1
|
Wu D, Thompson LU, Comelli EM. Cecal microbiota and mammary gland microRNA signatures are related and modifiable by dietary flaxseed with implications for breast cancer risk. Microbiol Spectr 2024; 12:e0229023. [PMID: 38059614 PMCID: PMC10783090 DOI: 10.1128/spectrum.02290-23] [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: 06/04/2023] [Accepted: 10/29/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE Breast cancer is a leading cause of cancer mortality worldwide. There is a growing interest in using dietary approaches, including flaxseed (FS) and its oil and lignan components, to mitigate breast cancer risk. Importantly, there is recognition that pubertal processes and lifestyle, including diet, are important for breast health throughout life. Mechanisms remain incompletely understood. Our research uncovers a link between mammary gland miRNA expression and the gut microbiota in young female mice. We found that this relationship is modifiable via a dietary intervention. Using data from The Cancer Genome Atlas, we also show that the expression of miRNAs involved in these relationships is altered in breast cancer in humans. These findings highlight a role for the gut microbiome as a modulator, and thus a target, of interventions aiming at reducing breast cancer risk. They also provide foundational knowledge to explore the effects of early life interventions and mechanisms programming breast health.
Collapse
Affiliation(s)
- Diana Wu
- Department of Nutritional Sciences, University of Toronto, Faculty of Medicine, Toronto, Canada
| | - Lilian U. Thompson
- Department of Nutritional Sciences, University of Toronto, Faculty of Medicine, Toronto, Canada
| | - Elena M. Comelli
- Department of Nutritional Sciences, University of Toronto, Faculty of Medicine, Toronto, Canada
- Joannah and Brian Lawson Centre for Child Nutrition, University of Toronto, Toronto, Canada
| |
Collapse
|
2
|
van Gogh M, Glaus Garzon JF, Sahin D, Knopfova L, Benes P, Boyman O, Jurisica I, Borsig L. Tumor Cell-Intrinsic c-Myb Upregulation Stimulates Antitumor Immunity in a Murine Colorectal Cancer Model. Cancer Immunol Res 2023; 11:1432-1444. [PMID: 37478172 PMCID: PMC10548106 DOI: 10.1158/2326-6066.cir-22-0912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/08/2023] [Accepted: 07/20/2023] [Indexed: 07/23/2023]
Abstract
The transcription factor c-Myb is overexpressed in many different types of solid tumors, including colorectal cancer. However, its exact role in tumorigenesis is unclear. In this study, we show that tumor-intrinsic c-Myb expression in mouse models of colon cancer and melanoma suppresses tumor growth. Although no differences in proliferation, apoptosis, and angiogenesis of tumors were evident in tumors with distinct levels of c-Myb expression, we observed changes in intratumoral immune cell infiltrates. MC38 tumors with upregulated c-Myb expression showed increased numbers of CD103+ dendritic cells and eosinophils, but decreased tumor-associated macrophages (TAM). Concomitantly, an increase in the number of activated cytotoxic CD8+ T cells upon c-Myb upregulation was observed, which correlated with a pro-inflammatory tumor microenvironment and increased numbers of M1 polarized TAMs. Mechanistically, c-Myb upregulation in immunogenic MC38 colon cancer cells resulted in enhanced expression of immunomodulatory genes, including those encoding β2-microglobulin and IFNβ, and decreased expression of the gene encoding the chemokine receptor CCR2. The increased numbers of activated cytotoxic CD8+ T cells contributed to tumor growth attenuation. In poorly immunogenic CT26, LLC, and B16-BL6 tumor cells, c-Myb upregulation did not affect the immunomodulatory gene expression. Despite this, c-Myb upregulation led to reduced B16-BL6 tumor growth but it did not affect tumor growth of CT26 and LLC tumors. Altogether, we postulate that c-Myb functions as a tumor suppressor in a tumor cell-type specific manner and modulates antitumor immunity.
Collapse
Affiliation(s)
- Merel van Gogh
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Dilara Sahin
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Lucia Knopfova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Petr Benes
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and, Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital (UHN), Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Faculty of Dentistry, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lubor Borsig
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, University Hospital of Zurich, Zurich, Switzerland
| |
Collapse
|
3
|
Wong SWH, Pastrello C, Kotlyar M, Faloutsos C, Jurisica I. USNAP: fast unique dense region detection and its application to lung cancer. Bioinformatics 2023; 39:btad477. [PMID: 37527019 PMCID: PMC10425186 DOI: 10.1093/bioinformatics/btad477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/09/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
MOTIVATION Many real-world problems can be modeled as annotated graphs. Scalable graph algorithms that extract actionable information from such data are in demand since these graphs are large, varying in topology, and have diverse node/edge annotations. When these graphs change over time they create dynamic graphs, and open the possibility to find patterns across different time points. In this article, we introduce a scalable algorithm that finds unique dense regions across time points in dynamic graphs. Such algorithms have applications in many different areas, including the biological, financial, and social domains. RESULTS There are three important contributions to this manuscript. First, we designed a scalable algorithm, USNAP, to effectively identify dense subgraphs that are unique to a time stamp given a dynamic graph. Importantly, USNAP provides a lower bound of the density measure in each step of the greedy algorithm. Second, insights and understanding obtained from validating USNAP on real data show its effectiveness. While USNAP is domain independent, we applied it to four non-small cell lung cancer gene expression datasets. Stages in non-small cell lung cancer were modeled as dynamic graphs, and input to USNAP. Pathway enrichment analyses and comprehensive interpretations from literature show that USNAP identified biologically relevant mechanisms for different stages of cancer progression. Third, USNAP is scalable, and has a time complexity of O(m+mc log nc+nc log nc), where m is the number of edges, and n is the number of vertices in the dynamic graph; mc is the number of edges, and nc is the number of vertices in the collapsed graph. AVAILABILITY AND IMPLEMENTATION The code of USNAP is available at https://www.cs.utoronto.ca/~juris/data/USNAP22.
