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Chen Z, Lu J, Zhao XM, Yu H, Li C. Energy Landscape Reveals the Underlying Mechanism of Cancer-Adipose Conversion in Gene Network Models. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404854. [PMID: 39258786 DOI: 10.1002/advs.202404854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Indexed: 09/12/2024]
Abstract
Cancer is a systemic heterogeneous disease involving complex molecular networks. Tumor formation involves an epithelial-mesenchymal transition (EMT), which promotes both metastasis and plasticity of cancer cells. Recent experiments have proposed that cancer cells can be transformed into adipocytes via a combination of drugs. However, the underlying mechanisms for how these drugs work, from a molecular network perspective, remain elusive. To reveal the mechanism of cancer-adipose conversion (CAC), this study adopts a systems biology approach by combing mathematical modeling and molecular experiments, based on underlying molecular regulatory networks. Four types of attractors are identified, corresponding to epithelial (E), mesenchymal (M), adipose (A) and partial/intermediate EMT (P) cell states on the CAC landscape. Landscape and transition path results illustrate that intermediate states play critical roles in the cancer to adipose transition. Through a landscape control approach, two new therapeutic strategies for drug combinations are identified, that promote CAC. These predictions are verified by molecular experiments in different cell lines. The combined computational and experimental approach provides a powerful tool to explore molecular mechanisms for cell fate transitions in cancer networks. The results reveal underlying mechanisms of intermediate cell states that govern the CAC, and identified new potential drug combinations to induce cancer adipogenesis.
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Affiliation(s)
- Zihao Chen
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, 200433, China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Jia Lu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Haiyang Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Haihe Laboratory of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Chunhe Li
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, 200433, China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
- School of Mathematical Sciences and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
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2
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Elfeky M, Matsuoka S, Yamamoto I, Elewa YHA, Nakamura K, Suzuki H, Kamikawa A, Okamatu-Ogura Y, Kimura K. Expression Patterns of Grainyhead-Like 2 and Ovo-Like 2 in Mouse Mammary Gland Development During Pregnancy, Lactation, and Weaning. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024; 30:552-563. [PMID: 38833344 DOI: 10.1093/mam/ozae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/03/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Grainyhead-like 2 (Grhl2) is a transcription factor that regulates cell adhesion genes in mammary ductal development and serves as a repressor of the epithelial-mesenchymal transition. Conversely, Ovo-like2 (Ovol2) is a target gene of Grhl2 but functions as a substitute in Grhl2-deficient mice, facilitating successful epithelial barrier formation and lumen expansion in kidney-collecting ductal epithelial cells. Our objective was to examine the expression patterns of Grhl2, Ovol2, and their associated genes during the intricate phases of mouse mammary gland development. The mRNA expression of Grhl2 and Ovol2 increased after pregnancy. We observed Grhl2 protein presence in the epithelial cell's region, coinciding with acini formation, and its signal significantly correlated with E-cadherin (Cdh1) expression. However, Ovol2 was present in the epithelial region without a correlation with Cdh1. Similarly, Zeb1, a mesenchymal transcription factor, showed Cdh1-independent expression. Subsequently, we explored the interaction between Rab25, a small G protein, and Grhl2/Ovol2. The expressions of Grhl2 and Ovol2 exhibited a strong correlation with Rab25 and claudin-4, a tight junction protein. These findings suggest that Grhl2 and Ovol2 may collaborate to regulate genes associated with cell adhesion and are crucial for maintaining epithelial integrity during the different phases of mammary gland development.
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Affiliation(s)
- Mohamed Elfeky
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Kita 18, Nishi 9, Sapporo 060-0818, Japan
- Department of Biochemistry, Faculty of Veterinary Medicine, Alexandria University, Al Azaritah, Alexandria 22758, Egypt
| | - Shinya Matsuoka
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Kita 18, Nishi 9, Sapporo 060-0818, Japan
| | - Izumi Yamamoto
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Kita 18, Nishi 9, Sapporo 060-0818, Japan
| | - Yaser Hosny Ali Elewa
- Department of Histology, Faculty of Veterinary Medicine, Zagazig University, El Tagneed St, Zagazig 44519, Egypt
- Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Kita 18, Nishi 9, Sapporo 060-0818, Japan
| | - Kazuki Nakamura
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Kita 18, Nishi 9, Sapporo 060-0818, Japan
| | - Hiroyoshi Suzuki
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Kita 18, Nishi 9, Sapporo 060-0818, Japan
| | - Akihiro Kamikawa
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Kita 18, Nishi 9, Sapporo 060-0818, Japan
| | - Yuko Okamatu-Ogura
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Kita 18, Nishi 9, Sapporo 060-0818, Japan
| | - Kazuhiro Kimura
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Kita 18, Nishi 9, Sapporo 060-0818, Japan
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3
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Bracken CP, Goodall GJ, Gregory PA. RNA regulatory mechanisms controlling TGF-β signaling and EMT in cancer. Semin Cancer Biol 2024; 102-103:4-16. [PMID: 38917876 DOI: 10.1016/j.semcancer.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024]
Abstract
Epithelial-mesenchymal transition (EMT) is a major contributor to metastatic progression and is prominently regulated by TGF-β signalling. Both EMT and TGF-β pathway components are tightly controlled by non-coding RNAs - including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) - that collectively have major impacts on gene expression and resulting cellular states. While miRNAs are the best characterised regulators of EMT and TGF-β signaling and the miR-200-ZEB1/2 feedback loop plays a central role, important functions for lncRNAs and circRNAs are also now emerging. This review will summarise our current understanding of the roles of non-coding RNAs in EMT and TGF-β signaling with a focus on their functions in cancer progression.
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Affiliation(s)
- Cameron P Bracken
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, SA 5000, Australia.
| | - Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, SA 5000, Australia.
| | - Philip A Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia.
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4
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Böpple K, Oren Y, Henry WS, Dong M, Weller S, Thiel J, Kleih M, Gaißler A, Zipperer D, Kopp HG, Aylon Y, Oren M, Essmann F, Liang C, Aulitzky WE. ATF3 characterizes aggressive drug-tolerant persister cells in HGSOC. Cell Death Dis 2024; 15:290. [PMID: 38658567 PMCID: PMC11043376 DOI: 10.1038/s41419-024-06674-x] [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: 07/18/2023] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
High-grade serous ovarian cancer (HGSOC) represents the most common and lethal subtype of ovarian cancer. Despite initial response to platinum-based standard therapy, patients commonly suffer from relapse that likely originates from drug-tolerant persister (DTP) cells. We generated isogenic clones of treatment-naïve and cisplatin-tolerant persister HGSOC cells. In addition, single-cell RNA sequencing of barcoded cells was performed in a xenograft model with HGSOC cell lines after platinum-based therapy. Published single-cell RNA-sequencing data from neo-adjuvant and non-treated HGSOC patients and patient data from TCGA were analyzed. DTP-derived cells exhibited morphological alterations and upregulation of epithelial-mesenchymal transition (EMT) markers. An aggressive subpopulation of DTP-derived cells showed high expression of the stress marker ATF3. Knockdown of ATF3 enhanced the sensitivity of aggressive DTP-derived cells to cisplatin-induced cell death, implying a role for ATF3 stress response in promoting a drug tolerant persister cell state. Furthermore, single cell lineage tracing to detect transcriptional changes in a HGSOC cell line-derived xenograft relapse model showed that cells derived from relapsed solid tumors express increased levels of EMT and multiple endoplasmic reticulum (ER) stress markers, including ATF3. Single cell RNA sequencing of epithelial cells from four HGSOC patients also identified a small cell population resembling DTP cells in all samples. Moreover, analysis of TCGA data from 259 HGSOC patients revealed a significant progression-free survival advantage for patients with low expression of the ATF3-associated partial EMT genes. These findings suggest that increased ATF3 expression together with partial EMT promote the development of aggressive DTP, and thereby relapse in HGSOC patients.
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Affiliation(s)
- Kathrin Böpple
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology and University of Tuebingen, Auerbachstr. 112, 70376, Stuttgart, Germany.
| | - Yaara Oren
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Whitney S Henry
- Whitehead Institute for Biomedical Research, 455 Main St., Cambridge, MA, 02142, USA
| | - Meng Dong
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology and University of Tuebingen, Auerbachstr. 112, 70376, Stuttgart, Germany
| | - Sandra Weller
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology and University of Tuebingen, Auerbachstr. 112, 70376, Stuttgart, Germany
- Robert Bosch Center for Tumor Diseases (RBCT), Auerbachstr. 110, 70376, Stuttgart, Germany
| | - Julia Thiel
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology and University of Tuebingen, Auerbachstr. 112, 70376, Stuttgart, Germany
| | - Markus Kleih
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology and University of Tuebingen, Auerbachstr. 112, 70376, Stuttgart, Germany
| | - Andrea Gaißler
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology and University of Tuebingen, Auerbachstr. 112, 70376, Stuttgart, Germany
| | - Damaris Zipperer
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology and University of Tuebingen, Auerbachstr. 112, 70376, Stuttgart, Germany
| | - Hans-Georg Kopp
- Robert Bosch Hospital, Auerbachstr. 110, 70376, Stuttgart, Germany
- Robert Bosch Center for Tumor Diseases (RBCT), Auerbachstr. 110, 70376, Stuttgart, Germany
| | - Yael Aylon
- Weizmann Institute of Science, 234 Herzl St, Rehovot, Israel
| | - Moshe Oren
- Weizmann Institute of Science, 234 Herzl St, Rehovot, Israel
| | - Frank Essmann
- Dr. Margarete Fischer-Bosch - Institute of Clinical Pharmacology and University of Tuebingen, Auerbachstr. 112, 70376, Stuttgart, Germany
- Robert Bosch Center for Tumor Diseases (RBCT), Auerbachstr. 110, 70376, Stuttgart, Germany
| | - Chunguang Liang
- Department of Bioinformatics, Biocenter Am Hubland, University of Wuerzburg, 97074, Wuerzburg, Germany.
- Institute of Immunology, Jena University Hospital, Friedrich-Schiller-University, Leutragraben 3, 07743, Jena, Germany.
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5
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Hong T, Xing J. Data- and theory-driven approaches for understanding paths of epithelial-mesenchymal transition. Genesis 2024; 62:e23591. [PMID: 38553870 PMCID: PMC11017362 DOI: 10.1002/dvg.23591] [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: 01/02/2024] [Revised: 02/16/2024] [Accepted: 03/16/2024] [Indexed: 04/02/2024]
Abstract
Reversible transitions between epithelial and mesenchymal cell states are a crucial form of epithelial plasticity for development and disease progression. Recent experimental data and mechanistic models showed multiple intermediate epithelial-mesenchymal transition (EMT) states as well as trajectories of EMT underpinned by complex gene regulatory networks. In this review, we summarize recent progress in quantifying EMT and characterizing EMT paths with computational methods and quantitative experiments including omics-level measurements. We provide perspectives on how these studies can help relating fundamental cell biology to physiological and pathological outcomes of EMT.
