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Liu Z, Wu B, Shi X, Zhou J, Huang H, Li Z, Yang M. Immune profiling of premalignant lesions in patients with Peutz-Jeghers syndrome. United European Gastroenterol J 2024. [PMID: 39174496 DOI: 10.1002/ueg2.12650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/12/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND Peutz-Jeghers syndrome (PJS), is a rare autosomal dominant hereditary disease characterized by an elevated risk of various cancers. Serine/Threonine Kinase 11 (STK11) gene is a major tumor suppressor crucial for immune evasion with and beyond tumorigenic cells. It has garnered increasing attention in the realm of oncology treatment, particularly in the context of immunotherapy development. OBJECTIVE This study aimed to assess the suitability of polyps obtained from individuals with PJS, resulting from germline STK11 deficiency, for immunotherapy. Additionally, we seek to identify potential shared mechanisms related to immune evasion between PJS polyps and cancers. To achieve this, we examined PJS polyps alongside familial adenomatous polyposis (FAP) and sporadic polyps. METHODS Polyps were compared among themselves and with either the paracancerous tissues or colon cancers. Pathological and gene expression profiling approaches were employed to characterize infiltrating immune cells and assess the expression of immune checkpoint genes. RESULTS Our findings revealed that PJS polyps exhibited a closer resemblance to cancer tissues than other polyps in terms of their immune microenvironment. Notably, PJS polyps displayed heightened expression of the immune checkpoint gene CD80 and an accumulation of myeloid cells, particularly myeloid-derived suppressor cells (MDSCs). CONCLUSION The findings suggest an immunobiological foundation for the increased cancer susceptibility in PJS patients, paving the way for potential immune therapy applications in this population. Furthermore, utilizing PJS as a model may facilitate the exploration of immune evasion mechanisms, benefiting both PJS and cancer patients.
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Affiliation(s)
- Zhongyue Liu
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Boda Wu
- Department of Gastroenterology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Xiaoliu Shi
- Department of Medical Genetics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Junfeng Zhou
- Endoscopic Medical Center, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Hui Huang
- Department of Medical Genetics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhihong Li
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mei Yang
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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2
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Hofer SJ, Daskalaki I, Bergmann M, Friščić J, Zimmermann A, Mueller MI, Abdellatif M, Nicastro R, Masser S, Durand S, Nartey A, Waltenstorfer M, Enzenhofer S, Faimann I, Gschiel V, Bajaj T, Niemeyer C, Gkikas I, Pein L, Cerrato G, Pan H, Liang Y, Tadic J, Jerkovic A, Aprahamian F, Robbins CE, Nirmalathasan N, Habisch H, Annerer E, Dethloff F, Stumpe M, Grundler F, Wilhelmi de Toledo F, Heinz DE, Koppold DA, Rajput Khokhar A, Michalsen A, Tripolt NJ, Sourij H, Pieber TR, de Cabo R, McCormick MA, Magnes C, Kepp O, Dengjel J, Sigrist SJ, Gassen NC, Sedej S, Madl T, De Virgilio C, Stelzl U, Hoffmann MH, Eisenberg T, Tavernarakis N, Kroemer G, Madeo F. Spermidine is essential for fasting-mediated autophagy and longevity. Nat Cell Biol 2024:10.1038/s41556-024-01468-x. [PMID: 39117797 DOI: 10.1038/s41556-024-01468-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/02/2024] [Indexed: 08/10/2024]
Abstract
Caloric restriction and intermittent fasting prolong the lifespan and healthspan of model organisms and improve human health. The natural polyamine spermidine has been similarly linked to autophagy enhancement, geroprotection and reduced incidence of cardiovascular and neurodegenerative diseases across species borders. Here, we asked whether the cellular and physiological consequences of caloric restriction and fasting depend on polyamine metabolism. We report that spermidine levels increased upon distinct regimens of fasting or caloric restriction in yeast, flies, mice and human volunteers. Genetic or pharmacological blockade of endogenous spermidine synthesis reduced fasting-induced autophagy in yeast, nematodes and human cells. Furthermore, perturbing the polyamine pathway in vivo abrogated the lifespan- and healthspan-extending effects, as well as the cardioprotective and anti-arthritic consequences of fasting. Mechanistically, spermidine mediated these effects via autophagy induction and hypusination of the translation regulator eIF5A. In summary, the polyamine-hypusination axis emerges as a phylogenetically conserved metabolic control hub for fasting-mediated autophagy enhancement and longevity.
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Affiliation(s)
- Sebastian J Hofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Ioanna Daskalaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Martina Bergmann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Jasna Friščić
- Department of Dermatology, Allergy and Venerology, University of Lübeck, Lübeck, Germany
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Melanie I Mueller
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Mahmoud Abdellatif
- BioTechMed Graz, Graz, Austria
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Sarah Masser
- BioTechMed Graz, Graz, Austria
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Sylvère Durand
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Alexander Nartey
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Mara Waltenstorfer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Sarah Enzenhofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Isabella Faimann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Verena Gschiel
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Thomas Bajaj
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Christine Niemeyer
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Ilias Gkikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Lukas Pein
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Giulia Cerrato
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Hui Pan
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - YongTian Liang
- Institute for Biology and Genetics, Freie Universität Berlin, Berlin, Germany
- Cluster of Excellence, NeuroCure, Berlin, Germany
| | - Jelena Tadic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Andrea Jerkovic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Fanny Aprahamian
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Christine E Robbins
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Nitharsshini Nirmalathasan
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Hansjörg Habisch
- Research Unit Integrative Structural Biology, Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, Graz, Austria
| | - Elisabeth Annerer
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | | | - Michael Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | - Daniel E Heinz
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Daniela A Koppold
- Institute of Social Medicine, Epidemiology and Health Economics, corporate member of Freie Universität Berlin and Humboldt-Universität, Charité-Universitätsmedizin, Berlin, Germany
- Department of Pediatrics, Division of Oncology and Hematology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Internal Medicine and Nature-based Therapies, Immanuel Hospital Berlin, Berlin, Germany
| | - Anika Rajput Khokhar
- Institute of Social Medicine, Epidemiology and Health Economics, corporate member of Freie Universität Berlin and Humboldt-Universität, Charité-Universitätsmedizin, Berlin, Germany
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Michalsen
- Institute of Social Medicine, Epidemiology and Health Economics, corporate member of Freie Universität Berlin and Humboldt-Universität, Charité-Universitätsmedizin, Berlin, Germany
- Department of Internal Medicine and Nature-based Therapies, Immanuel Hospital Berlin, Berlin, Germany
| | - Norbert J Tripolt
- Interdisciplinary Metabolic Medicine Trials Unit, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Harald Sourij
- Interdisciplinary Metabolic Medicine Trials Unit, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Thomas R Pieber
- BioTechMed Graz, Graz, Austria
- Interdisciplinary Metabolic Medicine Trials Unit, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- HEALTH - Institute for Biomedical Research and Technologies, Joanneum Research Forschungsgesellschaft, Graz, Austria
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Mark A McCormick
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Christoph Magnes
- HEALTH - Institute for Biomedical Research and Technologies, Joanneum Research Forschungsgesellschaft, Graz, Austria
| | - Oliver Kepp
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Stephan J Sigrist
- Institute for Biology and Genetics, Freie Universität Berlin, Berlin, Germany
- Cluster of Excellence, NeuroCure, Berlin, Germany
| | - Nils C Gassen
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Simon Sedej
- BioTechMed Graz, Graz, Austria
- Division of Cardiology, Medical University of Graz, Graz, Austria
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Tobias Madl
- BioTechMed Graz, Graz, Austria
- Research Unit Integrative Structural Biology, Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, Graz, Austria
| | | | - Ulrich Stelzl
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Markus H Hoffmann
- Department of Dermatology, Allergy and Venerology, University of Lübeck, Lübeck, Germany
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece.
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, Graz, Austria.
- BioTechMed Graz, Graz, Austria.
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3
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Plumber SA, Tate T, Al-Ahmadie H, Chen X, Choi W, Basar M, Lu C, Viny A, Batourina E, Li J, Gretarsson K, Alija B, Molotkov A, Wiessner G, Lee BHL, McKiernan J, McConkey DJ, Dinney C, Czerniak B, Mendelsohn CL. Rosiglitazone and trametinib exhibit potent anti-tumor activity in a mouse model of muscle invasive bladder cancer. Nat Commun 2024; 15:6538. [PMID: 39095358 PMCID: PMC11297265 DOI: 10.1038/s41467-024-50678-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Muscle invasive bladder cancers (BCs) can be divided into 2 major subgroups-basal/squamous (BASQ) tumors and luminal tumors. Since Pparg has low or undetectable expression in BASQ tumors, we tested the effects of rosiglitazone, Pparg agonist, in a mouse model of BASQ BC. We find that rosiglitazone reduces proliferation while treatment with rosiglitazone plus trametinib, a MEK inhibitor, induces apoptosis and reduces tumor volume by 91% after 1 month. Rosiglitazone and trametinib also induce a shift from BASQ to luminal differentiation in tumors, which our analysis suggests is mediated by retinoid signaling, a pathway known to drive the luminal differentiation program. Our data suggest that rosiglitazone, trametinib, and retinoids, which are all FDA approved, may be clinically active in BASQ tumors in patients.
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Affiliation(s)
- Sakina A Plumber
- Department of Urology, Columbia University Irving Medical Center, New York, NY, USA
| | - Tiffany Tate
- Department of Urology, Columbia University Irving Medical Center, New York, NY, USA
- Generation Bio, Cambridge, MA, USA
| | | | - Xiao Chen
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
- Marine College, Shandong University, Weihai, China
| | - Woonyoung Choi
- Johns Hopkins Greenberg Bladder Cancer Institute, Baltimore, MD, USA
| | - Merve Basar
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
- Harvard Medical School, Cambridge, MA, USA
| | - Chao Lu
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron Viny
- Department of Medicine, Division of Hematology & Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ekatherina Batourina
- Department of Urology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jiaqi Li
- Department of Urology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kristjan Gretarsson
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Besmira Alija
- Department of Medicine, Division of Hematology & Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Andrei Molotkov
- Department of Urology, Columbia University Irving Medical Center, New York, NY, USA
| | - Gregory Wiessner
- Department of Urology, Columbia University Irving Medical Center, New York, NY, USA
| | - Byron Hing Lung Lee
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James McKiernan
- Department of Urology, Columbia University Irving Medical Center, New York, NY, USA
| | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Baltimore, MD, USA
| | - Colin Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cathy Lee Mendelsohn
- Department of Urology, Columbia University Irving Medical Center, New York, NY, USA.
