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Tavakoli S, Evans A, Oommen OP, Creemers L, Nandi JB, Hilborn J, Varghese OP. Unveiling extracellular matrix assembly: Insights and approaches through bioorthogonal chemistry. Mater Today Bio 2023; 22:100768. [PMID: 37600348 PMCID: PMC10432810 DOI: 10.1016/j.mtbio.2023.100768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023] Open
Abstract
Visualizing cells, tissues, and their components specifically without interference with cellular functions, such as biochemical reactions, and cellular viability remains important for biomedical researchers worldwide. For an improved understanding of disease progression, tissue formation during development, and tissue regeneration, labeling extracellular matrix (ECM) components secreted by cells persists is required. Bioorthogonal chemistry approaches offer solutions to visualizing and labeling ECM constituents without interfering with other chemical or biological events. Although biorthogonal chemistry has been studied extensively for several applications, this review summarizes the recent advancements in using biorthogonal chemistry specifically for metabolic labeling and visualization of ECM proteins and glycosaminoglycans that are secreted by cells and living tissues. Challenges, limitations, and future directions surrounding biorthogonal chemistry involved in the labeling of ECM components are discussed. Finally, potential solutions for improvements to biorthogonal chemical approaches are suggested. This would provide theoretical guidance for labeling and visualization of de novo proteins and polysaccharides present in ECM that are cell-secreted for example during tissue remodeling or in vitro differentiation of stem cells.
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Affiliation(s)
- Shima Tavakoli
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Austin Evans
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Oommen P. Oommen
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Laura Creemers
- Department of Orthopedics, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Jharna Barman Nandi
- Department of Chemistry, Sarojini Naidu College for Women, 30 Jessore Road, Kolkata, 700028, India
| | - Jöns Hilborn
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Oommen P. Varghese
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
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Singh G, Satpathi S, Gopala Reddy BV, Singh MK, Sarangi S, Behera PK, Nayak B. Impact of various detergent-based immersion and perfusion decellularization strategies on the novel caprine pancreas derived extracellular matrix scaffold. Front Bioeng Biotechnol 2023; 11:1253804. [PMID: 37790257 PMCID: PMC10544968 DOI: 10.3389/fbioe.2023.1253804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/05/2023] [Indexed: 10/05/2023] Open
Abstract
Limited availability of the organs donors has facilitated the establishment of xenogeneic organ sources for transplantation. Numerous studies have decellularized several organs and assessed their implantability in order to provide such organs. Among all the decellularized organs studies for xenotransplantation, the pancreas has garnered very limited amount of research. The presently offered alternatives for pancreas transplantation are unable to liberate patients from donor dependence. The rat and mice pancreas are not of an accurate size for transplantation but can only be used for in-vitro studies mimicking in-vivo immune response in humans, while the porcine pancreas can cause zoonotic diseases as it carries porcine endogenous retrovirus (PERV- A/B/C). Therefore, we propose caprine pancreas as a substitute for these organs, which not only reduces donor dependence but also poses no risk of zoonosis. Upon decellularization the extracellular matrix (ECM) of different tissues responds differently to the detergents used for decellularization at physical and physiological level; this necessitates a comprehensive analysis of each tissue independently. This study investigates the impact of decellularization by ionic (SDS and SDC), non-ionic (Triton X-100 and Tween-20), and zwitterionic detergents (CHAPS). All these five detergents have been used to decellularize caprine pancreas via immersion (ID) and perfusion (PD) set-up. In this study, an extensive comparison of these two configurations (ID and PD) with regard to each detergent has been conducted. The final obtained scaffold with each set-up has been evaluated for the left-over cytosolic content, ECM components like sGAG, collagen, and fibronectin were estimated via Prussian blue and Immunohistochemical staining respectively, and finally for the tensile strength and antimicrobial activity. All the detergents performed consistently superior in PD than in ID. Conclusively, PD with SDS, SDC, and TX-100 successfully decellularizes caprine pancreatic tissue while retaining ECM architecture and mechanical properties. This research demonstrates the viability of caprine pancreatic tissue as a substitute scaffold for porcine organs and provides optimal decellularization protocol for this xenogeneic tissue. This research aims to establish a foundation for further investigations into potential regenerative strategies using this ECM in combination with other factors.
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Affiliation(s)
- Garima Singh
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, India
| | | | - Bora Venu Gopala Reddy
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Manish Kumar Singh
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Samchita Sarangi
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, India
| | | | - Bismita Nayak
- Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology, Rourkela, India
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Titmarsh HF, von Kriegsheim A, Wills JC, O’Connor RA, Dhaliwal K, Frame MC, Pattle SB, Dorward DA, Byron A, Akram AR. Quantitative proteomics identifies tumour matrisome signatures in patients with non-small cell lung cancer. Front Oncol 2023; 13:1194515. [PMID: 37397358 PMCID: PMC10313119 DOI: 10.3389/fonc.2023.1194515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The composition and remodelling of the extracellular matrix (ECM) are important factors in the development and progression of cancers, and the ECM is implicated in promoting tumour growth and restricting anti-tumour therapies through multiple mechanisms. The characterisation of differences in ECM composition between normal and diseased tissues may aid in identifying novel diagnostic markers, prognostic indicators and therapeutic targets for drug development. Methods Using tissue from non-small cell lung cancer (NSCLC) patients undergoing curative intent surgery, we characterised quantitative tumour-specific ECM proteome signatures by mass spectrometry. Results We identified 161 matrisome proteins differentially regulated between tumour tissue and nearby non-malignant lung tissue, and we defined a collagen hydroxylation functional protein network that is enriched in the lung tumour microenvironment. We validated two novel putative extracellular markers of NSCLC, the collagen cross-linking enzyme peroxidasin and a disintegrin and metalloproteinase with thrombospondin motifs 16 (ADAMTS16), for discrimination of malignant and non-malignant lung tissue. These proteins were up-regulated in lung tumour samples, and high PXDN and ADAMTS16 gene expression was associated with shorter survival of lung adenocarcinoma and squamous cell carcinoma patients, respectively. Discussion These data chart extensive remodelling of the lung extracellular niche and reveal tumour matrisome signatures in human NSCLC.