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Affiliation(s)
- Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville TN, USA
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, USA
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6
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Bhat GR, Sethi I, Sadida HQ, Rah B, Mir R, Algehainy N, Albalawi IA, Masoodi T, Subbaraj GK, Jamal F, Singh M, Kumar R, Macha MA, Uddin S, Akil ASAS, Haris M, Bhat AA. Cancer cell plasticity: from cellular, molecular, and genetic mechanisms to tumor heterogeneity and drug resistance. Cancer Metastasis Rev 2024; 43:197-228. [PMID: 38329598 PMCID: PMC11016008 DOI: 10.1007/s10555-024-10172-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
Cancer is a complex disease displaying a variety of cell states and phenotypes. This diversity, known as cancer cell plasticity, confers cancer cells the ability to change in response to their environment, leading to increased tumor diversity and drug resistance. This review explores the intricate landscape of cancer cell plasticity, offering a deep dive into the cellular, molecular, and genetic mechanisms that underlie this phenomenon. Cancer cell plasticity is intertwined with processes such as epithelial-mesenchymal transition and the acquisition of stem cell-like features. These processes are pivotal in the development and progression of tumors, contributing to the multifaceted nature of cancer and the challenges associated with its treatment. Despite significant advancements in targeted therapies, cancer cell adaptability and subsequent therapy-induced resistance remain persistent obstacles in achieving consistent, successful cancer treatment outcomes. Our review delves into the array of mechanisms cancer cells exploit to maintain plasticity, including epigenetic modifications, alterations in signaling pathways, and environmental interactions. We discuss strategies to counteract cancer cell plasticity, such as targeting specific cellular pathways and employing combination therapies. These strategies promise to enhance the efficacy of cancer treatments and mitigate therapy resistance. In conclusion, this review offers a holistic, detailed exploration of cancer cell plasticity, aiming to bolster the understanding and approach toward tackling the challenges posed by tumor heterogeneity and drug resistance. As articulated in this review, the delineation of cellular, molecular, and genetic mechanisms underlying tumor heterogeneity and drug resistance seeks to contribute substantially to the progress in cancer therapeutics and the advancement of precision medicine, ultimately enhancing the prospects for effective cancer treatment and patient outcomes.
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Affiliation(s)
- Gh Rasool Bhat
- Advanced Centre for Human Genetics, Sher-I-Kashmir Institute of Medical Sciences, Soura, Srinagar, Jammu and Kashmir, India
| | - Itty Sethi
- Institute of Human Genetics, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Hana Q Sadida
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Bilal Rah
- Iron Biology Group, Research Institute of Medical and Health Science, University of Sharjah, Sharjah, UAE
| | - Rashid Mir
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Prince Fahad Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | - Naseh Algehainy
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Prince Fahad Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Tariq Masoodi
- Laboratory of Cancer Immunology and Genetics, Sidra Medicine, Doha, Qatar
| | | | - Farrukh Jamal
- Dr. Rammanohar, Lohia Avadh University, Ayodhya, India
| | - Mayank Singh
- Department of Medical Oncology (Lab.), Institute of Medical Sciences (AIIMS), Dr. BRAIRCH, All India, New Delhi, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Jammu and Kashmir, India
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
- Laboratory Animal Research Centre, Qatar University, Doha, Qatar
| | - Ammira S Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Mohammad Haris
- Laboratory Animal Research Centre, Qatar University, Doha, Qatar.
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
| | - Ajaz A Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar.
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7
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Sunny SS, Lachova J, Kasparek P, Palkova M, Spoutil F, Prochazka J, Sedlacek R, Liskova P, Kozmik Z. Ovol2 promoter mutations in mice and human illuminate species-specific phenotypic divergence. Hum Mol Genet 2024; 33:491-500. [PMID: 37971355 DOI: 10.1093/hmg/ddad195] [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: 09/28/2023] [Revised: 11/06/2022] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Pathogenic variants in the highly conserved OVOL2 promoter region cause posterior polymorphous corneal dystrophy (PPCD) 1 by inducing an ectopic expression of the endothelial OVOL2 mRNA. Here we produced an allelic series of Ovol2 promoter mutations in the mouse model including the heterozygous c.-307T>C variant (RefSeq NM_021220.4) causing PPCD1 in humans. Despite the high evolutionary conservation of the Ovol2 promoter, only some alterations of its sequence had phenotypic consequences in mice. Four independent sequence variants in the distal part of the Ovol2 promoter had no significant effect on endothelial Ovol2 mRNA level or caused any ocular phenotype. In contrast, the mutation c.-307T>C resulted in increased Ovol2 expression in the corneal endothelium. However, only a small fraction of adult mice c.-307T>C heterozygotes developed ocular phenotypes such as irido-corneal adhesions, and corneal opacity. Interestingly, phenotypic penetrance was increased at embryonic stages. Notably, c.-307T>C mutation is located next to the Ovol1/Ovol2 transcription factor binding site. Mice carrying an allele with a deletion encompassing the Ovol2 binding site c.-307_-320del showed significant Ovol2 gene upregulation in the cornea endothelium and exhibited phenotypes similar to the c.-307T>C mutation. In conclusion, although the mutations c.-307T>C and -307_-320del lead to a comparably strong increase in endothelial Ovol2 expression as seen in PPCD1 patients, endothelial dystrophy was not observed in the mouse model, implicating species-specific differences in endothelial cell biology. Nonetheless, the emergence of dominant ocular phenotypes associated with Ovol2 promoter variants in mice implies a potential role of this gene in eye development and disease.
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Affiliation(s)
- Sweetu Susan Sunny
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Prague, Czech Republic
| | - Jitka Lachova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Prague, Czech Republic
| | - Petr Kasparek
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, 513 Parnassus Avenue, CA 94158, San Francisco, United States
| | - Marcela Palkova
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Frantisek Spoutil
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 121 08, Prague 2, Prague Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, U Nemocnice 2, 128 08, Prague 2, Prague, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Prague, Czech Republic
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Hu Q, Luo M, Wang R. Identifying critical regulatory interactions in cell fate decision and transition by systematic perturbation analysis. J Theor Biol 2024; 577:111673. [PMID: 37984586 DOI: 10.1016/j.jtbi.2023.111673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
One of the most significant challenges in biology is to elucidate the roles of various regulatory interactions in cell fate decision and transition. However, it remains to be fully clarified how they cooperate and determine fate transition. Here, a general framework based on statistical analysis and bifurcation theory is proposed to identify crucial regulatory interactions and how they play decisive roles in fate transition. More exactly, specific feedback loops determine occurrence of bifurcations by which cell fate transition can be realized. While regulatory interactions in the feedback loops determine the direction of transition. In addition, two-parameter bifurcation analysis further provides detailed understanding of how the fate transition based on statistical analysis occurs. Statistical analysis can also be used to reveal synergistic combinatorial perturbations by which fate transition can be more efficiently realized. The integrative analysis approach can be used to identify critical regulatory interactions in cell fate transition and reveal how specific cell fate transition occurs. To verify feasibility of the approach, the epithelial to mesenchymal transition (EMT) network is chosen as an illustrative example. In agreement with experimental observations, the approach reveals some critical regulatory interactions and underlying mechanisms in cell fate determination and transitions between three states. The approach can also be applied to analyze other regulatory networks related to cell fate decision and transition.
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Affiliation(s)
- Qing Hu
- Department of Mathematics, Shanghai University, Shanghai, 200444, China
| | - Min Luo
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Ruiqi Wang
- Department of Mathematics, Shanghai University, Shanghai, 200444, China; Newtouch Center for Mathematics of Shanghai University, Shanghai, 200444, China.
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9
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Mancheno-Ferris A, Immarigeon C, Rivero A, Depierre D, Schickele N, Fosseprez O, Chanard N, Aughey G, Lhoumaud P, Anglade J, Southall T, Plaza S, Payre F, Cuvier O, Polesello C. Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage. iScience 2024; 27:108624. [PMID: 38174321 PMCID: PMC10762455 DOI: 10.1016/j.isci.2023.108624] [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: 01/26/2023] [Revised: 07/05/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
The transcription factor Shavenbaby (Svb), the only member of the OvoL family in Drosophila, controls the fate of various epithelial embryonic cells and adult stem cells. Post-translational modification of Svb produces two protein isoforms, Svb-ACT and Svb-REP, which promote adult intestinal stem cell renewal or differentiation, respectively. To define Svb mode of action, we used engineered cell lines and develop an unbiased method to identify Svb target genes across different contexts. Within a given cell type, Svb-ACT and Svb-REP antagonistically regulate the expression of a set of target genes, binding specific enhancers whose accessibility is constrained by chromatin landscape. Reciprocally, Svb-REP can influence local chromatin marks of active enhancers to help repressing target genes. Along the intestinal lineage, the set of Svb target genes progressively changes, together with chromatin accessibility. We propose that Svb-ACT-to-REP transition promotes enterocyte differentiation of intestinal stem cells through direct gene regulation and chromatin remodeling.
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Affiliation(s)
- Alexandra Mancheno-Ferris
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Control of cell shape remodeling team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - Clément Immarigeon
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Control of cell shape remodeling team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - Alexia Rivero
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Control of cell shape remodeling team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - David Depierre
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Chromatin Dynamics and Cell Proliferation team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - Naomi Schickele
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Chromatin Dynamics and Cell Proliferation team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Fosseprez
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Chromatin Dynamics and Cell Proliferation team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - Nicolas Chanard
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Chromatin Dynamics and Cell Proliferation team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - Gabriel Aughey
- Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK
| | - Priscilla Lhoumaud
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Chromatin Dynamics and Cell Proliferation team, CBI, CNRS, UPS, 31062 Toulouse, France
- Institut Jacques Monod, Université Paris Cité/CNRS, 15 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Julien Anglade
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Chromatin Dynamics and Cell Proliferation team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - Tony Southall
- Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK
| | - Serge Plaza
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Laboratoire de Recherche en Sciences Végétales, CNRS/UPS/INPT, 31320 Auzeville-Tolosane, France
| | - François Payre
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Control of cell shape remodeling team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Cuvier
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Chromatin Dynamics and Cell Proliferation team, CBI, CNRS, UPS, 31062 Toulouse, France
| | - Cédric Polesello
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Integrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
- Control of cell shape remodeling team, CBI, CNRS, UPS, 31062 Toulouse, France
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10
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Proença C, Freitas M, Ribeiro D, Rufino AT, Fernandes E, Ferreira de Oliveira JMP. The role of flavonoids in the regulation of epithelial-mesenchymal transition in cancer: A review on targeting signaling pathways and metastasis. Med Res Rev 2023; 43:1878-1945. [PMID: 37147865 DOI: 10.1002/med.21966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 03/20/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
One of the hallmarks of cancer is metastasis, a process that entails the spread of cancer cells to distant regions in the body, culminating in tumor formation in secondary organs. Importantly, the proinflammatory environment surrounding cancer cells further contributes to cancer cell transformation and extracellular matrix destruction. During metastasis, front-rear polarity and emergence of migratory and invasive features are manifestations of epithelial-mesenchymal transition (EMT). A variety of transcription factors (TFs) are implicated in the execution of EMT, the most prominent belonging to the Snail Family Transcriptional Repressor (SNAI) and Zinc Finger E-Box Binding Homeobox (ZEB) families of TFs. These TFs are regulated by interaction with specific microRNAs (miRNAs), as miR34 and miR200. Among the several secondary metabolites produced in plants, flavonoids constitute a major group of bioactive molecules, with several described effects including antioxidant, antiinflammatory, antidiabetic, antiobesogenic, and anticancer effects. This review scrutinizes the modulatory role of flavonoids on the activity of SNAI/ZEB TFs and on their regulatory miRNAs, miR-34, and miR-200. The modulatory role of flavonoids can attenuate mesenchymal features and stimulate epithelial features, thereby inhibiting and reversing EMT. Moreover, this modulation is concomitant with the attenuation of signaling pathways involved in diverse processes as cell proliferation, cell growth, cell cycle progression, apoptosis inhibition, morphogenesis, cell fate, cell migration, cell polarity, and wound healing. The antimetastatic potential of these versatile compounds is emerging and represents an opportunity for the synthesis of more specific and potent agents.