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4
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Crombé A, Lucchesi C, Bertolo F, Kind M, Spalato-Ceruso M, Toulmonde M, Chaire V, Michot A, Coindre JM, Perret R, Le Loarer F, Bourdon A, Italiano A. Integration of pre-treatment computational radiomics, deep radiomics, and transcriptomics enhances soft-tissue sarcoma patient prognosis. NPJ Precis Oncol 2024; 8:129. [PMID: 38849448 PMCID: PMC11161510 DOI: 10.1038/s41698-024-00616-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/17/2024] [Indexed: 06/09/2024] Open
Abstract
Our objective was to capture subgroups of soft-tissue sarcoma (STS) using handcraft and deep radiomics approaches to understand their relationship with histopathology, gene-expression profiles, and metastatic relapse-free survival (MFS). We included all consecutive adults with newly diagnosed locally advanced STS (N = 225, 120 men, median age: 62 years) managed at our sarcoma reference center between 2008 and 2020, with contrast-enhanced baseline MRI. After MRI postprocessing, segmentation, and reproducibility assessment, 175 handcrafted radiomics features (h-RFs) were calculated. Convolutional autoencoder neural network (CAE) and half-supervised CAE (HSCAE) were trained in repeated cross-validation on representative contrast-enhanced slices to extract 1024 deep radiomics features (d-RFs). Gene-expression levels were calculated following RNA sequencing (RNAseq) of 110 untreated samples from the same cohort. Unsupervised classifications based on h-RFs, CAE, HSCAE, and RNAseq were built. The h-RFs, CAE, and HSCAE grouping were not associated with the transcriptomics groups but with prognostic radiological features known to correlate with lower survivals and higher grade and SARCULATOR groups (a validated prognostic clinical-histological nomogram). HSCAE and h-RF groups were also associated with MFS in multivariable Cox regressions. Combining HSCAE and transcriptomics groups significantly improved the prognostic performances compared to each group alone, according to the concordance index. The combined radiomic-transcriptomic group with worse MFS was characterized by the up-regulation of 707 genes and 292 genesets related to inflammation, hypoxia, apoptosis, and cell differentiation. Overall, subgroups of STS identified on pre-treatment MRI using handcrafted and deep radiomics were associated with meaningful clinical, histological, and radiological characteristics, and could strengthen the prognostic value of transcriptomics signatures.
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Affiliation(s)
- Amandine Crombé
- Department of Oncologic Imaging, Bergonié Institute, F-33076, Bordeaux, France.
- Department of Radiology, Pellegrin University Hospital, F-33076, Bordeaux, France.
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France.
| | - Carlo Lucchesi
- Department of Bioinformatics, Bergonié Institute, F-33076, Bordeaux, France
| | - Frédéric Bertolo
- Department of Bioinformatics, Bergonié Institute, F-33076, Bordeaux, France
| | - Michèle Kind
- Department of Oncologic Imaging, Bergonié Institute, F-33076, Bordeaux, France
| | - Mariella Spalato-Ceruso
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Medical Oncology, Bergonié Institute, F-33076, Bordeaux, France
| | - Maud Toulmonde
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Medical Oncology, Bergonié Institute, F-33076, Bordeaux, France
| | - Vanessa Chaire
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Pathology, Bergonié Institute, F-33076, Bordeaux, France
| | - Audrey Michot
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Oncologic Surgery, Bergonié Institute, F-33076, Bordeaux, France
| | - Jean-Michel Coindre
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Pathology, Bergonié Institute, F-33076, Bordeaux, France
| | - Raul Perret
- Department of Pathology, Bergonié Institute, F-33076, Bordeaux, France
| | - François Le Loarer
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Pathology, Bergonié Institute, F-33076, Bordeaux, France
| | - Aurélien Bourdon
- Department of Bioinformatics, Bergonié Institute, F-33076, Bordeaux, France
| | - Antoine Italiano
- Bordeaux Institute of Oncology, BRIC U1312, Sarcotarget team, INSERM, University of Bordeaux, Institut Bergonié, F-33000, Bordeaux, France
- Department of Medical Oncology, Bergonié Institute, F-33076, Bordeaux, France
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5
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Satish KS, Saraswathy GR, Ritesh G, Saravanan KS, Krishnan A, Bhargava J, Ushnaa K, Dsouza PL. Exploring cutting-edge strategies for drug repurposing in female cancers - An insight into the tools of the trade. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:355-415. [PMID: 38942544 DOI: 10.1016/bs.pmbts.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Female cancers, which include breast and gynaecological cancers, represent a significant global health burden for women. Despite advancements in research pertinent to unearthing crucial pathological characteristics of these cancers, challenges persist in discovering potential therapeutic strategies. This is further exacerbated by economic burdens associated with de novo drug discovery and clinical intricacies such as development of drug resistance and metastasis. Drug repurposing, an innovative approach leveraging existing FDA-approved drugs for new indications, presents a promising avenue to expedite therapeutic development. Computational techniques, including virtual screening and analysis of drug-target-disease relationships, enable the identification of potential candidate drugs. Integration of diverse data types, such as omics and clinical information, enhances the precision and efficacy of drug repurposing strategies. Experimental approaches, including high-throughput screening assays, in vitro, and in vivo models, complement computational methods, facilitating the validation of repurposed drugs. This review highlights various target mining strategies based on analysis of differential gene expression, weighted gene co-expression, protein-protein interaction network, and host-pathogen interaction, among others. To unearth drug candidates, the technicalities of leveraging information from databases such as DrugBank, STITCH, LINCS, and ChEMBL, among others are discussed. Further in silico validation techniques encompassing molecular docking, pharmacophore modelling, molecular dynamic simulations, and ADMET analysis are elaborated. Overall, this review delves into the exploration of individual case studies to offer a wide perspective of the ever-evolving field of drug repurposing, emphasizing the multifaceted approaches and methodologies employed for the same to confront female cancers.
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Affiliation(s)
- Kshreeraja S Satish
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Ganesan Rajalekshmi Saraswathy
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India.
| | - Giri Ritesh
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Kamatchi Sundara Saravanan
- Department of Pharmacognosy, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Aarti Krishnan
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Janhavi Bhargava
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Kuri Ushnaa
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Prizvan Lawrence Dsouza
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
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6
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Bucheli OTM, Rodrigues D, Portmann K, Linder A, Thoma M, Halin C, Eyer K. Single-B cell analysis correlates high-lactate secretion with stress and increased apoptosis. Sci Rep 2024; 14:8507. [PMID: 38605071 PMCID: PMC11009249 DOI: 10.1038/s41598-024-58868-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
While cellular metabolism was proposed to be a driving factor of the activation and differentiation of B cells and the function of the resulting antibody-secreting cells (ASCs), the study of correlations between cellular metabolism and functionalities has been difficult due to the absence of technologies enabling the parallel measurement. Herein, we performed single-cell transcriptomics and introduced a direct concurrent functional and metabolic flux quantitation of individual murine B cells. Our transcriptomic data identified lactate metabolism as dynamic in ASCs, but antibody secretion did not correlate with lactate secretion rates (LSRs). Instead, our study of all splenic B cells during an immune response linked increased lactate metabolism with acidic intracellular pH and the upregulation of apoptosis. T cell-dependent responses increased LSRs, and added TLR4 agonists affected the magnitude and boosted LSRhigh B cells in vivo, while resulting in only a few immunoglobulin-G secreting cells (IgG-SCs). Therefore, our observations indicated that LSRhigh cells were not differentiating into IgG-SCs, and were rather removed due to apoptosis.
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Affiliation(s)
- Olivia T M Bucheli
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093, Zürich, Switzerland
| | - Daniela Rodrigues
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093, Zürich, Switzerland
| | - Kevin Portmann
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093, Zürich, Switzerland
| | - Aline Linder
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093, Zürich, Switzerland
| | - Marina Thoma
- ETH Laboratory for Pharmaceutical Immunology, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093, Zürich, Switzerland
| | - Cornelia Halin
- ETH Laboratory for Pharmaceutical Immunology, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093, Zürich, Switzerland
| | - Klaus Eyer
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093, Zürich, Switzerland.
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark.
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7
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Idrees S, Paudel KR, Sadaf T, Hansbro PM. Uncovering domain motif interactions using high-throughput protein-protein interaction detection methods. FEBS Lett 2024; 598:725-742. [PMID: 38439692 DOI: 10.1002/1873-3468.14841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/09/2024] [Accepted: 02/18/2024] [Indexed: 03/06/2024]
Abstract
Protein-protein interactions (PPIs) are often mediated by short linear motifs (SLiMs) in one protein and domain in another, known as domain-motif interactions (DMIs). During the past decade, SLiMs have been studied to find their role in cellular functions such as post-translational modifications, regulatory processes, protein scaffolding, cell cycle progression, cell adhesion, cell signalling and substrate selection for proteasomal degradation. This review provides a comprehensive overview of the current PPI detection techniques and resources, focusing on their relevance to capturing interactions mediated by SLiMs. We also address the challenges associated with capturing DMIs. Moreover, a case study analysing the BioGrid database as a source of DMI prediction revealed significant known DMI enrichment in different PPI detection methods. Overall, it can be said that current high-throughput PPI detection methods can be a reliable source for predicting DMIs.
