PMID- 36993628
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240325
DP  - 2023 Aug 21
TI  - Long-read single-cell sequencing reveals expressions of hypermutation clusters of 
      isoforms in human liver cancer cells.
LID - 2023.03.16.532991 [pii]
LID - 10.1101/2023.03.16.532991 [doi]
AB  - 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 (UMAP) 
      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 (HLA) 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.
FAU - Liu, Silvia
AU  - Liu S
AD  - Department of Pathology, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - High Throughput Genome Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
FAU - Yu, Yan-Ping
AU  - Yu YP
AD  - Department of Pathology, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - High Throughput Genome Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
FAU - Ren, Bao-Guo
AU  - Ren BG
AD  - Department of Pathology, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - High Throughput Genome Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
FAU - Ben-Yehezkel, Tuval
AU  - Ben-Yehezkel T
AD  - Element Biosciences, Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 
      92121.
FAU - Obert, Caroline
AU  - Obert C
AD  - Element Biosciences, Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 
      92121.
FAU - Smith, Mat
AU  - Smith M
AD  - Element Biosciences, Inc, 10055 Barnes Canyon Road, Suite 100, San Diego, CA 
      92121.
FAU - Wang, Wenjia
AU  - Wang W
AD  - Biostatistics, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 
      15261.
FAU - Ostrowska, Alina
AU  - Ostrowska A
AD  - Department of Pathology, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
FAU - Soto-Gutierrez, Alejandro
AU  - Soto-Gutierrez A
AD  - Department of Pathology, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
FAU - Luo, Jian-Hua
AU  - Luo JH
AD  - Department of Pathology, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - High Throughput Genome Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
AD  - Pittsburgh Liver Research Center, University of Pittsburgh, 3550 Terrace Street, 
      Pittsburgh, PA 15261.
LA  - eng
GR  - P30 DK120531/DK/NIDDK NIH HHS/United States
GR  - R56 CA229262/CA/NCI NIH HHS/United States
GR  - S10 OD028483/OD/NIH HHS/United States
GR  - UL1 TR001857/TR/NCATS NIH HHS/United States
PT  - Preprint
DEP - 20230821
PL  - United States
TA  - bioRxiv
JT  - bioRxiv : the preprint server for biology
JID - 101680187
UIN - This article has been published with doi: 10.7554/eLife.87607.3
UIN - Elife. 2024 Jan 11;12:. PMID: 38206124
PMC - PMC10055174
COIS- Statement of conflict of interest: Tuval Ben-Yehezkel, Caroline Obert, and Mat 
      Smith are employees of Element Biosciences, Inc. Silvia Liu, Yan-Ping Yu, Bao-Guo 
      Ren, Wenjia Wang, Alina Ostrowska, Alejandro Soto-Gutierrez, and Jian-Hua Luo 
      declare no conflict of interest.
EDAT- 2023/03/31 06:00
MHDA- 2023/03/31 06:01
PMCR- 2023/08/22
CRDT- 2023/03/30 02:54
PHST- 2023/03/31 06:00 [pubmed]
PHST- 2023/03/31 06:01 [medline]
PHST- 2023/03/30 02:54 [entrez]
PHST- 2023/08/22 00:00 [pmc-release]
AID - 2023.03.16.532991 [pii]
AID - 10.1101/2023.03.16.532991 [doi]
PST - epublish
SO  - bioRxiv [Preprint]. 2023 Aug 21:2023.03.16.532991. doi: 
      10.1101/2023.03.16.532991.