Defining Anorectal Transition Zone Heterogeneity Using Single-Cell RNA Sequencing

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2023 Jun 13

PMID 37310626

Authors

Loucine Mitoyan

Charlyne Gard

Sebastien Nin

Beatrice Loriod

Geraldine Guasch

Affiliations

Soon will be listed here.

Abstract

Special regions called transition zones (TZs) are found at numerous places in the body. TZs represent the junction between two different types of epithelia and are located between the esophagus and the stomach, in the cervix, in the eye, and between the anal canal and the rectum. TZ is a heterogeneous population, and the detailed characterization of its populations requires an analysis at the single-cell level. In this chapter, we provide a protocol to do single-cell RNA sequencing primary analysis of anal canal, TZ, and rectum epithelia.

References

Wang X, Ouyang H, Yamamoto Y, Kumar P, Wei T, Dagher R . Residual embryonic cells as precursors of a Barrett's-like metaplasia. Cell. 2011; 145(7):1023-35. PMC: 3125107. DOI: 10.1016/j.cell.2011.05.026. View

Guasch G, Schober M, Pasolli H, Conn E, Polak L, Fuchs E . Loss of TGFbeta signaling destabilizes homeostasis and promotes squamous cell carcinomas in stratified epithelia. Cancer Cell. 2007; 12(4):313-27. PMC: 2424201. DOI: 10.1016/j.ccr.2007.08.020. View

Mitoyan L, Chevrier V, Hernandez-Vargas H, Ollivier A, Homayed Z, Pannequin J . A stem cell population at the anorectal junction maintains homeostasis and participates in tissue regeneration. Nat Commun. 2021; 12(1):2761. PMC: 8115161. DOI: 10.1038/s41467-021-23034-x. View

Herfs M, Yamamoto Y, Laury A, Wang X, Nucci M, McLaughlin-Drubin M . A discrete population of squamocolumnar junction cells implicated in the pathogenesis of cervical cancer. Proc Natl Acad Sci U S A. 2012; 109(26):10516-21. PMC: 3387104. DOI: 10.1073/pnas.1202684109. View

Amitai-Lange A, Altshuler A, Bubley J, Dbayat N, Tiosano B, Shalom-Feuerstein R . Lineage tracing of stem and progenitor cells of the murine corneal epithelium. Stem Cells. 2014; 33(1):230-9. DOI: 10.1002/stem.1840. View

McNairn A, Guasch G . Epithelial transition zones: merging microenvironments, niches, and cellular transformation. Eur J Dermatol. 2011; 21 Suppl 2:21-8. DOI: 10.1684/ejd.2011.1267. View

Tasic B . Single cell transcriptomics in neuroscience: cell classification and beyond. Curr Opin Neurobiol. 2018; 50:242-249. DOI: 10.1016/j.conb.2018.04.021. View

Navin N . Cancer genomics: one cell at a time. Genome Biol. 2014; 15(8):452. PMC: 4281948. DOI: 10.1186/s13059-014-0452-9. View

Dalerba P, Kalisky T, Sahoo D, Rajendran P, Rothenberg M, Leyrat A . Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol. 2011; 29(12):1120-7. PMC: 3237928. DOI: 10.1038/nbt.2038. View

10.

Treutlein B, Brownfield D, Wu A, Neff N, Mantalas G, Espinoza F . Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature. 2014; 509(7500):371-5. PMC: 4145853. DOI: 10.1038/nature13173. View

11.

Trapnell C . Defining cell types and states with single-cell genomics. Genome Res. 2015; 25(10):1491-8. PMC: 4579334. DOI: 10.1101/gr.190595.115. View

12.

Svensson V, Vento-Tormo R, Teichmann S . Exponential scaling of single-cell RNA-seq in the past decade. Nat Protoc. 2018; 13(4):599-604. DOI: 10.1038/nprot.2017.149. View

13.

Macosko E, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M . Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015; 161(5):1202-1214. PMC: 4481139. DOI: 10.1016/j.cell.2015.05.002. View