Collapse
Affiliation(s)
- Serene W H Wong
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder
Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil
Research Institute, University Health Network, 60 Leonard Avenue,
Toronto, ON M5T 0S8, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder
Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil
Research Institute, University Health Network, 60 Leonard Avenue,
Toronto, ON M5T 0S8, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder
Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil
Research Institute, University Health Network, 60 Leonard Avenue,
Toronto, ON M5T 0S8, Canada
| | - Christos Faloutsos
- Department of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue,
Pittsburgh, PA 15213, United States
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder
Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil
Research Institute, University Health Network, 60 Leonard Avenue,
Toronto, ON M5T 0S8, Canada
- Department of Computer Science, University of Toronto, 40 St. George Street, Room
4283, Toronto, ON, M5S 2E4, Canada
- Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer
Research Tower, MaRS Centre, 101 College Street, Room 15-701, Toronto, ON, M5G 1L7,
Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, vvi, Dubravská cesta 9, 845
10 Bratislava 45, Slovakia
| |
Collapse
|
4
|
Traumatic MicroRNAs: Deconvolving the Signal After Severe Traumatic Brain Injury. Cell Mol Neurobiol 2023; 43:1061-1075. [PMID: 35852739 DOI: 10.1007/s10571-022-01254-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/02/2022] [Indexed: 11/03/2022]
Abstract
History of traumatic brain injury (TBI) represents a significant risk factor for development of dementia and neurodegenerative disorders in later life. While histopathological sequelae and neurological diagnostics of TBI are well defined, the molecular events linking the post-TBI signaling and neurodegenerative cascades remain unknown. It is not only due to the brain's inaccessibility to direct molecular analysis but also due to the lack of well-defined and highly informative peripheral biomarkers. MicroRNAs (miRNAs) in blood are promising candidates to address this gap. Using integrative bioinformatics pipeline including miRNA:target identification, pathway enrichment, and protein-protein interactions analysis we identified set of genes, interacting proteins, and pathways that are connected to previously reported peripheral miRNAs, deregulated following severe traumatic brain injury (sTBI) in humans. This meta-analysis revealed a spectrum of genes closely related to critical biological processes, such as neuroregeneration including axon guidance and neurite outgrowth, neurotransmission, inflammation, proliferation, apoptosis, cell adhesion, and response to DNA damage. More importantly, we have identified molecular pathways associated with neurodegenerative conditions, including Alzheimer's and Parkinson's diseases, based on purely peripheral markers. The pathway signature after acute sTBI is similar to the one observed in chronic neurodegenerative conditions, which implicates a link between the post-sTBI signaling and neurodegeneration. Identified key hub interacting proteins represent a group of novel candidates for potential therapeutic targets or biomarkers.
Collapse
|
5
|
Chicco D, Alameer A, Rahmati S, Jurman G. Towards a potential pan-cancer prognostic signature for gene expression based on probesets and ensemble machine learning. BioData Min 2022; 15:28. [PMID: 36329531 PMCID: PMC9632055 DOI: 10.1186/s13040-022-00312-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
Cancer is one of the leading causes of death worldwide and can be caused by environmental aspects (for example, exposure to asbestos), by human behavior (such as smoking), or by genetic factors. To understand which genes might be involved in patients’ survival, researchers have invented prognostic genetic signatures: lists of genes that can be used in scientific analyses to predict if a patient will survive or not. In this study, we joined together five different prognostic signatures, each of them related to a specific cancer type, to generate a unique pan-cancer prognostic signature, that contains 207 unique probesets related to 187 unique gene symbols, with one particular probeset present in two cancer type-specific signatures (203072_at related to the MYO1E gene). We applied our proposed pan-cancer signature with the Random Forests machine learning method to 57 microarray gene expression datasets of 12 different cancer types, and analyzed the results. We also compared the performance of our pan-cancer signature with the performances of two alternative prognostic signatures, and with the performances of each cancer type-specific signature on their corresponding cancer type-specific datasets. Our results confirmed the effectiveness of our prognostic pan-cancer signature. Moreover, we performed a pathway enrichment analysis, which indicated an association between the signature genes and a protein-protein interaction analysis, that highlighted PIK3R2 and FN1 as key genes having a fundamental relevance in our signature, suggesting an important role in pan-cancer prognosis for both of them.
Collapse
Affiliation(s)
- Davide Chicco
- grid.17063.330000 0001 2157 2938Institute of Health Policy Management and Evaluation, University of Toronto, 155 College Street, M5T 3M7 Toronto, Ontario Canada
| | - Abbas Alameer
- grid.411196.a0000 0001 1240 3921Department of Biological Sciences, Kuwait University, 13 KH Firdous Street, 13060 Kuwait City, Kuwait
| | - Sara Rahmati
- grid.231844.80000 0004 0474 0428Krembil Research Institute, 135 Nassau Street, M5T 1M8 Toronto, Ontario Canada
| | - Giuseppe Jurman
- grid.11469.3b0000 0000 9780 0901Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo (Trento), Italy
| |
Collapse
|
6
|
Agapito G, Milano M, Cannataro M. A Python Clustering Analysis Protocol of Genes Expression Data Sets. Genes (Basel) 2022; 13:genes13101839. [PMID: 36292724 PMCID: PMC9601308 DOI: 10.3390/genes13101839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Gene expression and SNPs data hold great potential for a new understanding of disease prognosis, drug sensitivity, and toxicity evaluations. Cluster analysis is used to analyze data that do not contain any specific subgroups. The goal is to use the data itself to recognize meaningful and informative subgroups. In addition, cluster investigation helps data reduction purposes, exposes hidden patterns, and generates hypotheses regarding the relationship between genes and phenotypes. Cluster analysis could also be used to identify bio-markers and yield computational predictive models. The methods used to analyze microarrays data can profoundly influence the interpretation of the results. Therefore, a basic understanding of these computational tools is necessary for optimal experimental design and meaningful data analysis. This manuscript provides an analysis protocol to effectively analyze gene expression data sets through the K-means and DBSCAN algorithms. The general protocol enables analyzing omics data to identify subsets of features with low redundancy and high robustness, speeding up the identification of new bio-markers through pathway enrichment analysis. In addition, to demonstrate the effectiveness of our clustering analysis protocol, we analyze a real data set from the GEO database. Finally, the manuscript provides some best practice and tips to overcome some issues in the analysis of omics data sets through unsupervised learning.
Collapse
Affiliation(s)
- Giuseppe Agapito
- Department of Law, Economics and Social Sciences, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
- Data Analytics Research Center, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence:
| | - Marianna Milano
- Data Analytics Research Center, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
- Department of Medical and Clinical Surgery, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
| | - Mario Cannataro
- Data Analytics Research Center, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
- Department of Medical and Clinical Surgery, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
| |
Collapse
|
7
|
Taheri G, Habibi M. Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method. Appl Soft Comput 2022; 128:109510. [PMID: 35992221 PMCID: PMC9384336 DOI: 10.1016/j.asoc.2022.109510] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/07/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022]
Abstract
The World Health Organization (WHO) introduced “Coronavirus disease 19” or “COVID-19” as a novel coronavirus in March 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the fast discovery of effective treatments to fight this worldwide crisis. Artificial intelligence and bioinformatics analysis pipelines can assist with finding biomarkers, explanations, and cures. Artificial intelligence and machine learning methods provide powerful infrastructures for interpreting and understanding the available data. On the other hand, pathway enrichment analysis, as a dominant tool, could help researchers discover potential key targets present in biological pathways of host cells that are targeted by SARS-CoV-2. In this work, we propose a two-stage machine learning approach for pathway analysis. During the first stage, four informative gene sets that can represent important COVID-19 related pathways are selected. These “representative genes” are associated with the COVID-19 pathology. Then, two distinctive networks were constructed for COVID-19 related signaling and disease pathways. In the second stage, the pathways of each network are ranked with respect to some unsupervised scorning method based on our defined informative features. Finally, we present a comprehensive analysis of the top important pathways in both networks. Materials and implementations are available at: https://github.com/MahnazHabibi/Pathway.
