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Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues.
Bai, Zhiliang; Zhang, Dingyao; Gao, Yan; Tao, Bo; Zhang, Daiwei; Bao, Shuozhen; Enninful, Archibald; Wang, Yadong; Li, Haikuo; Su, Graham; Tian, Xiaolong; Zhang, Ningning; Xiao, Yang; Liu, Yang; Gerstein, Mark; Li, Mingyao; Xing, Yi; Lu, Jun; Xu, Mina L; Fan, Rong.
  • Bai Z; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. Electronic address: zhiliang.bai@yale.edu.
  • Zhang D; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
  • Gao Y; Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
  • Tao B; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
  • Zhang D; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
  • Bao S; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
  • Enninful A; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
  • Wang Y; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
  • Li H; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
  • Su G; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
  • Tian X; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
  • Zhang N; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
  • Xiao Y; Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA.
  • Liu Y; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
  • Gerstein M; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
  • Li M; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:
  • Xing Y; Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: xingyi@chop.edu.
  • Lu J; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address: jun.lu@yale.edu.
  • Xu ML; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address: mina.xu@yale.edu.
  • Fan R; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA; Human and Translational
Cell ; 2024 Sep 25.
Article en En | MEDLINE | ID: mdl-39353436
ABSTRACT
The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for 5 years. Furthermore, genome-wide single-nucleotide RNA variants can be captured to distinguish malignant subclones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Single-cell level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to aid in clinical pathology evaluation.
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Texto completo: 1 Banco de datos: MEDLINE Idioma: En Año: 2024 Tipo del documento: Article
Texto completo
Imprimir
XML
PubMed Links
Search on Google

Texto completo: 1 Banco de datos: MEDLINE Idioma: En Año: 2024 Tipo del documento: Article