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Affiliation(s)
- Carina Proença
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Marisa Freitas
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Daniela Ribeiro
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana T Rufino
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Eduarda Fernandes
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - José Miguel P Ferreira de Oliveira
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
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11
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Jain P, Pillai M, Duddu AS, Somarelli JA, Goyal Y, Jolly MK. Dynamical hallmarks of cancer: Phenotypic switching in melanoma and epithelial-mesenchymal plasticity. Semin Cancer Biol 2023; 96:48-63. [PMID: 37788736 DOI: 10.1016/j.semcancer.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023]
Abstract
Phenotypic plasticity was recently incorporated as a hallmark of cancer. This plasticity can manifest along many interconnected axes, such as stemness and differentiation, drug-sensitive and drug-resistant states, and between epithelial and mesenchymal cell-states. Despite growing acceptance for phenotypic plasticity as a hallmark of cancer, the dynamics of this process remains poorly understood. In particular, the knowledge necessary for a predictive understanding of how individual cancer cells and populations of cells dynamically switch their phenotypes in response to the intensity and/or duration of their current and past environmental stimuli remains far from complete. Here, we present recent investigations of phenotypic plasticity from a systems-level perspective using two exemplars: epithelial-mesenchymal plasticity in carcinomas and phenotypic switching in melanoma. We highlight how an integrated computational-experimental approach has helped unravel insights into specific dynamical hallmarks of phenotypic plasticity in different cancers to address the following questions: a) how many distinct cell-states or phenotypes exist?; b) how reversible are transitions among these cell-states, and what factors control the extent of reversibility?; and c) how might cell-cell communication be able to alter rates of cell-state switching and enable diverse patterns of phenotypic heterogeneity? Understanding these dynamic features of phenotypic plasticity may be a key component in shifting the paradigm of cancer treatment from reactionary to a more predictive, proactive approach.
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Affiliation(s)
- Paras Jain
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Maalavika Pillai
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA
| | | | - Jason A Somarelli
- Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India.
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12
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Jiang Y, Zhang Z. OVOL2: an epithelial lineage determiner with emerging roles in energy homeostasis. Trends Cell Biol 2023; 33:824-833. [PMID: 37336658 PMCID: PMC10524639 DOI: 10.1016/j.tcb.2023.05.008] [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] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/21/2023]
Abstract
Ovo like zinc finger 2 (OVOL2) is an evolutionarily conserved regulator of epithelial lineage determination and differentiation during embryogenesis. OVOL2 binds to DNA using zinc-finger domains to suppress epithelial-mesenchymal transition (EMT), which is critical for tumor metastasis. However, recent studies have suggested some noncanonical roles of OVOL2 that do not rely on the DNA binding of zinc-finger domains or regulation of EMT. OVOL2 and EMT regulators have emerging roles in adipogenesis, thermogenesis, and lipid metabolism. Here, we review different roles of OVOL2 from embryo development to adult tissue homeostasis, and discuss how OVOL2 and other EMT regulators orchestrate a regulatory network to control energy homeostasis. Last, we propose potential applications of targeting OVOL2 to reduce human obesity.
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Affiliation(s)
- Yiao Jiang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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13
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Park H. Unraveling the Molecular Puzzle: Exploring Gene Networks across Diverse EMT Status of Cell Lines. Int J Mol Sci 2023; 24:12784. [PMID: 37628965 PMCID: PMC10454379 DOI: 10.3390/ijms241612784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Understanding complex disease mechanisms requires a comprehensive understanding of the gene regulatory networks, as complex diseases are often characterized by the dysregulation and dysfunction of molecular networks, rather than abnormalities in single genes. Specifically, the exploration of cell line-specific gene networks can provide essential clues for precision medicine, as this methodology can uncover molecular interplays specific to particular cell line statuses, such as drug sensitivity, cancer progression, etc. In this article, we provide a comprehensive review of computational strategies for cell line-specific gene network analysis: (1) cell line-specific gene regulatory network estimation and analysis of gene networks under varying epithelial-mesenchymal transition (EMT) statuses of cell lines; and (2) an explainable artificial intelligence approach for interpreting the estimated massive multiple EMT-status-specific gene networks. The objective of this review is to help readers grasp the concept of computational network biology, which holds significant implications for precision medicine by offering crucial clues.
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Affiliation(s)
- Heewon Park
- School of Mathematics, Statistics and Data Science, Sungshin Women's University, Seoul 02844, Republic of Korea
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14
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He Y, Zhang Q, Chen Y, Wu Y, Quan Y, Chen W, Yao J, Zhang P. ZHX2 deficiency enriches hybrid MET cells through regulating E-cadherin expression. Cell Death Dis 2023; 14:444. [PMID: 37460540 DOI: 10.1038/s41419-023-05974-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/18/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
Growing evidence indicates that the epithelial to mesenchymal (E/M) hybrid state plays a key role in tumorigenesis. Importantly, a hybrid mesenchymal to epithelial transition (MET) state in which individual cells express both epithelial and mesenchymal markers was recently identified in vivo, further strengthening the bonds between the hybrid EMT state and cancer progression. However, the role and the molecular mechanisms by which the hybrid MET state is maintained in triple-negative breast cancer cells (TNBC) remain elusive. Here, we find that loss of ZHX2 expression results in the hybrid MET phenotype in mesenchymal TNBC cells. Mechanistically, through directly binding to the CDH1 promoter, depletion of ZHX2 specifically reactivates expression of CDH1 encoding E-cadherin, an epithelial marker that is crucial for maintaining epithelial phenotype. Functionally, loss of ZHX2 expression enriches the hybrid MET cells and inhibits the migration and dissemination of TNBC cells or organoids, which could be reversed by restoration of E-cadherin. Moreover, depletion of ZHX2 suppresses lung metastasis in preclinical models of TNBC. In patients with TNBC, ZHX2 expression was amplified and negatively correlated with the expression of E-cadherin. These findings suggest that loss of ZHX2 promotes the hybrid MET state to impair TNBC progression.
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Affiliation(s)
- Yan He
- National Engineering Research Center for Nanomedicine, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Qimin Zhang
- National Engineering Research Center for Nanomedicine, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanhong Chen
- National Engineering Research Center for Nanomedicine, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yingjian Wu
- National Engineering Research Center for Nanomedicine, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Quan
- Stem Cell Laboratory, the Second Affiliated Hospital, Fujian Medical University, Quanzhou, China.
| | - Weihua Chen
- National Engineering Research Center for Nanomedicine, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Yao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peijing Zhang
- National Engineering Research Center for Nanomedicine, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.
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15
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Suzuki T, Conant A, Curow C, Alexander A, Ioffe Y, Unternaehrer JJ. Role of epithelial-mesenchymal transition factor SNAI1 and its targets in ovarian cancer aggressiveness. JOURNAL OF CANCER METASTASIS AND TREATMENT 2023; 9:25. [PMID: 38009093 PMCID: PMC10673625 DOI: 10.20517/2394-4722.2023.34] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Ovarian cancer remains the most lethal gynecologic malignancy in the USA. For over twenty years, epithelial-mesenchymal transition (EMT) has been characterized extensively in development and disease. The dysregulation of this process in cancer has been identified as a mechanism by which epithelial tumors become more aggressive, allowing them to survive and invade distant tissues. This occurs in part due to the increased expression of the EMT transcription factor, SNAI1 (Snail). In the case of epithelial ovarian cancer, Snail has been shown to contribute to cancer invasion, stemness, chemoresistance, and metabolic changes. Thus, in this review, we focus on summarizing current findings on the role of EMT (specifically, factors downstream of Snail) in determining ovarian cancer aggressiveness.
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Affiliation(s)
- Tise Suzuki
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
| | - Ashlyn Conant
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
| | - Casey Curow
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
- University of Redlands, Department of Biology, Redlands, CA 92373, USA
| | - Audrey Alexander
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
- Division of Natural and Mathematical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA
| | - Yevgeniya Ioffe
- Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, Loma Linda University Medical Center, Loma Linda, CA 92354, USA
| | - Juli J Unternaehrer
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
- Department of Gynecology and Obstetrics, Loma Linda University, Loma Linda, CA 92354, USA
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16
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Saini M, Schmidleitner L, Moreno HD, Donato E, Falcone M, Bartsch JM, Klein C, Vogel V, Würth R, Pfarr N, Espinet E, Lehmann M, Königshoff M, Reitberger M, Haas S, Graf E, Schwarzmayr T, Strom TM, Spaich S, Sütterlin M, Schneeweiss A, Weichert W, Schotta G, Reichert M, Aceto N, Sprick MR, Trumpp A, Scheel CH. Resistance to mesenchymal reprogramming sustains clonal propagation in metastatic breast cancer. Cell Rep 2023; 42:112533. [PMID: 37257449 DOI: 10.1016/j.celrep.2023.112533] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 10/04/2022] [Accepted: 05/03/2023] [Indexed: 06/02/2023] Open
Abstract
The acquisition of mesenchymal traits is considered a hallmark of breast cancer progression. However, the functional relevance of epithelial-to-mesenchymal transition (EMT) remains controversial and context dependent. Here, we isolate epithelial and mesenchymal populations from human breast cancer metastatic biopsies and assess their functional potential in vivo. Strikingly, progressively decreasing epithelial cell adhesion molecule (EPCAM) levels correlate with declining disease propagation. Mechanistically, we find that persistent EPCAM expression marks epithelial clones that resist EMT induction and propagate competitively. In contrast, loss of EPCAM defines clones arrested in a mesenchymal state, with concomitant suppression of tumorigenicity and metastatic potential. This dichotomy results from distinct clonal trajectories impacting global epigenetic programs that are determined by the interplay between human ZEB1 and its target GRHL2. Collectively, our results indicate that susceptibility to irreversible EMT restrains clonal propagation, whereas resistance to mesenchymal reprogramming sustains disease spread in multiple models of human metastatic breast cancer, including patient-derived cells in vivo.