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Affiliation(s)
- Helen F. Titmarsh
- The EPSRC and MRC Centre for Doctoral Training in Optical Medical Imaging, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh Bioquarter, Edinburgh, United Kingdom
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh Bioquarter, Edinburgh, United Kingdom
| | - Alex von Kriegsheim
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Jimi C. Wills
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Richard A. O’Connor
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh Bioquarter, Edinburgh, United Kingdom
| | - Kevin Dhaliwal
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh Bioquarter, Edinburgh, United Kingdom
| | - Margaret C. Frame
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel B. Pattle
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - David A. Dorward
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh Bioquarter, Edinburgh, United Kingdom
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Adam Byron
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Ahsan R. Akram
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh Bioquarter, Edinburgh, United Kingdom
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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Staab-Weijnitz CA, Onursal C, Nambiar D, Vanacore R. Assessment of Collagen in Translational Models of Lung Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1413:213-244. [PMID: 37195533 DOI: 10.1007/978-3-031-26625-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The extracellular matrix (ECM) plays an important role in lung health and disease. Collagen is the main component of the lung ECM, widely used for the establishment of in vitro and organotypic models of lung disease, and as scaffold material of general interest for the field of lung bioengineering. Collagen also is the main readout for fibrotic lung disease, where collagen composition and molecular properties are drastically changed and ultimately result in dysfunctional "scarred" tissue. Because of the central role of collagen in lung disease, quantification, determination of molecular properties, and three-dimensional visualization of collagen is important for both development and characterization of translational models of lung research. In this chapter, we provide a comprehensive overview on the various methodologies currently available for quantification and characterization of collagen including their detection principles, advantages, and disadvantages.
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Affiliation(s)
- Claudia A Staab-Weijnitz
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Member of the German Center for Lung Research (DZL), Ludwig-Maximilians-Universität and Helmholtz Zentrum München, Munich, Germany.
| | - Ceylan Onursal
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Member of the German Center for Lung Research (DZL), Ludwig-Maximilians-Universität and Helmholtz Zentrum München, Munich, Germany
| | - Deepika Nambiar
- Center for Matrix Biology, Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Roberto Vanacore
- Center for Matrix Biology, Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.
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Reuten R, Mayorca-Guiliani AE, Erler JT. Matritecture: Mapping the extracellular matrix architecture during health and disease. Matrix Biol Plus 2022; 14:100102. [PMID: 35243299 PMCID: PMC8861423 DOI: 10.1016/j.mbplus.2022.100102] [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: 10/03/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
Abstract
All cells in multicellular organisms are housed in the extracellular matrix (ECM), an acellular edifice built up by more than a thousand proteins and glycans. Cells engage in a reciprocal relationship with the ECM; they build, inhabit, maintain, and remodel the ECM, while, in turn, the ECM regulates their behavior. The homeostatic balance of cell-ECM interactions can be lost, due to ageing, irritants or diseases, which results in aberrant cell behavior. The ECM can suppress or promote disease progression, depending on the information relayed to cells. Instructions come in the form of biochemical (e.g., composition), biophysical (e.g., stiffness), and topographical (e.g., structure) cues. While advances have been made in many areas, we only have a very limited grasp of ECM topography. A detailed atlas deciphering the spatiotemporal arrangement of all ECM proteins is lacking. We feel that such an extracellular matrix architecture (matritecture) atlas should be a priority goal for ECM research. In this commentary, we will discuss the need to resolve the spatiotemporal matritecture to identify potential disease triggers and therapeutic targets and present strategies to address this goal. Such a detailed matritecture atlas will not only identify disease-specific ECM structures but may also guide future strategies to restructure disease-related ECM patterns reverting to a normal pattern.
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Abstract
Evidence from genetic studies in human and mice indicates that defective skeletal development is one of the major phenotypic outcomes for aberrant UPR signaling. Visualization of morphological alterations in whole-mount skeleton and protein secretion and UPR activation on tissue sections is the very first step to investigate skeletal phenotypes of UPR-related mouse models. In this chapter, we introduce the major techniques that have been frequently used in our laboratory to study UPR-induced skeletal disorders with genetically modified mice and provide descriptive directions of mouse genotyping, bone tissue grossing, whole-mount skeletal staining, immunostaining assays of matrix secretion, and UPR activation.
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Affiliation(s)
- Chao Zheng
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Cheng Wang
- School of Biomedical Sciences, University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Qiang Jie
- Department of Orthopedic Surgery, HongHui Hospital, Xi'an Jiaotong University, College of Medicine, Xi'an, China.
| | - Liu Yang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.
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Rickelt S, Neyaz A, Condon C, Whittaker CA, Zaidi AH, Taylor MS, Abbruzzese G, Mattia AR, Zukerberg L, Shroff SG, Yilmaz OH, Yılmaz O, Wu EY, Choi WT, Jobe BA, Odze RD, Patil DT, Deshpande V, Hynes RO. Agrin loss in Barrett's esophagus-related neoplasia and its utility as a diagnostic and predictive biomarker. Clin Cancer Res 2021; 28:1167-1179. [PMID: 34785582 DOI: 10.1158/1078-0432.ccr-21-2822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/29/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE There is an unmet need for identifying novel biomarkers in Barrett's esophagus (BE) that could stratify patients with regards to neoplastic progression. We investigate the expression patterns of extracellular matrix (ECM) molecules in BE and BE-related neoplasia, and assess their value as biomarkers for the diagnosis of BE-related neoplasia and to predict neoplastic progression. EXPERIMENTAL DESIGN Gene expression analyses of ECM matrisome gene sets were performed using publicly available data on human BE, BE-related dysplasia, esophageal ADCA and normal esophagus. Immunohistochemical expression of basement membrane (BM) marker agrin (AGRN) and p53 was analyzed in biopsies of BE-related neoplasia from 321 patients in three independent cohorts. RESULTS Differential gene expression analysis revealed significant enrichment of ECM matrisome gene sets in dysplastic BE and ADCA compared with controls. Loss of BM AGRN expression was observed in both BE-related dysplasia and ADCA. The mean AGRN loss in BE glands was significantly higher in BErelated dysplasia and ADCA compared to non-dysplastic BE (NDBE; p<0.001; specificity=82.2% and sensitivity=96.4%). Loss of AGRN was significantly higher in NDBE samples from progressors compared to non-progressors (p<0.001) and identified patients who progressed to advanced neoplasia with a specificity of 80.2% and sensitivity of 54.8%. Moreover, the combination of AGRN loss and abnormal p53 staining identified progression to BE-related advanced neoplasia with a specificity and sensitivity of 86.5% and 58.7%. CONCLUSIONS We highlight ECM changes during BE progression to neoplasia. BM AGRN loss is a novel diagnostic biomarker that can identify NDBE patients at increased risk of developing advanced neoplasia.
