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Wang P, Wen X, Li H, Lang P, Li S, Lei Y, Shu H, Gao L, Zhao D, Zeng J. Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON. Nat Commun 2023; 14:8459. [PMID: 38123534 PMCID: PMC10733330 DOI: 10.1038/s41467-023-44103-3] [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: 02/07/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Single-cell technologies enable the dynamic analyses of cell fate mapping. However, capturing the gene regulatory relationships and identifying the driver factors that control cell fate decisions are still challenging. We present CEFCON, a network-based framework that first uses a graph neural network with attention mechanism to infer a cell-lineage-specific gene regulatory network (GRN) from single-cell RNA-sequencing data, and then models cell fate dynamics through network control theory to identify driver regulators and the associated gene modules, revealing their critical biological processes related to cell states. Extensive benchmarking tests consistently demonstrated the superiority of CEFCON in GRN construction, driver regulator identification, and gene module identification over baseline methods. When applied to the mouse hematopoietic stem cell differentiation data, CEFCON successfully identified driver regulators for three developmental lineages, which offered useful insights into their differentiation from a network control perspective. Overall, CEFCON provides a valuable tool for studying the underlying mechanisms of cell fate decisions from single-cell RNA-seq data.
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Affiliation(s)
- Peizhuo Wang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Xiao Wen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
| | - Han Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Peng Lang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Yipin Lei
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Hantao Shu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, 710071, Xi'an, Shaanxi Province, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China.
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2
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Deng H, Gao J, Cao B, Qiu Z, Li T, Zhao R, Li H, Wei B. LncRNA CCAT2 promotes malignant progression of metastatic gastric cancer through regulating CD44 alternative splicing. Cell Oncol (Dordr) 2023; 46:1675-1690. [PMID: 37354353 DOI: 10.1007/s13402-023-00835-4] [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] [Accepted: 05/30/2023] [Indexed: 06/26/2023] Open
Abstract
OBJECTIVE Gastric cancer (GC) is one of the most malignant tumors worldwide. Thus, it is necessary to explore the underlying mechanisms of GC progression and develop novel therapeutic regimens. Long non-coding RNAs (lncRNAs) have been demonstrated to be abnormally expressed and regulate the malignant behaviors of cancer cells. Our previous research demonstrated that lncRNA colon cancer-associated transcript 2 (CCAT2) has potential value for GC diagnosis and discrimination. However, the functional mechanisms of lncRNA CCAT2 in GC development remain to be explored. METHODS GC and normal adjacent tissues were collected to detect the expression of lncRNA CCAT2, ESRP1 and CD44 in clinical specimens and their clinical significance for GC patients. Cell counting kit-8, wound healing and transwell assays were conducted to investigate the malignant behaviors in vitro. The generation of nude mouse xenografts by subcutaneous, intraperitoneal and tail vein injection was performed to examine GC growth and metastasis in vivo. Co-immunoprecipitation, RNA-binding protein pull-down assay and fluorescence in situ hybridization were performed to reveal the binding relationships between ESRP1 and CD44. RESULTS In the present study, lncRNA CCAT2 was overexpressed in GC tissues compared to adjacent normal tissues and correlated with short survival time of patients. lncRNA CCAT2 promoted the proliferation, migration and invasion of GC cells. Its overexpression modulates alternative splicing of Cluster of differentiation 44 (CD44) variants and facilitates the conversion from the standard form to variable CD44 isoform 6 (CD44v6). Mechanistically, lncRNA CCAT2 upregulated CD44v6 expression by binding to epithelial splicing regulatory protein 1 (ESRP1), which subsequently mediates CD44 alternative splicing. The oncogenic role of the lncRNA CCAT2/ESRP1/CD44 axis in the promotion of malignant behaviors was verified by both in vivo and in vitro experiments. CONCLUSIONS Our findings identified a novel mechanism by which lncRNA CCAT2, as a type of protein-binding RNA, regulates alternative splicing of CD44 and promotes GC progression. This axis may become an effective target for clinical diagnosis and treatment.