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Affiliation(s)
- Massimo Saini
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany; Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
| | - Laura Schmidleitner
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany; Translational Pancreatic Cancer Research Center, Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany; Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Garching, Germany; Center for Organoid Systems (COS), Technical University of Munich (TUM), Garching, Germany; Munich Institute of Biomedical Engineering (MIBE), Technical University of Munich (TUM), Garching, Germany
| | - Helena Domínguez Moreno
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilian University of Munich (LMU), Munich, Germany
| | - Elisa Donato
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Mattia Falcone
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Johanna M Bartsch
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Corinna Klein
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Vanessa Vogel
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Roberto Würth
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich (TUM), Munich, Germany
| | - Elisa Espinet
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Mareike Lehmann
- Institute for Lung Health and Immunity (LHI) and Comprehensive Pneumology Center (CPC), Helmholtz Center Munich, Member of the German Center for Lung Research (DZL), Munich, Germany; Institute for Lung Research, Philipps-University Marburg, Member of the German Center for Lung Research (DZL), Marburg, Germany
| | - Melanie Königshoff
- Research Unit Lung Repair and Regeneration, Helmholtz Center Munich, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Manuel Reitberger
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Simon Haas
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Tim-Matthias Strom
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Saskia Spaich
- Department of Gynaecology and Obstetrics, University Women's Clinic, University Medical Centre Mannheim, Mannheim, Germany
| | - Marc Sütterlin
- Department of Gynaecology and Obstetrics, University Women's Clinic, University Medical Centre Mannheim, Mannheim, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich (TUM), Munich, Germany; German Cancer Consortium (DKTK), Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilian University of Munich (LMU), Munich, Germany
| | - Maximilian Reichert
- Translational Pancreatic Cancer Research Center, Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany; Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Garching, Germany; Center for Organoid Systems (COS), Technical University of Munich (TUM), Garching, Germany; Munich Institute of Biomedical Engineering (MIBE), Technical University of Munich (TUM), Garching, Germany; German Cancer Consortium (DKTK), Germany
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Martin R Sprick
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; German Cancer Consortium (DKTK), Germany.
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; German Cancer Consortium (DKTK), Germany.
| | - Christina H Scheel
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany.
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17
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Akhmetkaliyev A, Alibrahim N, Shafiee D, Tulchinsky E. EMT/MET plasticity in cancer and Go-or-Grow decisions in quiescence: the two sides of the same coin? Mol Cancer 2023; 22:90. [PMID: 37259089 DOI: 10.1186/s12943-023-01793-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/20/2023] [Indexed: 06/02/2023] Open
Abstract
Epithelial mesenchymal transition (EMT) and mesenchymal epithelial transition (MET) are genetic determinants of cellular plasticity. These programs operate in physiological (embryonic development, wound healing) and pathological (organ fibrosis, cancer) conditions. In cancer, EMT and MET interfere with various signalling pathways at different levels. This results in gross alterations in the gene expression programs, which affect most, if not all hallmarks of cancer, such as response to proliferative and death-inducing signals, tumorigenicity, and cell stemness. EMT in cancer cells involves large scale reorganisation of the cytoskeleton, loss of epithelial integrity, and gain of mesenchymal traits, such as mesenchymal type of cell migration. In this regard, EMT/MET plasticity is highly relevant to the Go-or-Grow concept, which postulates the dichotomous relationship between cell motility and proliferation. The Go-or-Grow decisions are critically important in the processes in which EMT/MET plasticity takes the central stage, mobilisation of stem cells during wound healing, cancer relapse, and metastasis. Here we outline the maintenance of quiescence in stem cell and metastatic niches, focusing on the implication of EMT/MET regulatory networks in Go-or-Grow switches. In particular, we discuss the analogy between cells residing in hybrid quasi-mesenchymal states and GAlert, an intermediate phase allowing quiescent stem cells to enter the cell cycle rapidly.
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Affiliation(s)
- Azamat Akhmetkaliyev
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, 020000, Kazakhstan
| | | | - Darya Shafiee
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, 020000, Kazakhstan
| | - Eugene Tulchinsky
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, 020000, Kazakhstan.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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18
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Verstappe J, Berx G. A role for partial epithelial-to-mesenchymal transition in enabling stemness in homeostasis and cancer. Semin Cancer Biol 2023; 90:15-28. [PMID: 36773819 DOI: 10.1016/j.semcancer.2023.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023]
Abstract
Stem cells have self-renewal capacities and the ability to give rise to differentiated cells thereby sustaining tissues during homeostasis and injury. This structural hierarchy extends to tumours which harbor stem-like cells deemed cancer stem cells that propagate the tumour and drive metastasis and relapse. The process of epithelial-to-mesenchymal transition (EMT), which plays an important role in development and cancer cell migration, was shown to be correlated with stemness in both homeostasis and cancer indicating that stemness can be acquired and is not necessarily an intrinsic trait. Nowadays it is experimentally proven that the activation of an EMT program does not necessarily drive cells towards a fully mesenchymal phenotype but rather to hybrid E/M states. This review offers the latest advances in connecting the EMT status and stem-cell state of both non-transformed and cancer cells. Recent literature clearly shows that hybrid EMT states have a higher probability of acquiring stem cell traits. The position of a cell along the EMT-axis which coincides with a stem cell-like state is known as the stemness window. We show how the original EMT-state of a cell dictates the EMT/MET inducing programmes required to reach stemness. Lastly we present the mechanism of stemness regulation and the regulatory feedback loops which position cells at a certain EMT state along the EMT axis.
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Affiliation(s)
- Jeroen Verstappe
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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19
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Subhadarshini S, Markus J, Sahoo S, Jolly MK. Dynamics of Epithelial-Mesenchymal Plasticity: What Have Single-Cell Investigations Elucidated So Far? ACS OMEGA 2023; 8:11665-11673. [PMID: 37033874 PMCID: PMC10077445 DOI: 10.1021/acsomega.2c07989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Epithelial-mesenchymal plasticity (EMP) is a key driver of cancer metastasis and therapeutic resistance, through which cancer cells can reversibly and dynamically alter their molecular and functional traits along the epithelial-mesenchymal spectrum. While cells in the epithelial phenotype are usually tightly adherent, less metastatic, and drug-sensitive, those in the hybrid epithelial/mesenchymal and/or mesenchymal state are more invasive, migratory, drug-resistant, and immune-evasive. Single-cell studies have emerged as a powerful tool in gaining new insights into the dynamics of EMP across various cancer types. Here, we review many recent studies that employ single-cell analysis techniques to better understand the dynamics of EMP in cancer both in vitro and in vivo. These single-cell studies have underlined the plurality of trajectories cells can traverse during EMP and the consequent heterogeneity of hybrid epithelial/mesenchymal phenotypes seen at both preclinical and clinical levels. They also demonstrate how diverse EMP trajectories may exhibit hysteretic behavior and how the rate of such cell-state transitions depends on the genetic/epigenetic background of recipient cells, as well as the dose and/or duration of EMP-inducing growth factors. Finally, we discuss the relationship between EMP and patient survival across many cancer types. We also present a next set of questions related to EMP that could benefit much from single-cell observations and pave the way to better tackle phenotypic switching and heterogeneity in clinic.
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Affiliation(s)
| | - Joel Markus
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sarthak Sahoo
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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20
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Groves SM, Panchy N, Tyson DR, Harris LA, Quaranta V, Hong T. Involvement of Epithelial-Mesenchymal Transition Genes in Small Cell Lung Cancer Phenotypic Plasticity. Cancers (Basel) 2023; 15:1477. [PMID: 36900269 PMCID: PMC10001072 DOI: 10.3390/cancers15051477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive cancer recalcitrant to treatment, arising predominantly from epithelial pulmonary neuroendocrine (NE) cells. Intratumor heterogeneity plays critical roles in SCLC disease progression, metastasis, and treatment resistance. At least five transcriptional SCLC NE and non-NE cell subtypes were recently defined by gene expression signatures. Transition from NE to non-NE cell states and cooperation between subtypes within a tumor likely contribute to SCLC progression by mechanisms of adaptation to perturbations. Therefore, gene regulatory programs distinguishing SCLC subtypes or promoting transitions are of great interest. Here, we systematically analyze the relationship between SCLC NE/non-NE transition and epithelial to mesenchymal transition (EMT)-a well-studied cellular process contributing to cancer invasiveness and resistance-using multiple transcriptome datasets from SCLC mouse tumor models, human cancer cell lines, and tumor samples. The NE SCLC-A2 subtype maps to the epithelial state. In contrast, SCLC-A and SCLC-N (NE) map to a partial mesenchymal state (M1) that is distinct from the non-NE, partial mesenchymal state (M2). The correspondence between SCLC subtypes and the EMT program paves the way for further work to understand gene regulatory mechanisms of SCLC tumor plasticity with applicability to other cancer types.
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Affiliation(s)
- Sarah M. Groves
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Nicholas Panchy
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Darren R. Tyson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
| | - Leonard A. Harris
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA
- Cancer Biology Program, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
- National Institute for Mathematical and Biological Synthesis, Knoxville, TN 37996, USA
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21
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Li D, Xia L, Huang P, Wang Z, Guo Q, Huang C, Leng W, Qin S. Heterogeneity and plasticity of epithelial-mesenchymal transition (EMT) in cancer metastasis: Focusing on partial EMT and regulatory mechanisms. Cell Prolif 2023:e13423. [PMID: 36808651 DOI: 10.1111/cpr.13423] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/05/2023] [Accepted: 01/27/2023] [Indexed: 02/22/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) or mesenchymal-epithelial transition (MET) plays critical roles in cancer metastasis. Recent studies, especially those based on single-cell sequencing, have revealed that EMT is not a binary process, but a heterogeneous and dynamic disposition with intermediary or partial EMT states. Multiple double-negative feedback loops involved by EMT-related transcription factors (EMT-TFs) have been identified. These feedback loops between EMT drivers and MET drivers finely regulate the EMT transition state of the cell. In this review, the general characteristics, biomarkers and molecular mechanisms of different EMT transition states were summarized. We additionally discussed the direct and indirect roles of EMT transition state in tumour metastasis. More importantly, this article provides direct evidence that the heterogeneity of EMT is closely related to the poor prognosis in gastric cancer. Notably, a seesaw model was proposed to explain how tumour cells regulate themselves to remain in specific EMT transition states, including epithelial state, hybrid/intermediate state and mesenchymal state. Additionally, this article also provides a review of the current status, limitations and future perspectives of EMT signalling in clinical applications.
