1
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Hulahan TS, Spruill L, Wallace EN, Park Y, West RB, Marks JR, Hwang ES, Drake RR, Angel PM. Extracellular Microenvironment Alterations in Ductal Carcinoma In Situ and Invasive Breast Cancer Pathologies by Multiplexed Spatial Proteomics. Int J Mol Sci 2024; 25:6748. [PMID: 38928454 PMCID: PMC11203487 DOI: 10.3390/ijms25126748] [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: 05/07/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Ductal carcinoma in situ (DCIS) is a heterogeneous breast disease that remains challenging to treat due to its unpredictable progression to invasive breast cancer (IBC). Contemporary literature has become increasingly focused on extracellular matrix (ECM) alterations with breast cancer progression. However, the spatial regulation of the ECM proteome in DCIS has yet to be investigated in relation to IBC. We hypothesized that DCIS and IBC present distinct ECM proteomes that could discriminate between these pathologies. Tissue sections of pure DCIS, mixed DCIS-IBC, or pure IBC (n = 22) with detailed pathological annotations were investigated by multiplexed spatial proteomics. Across tissues, 1,005 ECM peptides were detected in pathologically annotated regions and their surrounding extracellular microenvironments. A comparison of DCIS to IBC pathologies demonstrated 43 significantly altered ECM peptides. Notably, eight fibrillar collagen peptides could distinguish with high specificity and sensitivity between DCIS and IBC. Lesion-targeted proteomic imaging revealed heterogeneity of the ECM proteome surrounding individual DCIS lesions. Multiplexed spatial proteomics reported an invasive cancer field effect, in which DCIS lesions in closer proximity to IBC shared a more similar ECM profile to IBC than distal counterparts. Defining the ECM proteomic microenvironment provides novel molecular insights relating to DCIS and IBC.
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Affiliation(s)
- Taylor S. Hulahan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Elizabeth N. Wallace
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Yeonhee Park
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, USA;
| | - Robert B. West
- Department of Pathology Clinical, Stanford University, Stanford, CA 94305, USA;
| | - Jeffrey R. Marks
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - E. Shelley Hwang
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
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2
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Macdonald JK, Mehta AS, Drake RR, Angel PM. Molecular analysis of the extracellular microenvironment: from form to function. FEBS Lett 2024; 598:602-620. [PMID: 38509768 PMCID: PMC11049795 DOI: 10.1002/1873-3468.14852] [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: 11/29/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
The extracellular matrix (ECM) proteome represents an important component of the tissue microenvironment that controls chemical flux and induces cell signaling through encoded structure. The analysis of the ECM represents an analytical challenge through high levels of post-translational modifications, protease-resistant structures, and crosslinked, insoluble proteins. This review provides a comprehensive overview of the analytical challenges involved in addressing the complexities of spatially profiling the extracellular matrix proteome. A synopsis of the process of synthesizing the ECM structure, detailing inherent chemical complexity, is included to present the scope of the analytical challenge. Current chromatographic and spatial techniques addressing these challenges are detailed. Capabilities for multimodal multiplexing with cellular populations are discussed with a perspective on developing a holistic view of disease processes that includes both the cellular and extracellular microenvironment.
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Affiliation(s)
- Jade K Macdonald
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC
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3
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Chung HH, Huang P, Chen CL, Lee C, Hsu CC. Next-generation pathology practices with mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2023; 42:2446-2465. [PMID: 35815718 DOI: 10.1002/mas.21795] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful technique that reveals the spatial distribution of various molecules in biological samples, and it is widely used in pathology-related research. In this review, we summarize common MSI techniques, including matrix-assisted laser desorption/ionization and desorption electrospray ionization MSI, and their applications in pathological research, including disease diagnosis, microbiology, and drug discovery. We also describe the improvements of MSI, focusing on the accumulation of imaging data sets, expansion of chemical coverage, and identification of biological significant molecules, that have prompted the evolution of MSI to meet the requirements of pathology practices. Overall, this review details the applications and improvements of MSI techniques, demonstrating the potential of integrating MSI techniques into next-generation pathology practices.
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Affiliation(s)
- Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Penghsuan Huang
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chih-Lin Chen
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chuping Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
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4
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Conroy LR, Clarke HA, Allison DB, Valenca SS, Sun Q, Hawkinson TR, Young LEA, Ferreira JE, Hammonds AV, Dunne JB, McDonald RJ, Absher KJ, Dong BE, Bruntz RC, Markussen KH, Juras JA, Alilain WJ, Liu J, Gentry MS, Angel PM, Waters CM, Sun RC. Spatial metabolomics reveals glycogen as an actionable target for pulmonary fibrosis. Nat Commun 2023; 14:2759. [PMID: 37179348 PMCID: PMC10182559 DOI: 10.1038/s41467-023-38437-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high-dimensionality reduction/spatial clustering and histopathological annotation of matrix assisted laser desorption/ionization imaging datasets to assess tissue metabolic heterogeneity in human lung diseases. Using metabolic features identified from this pipeline, we hypothesize that metabolic channeling between glycogen and N-linked glycans is a critical metabolic process favoring pulmonary fibrosis progression. To test our hypothesis, we induced pulmonary fibrosis in two different mouse models with lysosomal glycogen utilization deficiency. Both mouse models displayed blunted N-linked glycan levels and nearly 90% reduction in endpoint fibrosis when compared to WT animals. Collectively, we provide conclusive evidence that lysosomal utilization of glycogen is required for pulmonary fibrosis progression. In summary, our study provides a roadmap to leverage spatial metabolomics to understand foundational biology in pulmonary diseases.