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Affiliation(s)
- Huan Deng
- Department of Gastrointestinal Surgery, Peking University First Hospital, Beijing, 100034, China
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, 28 Fuxing Rd, Beijing, 100853, China
- Medical School of Chinese PLA, Beijing, 100853, China
| | - Jingwang Gao
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, 28 Fuxing Rd, Beijing, 100853, China
- Medical School of Chinese PLA, Beijing, 100853, China
| | - Bo Cao
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, 28 Fuxing Rd, Beijing, 100853, China
- Medical School of Chinese PLA, Beijing, 100853, China
| | - Ziyu Qiu
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, 100091, China
| | - Tian Li
- School of Basic Medicine, The Fourth Military Medical University, Xi'an, 710021, China
| | - Ruiyang Zhao
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, 28 Fuxing Rd, Beijing, 100853, China
- Medical School of Chinese PLA, Beijing, 100853, China
| | - Hanghang Li
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, 28 Fuxing Rd, Beijing, 100853, China
- Medical School of Chinese PLA, Beijing, 100853, China
| | - Bo Wei
- Department of General Surgery, First Medical Center, Chinese PLA General Hospital, 28 Fuxing Rd, Beijing, 100853, China.
- Medical School of Chinese PLA, Beijing, 100853, China.
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Maltseva D, Tonevitsky A. RNA-binding proteins regulating the CD44 alternative splicing. Front Mol Biosci 2023; 10:1326148. [PMID: 38106992 PMCID: PMC10722200 DOI: 10.3389/fmolb.2023.1326148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
Alternative splicing is often deregulated in cancer, and cancer-specific isoform switches are part of the oncogenic transformation of cells. Accumulating evidence indicates that isoforms of the multifunctional cell-surface glycoprotein CD44 play different roles in cancer cells as compared to normal cells. In particular, the shift of CD44 isoforms is required for epithelial to mesenchymal transition (EMT) and is crucial for the maintenance of pluripotency in normal human cells and the acquisition of cancer stem cells phenotype for malignant cells. The growing and seemingly promising use of splicing inhibitors for treating cancer and other pathologies gives hope for the prospect of using such an approach to regulate CD44 alternative splicing. This review integrates current knowledge about regulating CD44 alternative splicing by RNA-binding proteins.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Giraud J, Seeneevassen L, Rousseau B, Bouriez D, Sifré E, Giese A, Nguyen TL, Tiffon C, Lippi Y, Azzi-Martin L, Pannequin J, Ménard A, Bessède E, Staedel C, Mégraud F, Belleannée G, Lehours P, Gronnier C, Dubus P, Varon C. CD44v3 is a marker of invasive cancer stem cells driving metastasis in gastric carcinoma. Gastric Cancer 2023; 26:234-249. [PMID: 36528833 PMCID: PMC9950191 DOI: 10.1007/s10120-022-01357-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Cancer stem cells (CSCs) are at the origin of tumour initiation and progression in gastric adenocarcinoma (GC). However, markers of metastasis-initiating cells remain unidentified in GC. In this study, we characterized CD44 variants expressed in GC and evaluated the tumorigenic and metastatic properties of CD44v3+ cells and their clinical significance in GC patients. METHODS Using GC cell lines and patient-derived xenografts, we evaluated CD44+ and CD44v3+ GC cells molecular signature and their tumorigenic, chemoresistance, invasive and metastatic properties, and expression in patients-derived tissues. RESULTS CD44v3+ cells, which represented a subpopulation of CD44+ cells, were detected in advanced preneoplastic lesions and presented CSCs chemoresistance and tumorigenic properties in vitro and in vivo. Molecular and functional analyses revealed two subpopulations of gastric CSCs: CD44v3+ CSCs with an epithelial-mesenchymal transition (EMT)-like signature, and CD44+/v3- CSCs with an epithelial-like signature; both were tumorigenic but CD44v3+ cells showed higher invasive and metastatic properties in vivo. CD44v3+ cells detected in the primary tumours of GC patients were associated with a worse prognosis. CONCLUSION CD44v3 is a marker of a subpopulation of CSCs with metastatic properties in GC. The identification of metastasis-initiating cells in GC represents a major advance for further development of anti-metastatic therapeutic strategies.