Collapse
Affiliation(s)
- Golnaz Taheri
- Department of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Mahnaz Habibi
- Department of Mathematics, Qazvin Branch, Islamic Azad University, Qazvin, Iran
| |
Collapse
|
8
|
Sotzny F, Filgueiras IS, Kedor C, Freitag H, Wittke K, Bauer S, Sepúlveda N, Mathias da Fonseca DL, Baiocchi GC, Marques AHC, Kim M, Lange T, Plaça DR, Luebber F, Paulus FM, De Vito R, Jurisica I, Schulze-Forster K, Paul F, Bellmann-Strobl J, Rust R, Hoppmann U, Shoenfeld Y, Riemekasten G, Heidecke H, Cabral-Marques O, Scheibenbogen C. Dysregulated autoantibodies targeting vaso- and immunoregulatory receptors in Post COVID Syndrome correlate with symptom severity. Front Immunol 2022; 13:981532. [PMID: 36238301 PMCID: PMC9552223 DOI: 10.3389/fimmu.2022.981532] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Most patients with Post COVID Syndrome (PCS) present with a plethora of symptoms without clear evidence of organ dysfunction. A subset of them fulfills diagnostic criteria of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Symptom severity of ME/CFS correlates with natural regulatory autoantibody (AAB) levels targeting several G-protein coupled receptors (GPCR). In this exploratory study, we analyzed serum AAB levels against vaso- and immunoregulatory receptors, mostly GPCRs, in 80 PCS patients following mild-to-moderate COVID-19, with 40 of them fulfilling diagnostic criteria of ME/CFS. Healthy seronegative (n=38) and asymptomatic post COVID-19 controls (n=40) were also included in the study as control groups. We found lower levels for various AABs in PCS compared to at least one control group, accompanied by alterations in the correlations among AABs. Classification using random forest indicated AABs targeting ADRB2, STAB1, and ADRA2A as the strongest classifiers (AABs stratifying patients according to disease outcomes) of post COVID-19 outcomes. Several AABs correlated with symptom severity in PCS groups. Remarkably, severity of fatigue and vasomotor symptoms were associated with ADRB2 AAB levels in PCS/ME/CFS patients. Our study identified dysregulation of AAB against various receptors involved in the autonomous nervous system (ANS), vaso-, and immunoregulation and their correlation with symptom severity, pointing to their role in the pathogenesis of PCS.
Collapse
Affiliation(s)
- Franziska Sotzny
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| | - Claudia Kedor
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Helma Freitag
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Kirsten Wittke
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Sandra Bauer
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Nuno Sepúlveda
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- CEAUL – Centro de Estatística e Aplicações da Universidade de Lisboa, Lisbon, Portugal
| | | | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre H. C. Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Myungjin Kim
- Data Science Initiative, Brown University, Providence, RI, United States
| | - Tanja Lange
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Finn Luebber
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Frieder M. Paulus
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Roberta De Vito
- Department of Biostatistics and the Data Science Initiative, Brown University, Providence, RI, United States
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Friedemann Paul
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- NeuroCure Clinical Research Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Judith Bellmann-Strobl
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Rebekka Rust
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Uta Hoppmann
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Affiliated with the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Hashomer, Israel
- Ariel University, Ariel, Israel
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | | | - Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Interunit PostGraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo, Sao Paulo, Brazil
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Sao Paulo, Brazil
- Department of Pharmacy, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| | - Carmen Scheibenbogen
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| |
Collapse
|
9
|
Laiakis EC, Pinheiro M, Nguyen T, Nguyen H, Beheshti A, Dutta SM, Russell WK, Emmett MR, Britten RA. Quantitative proteomic analytic approaches to identify metabolic changes in the medial prefrontal cortex of rats exposed to space radiation. Front Physiol 2022; 13:971282. [PMID: 36091373 PMCID: PMC9459391 DOI: 10.3389/fphys.2022.971282] [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: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
NASA’s planned mission to Mars will result in astronauts being exposed to ∼350 mSv/yr of Galactic Cosmic Radiation (GCR). A growing body of data from ground-based experiments indicates that exposure to space radiation doses (approximating those that astronauts will be exposed to on a mission to Mars) impairs a variety of cognitive processes, including cognitive flexibility tasks. Some studies report that 33% of individuals may experience severe cognitive impairment. Translating the results from ground-based rodent studies into tangible risk estimates for astronauts is an enormous challenge, but it would be germane for NASA to use the vast body of data from the rodent studies to start developing appropriate countermeasures, in the expectation that some level of space radiation (SR) -induced cognitive impairment could occur in astronauts. While some targeted studies have reported radiation-induced changes in the neurotransmission properties and/or increased neuroinflammation within space radiation exposed brains, there remains little information that can be used to start the development of a mechanism-based countermeasure strategy. In this study, we have employed a robust label-free mass spectrometry (MS) -based untargeted quantitative proteomic profiling approach to characterize the composition of the medial prefrontal cortex (mPFC) proteome in rats that have been exposed to 15 cGy of 600 MeV/n28Si ions. A variety of analytical techniques were used to mine the generated expression data, which in such studies is typically hampered by low and variable sample size. We have identified several pathways and proteins whose expression alters as a result of space radiation exposure, including decreased mitochondrial function, and a further subset of proteins differs in rats that have a high level of cognitive performance after SR exposure in comparison with those that have low performance levels. While this study has provided further insight into how SR impacts upon neurophysiology, and what adaptive responses can be invoked to prevent the emergence of SR-induced cognitive impairment, the main objective of this paper is to outline strategies that can be used by others to analyze sub-optimal data sets and to identify new information.