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Affiliation(s)
- Dandan Li
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China.,Laboratory of Tumor Biology, Academy of Bio-medicine Research, Hubei University of Medicine, Shiyan, China
| | - Lingyun Xia
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Pan Huang
- Laboratory of Tumor Biology, Academy of Bio-medicine Research, Hubei University of Medicine, Shiyan, China
| | - Zidi Wang
- Laboratory of Tumor Biology, Academy of Bio-medicine Research, Hubei University of Medicine, Shiyan, China
| | - Qiwei Guo
- Laboratory of Tumor Biology, Academy of Bio-medicine Research, Hubei University of Medicine, Shiyan, China
| | - Congcong Huang
- Laboratory of Tumor Biology, Academy of Bio-medicine Research, Hubei University of Medicine, Shiyan, China
| | - Weidong Leng
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Shanshan Qin
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China.,Laboratory of Tumor Biology, Academy of Bio-medicine Research, Hubei University of Medicine, Shiyan, China
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22
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Malagoli Tagliazucchi G, Wiecek AJ, Withnell E, Secrier M. Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer. Nat Commun 2023; 14:789. [PMID: 36774358 PMCID: PMC9922305 DOI: 10.1038/s41467-023-36439-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/31/2023] [Indexed: 02/13/2023] Open
Abstract
The epithelial to mesenchymal transition (EMT) is a key cellular process underlying cancer progression, with multiple intermediate states whose molecular hallmarks remain poorly characterised. To fill this gap, we present a method to robustly evaluate EMT transformation in individual tumours based on transcriptomic signals. We apply this approach to explore EMT trajectories in 7180 tumours of epithelial origin and identify three macro-states with prognostic and therapeutic value, attributable to epithelial, hybrid E/M and mesenchymal phenotypes. We show that the hybrid state is relatively stable and linked with increased aneuploidy. We further employ spatial transcriptomics and single cell datasets to explore the spatial heterogeneity of EMT transformation and distinct interaction patterns with cytotoxic, NK cells and fibroblasts in the tumour microenvironment. Additionally, we provide a catalogue of genomic events underlying distinct evolutionary constraints on EMT transformation. This study sheds light on the aetiology of distinct stages along the EMT trajectory, and highlights broader genomic and environmental hallmarks shaping the mesenchymal transformation of primary tumours.
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Affiliation(s)
| | - Anna J Wiecek
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Eloise Withnell
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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23
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Paul I, Bolzan D, Youssef A, Gagnon KA, Hook H, Karemore G, Oliphant MUJ, Lin W, Liu Q, Phanse S, White C, Padhorny D, Kotelnikov S, Chen CS, Hu P, Denis GV, Kozakov D, Raught B, Siggers T, Wuchty S, Muthuswamy SK, Emili A. Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT. Nat Commun 2023; 14:688. [PMID: 36755019 PMCID: PMC9908882 DOI: 10.1038/s41467-023-36122-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
A proper understanding of disease etiology will require longitudinal systems-scale reconstruction of the multitiered architecture of eukaryotic signaling. Here we combine state-of-the-art data acquisition platforms and bioinformatics tools to devise PAMAF, a workflow that simultaneously examines twelve omics modalities, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. We apply PAMAF in an established in vitro model of TGFβ-induced epithelial to mesenchymal transition (EMT) to quantify >61,000 molecules from 12 omics and 10 timepoints over 12 days. Bioinformatics analysis of this EMT-ExMap resource allowed us to identify; -topological coupling between omics, -four distinct cell states during EMT, -omics-specific kinetic paths, -stage-specific multi-omics characteristics, -distinct regulatory classes of genes, -ligand-receptor mediated intercellular crosstalk by integrating scRNAseq and subcellular proteomics, and -combinatorial drug targets (e.g., Hedgehog signaling and CAMK-II) to inhibit EMT, which we validate using a 3D mammary duct-on-a-chip platform. Overall, this study provides a resource on TGFβ signaling and EMT.
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Affiliation(s)
- Indranil Paul
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Dante Bolzan
- Department of Computer Science, University of Miami, 1356 Memorial Drive, Coral Gables, FL, 33146, USA
| | - Ahmed Youssef
- Graduate Program in Bioinformatics, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA
| | - Keith A Gagnon
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Heather Hook
- Department of Biology, Boston University, 24 Cummington Mall, Boston, MA, 02115, USA
- Biological Design Center, Boston University, 610 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Gopal Karemore
- Advanced Analytics, Novo Nordisk A/S, 2760, Måløv, Denmark
| | - Michael U J Oliphant
- Cancer Research Institute, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Weiwei Lin
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Qian Liu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Sadhna Phanse
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Carl White
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, 11794, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, 11794, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Christopher S Chen
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Pingzhao Hu
- Department of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Gerald V Denis
- Boston Medical Center Cancer Center, Boston University, Boston University, 72 East Concord Street, Boston, MA, 02118, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, 11794, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Brian Raught
- Discovery Tower (TMDT), 101 College St, Rm. 9-701A, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Trevor Siggers
- Department of Biology, Boston University, 24 Cummington Mall, Boston, MA, 02115, USA
- Biological Design Center, Boston University, 610 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, 1356 Memorial Drive, Coral Gables, FL, 33146, USA
| | - Senthil K Muthuswamy
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA.
- Department of Biology, Charles River Campus, Boston University, Life Science & Engineering (LSEB-602), 24 Cummington Mall, Boston, MA, 02215, USA.
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, USA.
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24
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Hari K, Harlapur P, Gopalan A, Ullanat V, Duddu AS, Jolly MK. Emergent properties of coupled bistable switches. J Biosci 2022. [DOI: 10.1007/s12038-022-00310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Network topology metrics explaining enrichment of hybrid epithelial mesenchymal phenotypes in metastasis. PLoS Comput Biol 2022; 18:e1010687. [DOI: 10.1371/journal.pcbi.1010687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/18/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Epithelial to Mesenchymal Transition (EMT) and its reverse—Mesenchymal to Epithelial Transition (MET) are hallmarks of metastasis. Cancer cells use this reversible cellular programming to switch among Epithelial (E), Mesenchymal (M), and hybrid Epithelial/Mesenchymal (hybrid E/M) state(s) and seed tumors at distant sites. Hybrid E/M cells are often more aggressive and metastatic than the “pure” E and M cells. Thus, identifying mechanisms to inhibit hybrid E/M cells can be promising in curtailing metastasis. While multiple gene regulatory networks (GRNs) based mathematical models for EMT/MET have been developed recently, identifying topological signatures enriching hybrid E/M phenotypes remains to be done. Here, we investigate the dynamics of 13 different GRNs and report an interesting association between “hybridness” and the number of negative/positive feedback loops across the networks. While networks having more negative feedback loops favor hybrid phenotype(s), networks having more positive feedback loops (PFLs) or many HiLoops–specific combinations of PFLs, support terminal (E and M) phenotypes. We also establish a connection between “hybridness” and network-frustration by showing that hybrid phenotypes likely result from non-reinforcing interactions among network nodes (genes) and therefore tend to be more frustrated (less stable). Our analysis, thus, identifies network topology-based signatures that can give rise to, as well as prevent, the emergence of hybrid E/M phenotype in GRNs underlying EMP. Our results can have implications in terms of targeting specific interactions in GRNs as a potent way to restrict switching to the hybrid E/M phenotype(s) to curtail metastasis.
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26
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Hari K, Ullanat V, Balasubramanian A, Gopalan A, Jolly MK. Landscape of epithelial-mesenchymal plasticity as an emergent property of coordinated teams in regulatory networks. eLife 2022; 11:e76535. [PMID: 36269057 PMCID: PMC9683792 DOI: 10.7554/elife.76535] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
Elucidating the design principles of regulatory networks driving cellular decision-making has fundamental implications in mapping and eventually controlling cell-fate decisions. Despite being complex, these regulatory networks often only give rise to a few phenotypes. Previously, we identified two 'teams' of nodes in a small cell lung cancer regulatory network that constrained the phenotypic repertoire and aligned strongly with the dominant phenotypes obtained from network simulations (Chauhan et al., 2021). However, it remained elusive whether these 'teams' exist in other networks, and how do they shape the phenotypic landscape. Here, we demonstrate that five different networks of varying sizes governing epithelial-mesenchymal plasticity comprised of two 'teams' of players - one comprised of canonical drivers of epithelial phenotype and the other containing the mesenchymal inducers. These 'teams' are specific to the topology of these regulatory networks and orchestrate a bimodal phenotypic landscape with the epithelial and mesenchymal phenotypes being more frequent and dynamically robust to perturbations, relative to the intermediary/hybrid epithelial/mesenchymal ones. Our analysis reveals that network topology alone can contain information about corresponding phenotypic distributions, thus obviating the need to simulate them. We propose 'teams' of nodes as a network design principle that can drive cell-fate canalization in diverse decision-making processes.
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Affiliation(s)
- Kishore Hari
- Centre for BioSystems Science and Engineering, Indian Institute of Science BangaloreBangaloreIndia
| | - Varun Ullanat
- Department of Biotechnology, RV College of EngineeringBangaloreIndia
| | | | - Aditi Gopalan
- Department of Biotechnology, RV College of EngineeringBangaloreIndia
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science BangaloreBangaloreIndia
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27
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Nordick B, Chae-Yeon Park M, Quaranta V, Hong T. Cooperative RNA degradation stabilizes intermediate epithelial-mesenchymal states and supports a phenotypic continuum. iScience 2022; 25:105224. [PMID: 36248730 PMCID: PMC9557027 DOI: 10.1016/j.isci.2022.105224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/21/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022] Open
Abstract
Multiple intermediate epithelial-mesenchymal transition (EMT) states reflecting hybrid epithelial and mesenchymal phenotypes were observed in physiological and pathological conditions. Previous theoretical models explaining multiple EMT states rely on regulatory loops involving transcriptional feedback, which produce three or four attractors. This is incompatible with the observed continuum-like EMT spectrum. Here, we used mass-action-based models to describe post-transcriptional regulations, finding that cooperative RNA degradation via multiple microRNA binding sites can generate four-attractor systems without transcriptional feedback. Furthermore, the newly identified intermediates-enabling circuits are common in the EMT regulatory network, and they can synergize with transcriptional feedback to support phenotypic continuum. Finally, our model predicted a role of miR-101 in multistate EMT, and we identified evidence from single-cell RNA-sequencing data that support the prediction. Our work reveals a previously unknown role of cooperative RNA degradation and microRNAs in EMT, providing a framework that can bridge the gap between mechanistic models and single-cell experiments.