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Affiliation(s)
- Lindsey R Conroy
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Markey Cancer Center, Lexington, KY, 40536, USA
| | - Harrison A Clarke
- Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Derek B Allison
- Markey Cancer Center, Lexington, KY, 40536, USA
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Samuel Santos Valenca
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - Qi Sun
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Tara R Hawkinson
- Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Lyndsay E A Young
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Juanita E Ferreira
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Autumn V Hammonds
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Jaclyn B Dunne
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics at the Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Robert J McDonald
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Kimberly J Absher
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Brittany E Dong
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - Ronald C Bruntz
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Kia H Markussen
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Jelena A Juras
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Markey Cancer Center, Lexington, KY, 40536, USA
| | - Warren J Alilain
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Spinal Cord and Brain Injury Research Center, Lexington, KY, 40536, USA
| | - Jinze Liu
- Department of Biostatistics, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Matthew S Gentry
- Markey Cancer Center, Lexington, KY, 40536, USA
- Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Center for Advanced Spatial Biomolecule Research, University of Florida, Gainesville, FL, 32610, USA
| | - Peggi M Angel
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics at the Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Christopher M Waters
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, 40536, USA.
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA.
| | - Ramon C Sun
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA.
- Markey Cancer Center, Lexington, KY, 40536, USA.
- Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
- Center for Advanced Spatial Biomolecule Research, University of Florida, Gainesville, FL, 32610, USA.
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5
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Wang EJY, Chen IH, Kuo BYT, Yu CC, Lai MT, Lin JT, Lin LYT, Chen CM, Hwang T, Sheu JJC. Alterations of Cytoskeleton Networks in Cell Fate Determination and Cancer Development. Biomolecules 2022; 12:biom12121862. [PMID: 36551290 PMCID: PMC9775460 DOI: 10.3390/biom12121862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Cytoskeleton proteins have been long recognized as structural proteins that provide the necessary mechanical architecture for cell development and tissue homeostasis. With the completion of the cancer genome project, scientists were surprised to learn that huge numbers of mutated genes are annotated as cytoskeletal or associated proteins. Although most of these mutations are considered as passenger mutations during cancer development and evolution, some genes show high mutation rates that can even determine clinical outcomes. In addition, (phospho)proteomics study confirms that many cytoskeleton-associated proteins, e.g., β-catenin, PIK3CA, and MB21D2, are important signaling mediators, further suggesting their biofunctional roles in cancer development. With emerging evidence to indicate the involvement of mechanotransduction in stemness formation and cell differentiation, mutations in these key cytoskeleton components may change the physical/mechanical properties of the cells and determine the cell fate during cancer development. In particular, tumor microenvironment remodeling triggered by such alterations has been known to play important roles in autophagy, metabolism, cancer dormancy, and immune evasion. In this review paper, we will highlight the current understanding of how aberrant cytoskeleton networks affect cancer behaviors and cellular functions through mechanotransduction.
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Affiliation(s)
- Evan Ja-Yang Wang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - I-Hsuan Chen
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
- Department of Pharmacy, College of Pharmacy and Health Care, Tajen University, Pingtung County 907391, Taiwan
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Brian Yu-Ting Kuo
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chia-Cheng Yu
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
- Department of Pharmacy, College of Pharmacy and Health Care, Tajen University, Pingtung County 907391, Taiwan
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114202, Taiwan
| | - Ming-Tsung Lai
- Department of Pathology, Taichung Hospital, Ministry of Health and Welfare, Taichung 403301, Taiwan
| | - Jen-Tai Lin
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813405, Taiwan
| | - Leo Yen-Ting Lin
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chih-Mei Chen
- Human Genetic Center, China Medical University Hospital, Taichung 404327, Taiwan
| | - Tritium Hwang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Institute of Biopharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Correspondence: ; Tel.: +886-7-5252000 (ext. 7102)
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6
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Clift CL, Saunders J, Drake RR, Angel PM. Perspectives on pediatric congenital aortic valve stenosis: Extracellular matrix proteins, post translational modifications, and proteomic strategies. Front Cardiovasc Med 2022; 9:1024049. [PMID: 36439995 PMCID: PMC9685993 DOI: 10.3389/fcvm.2022.1024049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
In heart valve biology, organization of the extracellular matrix structure is directly correlated to valve function. This is especially true in cases of pediatric congenital aortic valve stenosis (pCAVS), in which extracellular matrix (ECM) dysregulation is a hallmark of the disease, eventually leading to left ventricular hypertrophy and heart failure. Therapeutic strategies are limited, especially in pediatric cases in which mechanical and tissue engineered valve replacements may not be a suitable option. By identifying mechanisms of translational and post-translational dysregulation of ECM in CAVS, potential drug targets can be identified, and better bioengineered solutions can be developed. In this review, we summarize current knowledge regarding ECM proteins and their post translational modifications (PTMs) during aortic valve development and disease and contributing factors to ECM dysregulation in CAVS. Additionally, we aim to draw parallels between other fibrotic disease and contributions to ECM post-translational modifications. Finally, we explore the current treatment options in pediatrics and identify how the field of proteomics has advanced in recent years, highlighting novel characterization methods of ECM and PTMs that may be used to identify potential therapeutic strategies relevant to pCAVS.
