Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer
Authors: Dondi Arthur , Lischetti Ulrike , Jacob Francis , Singer Franziska , Borgsmüller Nico , Coelho Ricardo ,   Tumor Profiler Consortium, Aebersold Rudolf , Ak Melike , Al-Quaddoomi Faisal S. , Albert Silvana I. , Albinus Jonas , Alborelli Ilaria , Andani Sonali , Attinger Per-Olof , Bacac Marina , Baumhoer Daniel , Beck-Schimmer Beatrice , Beisel Christian , Bernasconi Lara , Bertolini Anne , Bodenmiller Bernd , Bonilla Ximena , Bosshard Lars , Calgua Byron , Casanova Ruben , Chevrier Stéphane , Chicherova Natalia , D’Costa Maya , Danenberg Esther , Davidson Natalie , Drăgan Monica-Andreea , Dummer Reinhard , Engler Stefanie , Erkens Martin , Eschbach Katja , Esposito Cinzia , Fedier André , Ferreira Pedro , Ficek Joanna , Frei Anja L. , Frey Bruno , Goetze Sandra , Grob Linda , Gut Gabriele , Günther Detlef , Haberecker Martina , Haeuptle Pirmin , Herter Sylvia , Holtackers Rene , Huesser Tamara , Immer Alexander , Irmisch Anja , Jacobs Andrea , Jaeger Tim M. , Jahn Katharina , James Alva R. , Jermann Philip M. , Kahles André , Kahraman Abdullah , Koelzer Viktor H. , Kuebler Werner , Kuipers Jack , Kunze Christian P. , Kurzeder Christian , Lehmann Kjong-Van , Levesque Mitchell , Lischetti Ulrike , Lugert Sebastian , Maass Gerd , Manz Markus G. , Markolin Philipp , Mehnert Martin , Mena Julien , Metzler Julian M. , Miglino Nicola , Milani Emanuela S. , Moch Holger , Muenst Simone , Murri Riccardo , Ng Charlotte K. Y. , Nicolet Stefan , Nowak Marta , Lopez Monica Nunez , Pedrioli Patrick G. A. , Pelkmans Lucas , Piscuoglio Salvatore , Prummer Michael , Rimmer Natalie , Ritter Mathilde , Rommel Christian , Rosano-González María L. , Rätsch Gunnar , Santacroce Natascha , del Castillo Jacobo Sarabia , Schlenker Ramona , Schwalie Petra C. , Schwan Severin , Schär Tobias , Senti Gabriela , Shao Wenguang , Sivapatham Sujana , Snijder Berend , Sobottka Bettina , Sreedharan Vipin T. , Stark Stefan , Stekhoven Daniel J. , Tanna Tanmay , Theocharides Alexandre P. A. , Thomas Tinu M. , Tolnay Markus , Tosevski Vinko , Toussaint Nora C. , Tuncel Mustafa A. , Tusup Marina , Van Drogen Audrey , Vetter Marcus , Vlajnic Tatjana , Weber Sandra , Weber Walter P. , Wegmann Rebekka , Weller Michael , Wendt Fabian , Wey Norbert , Wicki Andreas , Wildschut Mattheus H. E. , Wollscheid Bernd , Yu Shuqing , Ziegler Johanna , Zimmermann Marc , Zoche Martin , Zuend Gregor , Heinzelmann-Schwarz Viola , Beisel Christian , Beerenwinkel Niko 
Published: November 2023

Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read single-cell RNA sequencing (scRNA-seq) on clinical samples from three ovarian cancer patients presenting with omental metastasis and increase the PacBio sequencing depth to 12,000 reads per cell. Our approach captures 152,000 isoforms, of which over 52,000 were not previously reported. Isoform-level analysis accounting for non-coding isoforms reveals 20% overestimation of protein-coding gene expression on average. We also detect cell type-specific isoform and poly-adenylation site usage in tumor and mesothelial cells, and find that mesothelial cells transition into cancer-associated fibroblasts in the metastasis, partly through the TGF-β/miR-29/Collagen axis. Furthermore, we identify gene fusions, including an experimentally validated IGF2BP2::TESPA1 fusion, which is misclassified as high TESPA1 expression in matched short-read data, and call mutations confirmed by targeted NGS cancer gene panel results. With these findings, we envision long-read scRNA-seq to become increasingly relevant in oncology and personalized medicine.