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Seraj H, Nazari MA, Atai AA, Amanpour S, Azadi M. A Review: Biomechanical Aspects of the Fallopian Tube Relevant to its Function in Fertility. Reprod Sci 2024; 31:1456-1485. [PMID: 38472710 DOI: 10.1007/s43032-024-01479-x] [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: 12/06/2023] [Accepted: 02/07/2024] [Indexed: 03/14/2024]
Abstract
The fallopian tube (FT) plays a crucial role in the reproductive process by providing an ideal biomechanical and biochemical environment for fertilization and early embryo development. Despite its importance, the biomechanical functions of the FT that originate from its morphological aspects, and ultrastructural aspects, as well as the mechanical properties of FT, have not been studied nor used sufficiently, which limits the understanding of fertilization, mechanotrasduction, and mechanobiology during embryo development, as well as the replication of the FT in laboratory settings for infertility treatments. This paper reviews and revives valuable information on human FT reported in medical literature in the past five decades relevant to the biomechanical aspects of FT. In this review, we summarized the current state of knowledge concerning the morphological, ultrastructural aspects, and mechanical properties of the human FT. We also investigate the potential arising from a thorough consideration of the biomechanical functions and exploring often neglected mechanical aspects. Our investigation encompasses both macroscopic measurements (such as length, diameter, and thickness) and microscopic measurements (including the height of epithelial cells, the percentage of ciliated cells, cilia structure, and ciliary beat frequency). Our primary focus has been on healthy women of reproductive age. We have examined various measurement techniques, encompassing conventional metrology, 2D histological data as well as new spatial measurement techniques such as micro-CT.
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Affiliation(s)
- Hasan Seraj
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Mohammad Ali Nazari
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran.
- Department of Speech and Cognition, CNRS UMR 5216, Grenoble Institute of Technology, Grenoble, France.
| | - Ali Asghar Atai
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Saeid Amanpour
- Vali-E-Asr Reproductive Health Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Cancer Biology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojtaba Azadi
- School of Engineering, College of Science and Engineering, San Francisco State University, San Francisco, CA, USA.
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Atiya HI, Gorecki G, Garcia GL, Frisbie LG, Baruwal R, Coffman L. Stromal-Modulated Epithelial-to-Mesenchymal Transition in Cancer Cells. Biomolecules 2023; 13:1604. [PMID: 38002286 PMCID: PMC10669774 DOI: 10.3390/biom13111604] [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: 09/21/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
The ability of cancer cells to detach from the primary site and metastasize is the main cause of cancer- related death among all cancer types. Epithelial-to-mesenchymal transition (EMT) is the first event of the metastatic cascade, resulting in the loss of cell-cell adhesion and the acquisition of motile and stem-like phenotypes. A critical modulator of EMT in cancer cells is the stromal tumor microenvironment (TME), which can promote the acquisition of a mesenchymal phenotype through direct interaction with cancer cells or changes to the broader microenvironment. In this review, we will explore the role of stromal cells in modulating cancer cell EMT, with particular emphasis on the function of mesenchymal stromal/stem cells (MSCs) through the activation of EMT-inducing pathways, extra cellular matrix (ECM) remodeling, immune cell alteration, and metabolic rewiring.
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Affiliation(s)
- Huda I. Atiya
- Division of Hematology/Oncology, Department of Medicine, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Grace Gorecki
- Division of Hematology/Oncology, Department of Medicine, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Geyon L. Garcia
- Medical Scientist Training Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Leonard G. Frisbie
- Department of Integrative Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Roja Baruwal
- Molecular Pharmacology Graduate Program, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lan Coffman
- Division of Hematology/Oncology, Department of Medicine, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee Women’s Research Institute, Pittsburgh, PA15213, USA
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Petrov PB, Considine JM, Izzi V, Naba A. Matrisome AnalyzeR - a suite of tools to annotate and quantify ECM molecules in big datasets across organisms. J Cell Sci 2023; 136:jcs261255. [PMID: 37555624 PMCID: PMC10499032 DOI: 10.1242/jcs.261255] [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: 04/18/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
The extracellular matrix (ECM) is a complex meshwork of proteins that forms the scaffold of all tissues in multicellular organisms. It plays crucial roles in all aspects of life - from orchestrating cell migration during development, to supporting tissue repair. It also plays critical roles in the etiology or progression of diseases. To study this compartment, we have previously defined the compendium of all genes encoding ECM and ECM-associated proteins for multiple organisms. We termed this compendium the 'matrisome' and further classified matrisome components into different structural or functional categories. This nomenclature is now largely adopted by the research community to annotate '-omics' datasets and has contributed to advance both fundamental and translational ECM research. Here, we report the development of Matrisome AnalyzeR, a suite of tools including a web-based application and an R package. The web application can be used by anyone interested in annotating, classifying and tabulating matrisome molecules in large datasets without requiring programming knowledge. The companion R package is available to more experienced users, interested in processing larger datasets or in additional data visualization options.