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Affiliation(s)
- Cassandra L. Clift
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
- Division of Cardiovascular Medicine, Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Janet Saunders
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
- *Correspondence: Peggi M. Angel,
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7
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Morato NM, Brown HM, Garcia D, Middlebrooks EH, Jentoft M, Chaichana K, Quiñones-Hinojosa A, Cooks RG. High-throughput analysis of tissue microarrays using automated desorption electrospray ionization mass spectrometry. Sci Rep 2022; 12:18851. [PMID: 36344609 PMCID: PMC9640715 DOI: 10.1038/s41598-022-22924-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Tissue microarrays (TMAs) are commonly used for the rapid analysis of large numbers of tissue samples, often in morphological assessments but increasingly in spectroscopic analysis, where specific molecular markers are targeted via immunostaining. Here we report the use of an automated high-throughput system based on desorption electrospray ionization (DESI) mass spectrometry (MS) for the rapid generation and online analysis of high-density (6144 samples/array) TMAs, at rates better than 1 sample/second. Direct open-air analysis of tissue samples (hundreds of nanograms) not subjected to prior preparation, plus the ability to provide molecular characterization by tandem mass spectrometry (MS/MS), make this experiment versatile and applicable to both targeted and untargeted analysis in a label-free manner. These capabilities are demonstrated in a proof-of-concept study of frozen brain tissue biopsies where we showcase (i) a targeted MS/MS application aimed at identification of isocitrate dehydrogenase mutation in glioma samples and (ii) an untargeted MS tissue type classification using lipid profiles and correlation with tumor cell percentage estimates from histopathology. The small sample sizes and large sample numbers accessible with this methodology make for a powerful analytical system that facilitates the identification of molecular markers for later use in intraoperative applications to guide precision surgeries and ultimately improve patient outcomes.
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Affiliation(s)
- Nicolás M. Morato
- grid.169077.e0000 0004 1937 2197Department of Chemistry, Purdue Center for Cancer Research, and Bindley Bioscience Center, Purdue University, 560 Oval Drive, West Lafayette, IN 47907 USA
| | - Hannah Marie Brown
- grid.169077.e0000 0004 1937 2197Department of Chemistry, Purdue Center for Cancer Research, and Bindley Bioscience Center, Purdue University, 560 Oval Drive, West Lafayette, IN 47907 USA ,grid.4367.60000 0001 2355 7002Present Address: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO USA
| | - Diogo Garcia
- grid.417467.70000 0004 0443 9942Department of Neurosurgery, Mayo Clinic, Jacksonville, FL USA
| | - Erik H. Middlebrooks
- grid.417467.70000 0004 0443 9942Department of Neurosurgery, Mayo Clinic, Jacksonville, FL USA ,grid.417467.70000 0004 0443 9942Department of Radiology, Mayo Clinic, Jacksonville, FL USA
| | - Mark Jentoft
- grid.417467.70000 0004 0443 9942Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL USA
| | - Kaisorn Chaichana
- grid.417467.70000 0004 0443 9942Department of Neurosurgery, Mayo Clinic, Jacksonville, FL USA
| | | | - R. Graham Cooks
- grid.169077.e0000 0004 1937 2197Department of Chemistry, Purdue Center for Cancer Research, and Bindley Bioscience Center, Purdue University, 560 Oval Drive, West Lafayette, IN 47907 USA
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8
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Huang RX, Siriwanna D, Cho WC, Wan TK, Du YR, Bennett AN, He QE, Liu JD, Huang XT, Chan KHK. Lung adenocarcinoma-related target gene prediction and drug repositioning. Front Pharmacol 2022; 13:936758. [PMID: 36081949 PMCID: PMC9445420 DOI: 10.3389/fphar.2022.936758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Lung cancer is the leading cause of cancer deaths globally, and lung adenocarcinoma (LUAD) is the most common type of lung cancer. Gene dysregulation plays an essential role in the development of LUAD. Drug repositioning based on associations between drug target genes and LUAD target genes are useful to discover potential new drugs for the treatment of LUAD, while also reducing the monetary and time costs of new drug discovery and development. Here, we developed a pipeline based on machine learning to predict potential LUAD-related target genes through established graph attention networks (GATs). We then predicted potential drugs for the treatment of LUAD through gene coincidence-based and gene network distance-based methods. Using data from 535 LUAD tissue samples and 59 precancerous tissue samples from The Cancer Genome Atlas, 48,597 genes were identified and used for the prediction model building of the GAT. The GAT model achieved good predictive performance, with an area under the receiver operating characteristic curve of 0.90. 1,597 potential LUAD-related genes were identified from the GAT model. These LUAD-related genes were then used for drug repositioning. The gene overlap and network distance with the target genes were calculated for 3,070 drugs and 672 preclinical compounds approved by the US Food and Drug Administration. At which, bromoethylamine was predicted as a novel potential preclinical compound for the treatment of LUAD, and cimetidine and benzbromarone were predicted as potential therapeutic drugs for LUAD. The pipeline established in this study presents new approach for developing targeted therapies for LUAD.
