Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

Zhiliang Bai¹, Dingyao Zhang², Yan Gao³, Bo Tao⁴, Daiwei Zhang⁵, Shuozhen Bao⁶, Archibald Enninful⁶, Yadong Wang⁷, Haikuo Li⁶, Graham Su⁶, Xiaolong Tian⁶, Ningning Zhang⁷, Yang Xiao⁸, Yang Liu⁴, Mark Gerstein⁹, Mingyao Li¹⁰, Yi Xing¹¹, Jun Lu¹², Mina L Xu¹³, Rong Fan¹⁴

Affiliations

¹ Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. Electronic address: zhiliang.bai@yale.edu.
² 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.
³ Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
⁴ Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
⁵ Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
⁶ Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
⁷ Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
⁸ Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA.
⁹ Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
¹⁰ 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: mingyao@pennmedicine.upenn.edu.
¹¹ 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.
¹² 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.
¹³ Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address: mina.xu@yale.edu.
¹⁴ 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 Immunology, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address: rong.fan@yale.edu.

PMID: 39353436
PMCID: PMC11568911 (available on 2025-11-14)
DOI: 10.1016/j.cell.2024.09.001

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

Zhiliang Bai et al. Cell. 2024.

. 2024 Nov 14;187(23):6760-6779.e24.

doi: 10.1016/j.cell.2024.09.001. Epub 2024 Sep 30.

Authors

Affiliations

¹ Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. Electronic address: zhiliang.bai@yale.edu.
² 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.
³ Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
⁴ Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
⁵ Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
⁶ Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
⁷ Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
⁸ Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA.
⁹ Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
¹⁰ 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: mingyao@pennmedicine.upenn.edu.
¹¹ 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.
¹² 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.
¹³ Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address: mina.xu@yale.edu.
¹⁴ 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 Immunology, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address: rong.fan@yale.edu.

PMID: 39353436
PMCID: PMC11568911 (available on 2025-11-14)
DOI: 10.1016/j.cell.2024.09.001

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.

Keywords: RNA biology; clinical FFPE tissue; histopathology; microRNA; single-nucleotide RNA variants; spatial omics; spatiotemporal dynamics; splicing isoforms; whole transcriptome.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests Z.B. and R.F. are inventors of a patent application related to this work. R.F. is scientific founder and adviser for IsoPlexis, Singleron Biotechnologies, and AtlasXomics. The interests of R.F. were reviewed and managed by Yale University Provost’s Office in accordance with the University’s conflict of interest policies. M.L.X. has served as consultant for Treeline Biosciences, Pure Marrow, and Seattle Genetics. Daiwei Zhang and M.L. are co-founders or OmicPath AI LLC. M.L. receives research funding from Biogen Inc. unrelated to the current manuscript.

Update of

Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues.
Bai Z, Zhang D, Gao Y, Tao B, Bao S, Enninful A, Zhang D, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. Bai Z, et al. bioRxiv [Preprint]. 2024 Feb 8:2024.02.06.579143. doi: 10.1101/2024.02.06.579143. bioRxiv. 2024. Update in: Cell. 2024 Nov 14;187(23):6760-6779.e24. doi: 10.1016/j.cell.2024.09.001. PMID: 38370833 Free PMC article. Updated. Preprint.

References

1. Baysoy A, Bai Z, Satija R, and Fan R (2023). The technological landscape and applications of single-cell multi-omics. Nat Rev Mol Cell Biol 24, 695–713. 10.1038/s41580-023-00615-w. - DOI - PMC - PubMed
1. Bressan D, Battistoni G, and Hannon GJ (2023). The dawn of spatial omics. Science 381, eabq4964. doi:10.1126/science.abq4964. - DOI - PMC - PubMed
1. Deng Y, Bai Z, and Fan R (2023). Microtechnologies for single-cell and spatial multi-omics. Nature Reviews Bioengineering 1, 769–784. 10.1038/s44222-023-00084-y. - DOI
1. Chen J, Larsson L, Swarbrick A, and Lundeberg J (2024). Spatial landscapes of cancers: insights and opportunities. Nature Reviews Clinical Oncology. 10.1038/s41571-024-00926-7. - DOI - PubMed
1. Harries LW (2019). RNA Biology Provides New Therapeutic Targets for Human Disease. Front Genet 10, 205. 10.3389/fgene.2019.00205. - DOI - PMC - PubMed

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions
Actions
Actions

Grants and funding

LinkOut - more resources

Full Text Sources
- Elsevier Science
Molecular Biology Databases
- Mouse Genome Informatics (MGI)
- NIAID Data Ecosystem - Find datasets on Infectious and Immune-mediated Diseases

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

Affiliations

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

Authors

Affiliations

Abstract

Conflict of interest statement

Update of

References

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Molecular Biology Databases