Feasibility of an explainable AI-based therapeutic recommendation-tool utilizing tumor gene expression profiles in advanced and refractory solid tumors.

Authors

null

Ouissam Al Jarroudi

Department of translational medicine, Centre Léon Bérard, Lyon, France

Ouissam Al Jarroudi , Coralie Williams , Rita Santos , Armelle Dufresne , Valéry Attignon , Anthony Ferrari , Sandrine Boyault , Laurie Tonon , Séverine Tabone-Eglinger , Philippe Alexandre Cassier , Nadège Corradini , Armelle Vinceneux , Aurélie Swalduz , Alain Viari , Sylvie Chabaud , David Pérol , Mohammad Afshar , Jean-Yves Blay , Olivier Tredan , Pierre Saintigny

Organizations

Department of translational medicine, Centre Léon Bérard, Lyon, France, Ariana Pharmaceuticals, Paris, France, OmiCure Inc, Paris, France, Department of Medical Oncology, Centre Léon Bérard, Lyon, France, Platform of Cancer Genomics, Centre Léon Bérard, Lyon, France, Platform of Bioinformatics Gilles-Thomas, Centre Léon Bérard, Lyon, France, Biobank, Centre Léon Bérard, Lyon, France, Department of Medical Oncology, Centre Léon-Bérard, Lyon, France, Department of Pediatric Oncology, Institute of Pediatric Hematology and Oncology, Centre Leon Bérard, Lyon, France, Department of Clinical Research, Centre Léon Bérard, Lyon, France, Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France, Medical Oncology Department, Centre Léon Bérard, Lyon, France

Research Funding

Other

Background: Precision oncology aims to guide patient (pts) treatment decisions by matching biological features with available drugs. Extensive genomic analysis allows to identify an actionable alteration in 40-60% of patients. In a recent study of 50 pts with advanced refractory diseases included in PROFILER (NCT01774409), whole exome and fusion transcripts had a limited value over a 90-tumor gene panel (TGP) to increase molecular-based treatment recommendations (MBTR). Herein, we evaluated the feasibility, in the same cohort of pts, of the AI-transcriptional-based therapeutic recommendation-tool OncoKEM to guide treatment recommendations. Methods: 77 fresh frozen (FF) and/or FFPE samples including paired specimens for 53 pts with available RNA-Seq gene expression profiles were included. For each pts, a tumor transcriptional profile (TTP) was generated by identifying differentially expressed genes between the pts tumor and a cohort of matched healthy tissue. A large database of drug transcriptional signatures (DTS) was queried in order to identify a “reversal relationship” between the TTP and a DTS. A total of 205 drugs were ranked, including a subset of 61 FDA and/or EMA approved targeted therapies (aTT). Results: Most common diagnoses were breast cancers (21% of which 63% were TNBC), followed by ovarian cancers (OC, 18%) and soft-tissue sarcomas (STS, 13%). The median number of previous treatment lines was 4 (range: 1 - 10). Among the 77 tumor samples analyzed, 54 (70%) specimens led to the generation of an OncoKEM report, with no differences between FF and FFPE samples (p = 0.85). The overlap between the top 10 proposed drugs between paired FF and FFPE samples was 56% on average. All patients had at least 2 propositions (range: 2-9) of aTT among the top 10 ranked drugs in the Onco KEM reports. Most frequently proposed drugs among the top 10 were palbociclib, talazoparib, infigratinib in TNBC; bosutinib, sapanisertib, SAR125844 in OC; ipilimumab, cabozantinib, sapanisertib in STS. Among the 30 pts (79%) without any MBTR based on TGP/WES/fusion transcript analysis, all had at least 2 proposed aTT in the Onco KEM report (median: 4, range: 2-9). Top ranked drugs were MET (18%), VEGFR (12%), Abl (12%), FGFR (11%), PI3K/AKT/mTOR (11%), PARP (10%) and CDK4/6 inhibitors (7%). Conclusions: AI-transcriptional-based therapeutic recommendation-tool OncoKEM is feasible and has the potential to expand personalized cancer treatment in pts with advanced & refractory diseases without tractable genomic alterations. The clinical relevance assessment is planned in an upcoming clinical trial.

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Abstract Details

Meeting

2022 ASCO Annual Meeting

Session Type

Poster Session

Session Title

Care Delivery and Regulatory Policy

Track

Care Delivery and Quality Care

Sub Track

Clinical Informatics/Advanced Algorithms/Machine Learning

Citation

J Clin Oncol 40, 2022 (suppl 16; abstr 1554)

DOI

10.1200/JCO.2022.40.16_suppl.1554

Abstract #

1554

Poster Bd #

147

Abstract Disclosures