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Affiliation(s)
- Rui Xuan Huang
- >Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China
| | - Damrongrat Siriwanna
- >Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - William C. Cho
- >Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - Tsz Kin Wan
- >Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China
| | - Yan Rong Du
- >Department of Linguistics and Modern Languages, The Chinese University of Hong Kong, Hong Kong, China
| | - Adam N. Bennett
- >Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Qian Echo He
- >Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Jun Dong Liu
- >Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xiao Tai Huang
- >School of Computer Science and Technology, Xidian University, Xi’an, China
| | - Kei Hang Katie Chan
- >Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China
- >Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- >Department of Epidemiology and Center for Global Cardiometabolic Health, Brown University, Providence, RI, United States
- *Correspondence: Kei Hang Katie Chan,
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9
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Multiplex Tissue Imaging: Spatial Revelations in the Tumor Microenvironment. Cancers (Basel) 2022; 14:cancers14133170. [PMID: 35804939 PMCID: PMC9264815 DOI: 10.3390/cancers14133170] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Cancer is the leading cause of death worldwide, and the overall aging of the population results in an increased risk of a cancer diagnosis during a person’s lifetime. Diagnosis and treatment at an early stage will typically increase the chances of survival. Tumors can develop therapy resistance, and it is difficult to predict how individual patients will respond to therapy. Most studies that aim to resolve this problem have focused on studying the composition and characteristics of dissociated tumors, while ignoring the role of cell localization and interactions within the tumor microenvironment. In the past decade, technological innovations have enabled multiplex imaging analyses of intact tumors to study localization and interaction parameters, which can be used as biomarkers, or can be correlated with treatment responses and clinical outcomes. Abstract The tumor microenvironment is a complex ecosystem containing various cell types, such as immune cells, fibroblasts, and endothelial cells, which interact with the tumor cells. In recent decades, the cancer research field has gained insight into the cellular subtypes that are involved in tumor microenvironment heterogeneity. Moreover, it has become evident that cellular interactions in the tumor microenvironment can either promote or inhibit tumor development, progression, and drug resistance, depending on the context. Multiplex spatial analysis methods have recently been developed; these have offered insight into how cellular crosstalk dynamics and heterogeneity affect cancer prognoses and responses to treatment. Multiplex (imaging) technologies and computational analysis methods allow for the spatial visualization and quantification of cell–cell interactions and properties. These technological advances allow for the discovery of cellular interactions within the tumor microenvironment and provide detailed single-cell information on properties that define cellular behavior. Such analyses give insights into the prognosis and mechanisms of therapy resistance, which is still an urgent problem in the treatment of multiple types of cancer. Here, we provide an overview of multiplex imaging technologies and concepts of downstream analysis methods to investigate cell–cell interactions, how these studies have advanced cancer research, and their potential clinical implications.
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10
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Pally D, Goutham S, Bhat R. Extracellular matrix as a driver for intratumoral heterogeneity. Phys Biol 2022; 19. [PMID: 35545075 DOI: 10.1088/1478-3975/ac6eb0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 05/11/2022] [Indexed: 11/12/2022]
Abstract
The architecture of an organ is built through interactions between its native cells and its connective tissue consisting of stromal cells and the extracellular matrix (ECM). Upon transformation through tumorigenesis, such interactions are disrupted and replaced by a new set of intercommunications between malignantly transformed parenchyma, an altered stromal cell population, and a remodeled ECM. In this perspective, we propose that the intratumoral heterogeneity of cancer cell phenotypes is an emergent property of such reciprocal intercommunications, both biochemical and mechanical-physical, which engender and amplify the diversity of cell behavioral traits. An attempt to assimilate such findings within a framework of phenotypic plasticity furthers our understanding of cancer progression.
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Affiliation(s)
- Dharma Pally
- Molecular Reproduction Development and Genetics, Indian Institute of Science, GA 07, Bangalore, Karnataka, 560012, INDIA
| | - Shyamili Goutham
- Molecular Reproduction Development and Genetics, Indian Institute of Science, GA 07, Bangalore, Karnataka, 560012, INDIA
| | - Ramray Bhat
- Molecular Reproduction Development and Genetics, Indian Institute of Science, GA 07, Bangalore, Karnataka, 560012, INDIA
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11
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Lin M, Eberlin LS, Seeley EH. Reduced Hemoglobin Signal and Improved Detection of Endogenous Proteins in Blood-Rich Tissues for MALDI Mass Spectrometry Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:296-303. [PMID: 35061381 PMCID: PMC9041275 DOI: 10.1021/jasms.1c00300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Mass spectrometry imaging provides a powerful approach for the direct analysis and spatial visualization of molecules in tissue sections. Using matrix-assisted laser desorption/ionization mass spectrometry, intact protein imaging has been widely investigated for biomarker analysis and diagnosis in a variety of tissue types and diseases. However, blood-rich or highly vascular tissues present a challenge in molecular imaging due to the high ionization efficiency of hemoglobin, which leads to ion suppression of endogenous proteins. Here, we describe a protocol to selectively reduce hemoglobin signal in blood-rich tissues that can easily be integrated into mass spectrometry imaging workflows.