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Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Tayyaba Sadaf
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
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8
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Nolt GL, Keeble AR, Wen Y, Strong AC, Thomas NT, Valentino TR, Brightwell CR, Murach KA, Patrizia S, Weinstabl H, Gollner A, McCarthy JJ, Fry CS, Franti M, Filareto A, Peterson CA, Dungan CM. Inhibition of p53-MDM2 binding reduces senescent cell abundance and improves the adaptive responses of skeletal muscle from aged mice. GeroScience 2024; 46:2153-2176. [PMID: 37872294 PMCID: PMC10828311 DOI: 10.1007/s11357-023-00976-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023] Open
Abstract
Skeletal muscle adaptation to external stimuli, such as regeneration following injury and hypertrophy in response to resistance exercise, are blunted with advanced age. The accumulation of senescent cells, along with defects in myogenic progenitor cell (MPC) proliferation, have been strongly linked as contributing factors to age-associated impairment in muscle adaptation. p53 plays an integral role in all these processes, as upregulation of p53 causes apoptosis in senescent cells and prevents mitotic catastrophe in MPCs from old mice. The goal of this study was to determine if a novel pharmaceutical agent (BI01), which functions by upregulating p53 through inhibition of binding to MDM2, the primary p53 regulatory protein, improves muscle regeneration and hypertrophy in old mice. BI01 effectively reduced the number of senescent cells in vitro but had no effect on MPC survival or proliferation at a comparable dose. Following repeated oral gavage with 2 mg/kg of BI01 (OS) or vehicle (OV), old mice (24 months) underwent unilateral BaCl2 injury in the tibialis anterior (TA) muscle, with PBS injections serving as controls. After 7 days, satellite cell number was higher in the TA of OS compared to OV mice, as was the expression of genes involved in ATP production. By 35 days, old mice treated with BI01 displayed reduced senescent cell burden, enhanced regeneration (higher muscle mass and fiber cross-sectional area) and restoration of muscle function relative to OV mice. To examine the impact of 2 mg/kg BI01 on muscle hypertrophy, the plantaris muscle was subjected to 28 days of mechanical overload (MOV) in OS and OV mice. In response to MOV, OS mice had larger plantaris muscles and muscle fibers than OV mice, particularly type 2b + x fibers, associated with reduced senescent cells. Together our data show that BI01 is an effective senolytic agent that may also augment muscle metabolism to enhance muscle regeneration and hypertrophy in old mice.
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Affiliation(s)
- Georgia L Nolt
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - Alexander R Keeble
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - Yuan Wen
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physical Therapy, University of Kentucky, Lexington, KY, USA
| | - Aubrey C Strong
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - Nicholas T Thomas
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Taylor R Valentino
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - Camille R Brightwell
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Kevin A Murach
- Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
| | - Sini Patrizia
- Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Harald Weinstabl
- Boehringer Ingelheim RCV, Boehringer Ingelheim Pharmaceuticals Inc., Vienna, Austria
| | - Andreas Gollner
- Boehringer Ingelheim RCV, Boehringer Ingelheim Pharmaceuticals Inc., Vienna, Austria
| | - John J McCarthy
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - Christopher S Fry
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Michael Franti
- Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Antonio Filareto
- Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, Ridgefield, CT, 06877, USA.
| | - Charlotte A Peterson
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physical Therapy, University of Kentucky, Lexington, KY, USA
| | - Cory M Dungan
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA.
- Department of Physical Therapy, University of Kentucky, Lexington, KY, USA.
- Department of Health, Human Performance, and Recreation, Baylor University, One Bear Place #97313, Waco, TX, 76706, USA.
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9
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Mahmood N, Arakelian A, Szyf M, Rabbani SA. Methyl-CpG binding domain protein 2 (Mbd2) drives breast cancer progression through the modulation of epithelial-to-mesenchymal transition. Exp Mol Med 2024; 56:959-974. [PMID: 38556549 PMCID: PMC11058268 DOI: 10.1038/s12276-024-01205-2] [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: 12/04/2022] [Revised: 12/27/2023] [Accepted: 01/25/2024] [Indexed: 04/02/2024] Open
Abstract
Methyl-CpG-binding domain protein 2 (Mbd2), a reader of DNA methylation, has been implicated in different types of malignancies, including breast cancer. However, the exact role of Mbd2 in various stages of breast cancer growth and progression in vivo has not been determined. To test whether Mbd2 plays a causal role in mammary tumor growth and metastasis, we performed genetic knockout (KO) of Mbd2 in MMTV-PyMT transgenic mice and compared mammary tumor progression kinetics between the wild-type (PyMT-Mbd2+/+) and KO (PyMT-Mbd2-/-) groups. Our results demonstrated that deletion of Mbd2 in PyMT mice impedes primary tumor growth and lung metastasis at the experimental endpoint (postnatal week 20). Transcriptomic and proteomic analyses of primary tumors revealed that Mbd2 deletion abrogates the expression of several key determinants involved in epithelial-to-mesenchymal transition, such as neural cadherin (N-cadherin) and osteopontin. Importantly, loss of the Mbd2 gene impairs the activation of the PI3K/AKT pathway, which is required for PyMT-mediated oncogenic transformation, growth, and survival of breast tumor cells. Taken together, the results of this study provide a rationale for further development of epigenetic therapies targeting Mbd2 to inhibit the progression of breast cancer.
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Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University, Montréal, QC, H4A3J1, Canada
- Department of Biochemistry, McGill University, Montréal, QC, H3A1A3, Canada
| | - Ani Arakelian
- Department of Medicine, McGill University, Montréal, QC, H4A3J1, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, H3G1Y6, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University, Montréal, QC, H4A3J1, Canada.
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10
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Casanova NG, De Armond RL, Sammani S, Sun X, Sun B, Kempf C, Bime C, Garcia JGN, Parthasarathy S. Circadian disruption dysregulates lung gene expression associated with inflammatory lung injury. Front Immunol 2024; 15:1348181. [PMID: 38558813 PMCID: PMC10979643 DOI: 10.3389/fimmu.2024.1348181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 04/04/2024] Open
Abstract
Rationale Circadian systems drive the expression of multiple genes in nearly all cells and coordinate cellular-, tissue-, and system-level processes that are critical to innate immunity regulation. Objective We examined the effects of circadian rhythm disorganization, produced by light shift exposure, on innate immunity-mediated inflammatory lung responses including vascular permeability and gene expression in a C57BL/6J murine model of inflammatory lung injury. Methods A total of 32 C57BL/6J mice were assigned to circadian phase shifting (CPS) with intratracheal phosphate-buffered saline (PBS), CPS with intratracheal lipopolysaccharide (LPS), control (normal lighting) condition with intratracheal PBS, and control condition with intratracheal LPS. Bronchoalveolar lavage (BAL) protein, cell counts, tissue immunostaining, and differentially expressed genes (DEGs) were measured in lung tissues at 2 and 10 weeks. Measurements and results In mice exposed to both CPS and intratracheal LPS, both BAL protein and cell counts were increased at both 2 and 10 weeks compared to mice exposed to LPS alone. Multiple DEGs were identified in CPS-LPS-exposed lung tissues compared to LPS alone and were involved in transcriptional pathways associated with circadian rhythm disruption, regulation of lung permeability, inflammation with Rap1 signaling, and regulation of actin cytoskeleton. The most dysregulated pathways included myosin light chain kinase, MAP kinase, profilin 2, fibroblast growth factor receptor, integrin b4, and p21-activated kinase. Conclusion Circadian rhythm disruption results in exacerbated immune response and dysregulated expression of cytoskeletal genes involved in the regulation of epithelial and vascular barrier integrity-the mechanistic underpinnings of acute lung injury. Further studies need to explore circadian disorganization as a druggable target.
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Affiliation(s)
- Nancy G. Casanova
- Department of Molecular Medicine, University of Florida Scripps Biomedical Research, Jupiter, FL, United States
| | - Richard L. De Armond
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
- University of Arizona Health Science – Center for Sleep and Circadian Sciences, University of Arizona, Tucson, AZ, United States
| | - Saad Sammani
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Xiaoguang Sun
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Belinda Sun
- Department of Pathology, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Carrie Kempf
- Department of Molecular Medicine, University of Florida Scripps Biomedical Research, Jupiter, FL, United States
| | - Christian Bime
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
| | - Joe G. N. Garcia
- Department of Molecular Medicine, University of Florida Scripps Biomedical Research, Jupiter, FL, United States
| | - Sairam Parthasarathy
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, United States
- University of Arizona Health Science – Center for Sleep and Circadian Sciences, University of Arizona, Tucson, AZ, United States
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11
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Bereketoglu C, Häggblom I, Turanlı B, Pradhan A. Comparative analysis of diisononyl phthalate and di(isononyl)cyclohexane-1,2 dicarboxylate plasticizers in regulation of lipid metabolism in 3T3-L1 cells. ENVIRONMENTAL TOXICOLOGY 2024; 39:1245-1257. [PMID: 37927243 DOI: 10.1002/tox.24010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/04/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
Diisononyl phthalate (DINP) and di(isononyl)cyclohexane-1,2-dicarboxylate (DINCH) are plasticizers introduced to replace previously used phthalate plasticizers in polymeric products. Exposure to DINP and DINCH has been shown to impact lipid metabolism. However, there are limited studies that address the mechanisms of toxicity of these two plasticizers. Here, a comparative toxicity analysis has been performed to evaluate the impacts of DINP and DINCH on 3T3-L1 cells. The preadipocyte 3T3-L1 cells were exposed to 1, 10, and 100 μM of DINP or DINCH for 10 days and assessed for lipid accumulation, gene expression, and protein analysis. Lipid staining showed that higher concentrations of DINP and DINCH can induce adipogenesis. The gene expression analysis demonstrated that both DINP and DINCH could alter the expression of lipid-related genes involved in adipogenesis. DINP and DINCH upregulated Pparγ, Pparα, C/EBPα Fabp4, and Fabp5, while both compounds significantly downregulated Fasn and Gata2. Protein analysis showed that both DINP and DINCH repressed the expression of FASN. Additionally, we analyzed an independent transcriptome dataset encompassing temporal data on lipid differentiation within 3T3-L1 cells. Subsequently, we derived a gene set that accurately portrays significant pathways involved in lipid differentiation, which we subsequently subjected to experimental validation through quantitative polymerase chain reaction. In addition, we extended our analysis to encompass a thorough assessment of the expression profiles of this identical gene set across 40 discrete transcriptome datasets that have linked to diverse pathological conditions to foreseen any potential association with DINP and DINCH exposure. Comparative analysis indicated that DINP could be more effective in regulating lipid metabolism.