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Affiliation(s)
- Julie Giraud
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France
| | - Lornella Seeneevassen
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France
| | - Benoit Rousseau
- Animal Facility, University of Bordeaux, 33076 Bordeaux, France
| | - Damien Bouriez
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France ,Department of Digestive Surgery, Haut-Lévêque Hospital, 33000 Bordeaux, France ,CHU Bordeaux, 33076 Bordeaux, France
| | - Elodie Sifré
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France
| | - Alban Giese
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France
| | - Tra Ly Nguyen
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France
| | - Camille Tiffon
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France
| | - Yannick Lippi
- Toxalim Research Centre in Food Toxicology, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Lamia Azzi-Martin
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France
| | - Julie Pannequin
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Armelle Ménard
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France
| | - Emilie Bessède
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France
| | - Cathy Staedel
- INSERM U1212, ARNA, University of Bordeaux, 33076 Bordeaux, France
| | - Francis Mégraud
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France ,CHU Bordeaux, 33076 Bordeaux, France ,Centre National de Référence des Campylobacters et Helicobacters, Pellegrin Hospital, 33076 Bordeaux, France
| | - Geneviève Belleannée
- CHU Bordeaux, 33076 Bordeaux, France ,Department of Histology and Pathology, Haut-Lévêque Hospital, 33000 Bordeaux, France
| | - Philippe Lehours
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France ,CHU Bordeaux, 33076 Bordeaux, France ,Centre National de Référence des Campylobacters et Helicobacters, Pellegrin Hospital, 33076 Bordeaux, France
| | - Caroline Gronnier
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France ,Department of Digestive Surgery, Haut-Lévêque Hospital, 33000 Bordeaux, France ,CHU Bordeaux, 33076 Bordeaux, France
| | - Pierre Dubus
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076 Bordeaux, France ,CHU Bordeaux, 33076 Bordeaux, France ,Department of Histology and Pathology, Haut-Lévêque Hospital, 33000 Bordeaux, France
| | - Christine Varon
- INSERM U1312, Bordeaux Institute of Oncology, University of Bordeaux, 146 rue Leo Saignat, 33076, Bordeaux, France.
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Zhu H, Zhou W, Wan Y, Lu J, Ge K, Jia C. CD44V3, an Alternatively Spliced Form of CD44, Promotes Pancreatic Cancer Progression. Int J Mol Sci 2022; 23:ijms232012061. [PMID: 36292918 PMCID: PMC9603666 DOI: 10.3390/ijms232012061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/25/2022] [Accepted: 10/02/2022] [Indexed: 12/24/2022] Open
Abstract
Pancreatic cancer is one of the most lethal malignant tumors. However, the molecular mechanisms responsible for its progression are little known. This study aimed to understand the regulatory role of CD44V3 in pancreatic cancer. A Kaplan–Meier analysis was performed to reveal the correlation between CD44/CD44V3 expression and the prognosis of pancreatic cancer patients. CD44V3 and U2AF1 were knocked down using shRNAs. The proliferation, migration, invasion, and stemness of two pancreatic cell lines, BxPC-3 and AsPC-1, were examined. The expression of CD44V3, cancer-associated markers, and the activation of AKT signaling were detected by qRT-PCR and Western blot. Both CD44 and CD44V3 expression levels were associated with a poor prognosis in pancreatic cancer patients. Interestingly, the expression of CD44V3, instead of CD44, was greatly increased in tumor tissues. CD44V3 knockdown inhibited the proliferation, migration, invasion, and stemness of cancer cells. CD44V3 splicing was regulated by U2AF1 and downregulation of U2AF1 enhanced CD44V3 expression, which promoted pancreatic cancer progression. CD44V3 is an important cancer-promoting factor, which may serve as a potential candidate for pancreatic cancer intervention.
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6
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Qiu Y, Ching WK, Zou Q. Matrix factorization-based data fusion for the prediction of RNA-binding proteins and alternative splicing event associations during epithelial-mesenchymal transition. Brief Bioinform 2021; 22:6354719. [PMID: 34410342 DOI: 10.1093/bib/bbab332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/11/2021] [Accepted: 07/29/2021] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION The epithelial-mesenchymal transition (EMT) is a cellular-developmental process activated during tumor metastasis. Transcriptional regulatory networks controlling EMT are well studied; however, alternative RNA splicing also plays a critical regulatory role during this process. Unfortunately, a comprehensive understanding of alternative splicing (AS) and the RNA-binding proteins (RBPs) that regulate it during EMT remains largely unknown. Therefore, a great need exists to develop effective computational methods for predicting associations of RBPs and AS events. Dramatically increasing data sources that have direct and indirect information associated with RBPs and AS events have provided an ideal platform for inferring these associations. RESULTS In this study, we propose a novel method for RBP-AS target prediction based on weighted data fusion with sparse matrix tri-factorization (WDFSMF in short) that simultaneously decomposes heterogeneous data source matrices into low-rank matrices to reveal hidden associations. WDFSMF can select and integrate data sources by assigning different weights to those sources, and these weights can be assigned automatically. In addition, WDFSMF can identify significant RBP complexes regulating AS events and eliminate noise and outliers from the data. Our proposed method achieves an area under the receiver operating characteristic curve (AUC) of $90.78\%$, which shows that WDFSMF can effectively predict RBP-AS event associations with higher accuracy compared with previous methods. Furthermore, this study identifies significant RBPs as complexes for AS events during EMT and provides solid ground for further investigation into RNA regulation during EMT and metastasis. WDFSMF is a general data fusion framework, and as such it can also be adapted to predict associations between other biological entities.