Collapse
Affiliation(s)
- Evagelia C. Laiakis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, United States
- *Correspondence: Evagelia C. Laiakis,
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV, United States
| | - Hung Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV, United States
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, Mountain View, CA, United States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Sucharita M. Dutta
- Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, VA, United States
| | - William K. Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Mark R. Emmett
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
- Department of Radiation Oncology, University of Texas Medical Branch, Galveston, TX, United States
| | - Richard A. Britten
- Department of Radiation Oncology, Eastern Virginia Medical School, Norfolk, VA, United States
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, United States
- Center for Integrative Neuroinflammatory and Inflammatory Diseases, Eastern Virginia Medical School, Norfolk, VA, United States
| |
Collapse
|
10
|
Cabral-Marques O, Halpert G, Schimke LF, Ostrinski Y, Vojdani A, Baiocchi GC, Freire PP, Filgueiras IS, Zyskind I, Lattin MT, Tran F, Schreiber S, Marques AHC, Plaça DR, Fonseca DLM, Humrich JY, Müller A, Giil LM, Graßhoff H, Schumann A, Hackel A, Junker J, Meyer C, Ochs HD, Lavi YB, Scheibenbogen C, Dechend R, Jurisica I, Schulze-Forster K, Silverberg JI, Amital H, Zimmerman J, Heidecke H, Rosenberg AZ, Riemekasten G, Shoenfeld Y. Autoantibodies targeting GPCRs and RAS-related molecules associate with COVID-19 severity. Nat Commun 2022; 13:1220. [PMID: 35264564 PMCID: PMC8907309 DOI: 10.1038/s41467-022-28905-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/16/2022] [Indexed: 12/27/2022] Open
Abstract
COVID-19 shares the feature of autoantibody production with systemic autoimmune diseases. In order to understand the role of these immune globulins in the pathogenesis of the disease, it is important to explore the autoantibody spectra. Here we show, by a cross-sectional study of 246 individuals, that autoantibodies targeting G protein-coupled receptors (GPCR) and RAS-related molecules associate with the clinical severity of COVID-19. Patients with moderate and severe disease are characterized by higher autoantibody levels than healthy controls and those with mild COVID-19 disease. Among the anti-GPCR autoantibodies, machine learning classification identifies the chemokine receptor CXCR3 and the RAS-related molecule AGTR1 as targets for antibodies with the strongest association to disease severity. Besides antibody levels, autoantibody network signatures are also changing in patients with intermediate or high disease severity. Although our current and previous studies identify anti-GPCR antibodies as natural components of human biology, their production is deregulated in COVID-19 and their level and pattern alterations might predict COVID-19 disease severity.
Collapse
Affiliation(s)
- Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil.
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Sao Paulo, Brazil.
| | - Gilad Halpert
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Saint Petersburg State University, Saint-Petersburg, Russia
| | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Yuri Ostrinski
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Saint Petersburg State University, Saint-Petersburg, Russia
- Ariel University, Ariel, Israel
| | - Aristo Vojdani
- Department of Immunology, Immunosciences Laboratory, Inc., Los Angeles, CA, United States
- Cyrex Laboratories, LLC 2602S. 24th St., Phoenix, AZ, 85034, USA
| | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Paula Paccielli Freire
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Israel Zyskind
- Department of Pediatrics, NYU Langone Medical Center, New York, NY, USA
- Maimonides Medical Center, Brooklyn, NY, USA
| | - Miriam T Lattin
- Department of Biology, Yeshiva University, Manhatten, NY, USA
| | - Florian Tran
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Alexandre H C Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Dennyson Leandro M Fonseca
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Jens Y Humrich
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Antje Müller
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Lasse M Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Hanna Graßhoff
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Anja Schumann
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Alexander Hackel
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Juliane Junker
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Carlotta Meyer
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, USA
| | - Yael Bublil Lavi
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Carmen Scheibenbogen
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ralf Dechend
- Experimental and Clinical Research Center, a collaboration of Max Delbruck Center for Molecular Medicine and Charité Universitätsmedizin, and HELIOS Clinic, Department of Cardiology and Nephrology, Berlin, 13125, Germany
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN; Data Science Discovery Centre, Krembil Research Institute, UHN, Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Kai Schulze-Forster
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Jonathan I Silverberg
- School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Howard Amital
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Department of Medicine B, Sheba Medical Center, Tel Hashomer, Israel
| | | | - Harry Heidecke
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Gabriela Riemekasten
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany.
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel.
- Saint Petersburg State University, Saint-Petersburg, Russia.
- Ariel University, Ariel, Israel.
| |
Collapse
|
11
|
Pastrello C, Niu Y, Jurisica I. Pathway Enrichment Analysis of Microarray Data. Methods Mol Biol 2022; 2401:147-159. [PMID: 34902127 DOI: 10.1007/978-1-0716-1839-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microarray analyses usually result in a list of differential genes that need to be annotated to link them the phenotype being studied, help planning validation experiments and interpretation of the results. Pathway enrichment analyses are frequently used for such purpose, where pathways are human created models of molecular activities and processes. While different types of pathway enrichment are available, we focus this protocol on the most frequent type-overrepresentation analysis. Many databases collect different sets of pathways and curate different sets of genes for the same pathways, so it is important to carefully choose the most suitable pathway source to perform enrichment analysis. To provide a comprehensive pathway analysis, in this protocol we will use pathDIP, which supports comprehensive enrichment analysis by integrating 22 main pathway databases. We will also describe the steps needed to visualize the enriched pathways using GSOAP.
Collapse
Affiliation(s)
- Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Yun Niu
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada.
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
| |
Collapse
|
12
|
Hollander M, Do T, Will T, Helms V. Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data. FRONTIERS IN BIOINFORMATICS 2021; 1:724297. [PMID: 36303788 PMCID: PMC9581068 DOI: 10.3389/fbinf.2021.724297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/23/2021] [Indexed: 12/25/2022] Open
Abstract
Proteins rarely carry out their cellular functions in isolation. Instead, eukaryotic proteins engage in about six interactions with other proteins on average. The aggregated protein interactome of an organism forms a “hairy ball”-type protein-protein interaction (PPI) network. Yet, in a typical human cell, only about half of all proteins are expressed at a particular time. Hence, it has become common practice to prune the full PPI network to the subset of expressed proteins. If RNAseq data is available, one can further resolve the specific protein isoforms present in a cell or tissue. Here, we review various approaches, software tools and webservices that enable users to construct context-specific or tissue-specific PPI networks and how these are rewired between two cellular conditions. We illustrate their different functionalities on the example of the interactions involving the human TNR6 protein. In an outlook, we describe how PPI networks may be integrated with epigenetic data or with data on the activity of splicing factors.
Collapse
|
13
|
Zhao Y, Cai H, Zhang Z, Tang J, Li Y. Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data. Nat Commun 2021; 12:5261. [PMID: 34489404 PMCID: PMC8421403 DOI: 10.1038/s41467-021-25534-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
The advent of single-cell RNA sequencing (scRNA-seq) technologies has revolutionized transcriptomic studies. However, large-scale integrative analysis of scRNA-seq data remains a challenge largely due to unwanted batch effects and the limited transferabilty, interpretability, and scalability of the existing computational methods. We present single-cell Embedded Topic Model (scETM). Our key contribution is the utilization of a transferable neural-network-based encoder while having an interpretable linear decoder via a matrix tri-factorization. In particular, scETM simultaneously learns an encoder network to infer cell type mixture and a set of highly interpretable gene embeddings, topic embeddings, and batch-effect linear intercepts from multiple scRNA-seq datasets. scETM is scalable to over 106 cells and confers remarkable cross-tissue and cross-species zero-shot transfer-learning performance. Using gene set enrichment analysis, we find that scETM-learned topics are enriched in biologically meaningful and disease-related pathways. Lastly, scETM enables the incorporation of known gene sets into the gene embeddings, thereby directly learning the associations between pathways and topics via the topic embeddings.