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Affiliation(s)
- Ceyhun Bereketoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Isabel Häggblom
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
| | - Beste Turanlı
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
| | - Ajay Pradhan
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
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12
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Fan G, Yan Q, Chen Y, Han M, Wu Z, Ruan S, Zhuang H, Gou Q, Hou B. FLNB overexpression promotes tumor progression and associates with immune suppression, evasion and stemness in pancreatic cancer. Am J Cancer Res 2024; 14:709-726. [PMID: 38455418 PMCID: PMC10915313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/11/2024] [Indexed: 03/09/2024] Open
Abstract
Pancreatic cancer (PC) is an immunosuppressive cancer. Immune-based therapies that enhance or recruit antitumor immune cells into the tumor microenvironment (TME) remain promising strategies for PC treatment. Consequently, a deeper understanding of the molecular mechanisms involved in PC immune suppression is critical for developing immune-based therapies to improve survival rates. In this study, weighted gene co-expression network analysis (WGCNA) was used to identify Filamin B (FLNB) correlated with the infiltration of CD8+ T cells and tumor-associated macrophages (TAMs). The clinical significance and potential biological function of FLNB were evaluated using bioinformatic analysis. The oncogenic role of FLNB in PC was determined using in vitro and in vivo studies. We further analyzed possible associations between FLNB expression and tumor immunity using CIBERSORT, single sample gene set enrichment analysis, and ESTIMATE algorithms. We found FLNB was overexpressed in PC tissues and was correlated with poorer overall survival, tumor recurrence, larger tumor size, and higher histologic grade. Moreover, FLNB overexpression was associated with the mutation status and expression of driver genes, especially for KRAS and SMAD4. Functional enrichment analysis identified the role of FLNB in the regulation of cell cycle, focal adhesion, vascular formation, and immune regulation. Knockdown of FLNB expression inhibited cancer cell proliferation and migration in-vitro and suppressed tumor growth in-vivo. Furthermore, FLNB overexpression caused high infiltration of Treg cells, Th2 cells, and TAMs, but reduced infiltration of CD8+ T cells and Th1/Th2. Collectively, our findings suggest FLNB promotes PC progression and may be a novel biomarker for PC.
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Affiliation(s)
- Guoyong Fan
- Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical UniversityGuangzhou, Guangdong, China
| | - Qian Yan
- Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical UniversityGuangzhou, Guangdong, China
- School of Medicine South China University of TechnologyGuangzhou, Guangdong, China
| | - Yubin Chen
- Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical UniversityGuangzhou, Guangdong, China
- School of Medicine South China University of TechnologyGuangzhou, Guangdong, China
| | - Mingqian Han
- Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical UniversityGuangzhou, Guangdong, China
| | - Zelong Wu
- Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical UniversityGuangzhou, Guangdong, China
| | - Shiye Ruan
- Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical UniversityGuangzhou, Guangdong, China
| | - Hongkai Zhuang
- Sun Yat-sen University Cancer CenterGuangzhou, Guangdong, China
| | - Qing Gou
- Department of Interventional Radiology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical UniversityGuangzhou, Guangdong, China
| | - Baohua Hou
- Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical UniversityGuangzhou, Guangdong, China
- School of Medicine South China University of TechnologyGuangzhou, Guangdong, China
- Heyuan People’s HospitalHeyuan, Guangdong, China
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13
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Zhuang H, Tang C, Lin H, Zhang Z, Chen X, Wang W, Wang Q, Tan W, Yang L, Xie Z, Wang B, Chen B, Shang C, Chen Y. A novel risk score system based on immune subtypes for identifying optimal mRNA vaccination population in hepatocellular carcinoma. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00921-1. [PMID: 38315287 DOI: 10.1007/s13402-024-00921-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
PURPOSE Although mRNA vaccines have shown certain clinical benefits in multiple malignancies, their therapeutic efficacies against hepatocellular carcinoma (HCC) remains uncertain. This study focused on establishing a novel risk score system based on immune subtypes so as to identify optimal HCC mRNA vaccination population. METHODS GEPIA, cBioPortal and TIMER databases were utilized to identify candidate genes for mRNA vaccination in HCC. Subsequently, immune subtypes were constructed based on the candidate genes. According to the differential expressed genes among various immune subtypes, a risk score system was established using machine learning algorithm. Besides, multi-color immunofluorescence of tumor tissues from 72 HCC patients were applied to validate the feasibility and efficiency of the risk score system. RESULTS Twelve overexpressed and mutated genes associated with poor survival and APCs infiltration were identified as potential candidate targets for mRNA vaccination. Three immune subtypes (e.g. IS1, IS2 and IS3) with distinct clinicopathological and molecular profiles were constructed according to the 12 candidate genes. Based on the immune subtype, a risk score system was developed, and according to the risk score from low to high, HCC patients were classified into four subgroups on average (e.g. RS1, RS2, RS3 and RS4). RS4 mainly overlapped with IS3, RS1 with IS2, and RS2+RS3 with IS1. ROC analysis also suggested the significant capacity of the risk score to distinguish between the three immune subtypes. Higher risk score exhibited robustly predictive ability for worse survival, which was further independently proved by multi-color immunofluorescence of HCC samples. Notably, RS4 tumors exhibited an increased immunosuppressive phenotype, higher expression of the twelve potential candidate targets and increased genome altered fraction, and therefore might benefit more from vaccination. CONCLUSIONS This novel risk score system based on immune subtypes enabled the identification of RS4 tumor that, due to its highly immunosuppressive microenvironment, may benefit from HCC mRNA vaccination.
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Affiliation(s)
- Hongkai Zhuang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Chenwei Tang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Han Lin
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zedan Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Xinming Chen
- Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, 516400, China
| | - Wentao Wang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Qingbin Wang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wenliang Tan
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Lei Yang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Zhiqin Xie
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Bingkun Wang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Bo Chen
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
| | - Changzhen Shang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Yajin Chen
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.
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14
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Lan Y, Wu X, Zhong X, Song P, Liu L, Liu Y, Ai X, Han C, Zhang Z. Increased neutrophil-derived IL-17A identified in generalized pustular psoriasis. Exp Dermatol 2024; 33:e15026. [PMID: 38414093 DOI: 10.1111/exd.15026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/29/2024]
Abstract
Generalized pustular psoriasis (GPP) is considered to be a distinct clinical entity from psoriasis vulgaris (PV), with different clinical and histological manifestations. The pathogenesis of GPP has not been thoroughly elucidated, especially in those patients lacking interleukin (IL)36RN. In present study, we performed RNA sequence analysis on skin lesions from 10 GPP patients (4 with and 6 without IL36RN mutation) and 10 PV patients without IL36RN mutation. Compared with PV, significantly overexpressed genes in GPP patients were enriched in IL-17 signalling pathway (MMP1, MMP3, DEFB4A and DEFB4B, etc.) and associated with neutrophil infiltration (MMP1, MMP3, ANXA and SERPINB, etc.). GPP with IL36RN mutations evidenced WNT11 upregulation and IL36RN downregulation in comparison to those GPP without IL36RN mutations. The expression of IL-17A/IL-36 in skin or serum and the origin of IL-17A in skin were also investigated. IL-17A expression in skin was significantly higher in GPP than PV patients, whereas, there were no differences in skin IL-36α/IL-36γ/IL-36RA or serum IL-17A/IL-36α/IL-36γ between GPP than PV. Besides, double immunofluorescence staining of MPO/IL-17A or CD3/IL-17A further confirmed that the majority of IL-17A in GPP skin was derived from neutrophils, but not T cells. These data emphasized the role of neutrophil-derived IL-17A in the pathogenesis of GPP with or without IL36RN mutations. Targeting neutrophil-derived IL-17A might be a promising treatment for GPP.
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Affiliation(s)
- Yu Lan
- Department of Dermatology, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Xiaoyan Wu
- Department of Dermatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Xinyu Zhong
- Department of Dermatology, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Pengfei Song
- Department of Dermatology, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Leying Liu
- Department of Dermatology, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Yuhua Liu
- Department of Dermatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Xuechen Ai
- Department of Dermatology, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Changxu Han
- Department of Dermatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Zhenying Zhang
- Department of Dermatology, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
- Department of Dermatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
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15
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Kori M, Demirtas TY, Comertpay B, Arga KY, Sinha R, Gov E. A 19-Gene Signature of Serous Ovarian Cancer Identified by Machine Learning and Systems Biology: Prospects for Diagnostics and Personalized Medicine. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:90-101. [PMID: 38320250 DOI: 10.1089/omi.2023.0273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Ovarian cancer is a major cause of cancer deaths among women. Early diagnosis and precision/personalized medicine are essential to reduce mortality and morbidity of ovarian cancer, as with new molecular targets to accelerate drug discovery. We report here an integrated systems biology and machine learning (ML) approach based on the differential coexpression analysis to identify candidate systems biomarkers (i.e., gene modules) for serous ovarian cancer. Accordingly, four independent transcriptome datasets were statistically analyzed independently and common differentially expressed genes (DEGs) were identified. Using these DEGs, coexpressed gene pairs were unraveled. Subsequently, differential coexpression networks between the coexpressed gene pairs were reconstructed so as to identify the differentially coexpressed gene modules. Based on the established criteria, "SOV-module" was identified as being significant, consisting of 19 genes. Using independent datasets, the diagnostic capacity of the SOV-module was evaluated using principal component analysis (PCA) and ML techniques. PCA showed a sensitivity and specificity of 96.7% and 100%, respectively, and ML analysis showed an accuracy of up to 100% in distinguishing phenotypes in the present study sample. The prognostic capacity of the SOV-module was evaluated using survival and ML analyses. We found that the SOV-module's performance for prognostics was significant (p-value = 1.36 × 10-4) with an accuracy of 63% in discriminating between survival and death using ML techniques. In summary, the reported genomic systems biomarker candidate offers promise for personalized medicine in diagnosis and prognosis of serous ovarian cancer and warrants further experimental and translational clinical studies.