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Affiliation(s)
- Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | - Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital
| | - Charlene Condon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | - Charles A Whittaker
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | - Ali H Zaidi
- Esophageal and Lung Institute, Allegheny Health Network
| | | | - Genevieve Abbruzzese
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
| | | | | | | | - Omer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology
| | - Osman Yılmaz
- Pathology & Laboratory Medicine, Boston University School of Medicine
| | | | - Won-Tak Choi
- Department of Pathology, University of California, San Francisco
| | | | | | - Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School
| | - Richard O Hynes
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
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Sharma A, Sah N, Kannan S, Kannan RM. Targeted drug delivery for maternal and perinatal health: Challenges and opportunities. Adv Drug Deliv Rev 2021; 177:113950. [PMID: 34454979 PMCID: PMC8544131 DOI: 10.1016/j.addr.2021.113950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/06/2021] [Accepted: 08/24/2021] [Indexed: 12/18/2022]
Abstract
Pre-existing conditions at reproductive age, and complications arising during pregnancy can be detrimental to maternal and fetal health. Current therapies to combat obstetric disorders are limited due to the inherent complexity of pregnancy, and can have harmful effects on developing fetus. Emerging research shows intricate signaling between the cells from mother and fetus at maternal-fetal interface, providing unique opportunities for interventions specifically targeted to the mother, fetus, or placenta. Advancements in nanotechnology, stem-cell biology and gene therapy have resulted in target-specific treatments with promising results in pre-clinical maternal and fetal disorder models. Comprehensive understanding of the effect of physicochemical properties of delivery systems on their uptake, retention and accumulation across placenta will help in the better diagnosis and treatment of perinatal disorders. This review describes the factors leading to obstetric complications along with their effect on pregnancy outcomes, and discusses key targeted therapeutic strategies for addressing conditions related to maternal and fetal health.
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Affiliation(s)
- Anjali Sharma
- Center for Nanomedicine, Department of Ophthalmology, Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Nirnath Sah
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sujatha Kannan
- Center for Nanomedicine, Department of Ophthalmology, Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Hugo W. Moser Research Institute at Kennedy Krieger, Inc., Baltimore MD, 21205, USA
| | - Rangaramanujam M Kannan
- Center for Nanomedicine, Department of Ophthalmology, Wilmer Eye Institute Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Hugo W. Moser Research Institute at Kennedy Krieger, Inc., Baltimore MD, 21205, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore MD, 21218, USA.
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Ibrahim AM, Bilsland A, Rickelt S, Morris JS, Stein T. A matrisome RNA signature from early-pregnancy mouse mammary fibroblasts predicts distant metastasis-free breast cancer survival in humans. Breast Cancer Res 2021; 23:90. [PMID: 34565423 PMCID: PMC8474794 DOI: 10.1186/s13058-021-01470-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/14/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND During pregnancy, the mouse mammary ductal epithelium branches and grows into the surrounding stroma, requiring extensive extracellular matrix (ECM) and tissue remodelling. It therefore shows parallels to cancer invasion. We hypothesised that similar molecular mechanisms may be utilised in both processes, and that assessment of the stromal changes during pregnancy-associated branching may depict the stromal involvement during human breast cancer progression. METHODS Immunohistochemistry (IHC) was employed to assess the alterations within the mouse mammary gland extracellular matrix during early pregnancy when lateral branching of the primary ductal epithelium is initiated. Primary mouse mammary fibroblasts from three-day pregnant and age-matched non-pregnant control mice, respectively, were 3D co-cultured with mammary epithelial cells to assess differences in their abilities to induce branching morphogenesis in vitro. Transcriptome analysis was performed to identify the underlying molecular changes. A signature of the human orthologues of the differentially expressed matrisome RNAs was analysed by Kaplan-Meier and multi-variate analysis in two large breast cancer RNA datasets (Gene expression-based Outcome for Breast cancer Online (GOBO) und Kaplan-Meier Plotter), respectively, to test for similarities in expression between early-pregnancy mouse mammary gland development and breast cancer progression. RESULTS The ECM surrounding the primary ductal network showed significant differences in collagen and basement membrane protein distribution early during pregnancy. Pregnancy-associated fibroblasts (PAFs) significantly enhanced branching initiation compared to age-matched control fibroblast. A combined signature of 64 differentially expressed RNAs, encoding matrisome proteins, was a strong prognostic indicator of distant metastasis-free survival (DMFS) independent of other clinical parameters. The prognostic power could be significantly strengthened by using only a subset of 18 RNAs (LogRank P ≤ 1.00e-13; Hazard ratio (HR) = 2.42 (1.8-3.26); p = 5.61e-09). The prognostic power was confirmed in a second breast cancer dataset, as well as in datasets from ovarian and lung cancer patients. CONCLUSIONS Our results describe for the first time the early stromal changes that accompany pregnancy-associated branching morphogenesis in mice, specify the early pregnancy-associated molecular alterations in mouse mammary fibroblasts, and identify a matrisome signature as a strong prognostic indicator of human breast cancer progression, with particular strength in oestrogen receptor (ER)-negative breast cancers.