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Affiliation(s)
- Monica Lin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Livia S. Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
- Department of Surgery, Baylor College of Medicine, Houston, TX 77030
- to whom correspondence may be addressed: ,
| | - Erin H. Seeley
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
- to whom correspondence may be addressed: ,
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12
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Capturing the third dimension in drug discovery: Spatially-resolved tools for interrogation of complex 3D cell models. Biotechnol Adv 2021; 55:107883. [PMID: 34875362 DOI: 10.1016/j.biotechadv.2021.107883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023]
Abstract
Advanced three-dimensional (3D) cell models have proven to be capable of depicting architectural and microenvironmental features of several tissues. By providing data of higher physiological and pathophysiological relevance, 3D cell models have been contributing to a better understanding of human development, pathology onset and progression mechanisms, as well as for 3D cell-based assays for drug discovery. Nonetheless, the characterization and interrogation of these tissue-like structures pose major challenges on the conventional analytical methods, pushing the development of spatially-resolved technologies. Herein, we review recent advances and pioneering technologies suitable for the interrogation of multicellular 3D models, while capable of retaining biological spatial information. We focused on imaging technologies and omics tools, namely transcriptomics, proteomics and metabolomics. The advantages and shortcomings of these novel methodologies are discussed, alongside the opportunities to intertwine data from the different tools.
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13
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Clift CL, McLaughlin S, Muñoz M, Suuronen EJ, Rotstein BH, Mehta AS, Drake RR, Alarcon EI, Angel PM. Evaluation of Therapeutic Collagen-Based Biomaterials in the Infarcted Mouse Heart by Extracellular Matrix Targeted MALDI Imaging Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2746-2754. [PMID: 34713699 PMCID: PMC8639787 DOI: 10.1021/jasms.1c00189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The goal of this study was to develop strategies to localize human collagen-based hydrogels within an infarcted mouse heart, as well as analyze its impact on endogenous extracellular matrix (ECM) remodeling. Collagen is a natural polymer that is abundantly used in bioengineered hydrogels because of its biocompatibility, cell permeability, and biodegradability. However, without the use of tagging techniques, collagen peptides derived from hydrogels can be difficult to differentiate from the endogenous ECM within tissues. Imaging mass spectrometry is a robust tool capable of visualizing synthetic and natural polymeric molecular structures yet is largely underutilized in the field of biomaterials outside of surface characterization. In this study, our group leveraged a recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) technique to enzymatically target collagen and other ECM peptides within the tissue microenvironment that are both endogenous and hydrogel-derived. Using a multimodal approach of fluorescence microscopy and ECM-IMS techniques, we were able to visualize and relatively quantify significantly abundant collagen peptides in an infarcted mouse heart that were localized to regions of therapeutic hydrogel injection sites. On-tissue MALDI MS/MS was used to putatively identify sites of collagen peptide hydroxyproline site occupancy, a post-translational modification that is critical in collagen triple helical stability. Additionally, the technique could putatively identify over 35 endogenously expressed ECM peptides that were expressed in hydrogel-injected mouse hearts. Our findings show evidence for the use of MALDI-IMS in assessing the therapeutic application of collagen-based biomaterials.
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Affiliation(s)
- Cassandra L Clift
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Sarah McLaughlin
- Division of Cardiac Surgery, University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Marcelo Muñoz
- Division of Cardiac Surgery, University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Erik J Suuronen
- Division of Cardiac Surgery, University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Benjamin H Rotstein
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Emilio I Alarcon
- Division of Cardiac Surgery, University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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14
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Rujchanarong D, Lefler J, Saunders JE, Pippin S, Spruill L, Bethard JR, Ball LE, Mehta AS, Drake RR, Ostrowski MC, Angel PM. Defining the Tumor Microenvironment by Integration of Immunohistochemistry and Extracellular Matrix Targeted Imaging Mass Spectrometry. Cancers (Basel) 2021; 13:4419. [PMID: 34503228 PMCID: PMC8430776 DOI: 10.3390/cancers13174419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 12/11/2022] Open
Abstract
Breast stroma plays a significant role in breast cancer risk and progression yet remains poorly understood. In breast stroma, collagen is the most abundantly expressed protein and its increased deposition and alignment contributes to progression and poor prognosis. Collagen post-translation modifications such as hydroxylated-proline (HYP) control deposition and stromal organization. The clinical relevance of collagen HYP site modifications in cancer processes remains undefined due to technical issues accessing collagen from formalin-fixed, paraffin-embedded (FFPE) tissues. We previously developed a targeted approach for investigating collagen and other extracellular matrix proteins from FFPE tissue. Here, we hypothesized that immunohistochemistry staining for fibroblastic markers would not interfere with targeted detection of collagen stroma peptides and could reveal peptide regulation influenced by specific cell types. Our initial work demonstrated that stromal peptide peak intensities when using MALD-IMS following IHC staining (αSMA, FAP, P4HA3 and PTEN) were comparable to serial sections of nonstained tissue. Analysis of histology-directed IMS using PTEN on breast tissues and TMAs revealed heterogeneous PTEN staining patterns and suggestive roles in stromal protein regulation. This study sets the foundation for investigations of target cell types and their unique contribution to collagen regulation within extracellular matrix niches.
