Universität zu Köln

Kraemer, Max, Plum, Patrick S. ORCID: 0000-0002-8165-4553, Camacho, Oscar Velazquez, Folz-Donahue, Kat, Thelen, Martin ORCID: 0000-0002-2785-9726, Garcia-Marquez, Isabel, Woelwer, Christina, Buesker, Soeren, Wittig, Jana, Franitza, Marek, Altmueller, Janine, Loeser, Heike, Schloesser, Hans, Buettner, Reinhard, Schroeder, Wolfgang, Bruns, Christiane J., Alakus, Hakan, Quaas, Alexander, Chon, Seung-Hun ORCID: 0000-0002-8923-6428 and Hillmer, Axel M. (2020). Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics. Mol. Oncol., 14 (6). S. 1170 - 1185. HOBOKEN: WILEY. ISSN 1878-0261

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Abstract

Single-cell transcriptomics have revolutionized our understanding of the cell composition of tumors and allowed us to identify new subtypes of cells. Despite rapid technological advancements, single-cell analysis remains resource-intense hampering the scalability that is required to profile a sufficient number of samples for clinical associations. Therefore, more scalable approaches are needed to understand the contribution of individual cell types to the development and treatment response of solid tumors such as esophageal adenocarcinoma where comprehensive genomic studies have only led to a small number of targeted therapies. Due to the limited treatment options and late diagnosis, esophageal adenocarcinoma has a poor prognosis. Understanding the interaction between and dysfunction of individual cell populations provides an opportunity for the development of new interventions. In an attempt to address the technological and clinical needs, we developed a protocol for the separation of esophageal carcinoma tissue into leukocytes (CD45+), epithelial cells (EpCAM+), and fibroblasts (two out of PDGFR alpha, CD90, anti-fibroblast) by fluorescence-activated cell sorting and subsequent RNA sequencing. We confirm successful separation of the three cell populations by mapping their transcriptomic profiles to reference cell lineage expression data. Gene-level analysis further supports the isolation of individual cell populations with high expression of CD3, CD4, CD8, CD19, and CD20 for leukocytes, CDH1 and MUC1 for epithelial cells, and FAP, SMA, COL1A1, and COL3A1 for fibroblasts. As a proof of concept, we profiled tumor samples of nine patients and explored expression differences in the three cell populations between tumor and normal tissue. Interestingly, we found that angiogenesis-related genes were upregulated in fibroblasts isolated from tumors compared with normal tissue. Overall, we suggest our protocol as a complementary and more scalable approach compared with single-cell RNA sequencing to investigate associations between clinical parameters and transcriptomic alterations of specific cell populations in esophageal adenocarcinoma.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Kraemer, Max UNSPECIFIED UNSPECIFIED UNSPECIFIED Plum, Patrick S. UNSPECIFIED orcid.org/0000-0002-8165-4553 UNSPECIFIED Camacho, Oscar Velazquez UNSPECIFIED UNSPECIFIED UNSPECIFIED Folz-Donahue, Kat UNSPECIFIED UNSPECIFIED UNSPECIFIED Thelen, Martin UNSPECIFIED orcid.org/0000-0002-2785-9726 UNSPECIFIED Garcia-Marquez, Isabel UNSPECIFIED UNSPECIFIED UNSPECIFIED Woelwer, Christina UNSPECIFIED UNSPECIFIED UNSPECIFIED Buesker, Soeren UNSPECIFIED UNSPECIFIED UNSPECIFIED Wittig, Jana UNSPECIFIED UNSPECIFIED UNSPECIFIED Franitza, Marek UNSPECIFIED UNSPECIFIED UNSPECIFIED Altmueller, Janine UNSPECIFIED UNSPECIFIED UNSPECIFIED Loeser, Heike UNSPECIFIED UNSPECIFIED UNSPECIFIED Schloesser, Hans UNSPECIFIED UNSPECIFIED UNSPECIFIED Buettner, Reinhard UNSPECIFIED UNSPECIFIED UNSPECIFIED Schroeder, Wolfgang UNSPECIFIED UNSPECIFIED UNSPECIFIED Bruns, Christiane J. UNSPECIFIED UNSPECIFIED UNSPECIFIED Alakus, Hakan UNSPECIFIED UNSPECIFIED UNSPECIFIED Quaas, Alexander UNSPECIFIED UNSPECIFIED UNSPECIFIED Chon, Seung-Hun UNSPECIFIED orcid.org/0000-0002-8923-6428 UNSPECIFIED Hillmer, Axel M. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-336671
DOI:	10.1002/1878-0261.12680
Journal or Publication Title:	Mol. Oncol.
Volume:	14
Number:	6
Page Range:	S. 1170 - 1185
Date:	2020
Publisher:	WILEY
Place of Publication:	HOBOKEN
ISSN:	1878-0261
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language CANCER-ASSOCIATED FIBROBLASTS; STROMAL MYOFIBROBLASTS; FLOW-CYTOMETRY; EXPRESSION; HETEROGENEITY; MULTICENTER; SUPPRESSOR; ANTIGEN; GENE Multiple languages Oncology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/33667