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Affiliation(s)
- Ayman M Ibrahim
- Institute of Cancer Sciences, College of MVLS, University of Glasgow, Glasgow, G12 8QQ, UK.,Zoology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt.,Aswan Heart Centre, Aswan, 200, Egypt
| | - Alan Bilsland
- Glasgow Experimental Cancer Medicines Centre, Institute of Cancer Science, College of MVLS, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Joanna S Morris
- School of Veterinary Medicine, College of MVLS, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK
| | - Torsten Stein
- Institute of Cancer Sciences, College of MVLS, University of Glasgow, Glasgow, G12 8QQ, UK. .,School of Medicine, College of MVLS, University of Glasgow, Glasgow, G12 8QQ, UK. .,Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg 19b, 14163, Berlin, Germany.
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10
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Tian C, Huang Y, Clauser KR, Rickelt S, Lau AN, Carr SA, Vander Heiden MG, Hynes RO. Suppression of pancreatic ductal adenocarcinoma growth and metastasis by fibrillar collagens produced selectively by tumor cells. Nat Commun 2021; 12:2328. [PMID: 33879793 PMCID: PMC8058088 DOI: 10.1038/s41467-021-22490-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 03/16/2021] [Indexed: 12/21/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a collagen-rich dense extracellular matrix (ECM) that promotes malignancy of cancer cells and presents a barrier for drug delivery. Data analysis of our published mass spectrometry (MS)-based studies on enriched ECM from samples of progressive PDAC stages reveal that the C-terminal prodomains of fibrillar collagens are partially uncleaved in PDAC ECM, suggesting reduced procollagen C-proteinase activity. We further show that the enzyme responsible for procollagen C-proteinase activity, bone morphogenetic protein1 (BMP1), selectively suppresses tumor growth and metastasis in cells expressing high levels of COL1A1. Although BMP1, as a secreted proteinase, promotes fibrillar collagen deposition from both cancer cells and stromal cells, only cancer-cell-derived procollagen cleavage and deposition suppresses tumor malignancy. These studies reveal a role for cancer-cell-derived fibrillar collagen in selectively restraining tumor growth and suggest stratification of patients based on their tumor epithelial collagen I expression when considering treatments related to perturbation of fibrillar collagens.
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MESH Headings
- Animals
- Bone Morphogenetic Protein 1/metabolism
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/pathology
- Carcinoma, Pancreatic Ductal/secondary
- Cell Line, Tumor
- Collagen Type I/chemistry
- Collagen Type I/genetics
- Collagen Type I/metabolism
- Collagen Type I, alpha 1 Chain
- Disease Progression
- Extracellular Matrix/metabolism
- Extracellular Matrix Proteins/metabolism
- Fibrillar Collagens/chemistry
- Fibrillar Collagens/genetics
- Fibrillar Collagens/metabolism
- Humans
- Mice
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Mutagenesis
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/pathology
- Procollagen/chemistry
- Procollagen/genetics
- Procollagen/metabolism
- Protein Domains
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Chenxi Tian
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ying Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Steffen Rickelt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Allison N Lau
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Richard O Hynes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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11
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Michopoulou A, Montmasson M, Garnier C, Lambert E, Dayan G, Rousselle P. A novel mechanism in wound healing: Laminin 332 drives MMP9/14 activity by recruiting syndecan-1 and CD44. Matrix Biol 2020; 94:1-17. [PMID: 32621878 DOI: 10.1016/j.matbio.2020.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022]
Abstract
Re-epithelialization describes the resurfacing of a skin wound with new epithelium. In response to various stimuli including that of growth factors, cytokines and extracellular matrix (ECM), wound edge epidermal keratinocytes undergo cytoskeleton rearrangements compatible with their motile behavior and develop protrusive adhesion contacts. Matrix metalloproteinases (MMP) expression is crucial for proper cell movement and ECM remodeling; however, their deposition mechanism is unknown in keratinocytes. Here, we show that similar to cytokine IL-1ß, the precursor laminin 332 pro-migratory fragment G45 induces expression of the MMP-9 pro-enzyme, which together with MMP-14, further exerts its proteolytic activity within epithelial podosomes. This event strictly depends on the expression of the proteoglycan receptor syndecan-1 that was found in a ring surrounding the podosome core, co-localised with CD44. Our findings uncover that by directly recruiting both syndecan-1 and CD44, the laminin-332 G45 domain plays a major role in regulating mechanisms underlying keratinocyte / ECM remodeling during wound repair.
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Affiliation(s)
- Anna Michopoulou
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, Institut de Biologie et Chimie des Protéines, UMR 5305; CNRS; Univ. Lyon 1; SFR BioSciences Gerland-Lyon Sud, 7 passage du Vercors, 69367, Lyon, France
| | - Marine Montmasson
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, Institut de Biologie et Chimie des Protéines, UMR 5305; CNRS; Univ. Lyon 1; SFR BioSciences Gerland-Lyon Sud, 7 passage du Vercors, 69367, Lyon, France
| | - Cécile Garnier
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, Institut de Biologie et Chimie des Protéines, UMR 5305; CNRS; Univ. Lyon 1; SFR BioSciences Gerland-Lyon Sud, 7 passage du Vercors, 69367, Lyon, France
| | - Elise Lambert
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, Institut de Biologie et Chimie des Protéines, UMR 5305; CNRS; Univ. Lyon 1; SFR BioSciences Gerland-Lyon Sud, 7 passage du Vercors, 69367, Lyon, France
| | - Guila Dayan
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, Institut de Biologie et Chimie des Protéines, UMR 5305; CNRS; Univ. Lyon 1; SFR BioSciences Gerland-Lyon Sud, 7 passage du Vercors, 69367, Lyon, France
| | - Patricia Rousselle
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, Institut de Biologie et Chimie des Protéines, UMR 5305; CNRS; Univ. Lyon 1; SFR BioSciences Gerland-Lyon Sud, 7 passage du Vercors, 69367, Lyon, France.