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Affiliation(s)
- Medi Kori
- Faculty of Health Sciences, Acibadem Mehmet Ali Aydinlar University, İstanbul, Türkiye
| | - Talip Yasir Demirtas
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Betul Comertpay
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, İstanbul, Türkiye
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, İstanbul, Türkiye
| | - Raghu Sinha
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Esra Gov
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Türkeş Science and Technology University, Adana, Türkiye
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16
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Raja R, Khanum S, Aboulmouna L, Maurya MR, Gupta S, Subramaniam S, Ramkrishna D. Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach. Biophys J 2024; 123:221-234. [PMID: 38102827 PMCID: PMC10808046 DOI: 10.1016/j.bpj.2023.12.010] [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: 02/20/2023] [Revised: 09/18/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023] Open
Abstract
Quantitative understanding of cellular processes, such as cell cycle and differentiation, is impeded by various forms of complexity ranging from myriad molecular players and their multilevel regulatory interactions, cellular evolution with multiple intermediate stages, lack of elucidation of cause-effect relationships among the many system players, and the computational complexity associated with the profusion of variables and parameters. In this paper, we present a modeling framework based on the cybernetic concept that biological regulation is inspired by objectives embedding rational strategies for dimension reduction, process stage specification through the system dynamics, and innovative causal association of regulatory events with the ability to predict the evolution of the dynamical system. The elementary step of the modeling strategy involves stage-specific objective functions that are computationally determined from experiments, augmented with dynamical network computations involving endpoint objective functions, mutual information, change-point detection, and maximal clique centrality. We demonstrate the power of the method through application to the mammalian cell cycle, which involves thousands of biomolecules engaged in signaling, transcription, and regulation. Starting with a fine-grained transcriptional description obtained from RNA sequencing measurements, we develop an initial model, which is then dynamically modeled using the cybernetic-inspired method, based on the strategies described above. The cybernetic-inspired method is able to distill the most significant interactions from a multitude of possibilities. In addition to capturing the complexity of regulatory processes in a mechanistically causal and stage-specific manner, we identify the functional network modules, including novel cell cycle stages. Our model is able to predict future cell cycles consistent with experimental measurements. We posit that this innovative framework has the promise to extend to the dynamics of other biological processes, with a potential to provide novel mechanistic insights.
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Affiliation(s)
- Rubesh Raja
- The Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana
| | - Sana Khanum
- The Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana
| | - Lina Aboulmouna
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Mano R Maurya
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Shakti Gupta
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, La Jolla, California; Departments of Computer Science and Engineering, Cellular and Molecular Medicine, San Diego Supercomputer Center, and the Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, California.
| | - Doraiswami Ramkrishna
- The Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana.
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17
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Arwansyah A, Lewa AF, Muliani M, Warnasih S, Mustopa AZ, Arif AR. Molecular Recognition of Moringa oleifera Active Compounds for Stunted Growth Prevention Using Network Pharmacology and Molecular Modeling Approach. ACS OMEGA 2023; 8:44121-44138. [PMID: 38027368 PMCID: PMC10666129 DOI: 10.1021/acsomega.3c06379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
In this study, network pharmacology was used to analyze the active compounds of Moringa oleifera as food supplements for stunted growth prevention. Thirty-eight important proteins were discovered that may be strongly related to stunting. Those proteins were uploaded to several online tool platforms in order to determine the shared genes' pathways. Six pathways were identified that may be correlated with human growth. Furthermore, ligands for molecular docking analysis were retrieved from the top 5 active substances discovered through experimental investigation. In the meantime, the first-degree rank based on the protein-protein interaction (PPI) topological analysis was utilized to choose albumin protein (ALB) as a receptor. Our docking results showed that every ligand binds to the receptors, indicating that they can bind to the binding site of the ALB protein to form a complex formation. Further, MD simulation was used to verify the stability of the ligand in complex with the protein in the TIP3P water model. Based on the validation parameters, our results suggested that all models achieved a stable phase along the simulation. Additionally, the MM-GBSA method was used to calculate the binding energies of all models. Ligands 2 and 4 have strong binding to the binding pocket of ALB, followed by ligands 3, 5, and 2, suggesting that those ligands could be promising food supplements that can be utilized for the prevention of stunted growth in children.
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Affiliation(s)
- Arwansyah Arwansyah
- Department
of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu 94148, Indonesia
- Research
Center for Genetic Engineering, National
Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
| | - Abd Farid Lewa
- Department
of Nutrition, Poltekkes Kemenkes Palu, Palu 94148, Indonesia
| | - Muliani Muliani
- Department
of Midwife, Poltekkes Kemenkes Palu, Palu 94148, Indonesia
| | - Siti Warnasih
- Department
of Chemistry, Faculty of Mathematics and Natural Sciences, Pakuan University, Bogor 16129, Indonesia
| | - Apon Zaenal Mustopa
- Research
Center for Genetic Engineering, National
Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
| | - Abdur Rahman Arif
- Department
of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, 90245, Indonesia
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18
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Fan YW, Lu IC, Hsu MY, Kuo WT, Wu SY, Lan SH, Wang PY, Chen CY, Liu HS, Su CL. Synthetic lethality in human bladder cancer cells by curcumin via concurrent Aurora A inhibition and autophagy induction. J Nutr Biochem 2023; 121:109438. [PMID: 37666476 DOI: 10.1016/j.jnutbio.2023.109438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/24/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
Combination therapies to induce mixed-type cell death and synthetic lethality have the potential to overcome drug resistance in cancer. In this study, we demonstrated that the curcumin-enhanced cytotoxicity of cisplatin/carboplatin in combination with gemcitabine was associated with Aurora A suppression-mediated G2/M arrest, and thus apoptosis, as well as MEK/ERK-mediated autophagy in human bladder cancer cells. Animal study data confirmed that curcumin combined with cisplatin/gemcitabine reduced tumorigenesis of xenograft in mice and this phenomenon was associated with elevated expressions of p-ERK and reduced p-Aurora A in tumors. Gene analyses using data repositories further revealed that reduced Aurora A expression alone did not significantly elevate the sensitivity of human bladder carcinoma cells to these anticancer drugs. Unlike other major cancer types, human bladder urothelial carcinoma tissue coexpressed higher AURKA and lower MAP1LC3B than normal tissue, and reduced Aurora A and induction of autophagy have been clinically associated with a better prognosis in patients with early but not advanced stage bladder cancer. Therefore, our results suggest that treatment strategies can utilize the synthetic lethal pair to concurrently suppress oncogenic Aurora A and induce autophagy by coadministrating curcumin with anticancer drugs for early-stage bladder cancer with high expression of Aurora A.
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Affiliation(s)
- Ya-Wen Fan
- Department of Human Development and Family Studies, National Taiwan Normal University, Taipei, Taiwan
| | - I-Ching Lu
- Graduate Program of Nutrition Science, School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Man-Yuan Hsu
- Graduate Program of Nutrition Science, School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Wan-Ting Kuo
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shan-Ying Wu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Hui Lan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pao-Yuan Wang
- Graduate Program of Nutrition Science, School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ching-Ying Chen
- Graduate Program of Nutrition Science, School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiao-Sheng Liu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research Center, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Master of Science Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Li Su
- Department of Human Development and Family Studies, National Taiwan Normal University, Taipei, Taiwan; Graduate Program of Nutrition Science, School of Life Science, National Taiwan Normal University, Taipei, Taiwan.
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19
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Sha Z, Warrier V, Bethlehem RA, Schultz LM, Merikangas A, Sun KY, Gur RC, Gur RE, Shinohara RT, Seidlitz J, Almasy L, Andreassen OA, Alexander-Bloch AF. The overlapping genetic architecture of psychiatric disorders and cortical brain structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561040. [PMID: 37873315 PMCID: PMC10592957 DOI: 10.1101/2023.10.05.561040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Both psychiatric vulnerability and cortical structure are shaped by the cumulative effect of common genetic variants across the genome. However, the shared genetic underpinnings between psychiatric disorders and brain structural phenotypes, such as thickness and surface area of the cerebral cortex, remains elusive. In this study, we employed pleiotropy-informed conjunctional false discovery rate analysis to investigate shared loci across genome-wide association scans of regional cortical thickness, surface area, and seven psychiatric disorders in approximately 700,000 individuals of European ancestry. Aggregating regional measures, we identified 50 genetic loci shared between psychiatric disorders and surface area, as well as 26 genetic loci shared with cortical thickness. Risk alleles exhibited bidirectional effects on both cortical thickness and surface area, such that some risk alleles for each disorder increased regional brain size while other risk alleles decreased regional brain size. Due to bidirectional effects, in many cases we observed extensive pleiotropy between an imaging phenotype and a psychiatric disorder even in the absence of a significant genetic correlation between them. The impact of genetic risk for psychiatric disorders on regional brain structure did exhibit a consistent pattern across highly comorbid psychiatric disorders, with 80% of the genetic loci shared across multiple disorders displaying consistent directions of effect. Cortical patterning of genetic overlap revealed a hierarchical genetic architecture, with the association cortex and sensorimotor cortex representing two extremes of shared genetic influence on psychiatric disorders and brain structural variation. Integrating multi-scale functional annotations and transcriptomic profiles, we observed that shared genetic loci were enriched in active genomic regions, converged on neurobiological and metabolic pathways, and showed differential expression in postmortem brain tissue from individuals with psychiatric disorders. Cumulatively, these findings provide a significant advance in our understanding of the overlapping polygenic architecture between psychopathology and cortical brain structure.
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Affiliation(s)
- Zhiqiang Sha
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Varun Warrier
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychology, University of Cambridge, Cambridge, UK
| | | | - Laura M. Schultz
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Alison Merikangas
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kevin Y. Sun
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Ruben C. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Raquel E. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States
- Center for Biomedical Image Computing and Analytics (CBICA), Department of Radiology, Perelman School of Medicine, United States
| | - Jakob Seidlitz
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ole A. Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Aaron F. Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
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20
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Oliveras-Cañellas N, Latorre J, Santos-González E, Lluch A, Ortega F, Mayneris-Perxachs J, Fernández-Real JM, Moreno-Navarrete JM. Inflammatory response to bacterial lipopolysaccharide drives iron accumulation in human adipocytes. Biomed Pharmacother 2023; 166:115428. [PMID: 37677967 DOI: 10.1016/j.biopha.2023.115428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
The association among increased inflammation, disrupted iron homeostasis, and adipose tissue dysfunction in obesity has been widely recognized. However, the specific impact of inflammation on iron homeostasis during human adipogenesis and in adipocytes remains poorly understood. In this study, we investigated the effects of bacterial lipopolysaccharide (LPS) on iron homeostasis during human adipocyte differentiation, in fully differentiated adipocytes, and in human adipose tissue. We found that LPS-induced inflammation hindered adipogenesis and led to a gene expression profile indicative of intracellular iron accumulation. This was accompanied by increased expression of iron importers (TFRC and SLC11A2), markers of intracellular iron accumulation (FTH, CYBA, FTL, and LCN2), and decreased expression of iron exporter-related genes (SLC40A1), concomitant with elevated intracellular iron levels. Mechanistically, RNA-seq analysis and gene knockdown experiments revealed the significant involvement of iron importers SLC39A14, SLC39A8, and STEAP4 in LPS-induced intracellular iron accumulation in human adipocytes. Notably, markers of LPS signaling pathway-related inflammation were also associated with a gene expression pattern indicative of intracellular iron accumulation in human adipose tissue, corroborating the link between LPS-induced inflammation and iron accumulation at the tissue level. In conclusion, our findings demonstrate that induction of adipocyte inflammation disrupts iron homeostasis, resulting in adipocyte iron overload.