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Affiliation(s)
- Denys Rujchanarong
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC 29425, USA; (D.R.); (J.E.S.); (S.P.); (J.R.B.); (L.E.B.); (A.S.M.); (R.R.D.)
| | - Julia Lefler
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; (J.L.); (M.C.O.)
| | - Janet E. Saunders
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC 29425, USA; (D.R.); (J.E.S.); (S.P.); (J.R.B.); (L.E.B.); (A.S.M.); (R.R.D.)
| | - Sarah Pippin
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC 29425, USA; (D.R.); (J.E.S.); (S.P.); (J.R.B.); (L.E.B.); (A.S.M.); (R.R.D.)
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Jennifer R. Bethard
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC 29425, USA; (D.R.); (J.E.S.); (S.P.); (J.R.B.); (L.E.B.); (A.S.M.); (R.R.D.)
| | - Lauren E. Ball
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC 29425, USA; (D.R.); (J.E.S.); (S.P.); (J.R.B.); (L.E.B.); (A.S.M.); (R.R.D.)
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC 29425, USA; (D.R.); (J.E.S.); (S.P.); (J.R.B.); (L.E.B.); (A.S.M.); (R.R.D.)
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC 29425, USA; (D.R.); (J.E.S.); (S.P.); (J.R.B.); (L.E.B.); (A.S.M.); (R.R.D.)
| | - Michael C. Ostrowski
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; (J.L.); (M.C.O.)
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC 29425, USA; (D.R.); (J.E.S.); (S.P.); (J.R.B.); (L.E.B.); (A.S.M.); (R.R.D.)
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; (J.L.); (M.C.O.)
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15
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Jiang X, Gao Y, Zhang N, Yuan C, Luo Y, Sun W, Zhang J, Ren J, Gong Y, Xie C. Establishment of Immune-related Gene Pair Signature to Predict Lung Adenocarcinoma Prognosis. Cell Transplant 2021; 29:963689720977131. [PMID: 33334139 PMCID: PMC7873765 DOI: 10.1177/0963689720977131] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Tumor microenvironment (TME) has critical impacts on the pathogenesis of lung adenocarcinoma (LUAD). However, the molecular mechanism of TME effects on the prognosis of LUAD patients remains unclear. Our study aimed to establish an immune-related gene pair (IRGP) model for prognosis prediction and internal mechanism investigation. Based on 702 TME-related differentially expressed genes (DEGs) extracted from The Cancer Genome Atlas (TCGA) training cohort using the ESTIMATE algorithm, a 10-IRGP signature was established to predict LUAD patient prognosis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that DEGs were significantly associated with tumor immune response. In both TCGA training and Gene Expression Omnibus validation datasets, the risk score was an independent prognostic factor for LUAD patients using Lasso-Cox analysis, and patients in the high-risk group had poorer prognosis than those in the low-risk one. In the high-risk group, M2 macrophage and neutrophil infiltrations were higher, while the levels of T cell follicular helpers were significantly lower. The gene set enrichment analysis results showed that DNA repair signaling pathways were involved. In summary, we established an IRGP signature as a potential biomarker to predict the prognosis of LUAD patients.
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Affiliation(s)
- Xueping Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yanping Gao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Nannan Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Cheng Yuan
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yuan Luo
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wenjie Sun
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jianguo Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jiangbo Ren
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Human Genetics Resource Preservation Center of Hubei Province, Human Genetics Resource Preservation Center of Wuhan University, Wuhan, Hubei, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
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16
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Basu SS, Agar NYR. Bringing Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging to the Clinics. Clin Lab Med 2021; 41:309-324. [PMID: 34020766 DOI: 10.1016/j.cll.2021.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is an emerging analytical technique that promises to change tissue-based diagnostics. This article provides a brief introduction to MALDI MSI as well as clinical diagnostic workflows and opportunities to apply this powerful approach. It describes various MALDI MSI applications, from more clinically mature applications such as cancer to emerging applications such as infectious diseases and drug distribution. In addition, it discusses the analytical considerations that need to be considered when bringing these approaches to different diagnostic problems and settings.
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Affiliation(s)
- Sankha S Basu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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17
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Clift CL, Su YR, Bichell D, Jensen Smith HC, Bethard JR, Norris-Caneda K, Comte-Walters S, Ball LE, Hollingsworth MA, Mehta AS, Drake RR, Angel PM. Collagen fiber regulation in human pediatric aortic valve development and disease. Sci Rep 2021; 11:9751. [PMID: 33963260 PMCID: PMC8105334 DOI: 10.1038/s41598-021-89164-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/19/2021] [Indexed: 02/03/2023] Open
Abstract
Congenital aortic valve stenosis (CAVS) affects up to 10% of the world population without medical therapies to treat the disease. New molecular targets are continually being sought that can halt CAVS progression. Collagen deregulation is a hallmark of CAVS yet remains mostly undefined. Here, histological studies were paired with high resolution accurate mass (HRAM) collagen-targeting proteomics to investigate collagen fiber production with collagen regulation associated with human AV development and pediatric end-stage CAVS (pCAVS). Histological studies identified collagen fiber realignment and unique regions of high-density collagen in pCAVS. Proteomic analysis reported specific collagen peptides are modified by hydroxylated prolines (HYP), a post-translational modification critical to stabilizing the collagen triple helix. Quantitative data analysis reported significant regulation of collagen HYP sites across patient categories. Non-collagen type ECM proteins identified (26 of the 44 total proteins) have direct interactions in collagen synthesis, regulation, or modification. Network analysis identified BAMBI (BMP and Activin Membrane Bound Inhibitor) as a potential upstream regulator of the collagen interactome. This is the first study to detail the collagen types and HYP modifications associated with human AV development and pCAVS. We anticipate that this study will inform new therapeutic avenues that inhibit valvular degradation in pCAVS and engineered options for valve replacement.