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12
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Zou Y, Li S, Xu B, Guo H, Zhang S, Cai Y. Inhibition of Proprotein Convertase Subtilisin/Kexin Type 9 Ameliorates Liver Fibrosis via Mitigation of Intestinal Endotoxemia. Inflammation 2020; 43:251-263. [PMID: 31776890 DOI: 10.1007/s10753-019-01114-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lipopolysaccharide (LPS) is demonstrated to cause "two-hit" injury to liver. Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays an important role in LPS clearance. Hepatocyte nuclear factor-1 alpha (HNF-1α) and sterol regulatory element-binding protein 2 (SREBP2) were reported to be responsible for PCSK9 gene transcription and regulation. We aim to clarify the expression status of PCSK9 during the process of liver fibrosis and to verify the effect on liver fibrosis via PCSK9 inhibition. In this study, we found that PCSK9 increased significantly in human and BDL mouse injured liver tissues, so did HNF-1α and SREBP2. No significant difference of plasma PCSK9 was observed. Inhibited PCSK9 using CRISPR-PCSK9 adeno-associated virus in BDL mice ameliorated liver inflammation and fibrosis, with LPS decrease in serum, without any change in intestinal wall integrity. PCSK9 expression of L02 hepatocytes can be induced by LPS; however, they lose the ability at high content of LPS. L02 cells increased LPS uptake after PCSK9 knockout. Taken together, these results suggest that, with PCSK9 increasing during liver fibrosis advancement, its inhibition can ameliorate liver injury by enhancing LPS uptake in hepatocytes; however, the enhancement is limited for destruction to hepatocytes by high LPS.
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Affiliation(s)
- Yanting Zou
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Xuhui District, Shanghai, People's Republic of China
| | - Shuyu Li
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Xuhui District, Shanghai, People's Republic of China
| | - Beili Xu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Xuhui District, Shanghai, People's Republic of China
| | - Hongying Guo
- Department of Severe Hepatitis, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, People's Republic of China
| | - Shuncai Zhang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Xuhui District, Shanghai, People's Republic of China
| | - Yu Cai
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Xuhui District, Shanghai, People's Republic of China.
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13
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Bingham GC, Lee F, Naba A, Barker TH. Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology. Matrix Biol 2020; 91-92:152-166. [DOI: 10.1016/j.matbio.2020.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022]
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14
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Arteel GE, Naba A. The liver matrisome - looking beyond collagens. JHEP Rep 2020; 2:100115. [PMID: 32637906 PMCID: PMC7330160 DOI: 10.1016/j.jhepr.2020.100115] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/17/2020] [Accepted: 03/22/2020] [Indexed: 02/07/2023] Open
Abstract
The extracellular matrix (ECM) is a diverse microenvironment that maintains bidirectional communication with surrounding cells to regulate cell and tissue homeostasis. The classical definition of the ECM has more recently been extended to include non-fibrillar proteins that either interact or are structurally affiliated with the ECM, termed the 'matrisome.' In addition to providing the structure and architectural support for cells and tissue, the matrisome serves as a reservoir for growth factors and cytokines, as well as a signaling hub via which cells can communicate with their environment and vice-versa. The matrisome is a master regulator of tissue homeostasis and organ function, which can dynamically and appropriately respond to any stress or injury. Failure to properly regulate these responses can lead to changes in the matrisome that are maladaptive. Hepatic fibrosis is a canonical example of ECM dyshomeostasis, leading to accumulation of predominantly collagenous ECM; indeed, hepatic fibrosis is considered almost synonymous with collagen accumulation. However, the qualitative and quantitative alterations of the hepatic matrisome during fibrosis are much more diverse than simple accumulation of collagens and occur long before fibrosis is histologically detected. A deeper understanding of the hepatic matrisome and its response to injury could yield new mechanistic insights into disease progression and regression, as well as potentially identify new biomarkers for both. In this review, we discuss the role of the ECM in liver diseases and look at new "omic" approaches to study this compartment.
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Key Words
- AUROC, area under the receiver operating characteristic curve
- CCl4, carbon tetrachloride
- ECM
- ECM, extracellular matrix
- Extracellular matrix
- Fibrosis
- HCC, hepatocellular carcinoma
- Liver disease
- MMP, matrix metalloproteinase
- NAFLD, non-alcoholic fatty liver disease
- NPV, negative predictive value
- POSTN, periostin
- PPV, positive predictive values
- Proteomics
- Regeneration
- TGFβ, transforming growth factor beta
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Affiliation(s)
- Gavin E. Arteel
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, Pittsburgh, PA, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
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15
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Vaisar T, Hu JH, Airhart N, Fox K, Heinecke J, Nicosia RF, Kohler T, Potter ZE, Simon GM, Dix MM, Cravatt BF, Gharib SA, Dichek DA. Parallel Murine and Human Plaque Proteomics Reveals Pathways of Plaque Rupture. Circ Res 2020; 127:997-1022. [PMID: 32762496 PMCID: PMC7508285 DOI: 10.1161/circresaha.120.317295] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
RATIONALE Plaque rupture is the proximate cause of most myocardial infarctions and many strokes. However, the molecular mechanisms that precipitate plaque rupture are unknown. OBJECTIVE By applying proteomic and bioinformatic approaches in mouse models of protease-induced plaque rupture and in ruptured human plaques, we aimed to illuminate biochemical pathways through which proteolysis causes plaque rupture and identify substrates that are cleaved in ruptured plaques. METHODS AND RESULTS We performed shotgun proteomics analyses of aortas of transgenic mice with macrophage-specific overexpression of urokinase (SR-uPA+/0 mice) and of SR-uPA+/0 bone marrow transplant recipients, and we used bioinformatic tools to evaluate protein abundance and functional category enrichment in these aortas. In parallel, we performed shotgun proteomics and bioinformatics studies on extracts of ruptured and stable areas of freshly harvested human carotid plaques. We also applied a separate protein-analysis method (protein topography and migration analysis platform) to attempt to identify substrates and proteolytic fragments in mouse and human plaque extracts. Approximately 10% of extracted aortic proteins were reproducibly altered in SR-uPA+/0 aortas. Proteases, inflammatory signaling molecules, as well as proteins involved with cell adhesion, the cytoskeleton, and apoptosis, were increased. ECM (Extracellular matrix) proteins, including basement-membrane proteins, were decreased. Approximately 40% of proteins were altered in ruptured versus stable areas of human carotid plaques, including many of the same functional categories that were altered in SR-uPA+/0 aortas. Collagens were minimally altered in SR-uPA+/0 aortas and ruptured human plaques; however, several basement-membrane proteins were reduced in both SR-uPA+/0 aortas and ruptured human plaques. Protein topography and migration analysis platform did not detect robust increases in proteolytic fragments of ECM proteins in either setting. CONCLUSIONS Parallel studies of SR-uPA+/0 mouse aortas and human plaques identify mechanisms that connect proteolysis with plaque rupture, including inflammation, basement-membrane protein loss, and apoptosis. Basement-membrane protein loss is a prominent feature of ruptured human plaques, suggesting a major role for basement-membrane proteins in maintaining plaque stability.