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Affiliation(s)
- Yushan Qiu
- College of Mathematics and Statistics, Shenzhen University, 518000 Guangdong, China
| | - Wai-Ki Ching
- Department of Mathematics, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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7
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Fang Y, Shi L, Duan Z, Rohani S. Hyaluronic acid hydrogels, as a biological macromolecule-based platform for stem cells delivery and their fate control: A review. Int J Biol Macromol 2021; 189:554-566. [PMID: 34437920 DOI: 10.1016/j.ijbiomac.2021.08.140] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/27/2022]
Abstract
Stem cell-based therapies offer numerous potentials to repair damaged or defective organs. The therapeutic outcomes of human studies, however, fall far short from what is expected. Enhancing stem cells local density and longevity would possibly maximize their healing potential. One promising strategy is to administer stem cells via injectable hydrogels. However, stem cells differentiation process is a delicate matter which is easily affected by various factors such as their interaction with their surrounding materials. Among various biomaterial options for hydrogels' production, hyaluronic acid (HA) has shown great promise. HA is a naturally occurring biological macromolecule, a polysaccharide of large molecular weight which is involved in cell proliferation, cell migration, angiogenesis, fetal development, and tissue function. In the current study we will discuss the applications, prospects, and challenges of HA-based hydrogels in stem cell delivery and fate control.
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Affiliation(s)
- Yu Fang
- Henan Provincial Engineering and Technology Research Center for Precise Synthesis of Fluorine-Containing Drugs, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China; Key Laboratory of New Opto-Electronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China.
| | - Lele Shi
- Henan Provincial Engineering and Technology Research Center for Precise Synthesis of Fluorine-Containing Drugs, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China; Key Laboratory of New Opto-Electronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Zhiwei Duan
- Henan Provincial Engineering and Technology Research Center for Precise Synthesis of Fluorine-Containing Drugs, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China; Key Laboratory of New Opto-Electronic Functional Materials of Henan Province, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Saeed Rohani
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
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8
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Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep 2021; 35:109198. [PMID: 34077720 DOI: 10.1016/j.celrep.2021.109198] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
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Affiliation(s)
- Shlomi Dvir
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Chen Lesnik
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | | | | | - Michal Amit
- Accellta LTD, Haifa 320003, Israel; Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College, Karmiel 2161002, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel; Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel.
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9
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Navvabi N, Kolikova P, Hosek P, Zitricky F, Navvabi A, Vycital O, Bruha J, Palek R, Rosendorf J, Liska V, Pitule P. Altered Expression of MBNL Family of Alternative Splicing Factors in Colorectal Cancer. Cancer Genomics Proteomics 2021; 18:295-306. [PMID: 33893082 DOI: 10.21873/cgp.20260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND/AIM Colorectal cancer is currently the third leading cause of cancer-related deaths and recently, alternative splicing has risen as its important regulator and potential treatment target. In the present study, we analyzed gene expression of the MBNL family of regulators of alternative splicing in various stages of colorectal cancer development, together with the MBNL-target splicing events in FOXP1 and EPB41L3 genes and tumor-related CD44 variants. MATERIALS AND METHODS Samples of tumor tissue and non-malignant mucosa from 108 patients were collected. After RNA isolation and reverse transcription, the relative gene expression of a selected gene panel was tested by quantitative real-time PCR, followed by statistical analysis. RESULTS MBNL expression was decreased in tumor tissue compared to non-tumor mucosa. In addition, lower expression was observed for the variants of FOXP1 and EPB41L3, while higher expression in tumor tissue was detected both for total CD44 and its cancer-related variants 3 and 6. Transcript levels of the MBNL genes were not found to be related to any of the studied clinicopathological characteristics. Multiple significant associations were identified in the target gene panel, including higher transcript levels of FOXP1 and CD44v3 in patients with distant metastases and connections between recurrence-free survival and altered levels of FOXP1 and CD44v3. CONCLUSION Our results identified for the first-time deregulation of MBNL genes in colorectal cancer. Down-regulation of their transcripts in tumor tissue compared to matched non-tumor mucosa can lead to transition of alternative splicing patterns towards a less differentiated phenotype, which highlights the importance of alternative splicing regulation for tumor growth and propagation.