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Affiliation(s)
- Núria Oliveras-Cañellas
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - Jessica Latorre
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - Elena Santos-González
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - Aina Lluch
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - Francisco Ortega
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain
| | - José-Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain; Department of Medicine, Universitat de Girona, Girona, Spain.
| | - José María Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition, Institut d'Investigació Biomèdica de Girona (IdIBGi), CIBEROBN (CB06/03/010) and Instituto de Salud Carlos III (ISCIII), Girona, Spain.
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21
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Buljan M, Banaei-Esfahani A, Blattmann P, Meier-Abt F, Shao W, Vitek O, Tang H, Aebersold R. A computational framework for the inference of protein complex remodeling from whole-proteome measurements. Nat Methods 2023; 20:1523-1529. [PMID: 37749212 PMCID: PMC10555833 DOI: 10.1038/s41592-023-02011-w] [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: 12/30/2020] [Accepted: 08/16/2023] [Indexed: 09/27/2023]
Abstract
Protein complexes are responsible for the enactment of most cellular functions. For the protein complex to form and function, its subunits often need to be present at defined quantitative ratios. Typically, global changes in protein complex composition are assessed with experimental approaches that tend to be time consuming. Here, we have developed a computational algorithm for the detection of altered protein complexes based on the systematic assessment of subunit ratios from quantitative proteomic measurements. We applied it to measurements from breast cancer cell lines and patient biopsies and were able to identify strong remodeling of HDAC2 epigenetic complexes in more aggressive forms of cancer. The presented algorithm is available as an R package and enables the inference of changes in protein complex states by extracting functionally relevant information from bottom-up proteomic datasets.
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Affiliation(s)
- Marija Buljan
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
- EMPA, Swiss Federal Laboratories for Materials Science and Technology, St Gallen, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Idorsia Pharmaceuticals, Allschwil, Switzerland
| | - Fabienne Meier-Abt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Medical Oncology and Hematology, University and University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Wenguang Shao
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, and Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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22
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Blaser MC, Buffolo F, Halu A, Turner ME, Schlotter F, Higashi H, Pantano L, Clift CL, Saddic LA, Atkins SK, Rogers MA, Pham T, Vromman A, Shvartz E, Sukhova GK, Monticone S, Camussi G, Robson SC, Body SC, Muehlschlegel JD, Singh SA, Aikawa M, Aikawa E. Multiomics of Tissue Extracellular Vesicles Identifies Unique Modulators of Atherosclerosis and Calcific Aortic Valve Stenosis. Circulation 2023; 148:661-678. [PMID: 37427430 PMCID: PMC10527599 DOI: 10.1161/circulationaha.122.063402] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/02/2023] [Indexed: 07/11/2023]
Abstract
BACKGROUND Fewer than 50% of patients who develop aortic valve calcification have concomitant atherosclerosis, implying differential pathogenesis. Although circulating extracellular vesicles (EVs) act as biomarkers of cardiovascular diseases, tissue-entrapped EVs are associated with early mineralization, but their cargoes, functions, and contributions to disease remain unknown. METHODS Disease stage-specific proteomics was performed on human carotid endarterectomy specimens (n=16) and stenotic aortic valves (n=18). Tissue EVs were isolated from human carotid arteries (normal, n=6; diseased, n=4) and aortic valves (normal, n=6; diseased, n=4) by enzymatic digestion, (ultra)centrifugation, and a 15-fraction density gradient validated by proteomics, CD63-immunogold electron microscopy, and nanoparticle tracking analysis. Vesiculomics, comprising vesicular proteomics and small RNA-sequencing, was conducted on tissue EVs. TargetScan identified microRNA targets. Pathway network analyses prioritized genes for validation in primary human carotid artery smooth muscle cells and aortic valvular interstitial cells. RESULTS Disease progression drove significant convergence (P<0.0001) of carotid artery plaque and calcified aortic valve proteomes (2318 proteins). Each tissue also retained a unique subset of differentially enriched proteins (381 in plaques; 226 in valves; q<0.05). Vesicular gene ontology terms increased 2.9-fold (P<0.0001) among proteins modulated by disease in both tissues. Proteomics identified 22 EV markers in tissue digest fractions. Networks of proteins and microRNA targets changed by disease progression in both artery and valve EVs revealed shared involvement in intracellular signaling and cell cycle regulation. Vesiculomics identified 773 proteins and 80 microRNAs differentially enriched by disease exclusively in artery or valve EVs (q<0.05); multiomics integration found tissue-specific EV cargoes associated with procalcific Notch and Wnt signaling in carotid arteries and aortic valves, respectively. Knockdown of tissue-specific EV-derived molecules FGFR2, PPP2CA, and ADAM17 in human carotid artery smooth muscle cells and WNT5A, APP, and APC in human aortic valvular interstitial cells significantly modulated calcification. CONCLUSIONS The first comparative proteomics study of human carotid artery plaques and calcified aortic valves identifies unique drivers of atherosclerosis versus aortic valve stenosis and implicates EVs in advanced cardiovascular calcification. We delineate a vesiculomics strategy to isolate, purify, and study protein and RNA cargoes from EVs entrapped in fibrocalcific tissues. Integration of vesicular proteomics and transcriptomics by network approaches revealed novel roles for tissue EVs in modulating cardiovascular disease.
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Affiliation(s)
- Mark C. Blaser
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Fabrizio Buffolo
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Arda Halu
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mandy E. Turner
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Florian Schlotter
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lorena Pantano
- T H Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Cassandra L. Clift
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Louis A. Saddic
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Samantha K. Atkins
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Maximillian A. Rogers
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Tan Pham
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amélie Vromman
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Eugenia Shvartz
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Galina K Sukhova
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Silvia Monticone
- Division of Internal Medicine and Hypertension, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Giovanni Camussi
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Simon C. Robson
- Center for Inflammation Research, Department of Anesthesia, Critical Care and Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School
| | - Simon C. Body
- Boston University School of Medicine, Boston, MA, USA
| | - Jochen D. Muehlschlegel
- Center for Perioperative Genomics, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sasha A. Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elena Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Center for Excellence in Vascular Biology, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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23
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Jethalia M, Jani SP, Ceccarelli M, Mall R. Pancancer network analysis reveals key master regulators for cancer invasiveness. J Transl Med 2023; 21:558. [PMID: 37599366 PMCID: PMC10440887 DOI: 10.1186/s12967-023-04435-6] [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: 03/23/2023] [Accepted: 08/12/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Tumor invasiveness reflects numerous biological changes, including tumorigenesis, progression, and metastasis. To decipher the role of transcriptional regulators (TR) involved in tumor invasiveness, we performed a systematic network-based pan-cancer assessment of master regulators of cancer invasiveness. MATERIALS AND METHODS We stratified patients in The Cancer Genome Atlas (TCGA) into invasiveness high (INV-H) and low (INV-L) groups using consensus clustering based on an established robust 24-gene signature to determine the prognostic association of invasiveness with overall survival (OS) across 32 different cancers. We devise a network-based protocol to identify TRs as master regulators (MRs) unique to INV-H and INV-L phenotypes. We validated the activity of MRs coherently associated with INV-H phenotype and worse OS across cancers in TCGA on a series of additional datasets in the Prediction of Clinical Outcomes from the Genomic Profiles (PRECOG) repository. RESULTS Based on the 24-gene signature, we defined the invasiveness score for each patient sample and stratified patients into INV-H and INV-L clusters. We observed that invasiveness was associated with worse survival outcomes in almost all cancers and had a significant association with OS in ten out of 32 cancers. Our network-based framework identified common invasiveness-associated MRs specific to INV-H and INV-L groups across the ten prognostic cancers, including COL1A1, which is also part of the 24-gene signature, thus acting as a positive control. Downstream pathway analysis of MRs specific to INV-H phenotype resulted in the identification of several enriched pathways, including Epithelial into Mesenchymal Transition, TGF-β signaling pathway, regulation of Toll-like receptors, cytokines, and inflammatory response, and selective expression of chemokine receptors during T-cell polarization. Most of these pathways have connotations of inflammatory immune response and feasibility for metastasis. CONCLUSION Our pan-cancer study provides a comprehensive master regulator analysis of tumor invasiveness and can suggest more precise therapeutic strategies by targeting the identified MRs and downstream enriched pathways for patients across multiple cancers.
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Affiliation(s)
- Mahesh Jethalia
- Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Siddhi P Jani
- Centre of Brain Research, Indian Institute of Sciences, Bangalore, Karnataka, India
- Institute of Science, Nirma University, Ahmedabad, India
| | - Michele Ceccarelli
- Department of Public Health Sciences, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Raghvendra Mall
- St. Jude Children's Hospital, Memphis, TN, USA.
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates.