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Affiliation(s)
- Tomáš Vaisar
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Jie H Hu
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Nathan Airhart
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Kate Fox
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Jay Heinecke
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - Roberto F Nicosia
- Departments of Pathology and Laboratory Medicine (D.A.D., R.F.N.), University of Washington, Seattle.,Departments of Pathology and Laboratory Medicine (R.F.N.), VA Puget Sound Health Care System, Seattle, WA
| | - Ted Kohler
- Departments of Surgery (T.K.), University of Washington, Seattle.,Departments of Surgery (T.K.), VA Puget Sound Health Care System, Seattle, WA
| | - Zachary E Potter
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA (Z.E.P., M.M.D., B.F.C.)
| | | | - Melissa M Dix
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA (Z.E.P., M.M.D., B.F.C.)
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA (Z.E.P., M.M.D., B.F.C.)
| | - Sina A Gharib
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle
| | - David A Dichek
- Departments of Medicine (T.V., J.H.H., N.A., K.F., J.H., S.A.G., D.A.D.), University of Washington, Seattle.,Departments of Pathology and Laboratory Medicine (D.A.D., R.F.N.), University of Washington, Seattle
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16
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Rickelt S, Condon C, Mana M, Whittaker C, Pfirschke C, Roper J, Patil DT, Brown I, Mattia AR, Zukerberg L, Zhao Q, Chetty R, Lauwers GY, Neyaz A, Leijssen LGJ, Boylan K, Yilmaz OH, Deshpande V, Hynes RO. Agrin in the Muscularis Mucosa Serves as a Biomarker Distinguishing Hyperplastic Polyps from Sessile Serrated Lesions. Clin Cancer Res 2020; 26:1277-1287. [PMID: 31852835 PMCID: PMC7073301 DOI: 10.1158/1078-0432.ccr-19-2898] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/25/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023]
Abstract
PURPOSE Sessile serrated lesions (SSL) are precursors to colon carcinoma, and their distinction from other polyps, in particular hyperplastic polyps (HP), presents significant diagnostic challenges. We evaluated expression patterns in colonic polyps of previously identified colon carcinoma-associated extracellular matrix (ECM) proteins to identify markers distinguishing SSLs from other polyps. EXPERIMENTAL DESIGN Gene-expression analyses of ECM proteins were performed using publicly available data on preneoplastic colonic polyps. In parallel, we evaluated by IHC the expression of agrin (AGRN) in over 400 colonic polyps, including HP, SSL with and without dysplasia, traditional serrated adenomas (TSA), and tubular adenomas (TA), and compared the consistency of standard histologic diagnosis of SSLs by experienced gastrointestinal pathologists with that of AGRN IHC. RESULTS Differential gene expression analysis and IHC identified AGRN, serine peptidase inhibitor (SERPINE2), and TIMP metallopeptidase inhibitor 1 (TIMP1) elevated in SSLs and HPs but decreased in TAs and absent in normal colon. AGRN-positive basal laminae were noted in all TA, TSA, HP, and SSL in distinguishable patterns, whereas other polyps and normal mucosa were negative. SSL with or without dysplasia consistently showed IHC staining for AGRN in the muscularis mucosae, which was absent in HP, TSA, TA, and other polyps. In contrast, histologic evaluation showed only weak interobserver agreement (kappa value = 0.493) in distinguishing SSLs. CONCLUSIONS Muscularis mucosae-based AGRN immunostaining is a novel biomarker to distinguish SSL from HP, TSA, and TA, with a specificity of 97.1% and sensitivity of 98.9% and can assist in diagnosis of morphologically challenging colonic polyps.
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Affiliation(s)
- Steffen Rickelt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
| | - Charlene Condon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Swanson Biotechnology Center, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Miyeko Mana
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Charlie Whittaker
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Swanson Biotechnology Center, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christina Pfirschke
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, Massachusetts
| | - Jatin Roper
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Deepa T Patil
- Cleveland Clinic, Department of Pathology, Cleveland, Ohio
| | - Ian Brown
- Envoi Pathology, Kelvin Grove, Queensland, Australia
| | - Anthony R Mattia
- Department of Pathology, North Shore Medical Center, Salem, Massachusetts
| | - Lawrence Zukerberg
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Qing Zhao
- Department of Pathology and Laboratory Medicine, Boston University Medical Center, Boston, Massachusetts
| | - Runjan Chetty
- Department of Pathology, Toronto General Hospital, Toronto, Ontario, Canada
| | | | - Azfar Neyaz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Lieve G J Leijssen
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Katherine Boylan
- Department of Pathology, University of Utah, Huntsman Cancer Institute, Salt Lake City, Utah
| | - Omer H Yilmaz
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
| | - Richard O Hynes
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
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17
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The scaffold protein IQGAP1 is crucial for extravasation and metastasis. Sci Rep 2020; 10:2439. [PMID: 32051509 PMCID: PMC7015931 DOI: 10.1038/s41598-020-59438-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
IQGAP1 is a scaffold protein involved in a range of cellular activities, including migration, invasion, adhesion and proliferation. It is also oncogenic in a variety of cancers, promoting primary tumor growth and invasiveness. However, the role of IQGAP1 in tumor progression and metastasis remains unclear. In this study, we use both knockdown and knockout of IQGAP1 to investigate its role in the metastatic cascade of both melanoma and breast cancer cells in vivo. We find that reduction of IQGAP1 expression decreases the formation of both spontaneous and experimental metastases, without limiting primary or metastatic tumor growth. Furthermore, IQGAP1 knockout significantly inhibits extravasation of tumor cells from circulation, possibly involving invadopodial function. By expressing mutant forms of IQGAP1 in a knockout context, we also determine that IQGAP1’s pro-metastatic functions are dependent on multiple domains and functions. These data demonstrate that IQGAP1 is crucial for metastasis in vivo through regulation of extravasation and suggest that it may represent a valid therapeutic target for inhibiting metastasis.