Collapse
Affiliation(s)
- Yifan Zhao
- School of Computer Science, McGill University, Montreal, QC, Canada
- Harvard-MIT Health Sciences and Technology, Cambridge, MA, USA
| | - Huiyu Cai
- Department of Machine Intelligence, Peking University, Beijing, China
| | - Zuobai Zhang
- School of Computer Science, Fudan University, Shanghai, China
| | | | - Yue Li
- School of Computer Science, McGill University, Montreal, QC, Canada.
| |
Collapse
|
14
|
Insights into the pathogenesis of psoriatic arthritis from genetic studies. Semin Immunopathol 2021; 43:221-234. [PMID: 33712923 DOI: 10.1007/s00281-021-00843-2] [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: 11/16/2020] [Accepted: 01/19/2021] [Indexed: 12/20/2022]
Abstract
Psoriatic arthritis (PsA) is a relatively common inflammatory arthritis, a spondyloarthritis (SpA), that occurs most often in patients with psoriasis, a common immune-mediated inflammatory skin disease. Both psoriasis and PsA are highly heritable. Genetic and recent genomic studies have identified variants associated with psoriasis and PsA, but variants differentiating psoriasis from PsA are few. In this review, we describe recent developments in understanding the genetic burden of PsA, linkage, association and epigenetic studies. Using pathway analysis, we provide further insights into the similarities and differences between PsA and psoriasis, as well as between PsA and other immune-mediated inflammatory diseases, particularly ankylosing spondylitis, another SpA. Environmental factors that may trigger PsA in patients with psoriasis are also reviewed. To further understand the pathogenetic differences between PsA and psoriasis as well as other SpA, larger cohort studies of well-phenotyped subjects with integrated analysis of genomic, epigenomic, transcriptomic, proteomic and metabolomic data using interomic system biology approaches are required.
Collapse
|
15
|
Rahmati S, O'Rielly DD, Li Q, Codner D, Dohey A, Jenkins K, Jurisica I, Gladman DD, Chandran V, Rahman P. Rho-GTPase pathways may differentiate treatment response to TNF-alpha and IL-17A inhibitors in psoriatic arthritis. Sci Rep 2020; 10:21703. [PMID: 33303908 PMCID: PMC7728744 DOI: 10.1038/s41598-020-78866-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/01/2020] [Indexed: 12/14/2022] Open
Abstract
Biological therapies have dramatically improved the therapeutic landscape of psoriatic arthritis (PsA); however, 40–50% of patients are primary non-responders with response rates declining significantly with each successive biological therapy. Therefore, there is a pressing need to develop a coherent strategy for effective initial and subsequent selection of biologic agents. We interrogated 40 PsA patients initiating either tumour necrosis factor inhibitors (TNFi) or interleukin-17A inhibitors (17Ai) for active PsA. Patients achieving low disease activity according to the Disease Activity Index for PsA (DAPSA) at 3 months were classified as responders. Baseline and 3-month CD4+ transcript profiling were performed, and novel signaling pathways were identified using a multi-omics profiling and integrative computational analysis approach. Using transcriptomic data at initiation of therapy, we identified over 100 differentially expressed genes (DEGs) that differentiated IL-17Ai response from non-response and TNFi response from non-response. Integration of cell-type-specific DEGs with protein–protein interactions and further comprehensive pathway enrichment analysis revealed several pathways. Rho GTPase signaling pathway exhibited a strong signal specific to IL-17Ai response and the genes, RAC1 and ROCKs, are supported by results from prior research. Our detailed network and pathway analyses have identified the rewiring of Rho GTPase pathways as potential markers of response to IL17Ai but not TNFi. These results need further verification.
Collapse
Affiliation(s)
- Sara Rahmati
- Krembil Research Institute, UHN, 5-KD405, Krembil Discovery Tower, 60 Leonard Ave, Toronto, M5T 2S8, Canada.,Faculty of Medicine, Craig L Dobbin Genetics Research Centre, Memorial University, Suite 3M500, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada
| | - Darren D O'Rielly
- Faculty of Medicine, Craig L Dobbin Genetics Research Centre, Memorial University, Suite 3M500, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada
| | - Quan Li
- Krembil Research Institute, UHN, 5-KD405, Krembil Discovery Tower, 60 Leonard Ave, Toronto, M5T 2S8, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G1L7, Canada
| | - Dianne Codner
- Faculty of Medicine, Craig L Dobbin Genetics Research Centre, Memorial University, Suite 3M500, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada.,Faculty of Medicine, 5M202 Craig L Dobbin Genetics Research Centre, Memorial University, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada
| | - Amanda Dohey
- Faculty of Medicine, Craig L Dobbin Genetics Research Centre, Memorial University, Suite 3M500, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada.,Faculty of Medicine, 5M203 Craig L Dobbin Genetics Research Centre, Memorial University, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada
| | - Kari Jenkins
- Faculty of Medicine, Craig L Dobbin Genetics Research Centre, Memorial University, Suite 3M500, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada.,St. Clare's Mercy Hosptial, 154 LeMarchant Rd., St. John's, NL, A1C5B8, Canada
| | - Igor Jurisica
- Krembil Research Institute, UHN, 5-KD405, Krembil Discovery Tower, 60 Leonard Ave, Toronto, M5T 2S8, Canada.,University of Toronto, Toronto, Canada.,Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada
| | - Dafna D Gladman
- Krembil Research Institute, UHN, 5-KD405, Krembil Discovery Tower, 60 Leonard Ave, Toronto, M5T 2S8, Canada.,University of Toronto, Toronto, Canada.,Toronto Western Hospital, 399 Bathurst Street, 1E410B, Toronto, M5T 2S8, Canada
| | - Vinod Chandran
- Krembil Research Institute, UHN, 5-KD405, Krembil Discovery Tower, 60 Leonard Ave, Toronto, M5T 2S8, Canada.,Faculty of Medicine, Craig L Dobbin Genetics Research Centre, Memorial University, Suite 3M500, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada.,University of Toronto, Toronto, Canada.,Toronto Western Hospital, 399 Bathurst Street, 1E416, Toronto, M5T 2S8, Canada
| | - Proton Rahman
- Faculty of Medicine, Craig L Dobbin Genetics Research Centre, Memorial University, Suite 3M500, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada. .,St. Clare's Mercy Hosptial, 154 LeMarchant Rd., St. John's, NL, A1C5B8, Canada.
| |
Collapse
|
16
|
Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S. Towards a unified open access dataset of molecular interactions. Nat Commun 2020; 11:6144. [PMID: 33262342 PMCID: PMC7708836 DOI: 10.1038/s41467-020-19942-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The International Molecular Exchange (IMEx) Consortium provides scientists with a single body of experimentally verified protein interactions curated in rich contextual detail to an internationally agreed standard. In this update to the work of the IMEx Consortium, we discuss how this initiative has been working in practice, how it has ensured database sustainability, and how it is meeting emerging annotation challenges through the introduction of new interactor types and data formats. Additionally, we provide examples of how IMEx data are being used by biomedical researchers and integrated in other bioinformatic tools and resources.
