دورية أكاديمية
أعرض في EDS

Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells.

التفاصيل البيبلوغرافية
العنوان: Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells.
المؤلفون: Liu S; Department of Pathology, University of Pittsburgh, Pittsburgh, United States.; High Throughput Genome Center, University of Pittsburgh, Pittsburgh, United States.; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, United States., Yu YP; Department of Pathology, University of Pittsburgh, Pittsburgh, United States.; High Throughput Genome Center, University of Pittsburgh, Pittsburgh, United States.; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, United States., Ren BG; Department of Pathology, University of Pittsburgh, Pittsburgh, United States.; High Throughput Genome Center, University of Pittsburgh, Pittsburgh, United States.; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, United States., Ben-Yehezkel T; Element Biosciences Inc, San Diego, United States., Obert C; Element Biosciences Inc, San Diego, United States., Smith M; Element Biosciences Inc, San Diego, United States., Wang W; Biostatistics, University of Pittsburgh, Pittsburgh, United States., Ostrowska A; Department of Pathology, University of Pittsburgh, Pittsburgh, United States.; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, United States., Soto-Gutierrez A; Department of Pathology, University of Pittsburgh, Pittsburgh, United States.; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, United States., Luo JH; Department of Pathology, University of Pittsburgh, Pittsburgh, United States.; High Throughput Genome Center, University of Pittsburgh, Pittsburgh, United States.; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, United States.
المصدر: ELife [Elife] 2024 Jan 11; Vol. 12. Date of Electronic Publication: 2024 Jan 11.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: eLife Sciences Publications, Ltd Country of Publication: England NLM ID: 101579614 Publication Model: Electronic Cited Medium: Internet ISSN: 2050-084X (Electronic) Linking ISSN: 2050084X NLM ISO Abbreviation: Elife Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Cambridge, UK : eLife Sciences Publications, Ltd., 2012-
مواضيع طبية MeSH: Liver Neoplasms*/genetics , Carcinoma, Hepatocellular*/genetics , Artificial Cells*, Animals ; Humans ; Protein Isoforms/genetics ; Mammals
مستخلص: The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Genetic mutation is essential in species evolution and cancer development. Accurate long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPSeq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximation and Projection analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. The evolution pathways that led to the hyper-mutation clusters in single human leukocyte antigen molecules were identified. Novel fusion transcripts were detected. The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. In conclusion, LOOPSeq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome.
Competing Interests: SL, YY, BR, WW, AO, AS, JL No competing interests declared, TB He is an employee of Element Biosciences, Inc, CO She is an employee of Element Biosciences, Inc, MS MS is an employee of Element Biosciences, Inc
(© 2023, Liu et al.)
التعليقات: Update of: bioRxiv. 2023 Aug 21;:. (PMID: 36993628)
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معلومات مُعتمدة: UL1 TR001857 United States TR NCATS NIH HHS; R56 CA229262 United States CA NCI NIH HHS; P30 DK120531 United States DK NIDDK NIH HHS; S10 OD028483 United States OD NIH HHS; UL1TR001857 and S10OD028483 United States NH NIH HHS; 1R56CA229262-01 United States CA NCI NIH HHS; P30- DK120531-01 United States DK NIDDK NIH HHS
فهرسة مساهمة: Keywords: computational biology; human; mutation evolution pathway; mutation gene expression; mutation isoform expression; single-cell synthetic long-read sequencing; single-molecule mutation evolution; systems biology
سلسلة جزيئية: GEO GSE223743
المشرفين على المادة: 0 (Protein Isoforms)
تواريخ الأحداث: Date Created: 20240111 Date Completed: 20240112 Latest Revision: 20240325
رمز التحديث: 20240325
مُعرف محوري في PubMed: PMC10945587
DOI: 10.7554/eLife.87607
PMID: 38206124
قاعدة البيانات: MEDLINE
الوصف
تدمد:2050-084X
DOI:10.7554/eLife.87607