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18
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Raghunathan R, Sethi MK, Klein JA, Zaia J. Proteomics, Glycomics, and Glycoproteomics of Matrisome Molecules. Mol Cell Proteomics 2019; 18:2138-2148. [PMID: 31471497 PMCID: PMC6823855 DOI: 10.1074/mcp.r119.001543] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/26/2019] [Indexed: 12/21/2022] Open
Abstract
The most straightforward applications of proteomics database searching involve intracellular proteins. Although intracellular gene products number in the thousands, their well-defined post-translational modifications (PTMs) makes database searching practical. By contrast, cell surface and extracellular matrisome proteins pass through the secretory pathway where many become glycosylated, modulating their physicochemical properties, adhesive interactions, and diversifying their functions. Although matrisome proteins number only a few hundred, their high degree of complex glycosylation multiplies the number of theoretical proteoforms by orders of magnitude. Given that extracellular networks that mediate cell-cell and cell-pathogen interactions in physiology depend on glycosylation, it is important to characterize the proteomes, glycomes, and glycoproteomes of matrisome molecules that exist in a given biological context. In this review, we summarize proteomics approaches for characterizing matrisome molecules, with an emphasis on applications to brain diseases. We demonstrate the availability of methods that should greatly increase the availability of information on matrisome molecular structure associated with health and disease.
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Affiliation(s)
- Rekha Raghunathan
- Molecular and Translational Medicine Program, Boston University, Boston, MA 02218; Department of Biochemistry, Boston University, Boston, MA 02218
| | - Manveen K Sethi
- Department of Biochemistry, Boston University, Boston, MA 02218
| | - Joshua A Klein
- Bioinformatics Program, Boston University, Boston, MA 02218
| | - Joseph Zaia
- Molecular and Translational Medicine Program, Boston University, Boston, MA 02218; Department of Biochemistry, Boston University, Boston, MA 02218; Bioinformatics Program, Boston University, Boston, MA 02218.
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19
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Exploring the extracellular matrix in health and disease using proteomics. Essays Biochem 2019; 63:417-432. [DOI: 10.1042/ebc20190001] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023]
Abstract
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins that constitutes the scaffold of multicellular organisms. In addition to providing architectural and mechanical support to the surrounding cells, it conveys biochemical signals that regulate cellular processes including proliferation and survival, fate determination, and cell migration. Defects in ECM protein assembly, decreased ECM protein production or, on the contrary, excessive ECM accumulation, have been linked to many pathologies including cardiovascular and skeletal diseases, cancers, and fibrosis. The ECM thus represents a potential reservoir of prognostic biomarkers and therapeutic targets. However, our understanding of the global protein composition of the ECM and how it changes during pathological processes has remained limited until recently.
In this mini-review, we provide an overview of the latest methodological advances in sample preparation and mass spectrometry-based proteomics that have permitted the profiling of the ECM of now dozens of normal and diseased tissues, including tumors and fibrotic lesions.
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20
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Cheng CW, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty VL, Moreno M, Iqbal AM, Bauer-Rowe KE, Imada S, Ulutas MS, Mylonas C, Whary MT, Levine SS, Basbinar Y, Hynes RO, Mino-Kenudson M, Deshpande V, Boyer LA, Fox JG, Terranova C, Rai K, Piwnica-Worms H, Mihaylova MM, Regev A, Yilmaz ÖH. Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet. Cell 2019; 178:1115-1131.e15. [PMID: 31442404 PMCID: PMC6732196 DOI: 10.1016/j.cell.2019.07.048] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 06/03/2019] [Accepted: 07/25/2019] [Indexed: 01/18/2023]
Abstract
Little is known about how metabolites couple tissue-specific stem cell function with physiology. Here we show that, in the mammalian small intestine, the expression of Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthetase 2), the gene encoding the rate-limiting enzyme in the production of ketone bodies, including beta-hydroxybutyrate (βOHB), distinguishes self-renewing Lgr5+ stem cells (ISCs) from differentiated cell types. Hmgcs2 loss depletes βOHB levels in Lgr5+ ISCs and skews their differentiation toward secretory cell fates, which can be rescued by exogenous βOHB and class I histone deacetylase (HDAC) inhibitor treatment. Mechanistically, βOHB acts by inhibiting HDACs to reinforce Notch signaling, instructing ISC self-renewal and lineage decisions. Notably, although a high-fat ketogenic diet elevates ISC function and post-injury regeneration through βOHB-mediated Notch signaling, a glucose-supplemented diet has the opposite effects. These findings reveal how control of βOHB-activated signaling in ISCs by diet helps to fine-tune stem cell adaptation in homeostasis and injury.