Collapse
Affiliation(s)
- Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Elisabet Barrera
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alan Bridge
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland
| | - Noemi Del-Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Gianni Cesareni
- University of Rome Tor Vergata, Rome, Italy.,IRCCS Fondazione Santa Lucia, 00143, Rome, Italy
| | - Margaret Duesbury
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK.,UCLA-DOE Institute, University of California, Los Angeles, CA, 90095, USA
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada.,Departments of Medical Biophysics, and Computer Science, University of Toronto, Toronto, ON, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada
| | | | - Ruth C Lovering
- Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, WC1E 6JF, UK
| | - David J Lynn
- Computational and Systems Biology Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.,College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Birgit Meldal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Bindu Nanduri
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA
| | - Kalpana Paneerselvam
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Simona Panni
- Università della Calabria, Dipartimento di Biologia, Ecologia e Scienze della Terra, Via Pietro Bucci Cubo 6/C, Rende, CS, Italy
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, UCLA, Box 951606, Los Angeles, CA, 90095-1606, USA
| | - Livia Perfetto
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Negin Rahimzadeh
- UCLA-DOE Institute, University of California, Los Angeles, CA, 90095, USA
| | - Prashansa Ratan
- UCLA-DOE Institute, University of California, Los Angeles, CA, 90095, USA
| | - Sylvie Ricard-Blum
- ICBMS, UMR 5246 University Lyon 1 - CNRS, Univ. Lyon, 69622, Villeurbanne, France
| | - Lukasz Salwinski
- UCLA-DOE Institute, University of California, Los Angeles, CA, 90095, USA
| | - Gautam Shirodkar
- UCLA-DOE Institute, University of California, Los Angeles, CA, 90095, USA
| | - Anjalia Shrivastava
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Campus, Hinxton, Cambridge, CB10 1SD, UK.
| |
Collapse
|
17
|
Clotet-Freixas S, McEvoy CM, Batruch I, Pastrello C, Kotlyar M, Van JAD, Arambewela M, Boshart A, Farkona S, Niu Y, Li Y, Famure O, Bozovic A, Kulasingam V, Chen P, Kim SJ, Chan E, Moshkelgosha S, Rahman SA, Das J, Martinu T, Juvet S, Jurisica I, Chruscinski A, John R, Konvalinka A. Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection: A Proteomics Study. J Am Soc Nephrol 2020; 31:2705-2724. [PMID: 32900843 DOI: 10.1681/asn.2020030286] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Antibody-mediated rejection (AMR) accounts for >50% of kidney allograft loss. Donor-specific antibodies (DSA) against HLA and non-HLA antigens in the glomeruli and the tubulointerstitium cause AMR while inflammatory cytokines such as TNFα trigger graft injury. The mechanisms governing cell-specific injury in AMR remain unclear. METHODS Unbiased proteomic analysis of laser-captured and microdissected glomeruli and tubulointerstitium was performed on 30 for-cause kidney biopsy specimens with early AMR, acute cellular rejection (ACR), or acute tubular necrosis (ATN). RESULTS A total of 107 of 2026 glomerular and 112 of 2399 tubulointerstitial proteins was significantly differentially expressed in AMR versus ACR; 112 of 2026 glomerular and 181 of 2399 tubulointerstitial proteins were significantly dysregulated in AMR versus ATN (P<0.05). Basement membrane and extracellular matrix (ECM) proteins were significantly decreased in both AMR compartments. Glomerular and tubulointerstitial laminin subunit γ-1 (LAMC1) expression decreased in AMR, as did glomerular nephrin (NPHS1) and receptor-type tyrosine-phosphatase O (PTPRO). The proteomic analysis revealed upregulated galectin-1, which is an immunomodulatory protein linked to the ECM, in AMR glomeruli. Anti-HLA class I antibodies significantly increased cathepsin-V (CTSV) expression and galectin-1 expression and secretion in human glomerular endothelial cells. CTSV had been predicted to cleave ECM proteins in the AMR glomeruli. Glutathione S-transferase ω-1, an ECM-modifying enzyme, was significantly increased in the AMR tubulointerstitium and in TNFα-treated proximal tubular epithelial cells. CONCLUSIONS Basement membranes are often remodeled in chronic AMR. Proteomic analysis performed on laser-captured and microdissected glomeruli and tubulointerstitium identified early ECM remodeling, which may represent a new therapeutic opportunity.
Collapse
Affiliation(s)
- Sergi Clotet-Freixas
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Caitriona M McEvoy
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| | - Ihor Batruch
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Chiara Pastrello
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Julie Anh Dung Van
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Madhurangi Arambewela
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Alex Boshart
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Sofia Farkona
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Yun Niu
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Yanhong Li
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Olusegun Famure
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Andrea Bozovic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Peixuen Chen
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - S Joseph Kim
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| | - Emilie Chan
- Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| | - Sajad Moshkelgosha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Division of Respirology, Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Syed Ashiqur Rahman
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,Center for Systems Immunology, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jishnu Das
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,Center for Systems Immunology, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Tereza Martinu
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Division of Respirology, Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada.,Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, Ontario, Canada
| | - Stephen Juvet
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Division of Respirology, Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada.,Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, Ontario, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Andrzej Chruscinski
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, Ontario, Canada
| | - Rohan John
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ana Konvalinka
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada .,Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, Ontario, Canada
| |
Collapse
|
18
|
Perfetto L, Pastrello C, Del-Toro N, Duesbury M, Iannuccelli M, Kotlyar M, Licata L, Meldal B, Panneerselvam K, Panni S, Rahimzadeh N, Ricard-Blum S, Salwinski L, Shrivastava A, Cesareni G, Pellegrini M, Orchard S, Jurisica I, Hermjakob HH, Porras P. The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.16.153817. [PMID: 32587962 PMCID: PMC7310617 DOI: 10.1101/2020.06.16.153817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The current Coronavirus Disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions enables studying fine-grained resolution of the mechanisms behind the virus biology and the human organism response. Here we present a curated dataset of physical molecular interactions, manually extracted by IMEx Consortium curators focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family. Currently, the dataset comprises over 2,200 binarized interactions extracted from 86 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website ( www.ebi.ac.uk/intact ), and will be continuously updated as research on COVID-19 progresses.
