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Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer

Author

Listed:
  • Arthur Dondi

    (ETH Zurich, Department of Biosystems Science and Engineering
    SIB Swiss Institute of Bioinformatics)

  • Ulrike Lischetti

    (ETH Zurich, Department of Biosystems Science and Engineering
    University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine)

  • Francis Jacob

    (University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine)

  • Franziska Singer

    (SIB Swiss Institute of Bioinformatics
    ETH Zurich, NEXUS Personalized Health Technologies)

  • Nico Borgsmüller

    (ETH Zurich, Department of Biosystems Science and Engineering
    SIB Swiss Institute of Bioinformatics)

  • Ricardo Coelho

    (University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine)

  • Viola Heinzelmann-Schwarz

    (University Hospital Basel and University of Basel, Ovarian Cancer Research, Department of Biomedicine
    University Hospital Basel, Gynecological Cancer Center)

  • Christian Beisel

    (ETH Zurich, Department of Biosystems Science and Engineering)

  • Niko Beerenwinkel

    (ETH Zurich, Department of Biosystems Science and Engineering
    SIB Swiss Institute of Bioinformatics)

Abstract

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.

Suggested Citation

  • Arthur Dondi & Ulrike Lischetti & Francis Jacob & Franziska Singer & Nico Borgsmüller & Ricardo Coelho & Viola Heinzelmann-Schwarz & Christian Beisel & Niko Beerenwinkel, 2023. "Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43387-9
    DOI: 10.1038/s41467-023-43387-9
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    References listed on IDEAS

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    1. Ludmil B. Alexandrov & Serena Nik-Zainal & David C. Wedge & Samuel A. J. R. Aparicio & Sam Behjati & Andrew V. Biankin & Graham R. Bignell & Niccolò Bolli & Ake Borg & Anne-Lise Børresen-Dale & Sandri, 2013. "Correction: Corrigendum: Signatures of mutational processes in human cancer," Nature, Nature, vol. 502(7470), pages 258-258, October.
    2. Dafni A. Glinos & Garrett Garborcauskas & Paul Hoffman & Nava Ehsan & Lihua Jiang & Alper Gokden & Xiaoguang Dai & François Aguet & Kathleen L. Brown & Kiran Garimella & Tera Bowers & Maura Costello &, 2022. "Transcriptome variation in human tissues revealed by long-read sequencing," Nature, Nature, vol. 608(7922), pages 353-359, August.
    3. Nikolaus Fortelny & Christopher M. Overall & Paul Pavlidis & Gabriela V. Cohen Freue, 2017. "Can we predict protein from mRNA levels?," Nature, Nature, vol. 547(7664), pages 19-20, July.
    4. Zhuo-Xing Shi & Zhi-Chao Chen & Jia-Yong Zhong & Kun-Hua Hu & Ying-Feng Zheng & Ying Chen & Shang-Qian Xie & Xiao-Chen Bo & Feng Luo & Chong Tang & Chuan-Le Xiao & Yi-Zhi Liu, 2023. "High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    5. Jonathan A. Griffiths & Arianne C. Richard & Karsten Bach & Aaron T. L. Lun & John C. Marioni, 2018. "Detection and removal of barcode swapping in single-cell RNA-seq data," Nature Communications, Nature, vol. 9(1), pages 1-6, December.
    6. Ludmil B. Alexandrov & Serena Nik-Zainal & David C. Wedge & Samuel A. J. R. Aparicio & Sam Behjati & Andrew V. Biankin & Graham R. Bignell & Niccolò Bolli & Ake Borg & Anne-Lise Børresen-Dale & Sandri, 2013. "Signatures of mutational processes in human cancer," Nature, Nature, vol. 500(7463), pages 415-421, August.
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    1. Ashley Byrne & Daniel Le & Kostianna Sereti & Hari Menon & Samir Vaidya & Neha Patel & Jessica Lund & Ana Xavier-Magalhães & Minyi Shi & Yuxin Liang & Timothy Sterne-Weiler & Zora Modrusan & William S, 2024. "Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

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