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24
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Oliveras-Cañellas N, Castells-Nobau A, de la Vega-Correa L, Latorre-Luque J, Motger-Albertí A, Arnoriaga-Rodriguez M, Garre-Olmo J, Zapata-Tona C, Coll-Martínez C, Ramió-Torrentà L, Moreno-Navarrete JM, Puig J, Villarroya F, Ramos R, Casadó-Anguera V, Martín-García E, Maldonado R, Mayneris-Perxachs J, Fernández-Real JM. Adipose tissue coregulates cognitive function. SCIENCE ADVANCES 2023; 9:eadg4017. [PMID: 37566655 PMCID: PMC10421051 DOI: 10.1126/sciadv.adg4017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/10/2023] [Indexed: 08/13/2023]
Abstract
Obesity is associated with cognitive decline. Recent observations in mice propose an adipose tissue (AT)-brain axis. We identified 188 genes from RNA sequencing of AT in three cohorts that were associated with performance in different cognitive domains. These genes were mostly involved in synaptic function, phosphatidylinositol metabolism, the complement cascade, anti-inflammatory signaling, and vitamin metabolism. These findings were translated into the plasma metabolome. The circulating blood expression levels of most of these genes were also associated with several cognitive domains in a cohort of 816 participants. Targeted misexpression of candidate gene ortholog in the Drosophila fat body significantly altered flies memory and learning. Among them, down-regulation of the neurotransmitter release cycle-associated gene SLC18A2 improved cognitive abilities in Drosophila and in mice. Up-regulation of RIMS1 in Drosophila fat body enhanced cognitive abilities. Current results show previously unidentified connections between AT transcriptome and brain function in humans, providing unprecedented diagnostic/therapeutic targets in AT.
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Affiliation(s)
- Núria Oliveras-Cañellas
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Lisset de la Vega-Correa
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Jessica Latorre-Luque
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Anna Motger-Albertí
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Arnoriaga-Rodriguez
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Garre-Olmo
- Department of Nursing (Serra-Hunter Professor), University of Girona, Girona, Spain
| | - Cristina Zapata-Tona
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Clàudia Coll-Martínez
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Lluís Ramió-Torrentà
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
- Girona Neurodegeneration and Neuroinflammation Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - José Maria Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Puig
- Department of Radiology (IDI), Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
| | - Francesc Villarroya
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biology, University of Barcelona, Barcelona. Spain
| | - Rafel Ramos
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Vascular Health Research Group of Girona (ISV-Girona), Jordi Gol Institute for Primary Care Research (Institut Universitari per a la Recerca en Atenció Primària Jordi Gol I Gorina -IDIAPJGol), Girona, Spain
| | - Verònica Casadó-Anguera
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain
| | - Elena Martín-García
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
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25
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Mastropietro A, De Carlo G, Anagnostopoulos A. XGDAG: explainable gene-disease associations via graph neural networks. Bioinformatics 2023; 39:btad482. [PMID: 37531293 PMCID: PMC10421968 DOI: 10.1093/bioinformatics/btad482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/27/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023] Open
Abstract
MOTIVATION Disease gene prioritization consists in identifying genes that are likely to be involved in the mechanisms of a given disease, providing a ranking of such genes. Recently, the research community has used computational methods to uncover unknown gene-disease associations; these methods range from combinatorial to machine learning-based approaches. In particular, during the last years, approaches based on deep learning have provided superior results compared to more traditional ones. Yet, the problem with these is their inherent black-box structure, which prevents interpretability. RESULTS We propose a new methodology for disease gene discovery, which leverages graph-structured data using graph neural networks (GNNs) along with an explainability phase for determining the ranking of candidate genes and understanding the model's output. Our approach is based on a positive-unlabeled learning strategy, which outperforms existing gene discovery methods by exploiting GNNs in a non-black-box fashion. Our methodology is effective even in scenarios where a large number of associated genes need to be retrieved, in which gene prioritization methods often tend to lose their reliability. AVAILABILITY AND IMPLEMENTATION The source code of XGDAG is available on GitHub at: https://github.com/GiDeCarlo/XGDAG. The data underlying this article are available at: https://www.disgenet.org/, https://thebiogrid.org/, https://doi.org/10.1371/journal.pcbi.1004120.s003, and https://doi.org/10.1371/journal.pcbi.1004120.s004.
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Affiliation(s)
- Andrea Mastropietro
- Department of Computer, Control and Management Engineering “Antonio Ruberti”, Sapienza University of Rome, Rome 00185, Italy
| | - Gianluca De Carlo
- Department of Computer, Control and Management Engineering “Antonio Ruberti”, Sapienza University of Rome, Rome 00185, Italy
| | - Aris Anagnostopoulos
- Department of Computer, Control and Management Engineering “Antonio Ruberti”, Sapienza University of Rome, Rome 00185, Italy
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26
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Ngo D, Pratte KA, Flexeder C, Petersen H, Dang H, Ma Y, Keyes MJ, Gao Y, Deng S, Peterson BD, Farrell LA, Bhambhani VM, Palacios C, Quadir J, Gillenwater L, Xu H, Emson C, Gieger C, Suhre K, Graumann J, Jain D, Conomos MP, Tracy RP, Guo X, Liu Y, Johnson WC, Cornell E, Durda P, Taylor KD, Papanicolaou GJ, Rich SS, Rotter JI, Rennard SI, Curtis JL, Woodruff PG, Comellas AP, Silverman EK, Crapo JD, Larson MG, Vasan RS, Wang TJ, Correa A, Sims M, Wilson JG, Gerszten RE, O’Connor GT, Barr RG, Couper D, Dupuis J, Manichaikul A, O’Neal WK, Tesfaigzi Y, Schulz H, Bowler RP. Systemic Markers of Lung Function and Forced Expiratory Volume in 1 Second Decline across Diverse Cohorts. Ann Am Thorac Soc 2023; 20:1124-1135. [PMID: 37351609 PMCID: PMC10405603 DOI: 10.1513/annalsats.202210-857oc] [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: 10/11/2022] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airway obstruction and accelerated lung function decline. Our understanding of systemic protein biomarkers associated with COPD remains incomplete. Objectives: To determine what proteins and pathways are associated with impaired pulmonary function in a diverse population. Methods: We studied 6,722 participants across six cohort studies with both aptamer-based proteomic and spirometry data (4,566 predominantly White participants in a discovery analysis and 2,156 African American cohort participants in a validation). In linear regression models, we examined protein associations with baseline forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity (FVC). In linear mixed effects models, we investigated the associations of baseline protein levels with rate of FEV1 decline (ml/yr) in 2,777 participants with up to 7 years of follow-up spirometry. Results: We identified 254 proteins associated with FEV1 in our discovery analyses, with 80 proteins validated in the Jackson Heart Study. Novel validated protein associations include kallistatin serine protease inhibitor, growth differentiation factor 2, and tumor necrosis factor-like weak inducer of apoptosis (discovery β = 0.0561, Q = 4.05 × 10-10; β = 0.0421, Q = 1.12 × 10-3; and β = 0.0358, Q = 1.67 × 10-3, respectively). In longitudinal analyses within cohorts with follow-up spirometry, we identified 15 proteins associated with FEV1 decline (Q < 0.05), including elafin leukocyte elastase inhibitor and mucin-associated TFF2 (trefoil factor 2; β = -4.3 ml/yr, Q = 0.049; β = -6.1 ml/yr, Q = 0.032, respectively). Pathways and processes highlighted by our study include aberrant extracellular matrix remodeling, enhanced innate immune response, dysregulation of angiogenesis, and coagulation. Conclusions: In this study, we identify and validate novel biomarkers and pathways associated with lung function traits in a racially diverse population. In addition, we identify novel protein markers associated with FEV1 decline. Several protein findings are supported by previously reported genetic signals, highlighting the plausibility of certain biologic pathways. These novel proteins might represent markers for risk stratification, as well as novel molecular targets for treatment of COPD.
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Affiliation(s)
- Debby Ngo
- Cardiovascular Research Institute
- Division of Pulmonary, Critical Care, and Sleep Medicine, and
| | | | - Claudia Flexeder
- Institute of Epidemiology and
- Comprehensive Pneumology Center Munich (CPC-M) as member of the German Center for Lung Research (DZL), Munich, Germany
- Institute and Clinic for Occupational, Social, and Environmental Medicine, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Hans Petersen
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Hong Dang
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yanlin Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Yan Gao
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi; and
- Institute and Clinic for Occupational, Social, and Environmental Medicine, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | | | | | | | | | | | | | | | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Claire Emson
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Christian Gieger
- Institute of Epidemiology and
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine Qatar, Education City, Doha, Qatar
| | | | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Matthew P. Conomos
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA (University of California, Los Angeles) Medical Center, Torrance, California
| | - Yongmei Liu
- Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Elaine Cornell
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA (University of California, Los Angeles) Medical Center, Torrance, California
| | - George J. Papanicolaou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA (University of California, Los Angeles) Medical Center, Torrance, California
| | - Steven I. Rennard
- Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Prescott G. Woodruff
- Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | | | | | - Martin G. Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
| | - Ramachandran S. Vasan
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Division of Preventive Medicine and
- Division of Cardiology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Thomas J. Wang
- Department of Medicine, UT (University of Texas) Southwestern Medical Center, Dallas, Texas
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, and
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi; and
| | - Mario Sims
- Jackson Heart Study, Department of Medicine, and
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi; and
| | - James G. Wilson
- Cardiovascular Research Institute
- Jackson Heart Study, Department of Medicine, and
| | - Robert E. Gerszten
- Cardiovascular Research Institute
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - George T. O’Connor
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Pulmonary Center, Department of Medicine, Boston University, Boston, Massachusetts
| | - R. Graham Barr
- Department of Medicine and
- Department of Epidemiology, Columbia University, New York, New York
| | - David Couper
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Wanda K. O’Neal
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yohannes Tesfaigzi
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Holger Schulz
- Institute of Epidemiology and
- Comprehensive Pneumology Center Munich (CPC-M) as member of the German Center for Lung Research (DZL), Munich, Germany
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Sung J, Cheong J. Gene signature related to cancer stem cells and fibroblasts of stem-like gastric cancer predicts immunotherapy response. Clin Transl Med 2023; 13:e1347. [PMID: 37517036 PMCID: PMC10387327 DOI: 10.1002/ctm2.1347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/16/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Affiliation(s)
- Ji‐Yong Sung
- Center for Genome EngineeringInstitute for Basic ScienceDaejeonRepublic of Korea
| | - Jae‐Ho Cheong
- Department of SurgeryYonsei University College of MedicineSeoulRepublic of Korea
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Jennings P, Carta G, Singh P, da Costa Pereira D, Feher A, Dinnyes A, Exner TE, Wilmes A. Capturing time-dependent activation of genes and stress-response pathways using transcriptomics in iPSC-derived renal proximal tubule cells. Cell Biol Toxicol 2023; 39:1773-1793. [PMID: 36586010 PMCID: PMC10425493 DOI: 10.1007/s10565-022-09783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/06/2022] [Indexed: 01/01/2023]
Abstract
Transcriptomic analysis is a powerful method in the utilization of New Approach Methods (NAMs) for identifying mechanisms of toxicity and application to hazard characterization. With this regard, mapping toxicological events to time of exposure would be helpful to characterize early events. Here, we investigated time-dependent changes in gene expression levels in iPSC-derived renal proximal tubular-like cells (PTL) treated with five diverse compounds using TempO-Seq transcriptomics with the aims to evaluate the application of PTL for toxicity prediction and to report on temporal effects for the activation of cellular stress response pathways. PTL were treated with either 50 μM amiodarone, 10 μM sodium arsenate, 5 nM rotenone, or 300 nM tunicamycin over a temporal time course between 1 and 24 h. The TGFβ-type I receptor kinase inhibitor GW788388 (1 μM) was used as a negative control. Pathway analysis revealed the induction of key stress-response pathways, including Nrf2 oxidative stress response, unfolding protein response, and metal stress response. Early response genes per pathway were identified much earlier than 24 h and included HMOX1, ATF3, DDIT3, and several MT1 isotypes. GW788388 did not induce any genes within the stress response pathways above, but showed deregulation of genes involved in TGFβ inhibition, including downregulation of CYP24A1 and SERPINE1 and upregulation of WT1. This study highlights the application of iPSC-derived renal cells for prediction of cellular toxicity and sheds new light on the temporal and early effects of key genes that are involved in cellular stress response pathways.