Collapse
Affiliation(s)
- L Perfetto
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - C Pastrello
- Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
| | - N Del-Toro
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - M Duesbury
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- UCLA-DOE Institute, UCLA, Los Angeles, USA
| | - M Iannuccelli
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
| | - M Kotlyar
- Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
| | - L Licata
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
| | - B Meldal
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - K Panneerselvam
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - S Panni
- Department of Biology, Ecology and Earth Sciences, Università della Calabria, Rende, Italy
| | - N Rahimzadeh
- UCLA-DOE Institute, UCLA, Los Angeles, USA
- Providence John Wayne Cancer Institute, Santa Monica, USA
| | - S Ricard-Blum
- Univ Lyon, University Claude Bernard Lyon 1, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne, France
| | | | - A Shrivastava
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - G Cesareni
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
| | - M Pellegrini
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, USA
| | - S Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - I Jurisica
- Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada
| | - H H Hermjakob
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - P Porras
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| |
Collapse
|
19
|
Van JAD, Clotet-Freixas S, Hauschild AC, Batruch I, Jurisica I, Elia Y, Mahmud FH, Sochett E, Diamandis EP, Scholey JW, Konvalinka A. Urinary proteomics links keratan sulfate degradation and lysosomal enzymes to early type 1 diabetes. PLoS One 2020; 15:e0233639. [PMID: 32453760 PMCID: PMC7250451 DOI: 10.1371/journal.pone.0233639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/09/2020] [Indexed: 01/09/2023] Open
Abstract
Diabetes is the leading cause of end-stage renal disease worldwide. Our understanding of the early kidney response to chronic hyperglycemia remains incomplete. To address this, we first investigated the urinary proteomes of otherwise healthy youths with and without type 1 diabetes and subsequently examined the enriched pathways that might be dysregulated in early disease using systems biology approaches. This cross-sectional study included two separate cohorts for the discovery (N = 30) and internal validation (N = 30) of differentially excreted proteins. Discovery proteomics was performed on a Q Exactive Plus hybrid quadrupole-orbitrap mass spectrometer. We then searched the pathDIP, KEGG, and Reactome databases to identify enriched pathways in early diabetes; the Integrated Interactions Database to retrieve protein-protein interaction data; and the PubMed database to compare fold changes of our signature proteins with those published in similarly designed studies. Proteins were selected for internal validation based on pathway enrichment and availability of commercial enzyme-linked immunosorbent assay kits. Of the 2451 proteins identified, 576 were quantified in all samples from the discovery cohort; 34 comprised the urinary signature for early diabetes after Benjamini-Hochberg adjustment (Q < 0.05). The top pathways associated with this signature included lysosome, glycosaminoglycan degradation, and innate immune system (Q < 0.01). Notably, all enzymes involved in keratan sulfate degradation were significantly elevated in urines from youths with diabetes (|fold change| > 1.6). Increased urinary excretion of monocyte differentiation antigen CD14, hexosaminidase A, and lumican was also observed in the validation cohort (P < 0.05). Twenty-one proteins from our signature have been reported elsewhere as potential mediators of early diabetes. In this study, we identified a urinary proteomic signature for early type 1 diabetes, of which lysosomal enzymes were major constituents. Our findings highlight novel pathways such as keratan sulfate degradation in the early kidney response to hyperglycemia.
Collapse
Affiliation(s)
- Julie A. D. Van
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- * E-mail:
| | - Sergi Clotet-Freixas
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Anne-Christin Hauschild
- Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Mathematics & Computer Science, University of Marburg, Marburg, Germany
| | - Ihor Batruch
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Yesmino Elia
- Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, University of Toronto, Toronto, Canada
| | - James W. Scholey
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| | - Ana Konvalinka
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| |
Collapse
|
20
|
Pinheiro M, Lupinacci FCS, Santiago KM, Drigo SA, Marchi FA, Fonseca-Alves CE, Andrade SCDS, Aagaard MM, Basso TR, dos Reis MB, Villacis RAR, Roffé M, Hajj GNM, Jurisica I, Kowalski LP, Achatz MI, Rogatto SR. Germline Mutation in MUS81 Resulting in Impaired Protein Stability is Associated with Familial Breast and Thyroid Cancer. Cancers (Basel) 2020; 12:cancers12051289. [PMID: 32443704 PMCID: PMC7281423 DOI: 10.3390/cancers12051289] [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: 03/25/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 01/10/2023] Open
Abstract
Multiple primary thyroid cancer (TC) and breast cancer (BC) are commonly diagnosed, and the lifetime risk for these cancers is increased in patients with a positive family history of both TC and BC. Although this phenotype is partially explained by TP53 or PTEN mutations, a significant number of patients are negative for these alterations. We judiciously recruited patients diagnosed with BC and/or TC having a family history of these tumors and assessed their whole-exome sequencing. After variant prioritization, we selected MUS81 c.1292G>A (p.R431H) for further investigation. This variant was genotyped in a healthy population and sporadic BC/TC tissues and investigated at the protein level and cellular models. MUS81 c.1292G>A was the most frequent variant (25%) and the strongest candidate due to its function of double-strand break repair. This variant was confirmed in four relatives from two families. MUS81 p.R431H protein exhibited lower expression levels in tumors from patients positive for the germline variant, compared with wild-type BC, and normal breast and thyroid tissues. Using cell line models, we showed that c.1292G>A induced protein instability and affected DNA damage response. We suggest that MUS81 is a novel candidate involved in familial BC/TC based on its low frequency in healthy individuals and proven effect in protein stability.