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Affiliation(s)
- Cassandra L Clift
- Department of Cell and Molecular Pharmacology, MUSC Proteomics Center, Bruker-MUSC Clinical Glycomics Center of Excellence, Medical University of South Carolina, 173 Ashley Ave, BSB358, Charleston, SC, 29425, USA
| | - Yan Ru Su
- Division of Pediatric Cardiac Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David Bichell
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Heather C Jensen Smith
- Eppley Institute for Cancer Research and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | | | | | - M A Hollingsworth
- Eppley Institute for Cancer Research and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology, MUSC Proteomics Center, Bruker-MUSC Clinical Glycomics Center of Excellence, Medical University of South Carolina, 173 Ashley Ave, BSB358, Charleston, SC, 29425, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology, MUSC Proteomics Center, Bruker-MUSC Clinical Glycomics Center of Excellence, Medical University of South Carolina, 173 Ashley Ave, BSB358, Charleston, SC, 29425, USA
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology, MUSC Proteomics Center, Bruker-MUSC Clinical Glycomics Center of Excellence, Medical University of South Carolina, 173 Ashley Ave, BSB358, Charleston, SC, 29425, USA.
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18
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Baruffaldi D, Palmara G, Pirri C, Frascella F. 3D Cell Culture: Recent Development in Materials with Tunable Stiffness. ACS APPLIED BIO MATERIALS 2021; 4:2233-2250. [PMID: 35014348 DOI: 10.1021/acsabm.0c01472] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
It is widely accepted that three-dimensional cell culture systems simulate physiological conditions better than traditional 2D systems. Although extracellular matrix components strongly modulate cell behavior, several studies underlined the importance of mechanosensing in the control of different cell functions such as growth, proliferation, differentiation, and migration. Human tissues are characterized by different degrees of stiffness, and various pathologies (e.g., tumor or fibrosis) cause changes in the mechanical properties through the alteration of the extracellular matrix structure. Additionally, these modifications have an impact on disease progression and on therapy response. Hence, the development of platforms whose stiffness could be modulated may improve our knowledge of cell behavior under different mechanical stress stimuli. In this review, we have analyzed the mechanical diversity of healthy and diseased tissues, and we have summarized recently developed materials with a wide range of stiffness.
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Affiliation(s)
- Désirée Baruffaldi
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin 10129, Italy.,PolitoBIOMed Lab, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin 10129, Italy
| | - Gianluca Palmara
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin 10129, Italy.,PolitoBIOMed Lab, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin 10129, Italy
| | - Candido Pirri
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin 10129, Italy.,PolitoBIOMed Lab, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin 10129, Italy.,Center for Sustainable Futures@Polito, Istituto Italiano di Tecnologia, Via Livorno 60, Turin 10144, Italy
| | - Francesca Frascella
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin 10129, Italy.,PolitoBIOMed Lab, Politecnico di Torino, C.so Duca degli Abruzzi 24, Turin 10129, Italy
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19
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Tiwari S, Kajdacsy-Balla A, Whiteley J, Cheng G, Hewitt SM, Bhargava R. INFORM: INFrared-based ORganizational Measurements of tumor and its microenvironment to predict patient survival. SCIENCE ADVANCES 2021; 7:7/6/eabb8292. [PMID: 33536203 PMCID: PMC7857685 DOI: 10.1126/sciadv.abb8292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 12/11/2020] [Indexed: 05/14/2023]
Abstract
The structure and organization of a tumor and its microenvironment are often associated with cancer outcomes due to spatially varying molecular composition and signaling. A persistent challenge is to use this physical and chemical spatial organization to understand cancer progression. Here, we present a high-definition infrared imaging-based organizational measurement framework (INFORM) that leverages intrinsic chemical contrast of tissue to label unique components of the tumor and its microenvironment. Using objective and automated computational methods, further, we determine organization characteristics important for prediction. We show that the tumor spatial organization assessed with this framework is predictive of overall survival in colon cancer that adds to capability from clinical variables such as stage and grade, approximately doubling the risk of death in high-risk individuals. Our results open an all-digital avenue for measuring and studying the association between tumor spatial organization and disease progression.
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Affiliation(s)
- Saumya Tiwari
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andre Kajdacsy-Balla
- Department of Pathology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Joshua Whiteley
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rohit Bhargava
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Departments of Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering and Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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20
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Clift CL, Mehta A, Drake RR, Angel PM. Multiplexed Imaging Mass Spectrometry of Histological Staining, N-Glycan and Extracellular Matrix from One Tissue Section: A Tool for Fibrosis Research. Methods Mol Biol 2021; 2350:313-329. [PMID: 34331294 DOI: 10.1007/978-1-0716-1593-5_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We describe a multiplexed imaging mass spectrometry approach especially suitable for fibrosis research. Fibrosis is a process characterized by excessive extracellular matrix (ECM) secretion. Buildup of ECM impairs tissue and organ function to promote further progression of disease. It is an ongoing analytical challenge to access ECM for diagnosis and therapeutic treatment of fibrosis. Recently, we reported the use of the enzyme collagenase type III to target the ECM proteome in thin histological tissue sections of fibrotic diseases including hepatocellular carcinoma, breast cancer, prostate cancer, lung cancer and aortic valve stenosis. Detection of collagenase type III peptides by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) allows localization of ECM peptide sequences to specific regions of fibrosis. We have further identified that the ECM proteome accessed by collagenase type III has on average 3.7 sites per protein that may be differentially N-glycosylated. N-glycosylation is a major posttranslational modification of the ECM proteome, influencing protein folding, secretion, and organization. Understanding both N-glycosylation signaling and regulation of ECM expression significantly informs on ECM signaling in fibrosis.
