Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.

The purpose of this study was to evaluate the suitability of formalin-fixed and paraffin-embedded (FFPE) samples and fixed fresh (FF) samples for single-cell RNA se quencing (scRNAseq). To this end, we compared single-cell profiles from FFPE and matched FF tissue samples of one invasive carcinoma of...

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Authors: Palacios, José, Carretero-Barrio, Irene, Lanza, Val F., García-Cosío Piqueras, Mónica, Caniego-Casas, Tamara, Hardisson, David, Esteban-Rodríguez, Isabel, Cortés, Javier, Pérez-Mies, Belén, González-Martínez, Silvia|||/items/a6747706-be4e-48c8-b8a5-32737469f700
Format: article
Publication Date:2025
Country:España
Institution:Universidad Alfonso X el Sabio
Repository:Repositorio Institucional de la Universidad Alfonso X el Sabio
Language:English
OAI Identifier:oai:archive.uax.com:20.500.12080/54866
Online Access:https://hdl.handle.net/20.500.12080/54866
Access Level:Open access
Keyword:Secuenciación de ARN unicelular
Cáncer de mama
Células multiciliadas
Tejido fresco fijado
Tejido FFPE
Heterogeneidad tumoral
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spelling Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.Palacios, JoséCarretero-Barrio, IreneLanza, Val F.García-Cosío Piqueras, MónicaCaniego-Casas, TamaraHardisson, DavidEsteban-Rodríguez, IsabelCortés, JavierPérez-Mies, BelénGonzález-Martínez, Silvia|||/items/a6747706-be4e-48c8-b8a5-32737469f700Secuenciación de ARN unicelularCáncer de mamaCélulas multiciliadasTejido fresco fijadoTejido FFPEHeterogeneidad tumoralThe purpose of this study was to evaluate the suitability of formalin-fixed and paraffin-embedded (FFPE) samples and fixed fresh (FF) samples for single-cell RNA se quencing (scRNAseq). To this end, we compared single-cell profiles from FFPE and matched FF tissue samples of one invasive carcinoma of no special type carcinoma (invasive ductal carcinoma–IDC) and one invasive lobular carcinoma (ILC) to assess consistency in cell type distribution and molecular profiles. The results were validated using immunohis tochemistry (IHC), fluorescence in situ hybridization (FISH), and electron microscopy. Additionally, immune cell proportions identified by IHC were quantified using QuPath and compared to the scRNAseq results. FFPE- and FF-derived libraries demonstrated high-quality sequencing metrics, and cellular heterogeneity was similar. No exclusive cell populations were identified by either approach. The four samples analysis identified six types of epithelial cells, as well as tumoral microenvironment populations. The scR NAseq results from epithelial neoplastic cells were concordant with common IHC markers. The proportion of immune cells identified by IHC in FFPE sections were similar to those obtained by scRNAseq. We identified and validated a previously poorly recognized sub population of neoplastic multi-ciliated cells (MCCs) (FOXJ1, ROPN1L). Analysis of FOXJ1 in 214 ER-positive invasive carcinomas demonstrated protein expression in one third of tumors, suggesting frequent focal MCC differentiation. Our results support the suitability of scRNAseq analysis using FFPE tissue, and identified a subpopulation of neoplastic MCC in breast cancer.MDPIUAX -Campus MadridUAX Archive20252025-01-0120252025-01-01journal articlehttp://purl.org/coar/resource_type/c_6501info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/20.500.12080/54866reponame:Repositorio Institucional de la Universidad Alfonso X el Sabioinstname:Universidad Alfonso X el SabioInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:archive.uax.com:20.500.12080/548662026-05-28T12:40:21Z
dc.title.none.fl_str_mv Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.
title Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.
spellingShingle Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.