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Affiliation(s)
- Benjamin Nordick
- School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37916, USA
| | - Mary Chae-Yeon Park
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37916, USA
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN 37232, USA
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37916, USA
- National Institute for Mathematical and Biological Synthesis, Knoxville, TN 37916, USA
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28
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Stochastic population dynamics of cancer stemness and adaptive response to therapies. Essays Biochem 2022; 66:387-398. [PMID: 36073715 DOI: 10.1042/ebc20220038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 02/07/2023]
Abstract
Intratumoral heterogeneity can exist along multiple axes: Cancer stem cells (CSCs)/non-CSCs, drug-sensitive/drug-tolerant states, and a spectrum of epithelial-hybrid-mesenchymal phenotypes. Further, these diverse cell-states can switch reversibly among one another, thereby posing a major challenge to therapeutic efficacy. Therefore, understanding the origins of phenotypic plasticity and heterogeneity remains an active area of investigation. While genomic components (mutations, chromosomal instability) driving heterogeneity have been well-studied, recent reports highlight the role of non-genetic mechanisms in enabling both phenotypic plasticity and heterogeneity. Here, we discuss various processes underlying phenotypic plasticity such as stochastic gene expression, chromatin reprogramming, asymmetric cell division and the presence of multiple stable gene expression patterns ('attractors'). These processes can facilitate a dynamically evolving cell population such that a subpopulation of (drug-tolerant) cells can survive lethal drug exposure and recapitulate population heterogeneity on drug withdrawal, leading to relapse. These drug-tolerant cells can be both pre-existing and also induced by the drug itself through cell-state reprogramming. The dynamics of cell-state transitions both in absence and presence of the drug can be quantified through mathematical models. Such a dynamical systems approach to elucidating patterns of intratumoral heterogeneity by integrating longitudinal experimental data with mathematical models can help design effective combinatorial and/or sequential therapies for better clinical outcomes.
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29
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Xue Y, Song X, Fan S, Deng R. The role of tumor-associated macrophages in oral squamous cell carcinoma. Front Physiol 2022; 13:959747. [PMID: 36105288 PMCID: PMC9464857 DOI: 10.3389/fphys.2022.959747] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a common head and neck cancer with a high recurrence rate and a low 5-year survival rate. Tumor-associated macrophages (TAMs) are important immune cells in the tumor microenvironment, which play an important role in the progression of many tumors. This article reviews the origin, and the role of TAMs in the invasion, metastasis, angiogenesis and immunosuppression of OSCC. Therapeutic strategies targeting TAMs are also discussed in hopes of providing new ideas for the treatment of OSCC.
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Affiliation(s)
- Yiwen Xue
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Xiao Song
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Siyu Fan
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Runzhi Deng
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
- *Correspondence: Runzhi Deng,
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30
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Mendez MJ, Hoffman MJ, Cherry EM, Lemmon CA, Weinberg SH. A data-assimilation approach to predict population dynamics during epithelial-mesenchymal transition. Biophys J 2022; 121:3061-3080. [PMID: 35836379 PMCID: PMC9463646 DOI: 10.1016/j.bpj.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/30/2022] [Accepted: 07/08/2022] [Indexed: 11/02/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a biological process that plays a central role in embryonic development, tissue regeneration, and cancer metastasis. Transforming growth factor-β (TGFβ) is a potent inducer of this cellular transition, comprising transitions from an epithelial state to partial or hybrid EMT state(s), to a mesenchymal state. Recent experimental studies have shown that, within a population of epithelial cells, heterogeneous phenotypical profiles arise in response to different time- and TGFβ dose-dependent stimuli. This offers a challenge for computational models, as most model parameters are generally obtained to represent typical cell responses, not necessarily specific responses nor to capture population variability. In this study, we applied a data-assimilation approach that combines limited noisy observations with predictions from a computational model, paired with parameter estimation. Synthetic experiments mimic the biological heterogeneity in cell states that is observed in epithelial cell populations by generating a large population of model parameter sets. Analysis of the parameters for virtual epithelial cells with biologically significant characteristics (e.g., EMT prone or resistant) illustrates that these sub-populations have identifiable critical model parameters. We perform a series of in silico experiments in which a forecasting system reconstructs the EMT dynamics of each virtual cell within a heterogeneous population exposed to time-dependent exogenous TGFβ dose and either an EMT-suppressing or EMT-promoting perturbation. We find that estimating population-specific critical parameters significantly improved the prediction accuracy of cell responses. Thus, with appropriate protocol design, we demonstrate that a data-assimilation approach successfully reconstructs and predicts the dynamics of a heterogeneous virtual epithelial cell population in the presence of physiological model error and parameter uncertainty.
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Affiliation(s)
- Mario J Mendez
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio; Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia
| | - Matthew J Hoffman
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York
| | - Elizabeth M Cherry
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York; School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Christopher A Lemmon
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia
| | - Seth H Weinberg
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio; Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia; The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio.
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31
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Wu J, Luo D, Li S. Ovo Like Zinc Finger 2 (OVOL2) Suppresses Breast Cancer Stem Cell Traits and Correlates with Immune Cells Infiltration. BREAST CANCER: TARGETS AND THERAPY 2022; 14:211-227. [PMID: 35996562 PMCID: PMC9391936 DOI: 10.2147/bctt.s363114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/05/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Jiafa Wu
- School of Food and Bioengineering, Henan University of Science and Technology, Luoyang, People’s Republic of China
- Correspondence: Jiafa Wu, School of Food and Bioengineering, Henan University of Science and Technology, Kaiyuan Avenue 263, Luoyang, People’s Republic of China, Email
| | - Dongping Luo
- The First Affiliated Hospital, Henan University of Science and Technology, Luoyang, People’s Republic of China
| | - Shengnan Li
- School of Medicine, Henan Polytechnic University, Jiaozuo, People’s Republic of China
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32
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Panchy N, Watanabe K, Takahashi M, Willems A, Hong T. Comparative single-cell transcriptomes of dose and time dependent epithelial–mesenchymal spectrums. NAR Genom Bioinform 2022; 4:lqac072. [PMID: 36159174 PMCID: PMC9492285 DOI: 10.1093/nargab/lqac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/17/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Epithelial–mesenchymal transition (EMT) is a cellular process involved in development and disease progression. Intermediate EMT states were observed in tumors and fibrotic tissues, but previous in vitro studies focused on time-dependent responses with single doses of signals; it was unclear whether single-cell transcriptomes support stable intermediates observed in diseases. Here, we performed single-cell RNA-sequencing with human mammary epithelial cells treated with multiple doses of TGF-β. We found that dose-dependent EMT harbors multiple intermediate states at nearly steady state. Comparisons of dose- and time-dependent EMT transcriptomes revealed that the dose-dependent data enable higher sensitivity to detect genes associated with EMT. We identified cell clusters unique to time-dependent EMT, reflecting cells en route to stable states. Combining dose- and time-dependent cell clusters gave rise to accurate prognosis for cancer patients. Our transcriptomic data and analyses uncover a stable EMT continuum at the single-cell resolution, and complementary information of two types of single-cell experiments.
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Affiliation(s)
- Nicholas Panchy
- Department of Biochemistry & Cellular and Molecular Biology. The University of Tennessee , Knoxville, Knoxville, TN 37996, USA
| | - Kazuhide Watanabe
- RIKEN Center for Integrative Medical Sciences , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Masataka Takahashi
- RIKEN Center for Integrative Medical Sciences , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Andrew Willems
- School of Genome Science and Technology, The University of Tennessee , Knoxville, Knoxville, TN 37916, USA
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology. The University of Tennessee , Knoxville, Knoxville, TN 37996, USA
- National Institute for Mathematical and Biological Synthesis , Knoxville, TN 37996, USA
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33
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Mullins R, Pal A, Barrett TF, Neal MEH, Puram SV. Epithelial-Mesenchymal Plasticity in Tumor Immune Evasion. Cancer Res 2022; 82:2329-2343. [PMID: 35363853 PMCID: PMC9256788 DOI: 10.1158/0008-5472.can-21-4370] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/05/2022] [Accepted: 03/29/2022] [Indexed: 01/07/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is a fundamental process that occurs during embryogenesis and tissue repair. However, EMT can be hijacked by malignant cells, where it may promote immune evasion and metastasis. Classically considered a dichotomous transition, EMT in cancer has recently been considered a plastic process whereby malignant cells display and interconvert among hybrid epithelial/mesenchymal (E/M) states. Epithelial-mesenchymal plasticity (EMP) and associated hybrid E/M states are divergent from classical EMT, with unique immunomodulatory effects. Here, we review recent insights into the EMP-immune cross-talk, highlighting possible mechanisms of immune evasion conferred by hybrid E/M states and roles of immune cells in EMP.
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Affiliation(s)
- Riley Mullins
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A
| | - Ananya Pal
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A
| | - Thomas F Barrett
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A
| | - Molly E Heft Neal
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A
| | - Sidharth V Puram
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, Missouri, U.S.A.,Corresponding author: Sidharth V. Puram, MD PhD, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8115, St. Louis, MO 63110, (314) 362-7509,
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Sirtuins and Hypoxia in EMT Control. Pharmaceuticals (Basel) 2022; 15:ph15060737. [PMID: 35745656 PMCID: PMC9228842 DOI: 10.3390/ph15060737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 05/25/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Epithelial–mesenchymal transition (EMT), a physiological process during embryogenesis, can become pathological in the presence of different driving forces. Reduced oxygen tension or hypoxia is one of these forces, triggering a large number of molecular pathways with aberrant EMT induction, resulting in cancer and fibrosis onset. Both hypoxia-induced factors, HIF-1α and HIF-2α, act as master transcription factors implicated in EMT. On the other hand, hypoxia-dependent HIF-independent EMT has also been described. Recently, a new class of seven proteins with deacylase activity, called sirtuins, have been implicated in the control of both hypoxia responses, HIF-1α and HIF-2α activation, as well as EMT induction. Intriguingly, different sirtuins have different effects on hypoxia and EMT, acting as either activators or inhibitors, depending on the tissue and cell type. Interestingly, sirtuins and HIF can be activated or inhibited with natural or synthetic molecules. Moreover, recent studies have shown that these natural or synthetic molecules can be better conveyed using nanoparticles, representing a valid strategy for EMT modulation. The following review, by detailing the aspects listed above, summarizes the interplay between hypoxia, sirtuins, and EMT, as well as the possible strategies to modulate them by using a nanoparticle-based approach.
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35
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Sundararajan V, Burk UC, Bajdak-Rusinek K. Revisiting the miR-200 Family: A Clan of Five Siblings with Essential Roles in Development and Disease. Biomolecules 2022; 12:biom12060781. [PMID: 35740906 PMCID: PMC9221129 DOI: 10.3390/biom12060781] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 12/07/2022] Open
Abstract
Over two decades of studies on small noncoding RNA molecules illustrate the significance of microRNAs (miRNAs/miRs) in controlling multiple physiological and pathological functions through post-transcriptional and spatiotemporal gene expression. Among the plethora of miRs that are essential during animal embryonic development, in this review, we elaborate the indispensable role of the miR-200 family (comprising miR-200a, -200b, 200c, -141, and -429) in governing the cellular functions associated with epithelial homeostasis, such as epithelial differentiation and neurogenesis. Additionally, in pathological contexts, miR-200 family members are primarily involved in tumor-suppressive roles, including the reversal of the cancer-associated epithelial–mesenchymal transition dedifferentiation process, and are dysregulated during organ fibrosis. Moreover, recent eminent studies have elucidated the crucial roles of miR-200s in the pathophysiology of multiple neurodegenerative diseases and tissue fibrosis. Lastly, we summarize the key studies that have recognized the potential use of miR-200 members as biomarkers for the diagnosis and prognosis of cancers, elaborating the application of these small biomolecules in aiding early cancer detection and intervention.