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Affiliation(s)
- Cassandra L Clift
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
| | - Anand Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA.
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21
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Angel PM, Spruill L, Jefferson M, Bethard JR, Ball LE, Hughes-Halbert C, Drake RR. Zonal regulation of collagen-type proteins and posttranslational modifications in prostatic benign and cancer tissues by imaging mass spectrometry. Prostate 2020; 80:1071-1086. [PMID: 32687633 PMCID: PMC7857723 DOI: 10.1002/pros.24031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND The emergence of reactive stroma is a hallmark of prostate cancer (PCa) progression and a potential source for prognostic and diagnostic markers of PCa. Collagen is a main component of reactive stroma and changes systematically and quantitatively to reflect the course of PCa, yet has remained undefined due to a lack of tools that can define collagen protein structure. Here we use a novel collagen-targeting proteomics approach to investigate zonal regulation of collagen-type proteins in PCa prostatectomies. METHODS Prostatectomies from nine patients were divided into zones containing 0%, 5%, 20%, 70% to 80% glandular tissue and 0%, 5%, 25%, 70% by mass of PCa tumor following the McNeal model. Tissue sections from zones were graded by a pathologist for Gleason score, percent tumor present, percent prostatic intraepithelial neoplasia and/or inflammation (INF). High-resolution accurate mass collagen targeting proteomics was done on a select subset of tissue sections from patient-matched tumor or nontumor zones. Imaging mass spectrometry was used to investigate collagen-type regulation corresponding to pathologist-defined regions. RESULTS Complex collagen proteomes were detected from all zones. COL17A and COL27A increased in zones of INF compared with zones with tumor present. COL3A1, COL4A5, and COL8A2 consistently increased in zones with tumor content, independent of tumor size. Collagen hydroxylation of proline (HYP) was altered in tumor zones compared with zones with INF and no tumor. COL3A1 and COL5A1 showed significant changes in HYP peptide ratios within tumor compared with zones of INF (2.59 ± 0.29, P value: .015; 3.75 ± 0.96 P value .036, respectively). By imaging mass spectrometry COL3A1 showed defined localization and regulation to tumor pathology. COL1A1 and COL1A2 showed gradient regulation corresponding to PCa pathology across zones. Pathologist-defined tumor regions showed significant increases in COL1A1 HYP modifications compared with COL1A2 HYP modifications. Certain COL1A1 and COL1A2 peptides could discriminate between pathologist-defined tumor and inflammatory regions. CONCLUSIONS Site-specific posttranslational regulation of collagen structure by proline hydroxylation may be involved in reactive stroma associated with PCa progression. Translational and posttranslational regulation of collagen protein structure has potential for new markers to understand PCa progression and outcomes.
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Affiliation(s)
- Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Proteomics Center, Medical University of South Carolina, Charleston, SC
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC
| | - Melanie Jefferson
- Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina, Charleston, SC
| | - Jennifer R. Bethard
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Proteomics Center, Medical University of South Carolina, Charleston, SC
| | - Lauren E. Ball
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Proteomics Center, Medical University of South Carolina, Charleston, SC
| | - Chanita Hughes-Halbert
- Department of Psychiatry & Behavioral Sciences, Medical University of South Carolina, Charleston, SC
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Proteomics Center, Medical University of South Carolina, Charleston, SC
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Resolving Metabolic Heterogeneity in Experimental Models of the Tumor Microenvironment from a Stable Isotope Resolved Metabolomics Perspective. Metabolites 2020; 10:metabo10060249. [PMID: 32549391 PMCID: PMC7345423 DOI: 10.3390/metabo10060249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022] Open
Abstract
The tumor microenvironment (TME) comprises complex interactions of multiple cell types that determines cell behavior and metabolism such as nutrient competition and immune suppression. We discuss the various types of heterogeneity that exist in solid tumors, and the complications this invokes for studies of TME. As human subjects and in vivo model systems are complex and difficult to manipulate, simpler 3D model systems that are compatible with flexible experimental control are necessary for studying metabolic regulation in TME. Stable Isotope Resolved Metabolomics (SIRM) is a valuable tool for tracing metabolic networks in complex systems, but at present does not directly address heterogeneous metabolism at the individual cell level. We compare the advantages and disadvantages of different model systems for SIRM experiments, with a focus on lung cancer cells, their interactions with macrophages and T cells, and their response to modulators in the immune microenvironment. We describe the experimental set up, illustrate results from 3D cultures and co-cultures of lung cancer cells with human macrophages, and outline strategies to address the heterogeneous TME.
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