Biology subjects

Cantor, C. R.

Publications and source records attributed to Cantor, C. R..

2 recordsLinked to original sources

bioRxiv2024

A Graph Curvature-Based Pipeline for Discovering Immune Checkpoint Response Biomarkers

Immune checkpoint inhibitors (ICIs), also called immune checkpoint blockers, are a promising category of targeted therapy for solid tumors. Predicting which patients will respond to ICI therapy remains an open problem under active investigation. This paper adds to this effort by developing a modular pipeline for the discovery of biomarkers from tumor RNA-sequencing data. We contextualize gene expression measurements using a protein-protein interaction (PPI) network and use a notion of graph curvature to find (pairs of) genes in the PPI that could serve as potential biomarkers. Our candidate biomarkers are evaluated using an extensive literature search and transfer learning experiments. We also provide a harmonized collection of drug-specific candidate markers found through rank aggregation that we believe merit further study.

cancer biology↗

bioRxiv2024

Discrete Ollivier-Ricci Flow Finds Distinct Subpopulations of Patients Treated with PD-1 Inhibition

In recent years immune checkpoint inhibitors (ICIs), also called immune checkpoint blockers, have revolutionized the standard of care for patients with cancers of many types. Researchers across many disciplines have endeavored to find biomarkers of response to ICI therapy but so far little consensus has been reached. In this paper we attempt to cluster patients in an unsupervised manner using discrete Ollivier-Ricci Flow (ORF). Our method surfaces populations with distinct survival curves which in turn allows us to find many potential biomarkers, including gene expression modules. We believe the algorithm may be of independent interest for clustering other datasets in a diverse set of research areas.

bioinformatics↗