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iScience2024;27(6):109928.June 21, 2024Journal Article

Single-cell transcriptomic-informed deconvolution of bulk data identifies immune checkpoint blockade resistance in urothelial cancer.

Li Wang1,2, Sudeh Izadmehr2, John P Sfakianos3, Michelle Tran2,4, Kristin G Beaumont5, Rachel Brody6, Carlos Cordon-Cardo6, Amir Horowitz4, Robert Sebra5, William K Oh2, Nina Bhardwaj2,4, Matthew D Galsky2, Jun Zhu2
1Department of Precision Medicine, Aitia, Somerville, MA 02143, USA.
2Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA.
3Department of Urology; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
4The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
5Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
6Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
PubMed PMC DOI PDF

Abstract

Interactions within the tumor microenvironment (TME) significantly influence tumor progression and treatment responses. While single-cell RNA sequencing (scRNA-seq) and spatial genomics facilitate TME exploration, many clinical cohorts are assessed at the bulk tissue level. Integrating scRNA-seq and bulk tissue RNA-seq data through computational deconvolution is essential for obtaining clinically…

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