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Affiliation(s)
- Vignesh Sundararajan
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore 117599, Singapore;
| | - Ulrike C. Burk
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany;
| | - Karolina Bajdak-Rusinek
- Department of Medical Genetics, Faculty of Medical Sciences, Medical University of Silesia, 40-752 Katowice, Poland
- Correspondence: ; Tel.: +48-32-208-8382
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Lee MK, Brown MS, Wilkins OM, Pattabiraman DR, Christensen BC. Distinct cytosine modification profiles define epithelial-to-mesenchymal cell-state transitions. Epigenomics 2022; 14:519-535. [PMID: 35382559 PMCID: PMC9118069 DOI: 10.2217/epi-2022-0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Epithelial-to-mesenchymal transition (EMT) is an early step in the invasion-metastasis cascade, involving progression through intermediate cell states. Due to challenges with isolating intermediate cell states, genome-wide cytosine modifications that define transition are not completely understood. Methods: The authors measured multiple DNA cytosine modification marks and chromatin accessibility across clonal populations residing in specific EMT states. Results: Clones exhibiting more intermediate EMT phenotypes demonstrated increased 5-hydroxymethylcytosine and decreased 5-methylcytosine. Open chromatin regions containing increased 5-hydroxymethylcytosine CpG loci were enriched in EMT transcription factor motifs and were associated with Rho GTPases. Conclusion: The results indicate the importance of both distinct and shared epigenetic profiles associated with EMT processes that may be targeted to prevent EMT progression.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Meredith S Brown
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Owen M Wilkins
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Diwakar R Pattabiraman
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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37
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Cancer: More than a geneticist’s Pandora’s box. J Biosci 2022. [DOI: 10.1007/s12038-022-00254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Kong W, Fu YC, Holloway EM, Garipler G, Yang X, Mazzoni EO, Morris SA. Capybara: A computational tool to measure cell identity and fate transitions. Cell Stem Cell 2022; 29:635-649.e11. [PMID: 35354062 PMCID: PMC9040453 DOI: 10.1016/j.stem.2022.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/18/2022] [Accepted: 03/03/2022] [Indexed: 01/14/2023]
Abstract
Measuring cell identity in development, disease, and reprogramming is challenging as cell types and states are in continual transition. Here, we present Capybara, a computational tool to classify discrete cell identity and intermediate "hybrid" cell states, supporting a metric to quantify cell fate transition dynamics. We validate hybrid cells using experimental lineage tracing data to demonstrate the multi-lineage potential of these intermediate cell states. We apply Capybara to diagnose shortcomings in several cell engineering protocols, identifying hybrid states in cardiac reprogramming and off-target identities in motor neuron programming, which we alleviate by adding exogenous signaling factors. Further, we establish a putative in vivo correlate for induced endoderm progenitors. Together, these results showcase the utility of Capybara to dissect cell identity and fate transitions, prioritizing interventions to enhance the efficiency and fidelity of stem cell engineering.
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Affiliation(s)
- Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Yuheng C Fu
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Emily M Holloway
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | - Görkem Garipler
- Department of Biology, New York University, New York, NY 10003, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA
| | | | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, MO 63110, USA.
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39
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Nordick B, Yu PY, Liao G, Hong T. Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression. Nucleic Acids Res 2022; 50:3693-3708. [PMID: 35380686 PMCID: PMC9023291 DOI: 10.1093/nar/gkac217] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/13/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
Periodic gene expression dynamics are key to cell and organism physiology. Studies of oscillatory expression have focused on networks with intuitive regulatory negative feedback loops, leaving unknown whether other common biochemical reactions can produce oscillations. Oscillation and noise have been proposed to support mammalian progenitor cells’ capacity to restore heterogenous, multimodal expression from extreme subpopulations, but underlying networks and specific roles of noise remained elusive. We use mass-action-based models to show that regulated RNA degradation involving as few as two RNA species—applicable to nearly half of human protein-coding genes—can generate sustained oscillations without explicit feedback. Diverging oscillation periods synergize with noise to robustly restore cell populations’ bimodal expression on timescales of days. The global bifurcation organizing this divergence relies on an oscillator and bistable switch which cannot be decomposed into two structural modules. Our work reveals surprisingly rich dynamics of post-transcriptional reactions and a potentially widespread mechanism underlying development, tissue regeneration, and cancer cell heterogeneity.
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Affiliation(s)
- Benjamin Nordick
- School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee 37916, USA
| | - Polly Y Yu
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Guangyuan Liao
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37916, USA
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37916, USA.,National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee 37916, USA
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40
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Morin C, Moyret-Lalle C, Mertani HC, Diaz JJ, Marcel V. Heterogeneity and dynamic of EMT through the plasticity of ribosome and mRNA translation. Biochim Biophys Acta Rev Cancer 2022; 1877:188718. [PMID: 35304296 DOI: 10.1016/j.bbcan.2022.188718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/02/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
Growing evidence exposes translation and its translational machinery as key players in establishing and maintaining physiological and pathological biological processes. Examining translation may not only provide new biological insight but also identify novel innovative therapeutic targets in several fields of biology, including that of epithelial-to-mesenchymal transition (EMT). EMT is currently considered as a dynamic and reversible transdifferentiation process sustaining the transition from an epithelial to mesenchymal phenotype, known to be mainly driven by transcriptional reprogramming. However, it seems that the characterization of EMT plasticity is challenging, relying exclusively on transcriptomic and epigenetic approaches. Indeed, heterogeneity in EMT programs was reported to depend on the biological context. Here, by reviewing the involvement of translational control, translational machinery and ribosome biogenesis characterizing the different types of EMT, from embryonic and adult physiological to pathological contexts, we discuss the added value of integrating translational control and its machinery to depict the heterogeneity and dynamics of EMT programs.
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Affiliation(s)
- Chloé Morin
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Caroline Moyret-Lalle
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Hichem C Mertani
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France.
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41
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Transcriptional and post-transcriptional control of epithelial-mesenchymal plasticity: why so many regulators? Cell Mol Life Sci 2022; 79:182. [PMID: 35278142 PMCID: PMC8918127 DOI: 10.1007/s00018-022-04199-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 01/18/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022]
Abstract
The dynamic transition between epithelial-like and mesenchymal-like cell states has been a focus for extensive investigation for decades, reflective of the importance of Epithelial-Mesenchymal Transition (EMT) through development, in the adult, and the contributing role EMT has to pathologies including metastasis and fibrosis. Not surprisingly, regulation of the complex genetic networks that underlie EMT have been attributed to multiple transcription factors and microRNAs. What is surprising, however, are the sheer number of different regulators (hundreds of transcription factors and microRNAs) for which critical roles have been described. This review seeks not to collate these studies, but to provide a perspective on the fundamental question of whether it is really feasible that so many regulators play important roles and if so, what does this tell us about EMT and more generally, the genetic machinery that controls complex biological processes.
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Guan D, Zhou W, Wei H, Wang T, Zheng K, Yang C, Feng R, Xu R, Fu Y, Li C, Li Y, Li C. Ferritinophagy-Mediated Ferroptosis and Activation of Keap1/Nrf2/HO-1 Pathway Were Conducive to EMT Inhibition of Gastric Cancer Cells in Action of 2,2'-Di-pyridineketone Hydrazone Dithiocarbamate Butyric Acid Ester. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3920664. [PMID: 35237380 PMCID: PMC8885181 DOI: 10.1155/2022/3920664] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/31/2022] [Indexed: 01/02/2023]
Abstract
In metastasis of cancer cells, the epithelial-mesenchymal transition (EMT) is prerequired. Ferroptosis is an iron-mediated cellular death process, but whether it involves EMT regulation remains elusive. In addition, how stress responders (Nrf2) respond to the redox alteration and cross-talking between them needs to be determined. Our data revealed that DpdtbA (2,2'-di-pyridineketone hydrazone dithiocarbamate butyric acid ester) resisted TGF-β1-induced EMT in gastric cancer lines (SGC-7901 and MGC-823) through ferritinophagy-mediated ROS production. Furthermore, the depletion of Gpx4 and xCT as well as enhanced lipid peroxidation indicated that DpdtbA acted as Erastin did in ferroptosis induction, which thus provided chance to explore the causal relationship between ferroptosis and EMT. Our data illustrated that ferritinophagy-mediated ferroptosis promoted the EMT inhibition. In addition, activated Nrf2 involved the regulation on both ferroptosis and EMT in response to the alteration in the cellular redox environment. In brief, ferritinophagy-mediated ferroptosis and activation of the Keap1/Nrf2/HO-1 pathway were conducive to the EMT inhibition.
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Affiliation(s)
- Deng Guan
- College of Pharmacy, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
- College of Basic Medical Science, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
- College of Basic Medical Science, Xinxiang Medical University, Xinxiang, Henan, China 453003
| | - Wei Zhou
- College of Basic Medical Science, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Huiping Wei
- College of Basic Medical Science, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Ting Wang
- Experimental Teaching Center of Biology and Basic Medical Sciences, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Kangwei Zheng
- College of Pharmacy, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Chunjie Yang
- College of Pharmacy, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Rui Feng
- Experimental Teaching Center of Biology and Basic Medical Sciences, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Ruifang Xu
- Experimental Teaching Center of Biology and Basic Medical Sciences, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Yun Fu
- College of Basic Medical Science, Xinxiang Medical University, Xinxiang, Henan, China 453003
| | - Cuiping Li
- College of Basic Medical Science, Xinxiang Medical University, Xinxiang, Henan, China 453003
| | - Yongli Li
- College of Basic Medical Science, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Changzheng Li
- College of Pharmacy, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
- College of Basic Medical Science, Xinxiang Medical University, Xinxiang, Henan, China 453003
- Experimental Teaching Center of Biology and Basic Medical Sciences, Sanquan College of Xinxiang Medical University, Xinxiang, Henan, China
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Naitou Y, Nagamatsu G, Hamazaki N, Shirane K, Hayashi M, Hayashi M, Kobayashi S, Hayashi K. Dual role of Ovol2 on the germ cell lineage segregation during gastrulation in mouse embryogenesis. Development 2022; 149:274415. [DOI: 10.1242/dev.200319] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022]
Abstract
ABSTRACT
In mammals, primordial germ cells (PGCs), the origin of the germ line, are specified from the epiblast at the posterior region where gastrulation simultaneously occurs, yet the functional relationship between PGC specification and gastrulation remains unclear. Here, we show that OVOL2, a transcription factor conserved across the animal kingdom, balances these major developmental processes by repressing the epithelial-to-mesenchymal transition (EMT) that drives gastrulation and the upregulation of genes associated with PGC specification. Ovol2a, a splice variant encoding a repressor domain, directly regulates EMT-related genes and, consequently, induces re-acquisition of potential pluripotency during PGC specification, whereas Ovol2b, another splice variant missing the repressor domain, directly upregulates genes associated with PGC specification. Taken together, these results elucidate the molecular mechanism underlying allocation of the germ line among epiblast cells differentiating into somatic cells through gastrulation.