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Affiliation(s)
- Nazila Navvabi
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavla Kolikova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Petr Hosek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Frantisek Zitricky
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Azita Navvabi
- Biological Center, Faculty of Marine Sciences and Technologies in Bandar Abbas, Hormozgan University, Hormozgan, Iran
| | - Ondrej Vycital
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Surgery, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jan Bruha
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Surgery, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Richard Palek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Surgery, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jachym Rosendorf
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Surgery, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Vaclav Liska
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Surgery, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavel Pitule
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic; .,Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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10
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Chang PH, Chao HM, Chern E, Hsu SH. Chitosan 3D cell culture system promotes naïve-like features of human induced pluripotent stem cells: A novel tool to sustain pluripotency and facilitate differentiation. Biomaterials 2020; 268:120575. [PMID: 33341735 DOI: 10.1016/j.biomaterials.2020.120575] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/03/2020] [Accepted: 11/21/2020] [Indexed: 12/14/2022]
Abstract
A simplified and cost-effective culture system for maintaining the pluripotency of human induced pluripotent stem cells (hiPSCs) is crucial for stem cell applications. Although recombinant protein-based feeder-free hiPSC culture systems have been developed, their manufacturing processes are expensive and complicated, which hinders hiPSC technology progress. Chitosan, a versatile biocompatible polysaccharide, has been reported as a biomaterial for three-dimensional (3D) cell culture system that promotes the physiological activities of mesenchymal stem cells and cancer cells. In the current study, we demonstrated that chitosan membranes sustained proliferation and pluripotency of hiPSCs in long-term culture (up to 365 days). Moreover, using vitronectin as the comparison group, the pluripotency of hiPSCs grown on the membranes was altered into a naïve-like state, which, for pluripotent stem cells, is an earlier developmental stage with higher stemness. On the chitosan membranes, hiPSCs self-assembled into 3D spheroids with an average diameter of ~100 μm. These hiPSC spheroids could be directly differentiated into lineage-specific cells from the three germ layers with 3D structures. Collectively, chitosan membranes not only promoted the naïve pluripotent features of hiPSCs but also provided a novel 3D differentiation platform. This convenient biomaterial-based culture system may enable the effective expansion and accessibility of hiPSCs for regenerative medicine, disease modeling, and drug screening.
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Affiliation(s)
- Po-Hsiang Chang
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsiao-Mei Chao
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan; Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan
| | - Edward Chern
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617, Taiwan.
| | - Shan-Hui Hsu
- Institute of Polymer Science and Engineering, National Taiwan University, Taipei 10617, Taiwan.
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Kanitz A, Syed AP, Kaji K, Zavolan M. Conserved regulation of RNA processing in somatic cell reprogramming. BMC Genomics 2019; 20:100. [PMID: 30704403 PMCID: PMC6357513 DOI: 10.1186/s12864-019-5438-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific transcript isoforms and 3' untranslated regions. A number of studies have uncovered RNA processing factors that modulate the efficiency of the reprogramming process. However, a comprehensive evaluation of the involvement of RNA processing factors in the reprogramming of somatic mammalian cells is lacking. RESULTS Here, we used data from a large number of studies carried out in three mammalian species, mouse, chimpanzee and human, to uncover consistent changes in gene expression upon reprogramming of somatic cells. We found that a core set of nine splicing factors have consistent changes across the majority of data sets in all three species. Most striking among these are ESRP1 and ESRP2, which accelerate and enhance the efficiency of somatic cell reprogramming by promoting isoform expression changes associated with mesenchymal-to-epithelial transition. We further identify genes and processes in which splicing changes are observed in both human and mouse. CONCLUSIONS Our results provide a general resource for gene expression and splicing changes that take place during somatic cell reprogramming. Furthermore, they support the concept that splicing factors with evolutionarily conserved, cell type-specific expression can modulate the efficiency of the process by reinforcing intermediate states resembling the cell types in which these factors are normally expressed.
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Affiliation(s)
- Alexander Kanitz
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Afzal Pasha Syed
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Keisuke Kaji
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
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