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Affiliation(s)
- Chia-Wei Cheng
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Moshe Biton
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,These authors contributed equally to this work
| | - Adam L. Haber
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,These authors contributed equally to this work
| | - Nuray Gunduz
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey 06800
| | - George Eng
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Liam T. Gaynor
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston MA, 02215, USA
| | - Surya Tripathi
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Gizem Calibasi-Kocal
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Dokuz Eylul University, Institute of Oncology, Department of Translational Oncology, Izmir, Turkey
| | - Steffen Rickelt
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Vincent L. Butty
- BioMicro Center, at MIT, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Marta Moreno
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | - Ameena M Iqbal
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA
| | | | - Shinya Imada
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University,1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Mehmet Sefa Ulutas
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Biology, Siirt University, Science and Arts Faculty, 56100 Siirt, Turkey
| | | | - Mark T. Whary
- Division of Comparative Medicine, Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Stuart S. Levine
- BioMicro Center, at MIT, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Yasemin Basbinar
- Dokuz Eylul University, Institute of Oncology, Department of Translational Oncology, Izmir, Turkey
| | - Richard O. Hynes
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Laurie A. Boyer
- Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
| | - James G. Fox
- Division of Comparative Medicine, Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Christopher Terranova
- Genomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kunal Rai
- Genomic Medicine Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria M. Mihaylova
- The Ohio State Comprehensive Cancer Center, Department of Biological Chemistry and Pharmacology, Ohio State University, 308 Wiseman Hall, Columbus, OH 43210, USA
| | - Aviv Regev
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Ömer H. Yilmaz
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts 02139, USA,Department of Biology, MIT, Cambridge, Massachusetts 02139, USA,Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, Massachusetts 02114, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA,Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA,Lead Contact,Correspondence: Ömer H. Yilmaz () (Ö.H.Y)
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21
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Jailkhani N, Ingram JR, Rashidian M, Rickelt S, Tian C, Mak H, Jiang Z, Ploegh HL, Hynes RO. Noninvasive imaging of tumor progression, metastasis, and fibrosis using a nanobody targeting the extracellular matrix. Proc Natl Acad Sci U S A 2019; 116:14181-14190. [PMID: 31068469 PMCID: PMC6628802 DOI: 10.1073/pnas.1817442116] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Extracellular matrix (ECM) deposition is a hallmark of many diseases, including cancer and fibroses. To exploit the ECM as an imaging and therapeutic target, we developed alpaca-derived libraries of "nanobodies" against disease-associated ECM proteins. We describe here one such nanobody, NJB2, specific for an alternatively spliced domain of fibronectin expressed in disease ECM and neovasculature. We showed by noninvasive in vivo immuno-PET/CT imaging that NJB2 detects primary tumors and metastatic sites with excellent specificity in multiple models of breast cancer, including human and mouse triple-negative breast cancer, and in melanoma. We also imaged mice with pancreatic ductal adenocarcinoma (PDAC) in which NJB2 was able to detect not only PDAC tumors but also early pancreatic lesions called pancreatic intraepithelial neoplasias, which are challenging to detect by any current imaging modalities, with excellent clarity and signal-to-noise ratios that outperformed conventional 2-fluorodeoxyglucose PET/CT imaging. NJB2 also detected pulmonary fibrosis in a bleomycin-induced fibrosis model. We propose NJB2 and similar anti-ECM nanobodies as powerful tools for noninvasive detection of tumors, metastatic lesions, and fibroses. Furthermore, the selective recognition of disease tissues makes NJB2 a promising candidate for nanobody-based therapeutic applications.
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Affiliation(s)
- Noor Jailkhani
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jessica R Ingram
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, MA 02115
| | - Mohammad Rashidian
- Program in Molecular and Cellular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Steffen Rickelt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Chenxi Tian
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Howard Mak
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Zhigang Jiang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hidde L Ploegh
- Program in Molecular and Cellular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Richard O Hynes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
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22
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New automatic quantification method of immunofluorescence and histochemistry in whole histological sections. Cell Signal 2019; 62:109335. [PMID: 31170471 DOI: 10.1016/j.cellsig.2019.05.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 12/12/2022]
Abstract
Immunofluorescent staining is a widespread tool in basic science to understand organ morphology and (patho-) physiology. The analysis of imaging data is often performed manually, limiting throughput and introducing human bias. Quantitative analysis is particularly challenging for organs with complex structure such as the kidney. In this study we present an approach for automatic quantification of fluorescent markers and histochemical stainings in whole organ sections using open source software. We validate our novel method in multiple typical challenges of basic kidney research and demonstrate its general relevance and applicability to other complex solid organs for a variety of different markers and stainings. Our newly developed software tool "AQUISTO", applied as a standard in primary data analysis, facilitates efficient large scale evaluation of cellular populations in various types of histological samples. Thereby it contributes to the characterization and understanding of (patho-) physiological processes.
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23
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Jin C, Lagoudas GK, Zhao C, Bullman S, Bhutkar A, Hu B, Ameh S, Sandel D, Liang XS, Mazzilli S, Whary MT, Meyerson M, Germain R, Blainey PC, Fox JG, Jacks T. Commensal Microbiota Promote Lung Cancer Development via γδ T Cells. Cell 2019; 176:998-1013.e16. [PMID: 30712876 DOI: 10.1016/j.cell.2018.12.040] [Citation(s) in RCA: 565] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/01/2018] [Accepted: 12/21/2018] [Indexed: 12/12/2022]
Abstract
Lung cancer is closely associated with chronic inflammation, but the causes of inflammation and the specific immune mediators have not been fully elucidated. The lung is a mucosal tissue colonized by a diverse bacterial community, and pulmonary infections commonly present in lung cancer patients are linked to clinical outcomes. Here, we provide evidence that local microbiota provoke inflammation associated with lung adenocarcinoma by activating lung-resident γδ T cells. Germ-free or antibiotic-treated mice were significantly protected from lung cancer development induced by Kras mutation and p53 loss. Mechanistically, commensal bacteria stimulated Myd88-dependent IL-1β and IL-23 production from myeloid cells, inducing proliferation and activation of Vγ6+Vδ1+ γδ T cells that produced IL-17 and other effector molecules to promote inflammation and tumor cell proliferation. Our findings clearly link local microbiota-immune crosstalk to lung tumor development and thereby define key cellular and molecular mediators that may serve as effective targets in lung cancer intervention.
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Affiliation(s)
- Chengcheng Jin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Georgia K Lagoudas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chen Zhao
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Susan Bullman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Bo Hu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Samuel Ameh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Demi Sandel
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Xu Sue Liang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sarah Mazzilli
- Department of Medicine, Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark T Whary
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Matthew Meyerson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ronald Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Paul C Blainey
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - James G Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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