This article has an associated ‘The people behind the papers’ interview.
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Affiliation(s)
- Yuki Naitou
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Go Nagamatsu
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nobuhiko Hamazaki
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kenjiro Shirane
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masafumi Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Makoto Hayashi
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Satoru Kobayashi
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Germline Genetics, Graduate School of Medicine, Osaka University, Suita 565-0871, Osaka, Japan
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44
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Wang HY, Zhang XP, Wang W. Regulation of epithelial-to-mesenchymal transition in hypoxia by the HIF-1α network. FEBS Lett 2022; 596:338-349. [PMID: 34905218 DOI: 10.1002/1873-3468.14258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) plays a significant role in cancer metastasis. A series of models have focused on EMT regulation by TGF-β network. However, how EMT is regulated under hypoxia is less understood. We developed a model of HIF-1α network to explore the potential link between EMT and the network topology. Our results revealed that three positive feedback loops, composed of HIF-1α and its three targets SNAIL, TWIST, and miR-210, should be sequentially activated to induce EMT under aggravating hypoxia. We suggested that the number of the positive feedback loops is critical for determining the number of stable states in EMT. Our work may advance the understanding of the significance of network topology in the regulation of EMT.
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Affiliation(s)
- Hang-Yu Wang
- Kuang Yaming Honors School, Nanjing University, China
| | - Xiao-Peng Zhang
- Kuang Yaming Honors School, Nanjing University, China
- Institute for Brain Sciences, Nanjing University, China
| | - Wei Wang
- Institute for Brain Sciences, Nanjing University, China
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, China
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45
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Kisoda S, Mouri Y, Kitamura N, Yamamoto T, Miyoshi K, Kudo Y. The role of partial-EMT in the progression of head and neck squamous cell carcinoma. J Oral Biosci 2022; 64:176-182. [DOI: 10.1016/j.job.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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46
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Jia W, Jolly MK, Levine H. NRF2-dependent Epigenetic Regulation can Promote the Hybrid Epithelial/Mesenchymal Phenotype. Front Cell Dev Biol 2022; 9:828250. [PMID: 35118079 PMCID: PMC8803900 DOI: 10.3389/fcell.2021.828250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/28/2021] [Indexed: 11/17/2022] Open
Abstract
The epithelial-mesenchymal transition (EMT) is a cellular process critical for wound healing, cancer metastasis and embryonic development. Recent efforts have identified the role of hybrid epithelial/mesenchymal states, having both epithelial and mesehncymal traits, in enabling cancer metastasis and resistance to various therapies. Also, previous work has suggested that NRF2 can act as phenotypic stability factor to help stablize such hybrid states. Here, we incorporate a phenomenological epigenetic feedback effect into our previous computational model for EMT signaling. We show that this type of feedback can stabilize the hybrid state as compared to the fully mesenchymal phenotype if NRF2 can influence SNAIL at an epigenetic level, as this link makes transitions out of hybrid state more difficult. However, epigenetic regulation on other NRF2-related links do not significantly change the EMT dynamics. Finally, we considered possible cell division effects in our epigenetic regulation model, and our results indicate that the degree of epigenetic inheritance does not appear to be a critical factor for the hybrid E/M state stabilizing behavior of NRF2.
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Affiliation(s)
- Wen Jia
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, United States
- Department of Physics and Astronomy, Rice University, Houston, TX, United States
- Department of Physics, Northeastern University, Boston, MA, United States
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- *Correspondence: Mohit Kumar Jolly, ; Herbert Levine,
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, United States
- Department of Physics, Northeastern University, Boston, MA, United States
- Department of Bioengineering, Northeastern University, Boston, MA, United States
- *Correspondence: Mohit Kumar Jolly, ; Herbert Levine,
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47
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Han Y, Villarreal-Ponce A, Gutierrez G, Nguyen Q, Sun P, Wu T, Sui B, Berx G, Brabletz T, Kessenbrock K, Zeng YA, Watanabe K, Dai X. Coordinate control of basal epithelial cell fate and stem cell maintenance by core EMT transcription factor Zeb1. Cell Rep 2022; 38:110240. [PMID: 35021086 PMCID: PMC9894649 DOI: 10.1016/j.celrep.2021.110240] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/30/2021] [Accepted: 12/16/2021] [Indexed: 02/04/2023] Open
Abstract
Maintenance of undifferentiated, long-lived, and often quiescent stem cells in the basal compartment is important for homeostasis and regeneration of multiple epithelial tissues, but the molecular mechanisms that coordinately control basal cell fate and stem cell quiescence are elusive. Here, we report an epithelium-intrinsic requirement for Zeb1, a core transcriptional inducer of epithelial-to-mesenchymal transition, for mammary epithelial ductal side branching and for basal cell regenerative capacity. Our findings uncover an evolutionarily conserved role of Zeb1 in promoting basal cell fate over luminal differentiation. We show that Zeb1 loss results in increased basal cell proliferation at the expense of quiescence and self-renewal. Moreover, Zeb1 cooperates with YAP to activate Axin2 expression, and inhibition of Wnt signaling partially restores stem cell function to Zeb1-deficient basal cells. Thus, Zeb1 is a transcriptional regulator that maintains both basal cell fate and stem cell quiescence, and it functions in part through suppressing Wnt signaling.
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Affiliation(s)
- Yingying Han
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,These authors contributed equally
| | - Alvaro Villarreal-Ponce
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,These authors contributed equally
| | - Guadalupe Gutierrez
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Peng Sun
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Ting Wu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China
| | - Benjamin Sui
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Geert Berx
- Molecular and Cellular Oncology Lab, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium,Cancer Research Institute Ghent, Ghent, Belgium
| | - Thomas Brabletz
- Department of Experimental Medicine, Nikolaus-Fiebiger-Center for Molecular Medicine I, University, Erlangen-Nuernberg Glueckstr. 6, 91054 Erlangen, Germany
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA
| | - Yi Arial Zeng
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China
| | - Kazuhide Watanabe
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Xing Dai
- Department of Biological Chemistry, School of Medicine, D250 Med Sci I, University of California, Irvine, Irvine, CA 92697-1700, USA,Lead contact,Correspondence:
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48
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Sahoo S, Ashraf B, Duddu AS, Biddle A, Jolly MK. Interconnected high-dimensional landscapes of epithelial-mesenchymal plasticity and stemness in cancer. Clin Exp Metastasis 2022; 39:279-290. [PMID: 34993766 DOI: 10.1007/s10585-021-10139-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023]
Abstract
Establishing macrometastases at distant organs is a highly challenging process for cancer cells, with extremely high attrition rates. A very small percentage of disseminated cells have the ability to dynamically adapt to their changing micro-environments through reversibly switching to another phenotype, aiding metastasis. Such plasticity can be exhibited along one or more axes-epithelial-mesenchymal plasticity (EMP) and cancer stem cells (CSCs) being the two most studied, and often tacitly assumed to be synonymous. Here, we review the emerging concepts related to EMP and CSCs across multiple cancers. Both processes are multi-dimensional in nature; for instance, EMP can be defined on morphological, molecular and functional changes, which may or may not be synchronized. Similarly, self-renewal, multi-lineage potential, and resistance to anoikis and/or therapy may not all occur simultaneously in CSCs. Thus, understanding the complexity in defining EMP and CSCs is essential if we are to understand their contribution to cancer metastasis. This will require a more comprehensive understanding of the non-linearity of these processes. These processes are dynamic, reversible, and semi-independent in nature; cells traverse the inter-connected high-dimensional EMP and CSC landscapes in diverse paths, each of which may exhibit a distinct EMP-CSC coupling. Our proposed model offers a potential unifying framework for elucidating the coupled decision-making along these dimensions and highlights a key set of open questions to be answered.
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Affiliation(s)
- Sarthak Sahoo
- Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore, 560012, India.,UG Programme, Indian Institute of Science, Bangalore, 560012, India
| | - Bazella Ashraf
- Department of Biotechnology, Central University of Kashmir, Ganderbal, India
| | - Atchuta Srinivas Duddu
- Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore, 560012, India
| | - Adrian Biddle
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore, 560012, India.
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49
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Sahoo S, Nayak SP, Hari K, Purkait P, Mandal S, Kishore A, Levine H, Jolly MK. Immunosuppressive Traits of the Hybrid Epithelial/Mesenchymal Phenotype. Front Immunol 2022; 12:797261. [PMID: 34975907 PMCID: PMC8714906 DOI: 10.3389/fimmu.2021.797261] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
Recent preclinical and clinical data suggests enhanced metastatic fitness of hybrid epithelial/mesenchymal (E/M) phenotypes, but mechanistic details regarding their survival strategies during metastasis remain unclear. Here, we investigate immune-evasive strategies of hybrid E/M states. We construct and simulate the dynamics of a minimalistic regulatory network encompassing the known associations among regulators of EMT (epithelial-mesenchymal transition) and PD-L1, an established immune-suppressor. Our simulations for the network consisting of SLUG, ZEB1, miR-200, CDH1 and PD-L1, integrated with single-cell and bulk RNA-seq data analysis, elucidate that hybrid E/M cells can have high levels of PD-L1, similar to those seen in cells with a full EMT phenotype, thus obviating the need for cancer cells to undergo a full EMT to be immune-evasive. Specifically, in breast cancer, we show the co-existence of hybrid E/M phenotypes, enhanced resistance to anti-estrogen therapy and increased PD-L1 levels. Our results underscore how the emergent dynamics of interconnected regulatory networks can coordinate different axes of cellular fitness during metastasis.
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Affiliation(s)
- Sarthak Sahoo
- Undergraduate Program, Indian Institute of Science, Bangalore, India.,Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | | | - Kishore Hari
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Prithu Purkait
- Undergraduate Program, Indian Institute of Science, Bangalore, India
| | - Susmita Mandal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Akash Kishore
- Department of Computer Science & Engineering, Sri Sivasubramaniya Nadar (SSN) College of Engineering, Chennai, India
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, United States.,Departments of Physics and Bioengineering, Northeastern University, Boston, MA, United States
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
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50
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Lang J, Li C. Unraveling the stochastic transition mechanism between oscillation states by landscape and minimum action path theory. Phys Chem Chem Phys 2022; 24:20050-20063. [DOI: 10.1039/d2cp01385a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cell fate transitions have been studied from various perspectives, such as the transition between stable states, or the transition between stable states and oscillation states. However, there is a lack...
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