Palacios, José
Secuenciación de ARN unicelular
Cáncer de mama
Células multiciliadas
Tejido fresco fijado
Tejido FFPE
Heterogeneidad tumoral
title_short Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.
title_full Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.
title_fullStr Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.
title_full_unstemmed Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.
title_sort Single-Cell RNA Sequencing on Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Identified Multi-Ciliary Cells in Breast Cancer.
dc.creator.none.fl_str_mv Palacios, José
Carretero-Barrio, Irene
Lanza, Val F.
García-Cosío Piqueras, Mónica
Caniego-Casas, Tamara
Hardisson, David
Esteban-Rodríguez, Isabel
Cortés, Javier
Pérez-Mies, Belén
González-Martínez, Silvia|||/items/a6747706-be4e-48c8-b8a5-32737469f700
author Palacios, José
author_facet Palacios, José
Carretero-Barrio, Irene
Lanza, Val F.
García-Cosío Piqueras, Mónica
Caniego-Casas, Tamara
Hardisson, David
Esteban-Rodríguez, Isabel
Cortés, Javier
Pérez-Mies, Belén
González-Martínez, Silvia|||/items/a6747706-be4e-48c8-b8a5-32737469f700
author_role author
author2 Carretero-Barrio, Irene
Lanza, Val F.
García-Cosío Piqueras, Mónica
Caniego-Casas, Tamara
Hardisson, David
Esteban-Rodríguez, Isabel
Cortés, Javier
Pérez-Mies, Belén
González-Martínez, Silvia|||/items/a6747706-be4e-48c8-b8a5-32737469f700
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv UAX -Campus Madrid
UAX Archive
dc.subject.none.fl_str_mv Secuenciación de ARN unicelular
Cáncer de mama
Células multiciliadas
Tejido fresco fijado
Tejido FFPE
Heterogeneidad tumoral
topic Secuenciación de ARN unicelular
Cáncer de mama
Células multiciliadas
Tejido fresco fijado
Tejido FFPE
Heterogeneidad tumoral
description The purpose of this study was to evaluate the suitability of formalin-fixed and paraffin-embedded (FFPE) samples and fixed fresh (FF) samples for single-cell RNA se quencing (scRNAseq). To this end, we compared single-cell profiles from FFPE and matched FF tissue samples of one invasive carcinoma of no special type carcinoma (invasive ductal carcinoma–IDC) and one invasive lobular carcinoma (ILC) to assess consistency in cell type distribution and molecular profiles. The results were validated using immunohis tochemistry (IHC), fluorescence in situ hybridization (FISH), and electron microscopy. Additionally, immune cell proportions identified by IHC were quantified using QuPath and compared to the scRNAseq results. FFPE- and FF-derived libraries demonstrated high-quality sequencing metrics, and cellular heterogeneity was similar. No exclusive cell populations were identified by either approach. The four samples analysis identified six types of epithelial cells, as well as tumoral microenvironment populations. The scR NAseq results from epithelial neoplastic cells were concordant with common IHC markers. The proportion of immune cells identified by IHC in FFPE sections were similar to those obtained by scRNAseq. We identified and validated a previously poorly recognized sub population of neoplastic multi-ciliated cells (MCCs) (FOXJ1, ROPN1L). Analysis of FOXJ1 in 214 ER-positive invasive carcinomas demonstrated protein expression in one third of tumors, suggesting frequent focal MCC differentiation. Our results support the suitability of scRNAseq analysis using FFPE tissue, and identified a subpopulation of neoplastic MCC in breast cancer.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025-01-01
2025
2025-01-01
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/20.500.12080/54866
url https://hdl.handle.net/20.500.12080/54866
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Repositorio Institucional de la Universidad Alfonso X el Sabio
instname:Universidad Alfonso X el Sabio
instname_str Universidad Alfonso X el Sabio
reponame_str Repositorio Institucional de la Universidad Alfonso X el Sabio
collection Repositorio Institucional de la Universidad Alfonso X el Sabio
repository.name.fl_str_mv
repository.mail.fl_str_mv
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