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Gómez-Matas J, Duran-Sanchon S, Lozano JJ, Ferrero G, Tarallo S, Pardini B, Naccarati A, Castells A, Gironella M. SnoRNA profiling in colorectal cancer and assessment of non-invasive biomarker capacity by ddPCR in fecal samples. iScience 2024; 27:109283. [PMID: 38450150 PMCID: PMC10915595 DOI: 10.1016/j.isci.2024.109283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/26/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) have been identified dysregulated in several pathologies, and these alterations can be detected in tissues and in circulation. The main aim of this study was to analyze the whole snoRNome in advanced colorectal neoplasms and to identify new potential non-invasive snoRNA-based biomarkers in fecal samples by different analytical approaches. SNORA51, SNORD15B, SNORA54, SNORD12B, SNORD12C, SNORD72, SNORD89, and several members of SNORD115 and SNORD116 clusters were consistently deregulated in both tissue sets. After technical validation, SNORA51 and SNORD15B were detected in FIT+ samples. SNORA51 was significantly upregulated in FIT+ samples from CRC patients compared to healthy controls. This upregulation, together with the fecal hemoglobin concentration, was sufficient to identify, among FIT+ individuals, patients with CRC (AUC = 0.86) and individuals with advanced adenomas (AUC = 0.68). These findings portray snoRNAs as an alternative source of candidates for further studies and SNORA51 appears as a potential non-invasive biomarker for CRC detection.
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Affiliation(s)
- Javier Gómez-Matas
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
| | - Saray Duran-Sanchon
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
| | | | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Antoni Castells
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
| | - Meritxell Gironella
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona-Spanish National Research Council (IIBB-CSIC), Barcelona, Spain
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Pastorino GA, Sheraj I, Huebner K, Ferrero G, Kunze P, Hartmann A, Hampel C, Husnugil HH, Maiuthed A, Gebhart F, Schlattmann F, Gulec Taskiran AE, Oral G, Palmisano R, Pardini B, Naccarati A, Erlenbach-Wuensch K, Banerjee S, Schneider-Stock R. A partial epithelial-mesenchymal transition signature for highly aggressive colorectal cancer cells that survive under nutrient restriction. J Pathol 2024; 262:347-361. [PMID: 38235615 DOI: 10.1002/path.6240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 10/12/2023] [Accepted: 11/21/2023] [Indexed: 01/19/2024]
Abstract
Partial epithelial-mesenchymal transition (p-EMT) has recently been identified as a hybrid state consisting of cells with both epithelial and mesenchymal characteristics and is associated with the migration, metastasis, and chemoresistance of cancer cells. Here, we describe the induction of p-EMT in starved colorectal cancer (CRC) cells and identify a p-EMT gene signature that can predict prognosis. Functional characterisation of starvation-induced p-EMT in HCT116, DLD1, and HT29 cells showed changes in proliferation, morphology, and drug sensitivity, supported by in vivo studies using the chorioallantoic membrane model. An EMT-specific quantitative polymerase chain reaction (qPCR) array was used to screen for deregulated genes, leading to the establishment of an in silico gene signature that was correlated with poor disease-free survival in CRC patients along with the CRC consensus molecular subtype CMS4. Among the significantly deregulated p-EMT genes, a triple-gene signature consisting of SERPINE1, SOX10, and epidermal growth factor receptor (EGFR) was identified. Starvation-induced p-EMT was characterised by increased migratory potential and chemoresistance, as well as E-cadherin processing and internalisation. Both gene signature and E-cadherin alterations could be reversed by the proteasomal inhibitor MG132. Spatially resolving EGFR expression with high-resolution immunofluorescence imaging identified a proliferation stop in starved CRC cells caused by EGFR internalisation. In conclusion, we have gained insight into a previously undiscovered EMT mechanism that may become relevant when tumour cells are under nutrient stress, as seen in early stages of metastasis. Targeting this process of tumour cell dissemination might help to prevent EMT and overcome drug resistance. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Gil A Pastorino
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ilir Sheraj
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
| | - Kerstin Huebner
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Philipp Kunze
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Chuanpit Hampel
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Arnatchai Maiuthed
- Department of Pharmacology, Mahidol University, Bangkok, Thailand
- Centre of Biopharmaceutical Science for Healthy Ageing, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Florian Gebhart
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Fynn Schlattmann
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Aliye Ezgi Gulec Taskiran
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
- Department of Molecular Biology and Genetics, Baskent University, Ankara, Turkey
| | - Goksu Oral
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
| | - Ralph Palmisano
- Optical Imaging Competence Centre FAU OICE, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o FPO-IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o FPO-IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Katharina Erlenbach-Wuensch
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sreeparna Banerjee
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
- Cancer Systems Biology Laboratory (CanSyl), Orta Dogu Teknik Universitesi, Ankara, Turkey
| | - Regine Schneider-Stock
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
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