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Affiliation(s)
- Petar B. Petrov
- Infotech Institute, University of Oulu, FI-90014 Oulu, Finland
| | - James M. Considine
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine & Faculty of Medicine, BioIM Unit, University of Oulu, FI-90014 Oulu, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, Fl-00290 Helsinki, Finland
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
- University of Illinois Cancer Center, Chicago, IL 60612, USA
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Petrov PB, Considine JM, Izzi V, Naba A. Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537378. [PMID: 37131773 PMCID: PMC10153148 DOI: 10.1101/2023.04.18.537378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The extracellular matrix (ECM) is a complex meshwork of proteins that forms the scaffold of all tissues in multicellular organisms. It plays critical roles in all aspects of life: from orchestrating cell migration during development, to supporting tissue repair. It also plays critical roles in the etiology or progression of diseases. To study this compartment, we defined the compendium of all genes encoding ECM and ECM-associated proteins for multiple organisms. We termed this compendium the "matrisome" and further classified matrisome components into different structural or functional categories. This nomenclature is now largely adopted by the research community to annotate -omics datasets and has contributed to advance both fundamental and translational ECM research. Here, we report the development of Matrisome AnalyzeR, a suite of tools including a web-based application ( https://sites.google.com/uic.edu/matrisome/tools/matrisome-analyzer ) and an R package ( https://github.com/Matrisome/MatrisomeAnalyzeR ). The web application can be used by anyone interested in annotating, classifying, and tabulating matrisome molecules in large datasets without requiring programming knowledge. The companion R package is available to more experienced users, interested in processing larger datasets or in additional data visualization options. SUMMARY STATEMENT Matrisome AnalyzeR is a suite of tools, including a web-based app and an R package, designed to facilitate the annotation and quantification of extracellular matrix components in big datasets.
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Affiliation(s)
- Petar B. Petrov
- Infotech Institute, University of Oulu, FI-90014 Oulu, Finland
| | - James M. Considine
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine & Faculty of Medicine, BioIM Unit, University of Oulu, FI-90014 Oulu, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, Helsinki, Finland
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA
- University of Illinois Cancer Center, Chicago, IL 60612, USA
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Shao X, Gomez CD, Kapoor N, Considine JM, Grams C, Gao Y(T, Naba A. MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. Nucleic Acids Res 2022; 51:D1519-D1530. [PMID: 36399478 PMCID: PMC9825471 DOI: 10.1093/nar/gkac1009] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that constitutes the scaffold organizing cells, tissues, and organs. Over the past decade, mass-spectrometry-based proteomics has become the method of choice to profile the composition of the ECM, or the matrisome, of tissues. To assist non-specialists with the reuse of ECM proteomic datasets, we released MatrisomeDB (https://matrisomedb.org) in 2020. Here, we report the expansion of the database to include 25 new curated studies on the ECM of 24 new tissues in addition to datasets on tissues previously included, more than doubling the size of the original database and achieving near-complete coverage of the in-silico predicted matrisome. We further enhanced data visualization by maps of peptides and post-translational-modifications detected onto domain-based representations and 3D structures of ECM proteins. We also referenced external resources to facilitate the design of targeted mass spectrometry assays. Last, we implemented an abstract-mining tool that generates an enrichment word cloud from abstracts of studies in which a queried protein is found with higher confidence and higher abundance relative to other studies in MatrisomeDB.
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Affiliation(s)
- Xinhao Shao
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Clarissa D Gomez
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Nandini Kapoor
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - James M Considine
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Christopher Grams
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Yu (Tom) Gao
- Correspondence may also be addressed to Dr. Yu (Tom) Gao. Tel: +1 312 996 8087;
| | - Alexandra Naba
- To whom correspondence should be addressed. Tel: +1 312 355 5417;
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Feng S, Xu Y, Dai Z, Yin H, Zhang K, Shen Y. Integrative Analysis From Multicenter Studies Identifies a WGCNA-Derived Cancer-Associated Fibroblast Signature for Ovarian Cancer. Front Immunol 2022; 13:951582. [PMID: 35874760 PMCID: PMC9304893 DOI: 10.3389/fimmu.2022.951582] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/06/2022] [Indexed: 01/23/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs) are a major contributor to tumor stromal crosstalk in the tumor microenvironment (TME) and boost tumor progression by promoting angiogenesis and lymphangiogenesis. This study aimed to identify prognostic genes associated with CAFs that lead to high morbidity and mortality in ovarian cancer (OC) patients. We performed bioinformatics analysis in 16 multicenter studies (2,742 patients) and identified CAF-associated hub genes using the weighted gene co-expression network analysis (WGCNA). A machine learning methodology was used to identify COL16A1, COL5A2, GREM1, LUM, SRPX, and TIMP3 and construct a prognostic signature. Subsequently, a series of bioinformatics algorithms indicated risk stratification based on the above signature, suggesting that high-risk patients have a worse prognosis, weaker immune response, and lower tumor mutational burden (TMB) status but may be more sensitive to routine chemotherapeutic agents. Finally, we characterized prognostic markers using cell lines, immunohistochemistry, and single-cell sequencing. In conclusion, these results suggest that the CAF-related signature may be a novel pretreatment guide for anti-CAFs, and prognostic markers in CAFs may be potential therapeutic targets to inhibit OC progression.
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Affiliation(s)
- Songwei Feng
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Yi Xu
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Zhu Dai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Han Yin
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Ke Zhang
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Yang Shen
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
- *Correspondence: Yang Shen,
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