personal, Stocks/Shares, I hold equity in Precede Biosciences: Precede Biosciences. T.K. Choueiri: Financial Interests, Personal, Advisory Board, Advice on GU/RCC drugs: BMS, Pfizer, Merck, Exelixis, AstraZeneca; Financial Interests, Personal, Advisory Board, Advice on Onc drugs: Lilly, EMD Serono, Infinity; Financial Interests, Personal, Advisory Board, Advice on RCC drug: Calithera; Financial Interests, Personal, Invited Speaker, RCC drug: Ipsen; Financial Interests, Personal, Advisory Board, Advice on GU Onc drugs: Surface Oncology; Financial Interests, Personal, Other, Consultant on onc drugs: Analysis Group; Financial Interests, Personal, Invited Speaker, CME, ww2.peerview.com: Peerview; Financial Interests, Personal, Invited Speaker, CME, gotoper.com: PER; Financial Interests, Personal, Invited Speaker, CME, researchtopractice.com: ResearchToPractice; Financial Interests, Personal, Invited Speaker, National Association of Managed Care: NAMC; Financial Interests, Personal, Invited Speaker, ASCO-related event: ASCO-SITC; Financial Interests, Personal, Other, Grant review to Orien Network ($400): ORIEN; Financial Interests, Personal, Advisory Board, Advising oncology strategy: Aptitude Health; Financial Interests, Personal, Invited Speaker, Best of ASCO19 talk: Advent health; Financial Interests, Personal, Invited Speaker, Best of ESMO20 talk ($1000): UAE Society of Onc; Financial Interests, Personal, Invited Speaker, CME, mjhlifesciences.com (OncLive): MJH life sciences; Financial Interests, Personal, Invited Speaker, Grand Rounds: MDACC; Financial Interests, Personal, Invited Speaker, RCC webinar: Cancernet; Financial Interests, Personal, Invited Speaker, CME, Kidney Cancer Association ($1300): France Foundation; Financial Interests, Personal, Invited Speaker, CME, RCC: Springer, WebMed; Financial Interests, Personal, Invited Speaker, CME, ImmunoOncology in RCC: ASiM, CE; Financial Interests, Personal, Invited Speaker, CME, PodCast in RCC ($500.00): Caribou Publishing; Financial Interests, Personal, Invited Speaker, Reimbursement ($432.00): Kidney Cancer Association; Financial Interests, Personal, Other, member of the DSMB for clinical trial: Aravive; Financial Interests, Personal, Advisory Board, GU cancer drug development: alkermes, Gilead; Financial Interests, Personal, Other, Study section reviewer. $200.00 per day for 1 day: National Cancer Institute; Financial Interests, Personal, Other, Cancer Center Grand Rounds: Cleveland Clinic; Financial Interests, Personal, Advisory Board, Advisory Board/month: CURESPONSE; Financial Interests, Personal, Advisory Board: Tempest, Precede Bio (not publicly traded)); Financial Interests, Personal, Member of Board of Directors, unpaidhttps://www.accru.org/main/public/index.xhtml: ACCRU; Financial Interests, Personal, Member of Board of Directors, Unpaidhttps://kidneycan.org: KidneyCan; Financial Interests, Personal, Other, External Advisory Board Member: Gustave Roussy; Financial Interests, Personal, Stocks/Shares, advisor: Pionyr (not publicly traded), Tempest (publicly traded), Osel (not publicly traded), Precede Bio (not publicly traded)), CURESPONSE (not publicly traded), Inndura; Financial Interests, Personal, Stocks/Shares: Primium; Financial Interests, Personal, Royalties, For writing and updating chapters in GU Oncology: Up-To-Date online textbook; Financial Interests, Institutional, Funding, National Chair: BMS, Merck, Exelixis, AstraZeneca, Takeda, Tracon; Financial Interests, Institutional, Local PI, National Chair: Roche; Financial Interests, Institutional, Funding, National co-chair: Pfizer, EMD-Serono; Financial Interests, Institutional, Funding, Chair of trial: Lilly; Financial Interests, Institutional, Local PI: Surface Oncology, GSK; Financial Interests, Institutional, Funding, SC member: Eisai; Financial Interests, Institutional, Funding, National co-chair on 3 ongoing trials: ALLIANCE Cooperative Group; Financial Interests, Institutional, Research Grant, for GU oncology translational research through IION program: BMS; Financial Interests, Institutional, Research Grant, for GU oncology translational research: Exelixis; Financial Interests, Institutional, Research Grant, For Health outcomes research: Roche; Financial Interests, Institutional, Local PI, leads trials as PI: Nikang; Non-Financial Interests, Leadership Role, Co-Chair of the meeting, 2019- current and BOD member (unpaid): Kidney Cancer Research Summit of KidneyCAN; Non-Financial Interests, Principal Investigator, Trial Global and National PI with GU Cancers, mostly Kidney Cancer: Multiple Academic and Industry entities; Non-Financial Interests, Personal, Other, Track Leader/Session chair/Speaker/Discussant: ASCO; Non-Financial Interests, Personal, Other, Speaker/Discussant/Track Leader: ESMO; Non-Financial Interests, Institutional, Other, Access to genomic database: Foundation Med, Guardant, Invitae; Non-Financial Interests, Personal, Other, Grants reviewers: AACR; Non-Financial Interests, Personal, Other, Reviewer of papers: Various journals (e.g. NEJM, Lancet, JCO); Non-Financial Interests, Personal, Other, Medical writing and editorial assistance support (e.g. ClinicalThinking, Envision Pharma Group, Fishawack Group of Companies, Health Interactions, Parexel, Oxford PharmaGenesis, Pharmagenesis, and others). However, first draft frequently initiated by myself when I am 1st author: Medical Communication; Non-Financial Interests, Member: ASCO, AACR; Non-Financial Interests, Other, Political vote usually as “independent”, not a member of any political party. I am an issue voter: General US Politics; Other, Employee at DFCI. Please see https://www.dana-farber.org/ for mission statement (non-profit hospital). I am also the past President of Medical Staff at DFCI 2015-2018: Dana-Farber Cancer Institute (DFCI); Other, Professor at HMS, Please see https://hms.harvard.edu/ for mission statement (non-profit school): Harvard Medical School (HMS); Other, The institution filed patents related to biomarkers of immune checkpoint blockers, and circulating tumor DNA. No money made and some patents were abandoned: Filed patents. S. Baca: Financial Interests, Personal, Stocks or ownership: Precede biosciences. S. Viswanathan: Financial Interests, Personal, Speaker, Consultant, Advisor: Jnana Therapeutics. All other authors have declared no conflicts of interest.