Collapse
Affiliation(s)
- Maisa Pinheiro
- Faculty of Medicine, Sao Paulo State University, UNESP, Botucatu SP 18618-687, Brazil;
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Fernanda Cristina Sulla Lupinacci
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Karina Miranda Santiago
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Sandra Aparecida Drigo
- Department of Surgery and Orthopedics, Experimental Research Unity, Faculty of Medicine, São Paulo State University, UNESP, Botucatu SP 18618-687, Brazil;
| | - Fabio Albuquerque Marchi
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Carlos Eduardo Fonseca-Alves
- Department of Veterinary Surgery and Anesthesiology, São Paulo State University, UNESP, Botucatu SP 18618-681, Brazil;
| | | | - Mads Malik Aagaard
- Department of Clinical Genetics, Vejle University Hospital, 7100 Vejle, Denmark;
| | - Tatiane Ramos Basso
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Mariana Bisarro dos Reis
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Rolando André Rios Villacis
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, UnB, Brasília DF 70910-900, Brazil;
| | - Martin Roffé
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Glaucia Noeli Maroso Hajj
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Igor Jurisica
- Krembil Research Institute, UHN, University of Toronto, Toronto, ON M5G 2C4, Canada;
- Institute of Neuroimmunology, Slovak Academy of Sciences, 845 10 Bratislava, Slovakia
| | - Luiz Paulo Kowalski
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Maria Isabel Achatz
- Cancer Genetics Unit, Centro de Oncologia, Hospital Sirio Libanês, São Paulo SP 01308-050, Brazil;
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, Vejle University Hospital, Institute of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
- Correspondence:
| |
Collapse
|
21
|
Sinsky J, Majerova P, Kovac A, Kotlyar M, Jurisica I, Hanes J. Physiological Tau Interactome in Brain and Its Link to Tauopathies. J Proteome Res 2020; 19:2429-2442. [PMID: 32357304 DOI: 10.1021/acs.jproteome.0c00137] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Alzheimer's disease (AD) and most of the other tauopathies are incurable neurodegenerative diseases with unpleasant symptoms and consequences. The common hallmark of all of these diseases is tau pathology, but its connection with disease progress has not been completely understood so far. Therefore, uncovering novel tau-interacting partners and pathology affected molecular pathways can reveal the causes of diseases as well as potential targets for the development of AD treatment. Despite the large number of known tau-interacting partners, a limited number of studies focused on in vivo tau interactions in disease or healthy conditions are available. Here, we applied an in vivo cross-linking approach, capable of capturing weak and transient protein-protein interactions, to a unique transgenic rat model of progressive tau pathology similar to human AD. We have identified 175 potential novel and known tau-interacting proteins by MALDI-TOF mass spectrometry. Several of the most promising candidates for possible drug development were selected for validation by coimmunoprecipitation and colocalization experiments in animal and cellular models. Three proteins, Baiap2, Gpr37l1, and Nptx1, were confirmed as novel tau-interacting partners, and on the basis of their known functions and implications in neurodegenerative or psychiatric disorders, we proposed their potential role in tau pathology.
Collapse
Affiliation(s)
- Jakub Sinsky
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia.,AXON Neuroscience R&D Services SE, Dvorakovo nabrezie 10, Bratislava 811 02, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia.,AXON Neuroscience R&D Services SE, Dvorakovo nabrezie 10, Bratislava 811 02, Slovakia
| | - Max Kotlyar
- Krembil Research Institute, UHN, 60 Leonard Avenue, Toronto, Ontario M5T 0S8, Canada
| | - Igor Jurisica
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia.,Krembil Research Institute, UHN, 60 Leonard Avenue, Toronto, Ontario M5T 0S8, Canada.,Departments of Medical Biophysics and Computer Science, University of Toronto, 27 King's College Circle, Toronto, Ontario ON M5S, Canada
| | - Jozef Hanes
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia.,AXON Neuroscience R&D Services SE, Dvorakovo nabrezie 10, Bratislava 811 02, Slovakia
| |
Collapse
|
22
|
Abstract
PURPOSE OF THE REVIEW To provide a general overview and current challenges regarding the genetics of psoriatic disease. With the use of integrative medicine, multiple candidate loci identified to date in psoriatic disease will be annotated, summarized, and visualized. Recent studies reporting differences in genetic architecture between psoriatic arthritis and cutaneous-only psoriasis will be highlighted. RECENT FINDINGS Focusing on functional pathways that connect previously identified genetic variants can increase our understanding of psoriatic diseases. The genetic architecture differs between psoriatic arthritis and cutaneous-only psoriasis with arthritis-specific signals in linkage disequilibrium independent of the published psoriasis signals. Integrative medicine is helpful in understanding cellular mechanisms of psoriatic diseases. Careful selection of the psoriatic disease cohort has translated into mechanistic differences among psoriatic arthritis and cutaneous psoriasis.
Collapse
Affiliation(s)
- Sara Rahmati
- Department of Medicine, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, A1B 3X9, Canada
- Krembil Research Institute, University Health Network, Toronto, Ontario, M5S 1A8, Canada
| | - Lam Tsoi
- Department of Computational Medicine & Bioinformatics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Darren O'Rielly
- Department of Medicine, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, A1B 3X9, Canada
| | - Vinod Chandran
- Department of Medicine, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, A1B 3X9, Canada
- Krembil Research Institute, University Health Network, Toronto, Ontario, M5S 1A8, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Proton Rahman
- Department of Medicine, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, A1B 3X9, Canada.
| |
Collapse
|
23
|
Perfetto L, Pastrello C, del-Toro N, Duesbury M, Iannuccelli M, Kotlyar M, Licata L, Meldal B, Panneerselvam K, Panni S, Rahimzadeh N, Ricard-Blum S, Salwinski L, Shrivastava A, Cesareni G, Pellegrini M, Orchard S, Jurisica I, Hermjakob H, Porras P. The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. Database (Oxford) 2020; 2020:baaa096. [PMID: 33206959 PMCID: PMC7673336 DOI: 10.1093/database/baaa096] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022]
Abstract
The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions can provide fine-grained resolution of the mechanisms behind the virus biology and the human organism response. We present a curated dataset of physical molecular interactions focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family that has been manually extracted by International Molecular Exchange (IMEx) Consortium curators. Currently, the dataset comprises over 4400 binarized interactions extracted from 151 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (https://www.ebi.ac.uk/intact) and will be continuously updated as research on COVID-19 progresses.
Collapse
Affiliation(s)
- L Perfetto
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - C Pastrello
- Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
| | - N del-Toro
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - M Duesbury
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
- UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA
| | - M Iannuccelli
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - M Kotlyar
- Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
| | - L Licata
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - B Meldal
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - K Panneerselvam
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - S Panni
- Department of Biology, Ecology and Earth Sciences, Università della Calabria, Rende, 87036, Italy
| | - N Rahimzadeh
- UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA
- Providence John Wayne Cancer Institute, Department of Translational Molecular, Santa Monica, CA 90404, USA
| | - S Ricard-Blum
- Univ Lyon, University Claude Bernard Lyon 1, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Villeurbanne, 69622, France
| | - L Salwinski
- UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA
| | - A Shrivastava
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - G Cesareni
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - M Pellegrini
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA 90095, USA
| | - S Orchard
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - I Jurisica
- Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, M5T 0S8, Canada
| | - H Hermjakob
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| | - P Porras
- European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK
| |
Collapse
|