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Affiliation(s)
- Paul Jennings
- Division of Molecular and Computational Toxicology, Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Giada Carta
- Division of Molecular and Computational Toxicology, Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Pranika Singh
- Edelweiss Connect GmbH, Technology Park Basel, Hochbergerstrasse 60C, 4057, Basel, Switzerland
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Daniel da Costa Pereira
- Division of Molecular and Computational Toxicology, Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anita Feher
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary
| | - Andras Dinnyes
- BioTalentum Ltd, Aulich Lajos Street 26, Gödöllő, 2100, Hungary
- HCEMM-USZ Stem Cell Research Group, Hungarian Centre of Excellence for Molecular Medicine, Szeged, 6723, Hungary
| | - Thomas E Exner
- Seven Past Nine d.o.o., Hribljane 10, 1380, Cerknica, Slovenia
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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29
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Farr Zuend C, Lamont A, Noel-Romas L, Knodel S, Birse K, Kratzer K, McQueen P, Perner M, Ayele H, Mutch S, Berard AR, Schellenberg JJ, Senturk F, McCorrister S, Westmacott G, Mulhall F, Sandberg B, Yu A, Burnett M, Poliquin V, Burgener AD. Increased genital mucosal cytokines in Canadian women associate with higher antigen-presenting cells, inflammatory metabolites, epithelial barrier disruption, and the depletion of L. crispatus. MICROBIOME 2023; 11:159. [PMID: 37491398 PMCID: PMC10367425 DOI: 10.1186/s40168-023-01594-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/05/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND Cervicovaginal inflammation has been linked to negative reproductive health outcomes including the acquisition of HIV, other sexually transmitted infections, and cervical carcinogenesis. While changes to the vaginal microbiome have been linked to genital inflammation, the molecular relationships between the functional components of the microbiome with cervical immunology in the reproductive tract are understudied, limiting our understanding of mucosal biology that may be important for reproductive health. RESULTS In this study, we used a multi'-omics approach to profile cervicovaginal samples collected from 43 Canadian women to characterize host, immune, functional microbiome, and metabolome features of cervicovaginal inflammation. We demonstrate that inflammation is associated with lower amounts of L. crispatus and higher levels of cervical antigen-presenting cells (APCs). Proteomic analysis showed an upregulation of pathways related to neutrophil degranulation, complement, and leukocyte migration, with lower levels of cornified envelope and cell-cell adherens junctions. Functional microbiome analysis showed reductions in carbohydrate metabolism and lactic acid, with increases in xanthine and other metabolites. Bayesian network analysis linked L. crispatus with glycolytic and nucleotide metabolism, succinate and xanthine, and epithelial proteins SCEL and IVL as major molecular features associated with pro-inflammatory cytokines and increased APCs. CONCLUSIONS This study identified key molecular and immunological relationships with cervicovaginal inflammation, including higher APCs, bacterial metabolism, and proteome alterations that underlie inflammation. As APCs are involved in HIV transmission, parturition, and cervical cancer progression, further studies are needed to explore the interactions between these cells, bacterial metabolism, mucosal immunity, and their relationship to reproductive health. Video Abstract.
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Affiliation(s)
- Christina Farr Zuend
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA.
| | - Alana Lamont
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Laura Noel-Romas
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Samantha Knodel
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Kenzie Birse
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Kateryna Kratzer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Peter McQueen
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Michelle Perner
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Hossaena Ayele
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Sarah Mutch
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Alicia R Berard
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - John J Schellenberg
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Faruk Senturk
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA
| | - Stuart McCorrister
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Garrett Westmacott
- JC Wilt Infectious Disease Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | | | | | - Adelicia Yu
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Margaret Burnett
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Vanessa Poliquin
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada
| | - Adam D Burgener
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, USA.
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Canada.
- Unit of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden.
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Haque R, Lee J, Chung JY, Shin HY, Kim H, Kim JH, Yun JW, Kang ES. VGLL3 expression is associated with macrophage infiltration and predicts poor prognosis in epithelial ovarian cancer. Front Oncol 2023; 13:1152991. [PMID: 37342190 PMCID: PMC10277618 DOI: 10.3389/fonc.2023.1152991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/09/2023] [Indexed: 06/22/2023] Open
Abstract
Background/objective High-grade serous ovarian carcinoma (HGSOC) is the most common histologic type of epithelial ovarian cancer (EOC). Due to its poor survival outcomes, it is essential to identify novel biomarkers and therapeutic targets. The hippo pathway is crucial in various cancers, including gynaecological cancers. Herein, we examined the expression of the key genes of the hippo pathway and their relationship with clinicopathological significance, immune cells infiltration and the prognosis of HGSOC. Methods The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) data were curated to analyse the mRNA expression as well as the clinicopathological association and correlation with immune cell infiltration in HGSOC. The protein levels of significant genes in the HGSOC tissue were analysed using Tissue Microarray (TMA)-based immunohistochemistry. Finally, DEGs pathway analysis was performed to find the signalling pathways associated with VGLL3. Results VGLL3 mRNA expression was significantly correlated with both advanced tumor stage and poor overall survival (OS) (p=0.046 and p=0.003, respectively). The result of IHC analysis also supported the association of VGLL3 protein with poor OS. Further, VGLL3 expression was significantly associated with tumor infiltrating macrophages. VGLL3 expression and macrophages infiltration were both found to be independent prognostic factors (p=0.003 and p=0.024, respectively) for HGSOC. VGLL3 was associated with four known and three novel cancer-related signalling pathways, thus implying that VGLL3 is involved in the deregulation of many genes and pathways. Conclusion Our study revealed that VGLL3 may play a distinct role in clinical outcomes and immune cell infiltration in patients with HGSOC and that it could potentially be a prognostic marker of EOC.
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Affiliation(s)
- Razaul Haque
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Seoul, Republic of Korea
- School of Medicine, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jaebon Lee
- School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
| | - Joon-Yong Chung
- Molecular Imaging Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ha-Yeon Shin
- Department of Obstetrics and Gynaecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyosun Kim
- Department of Obstetrics and Gynaecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae-Hoon Kim
- Department of Obstetrics and Gynaecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Won Yun
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Eun-Suk Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Seoul, Republic of Korea
- School of Medicine, Sungkyunkwan University, Suwon, Republic of Korea
- Cell and Gene Therapy Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
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31
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Gundesli H, Kori M, Arga KY. The Versatility of Plectin in Cancer: A Pan-Cancer Analysis on Potential Diagnostic and Prognostic Impacts of Plectin Isoforms. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023. [PMID: 37262182 DOI: 10.1089/omi.2023.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Plectin, encoded by PLEC, is a cytoskeletal and scaffold protein with a number of unique isoforms that act on various cellular functions such as cell adhesion, signal transduction, cancer cell invasion, and migration. While plectin has been shown to display high expression and mislocalization in tumor cells, our knowledge of the biological significance of plectin and its isoforms in tumorigenesis remain limited. In this study, we first performed pathway enrichment analysis to identify cancer hallmark proteins associated with plectin. Then, a pan-cancer analysis was performed using RNA-seq data collected from the Cancer Genome Atlas (TCGA) to detect the mRNA expression levels of PLEC and its transcript isoforms, and the prognostic as well as diagnostic significance of the transcript isoforms was evaluated considering cancer stages. We show here that several tissue specific PLEC isoforms are dysregulated in different cancer types and stages but not the expression of PLEC. Among them, PLEC 1d and PLEC 1f are potential biomarker candidates and call for further translational and personalized medicine research. This study makes a contribution as a stride to unravel the molecular mechanisms underpinning plectin isoforms in cancer development and progression by revealing the potent plectin isoforms in different stages of cancer as potential early cancer detection biomarkers. Importantly, uncovering how plectin isoforms guide malignancy and particular cancer types by comprehensive functional studies might open new avenues toward novel cancer therapeutics.
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Affiliation(s)
- Hulya Gundesli
- Gulhane Faculty of Medicine, University of Health Sciences, Ankara, Turkey
| | - Medi Kori
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
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Merchant JP, Zhu K, Henrion MYR, Zaidi SSA, Lau B, Moein S, Alamprese ML, Pearse RV, Bennett DA, Ertekin-Taner N, Young-Pearse TL, Chang R. Predictive network analysis identifies JMJD6 and other potential key drivers in Alzheimer's disease. Commun Biol 2023; 6:503. [PMID: 37188718 PMCID: PMC10185548 DOI: 10.1038/s42003-023-04791-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/31/2023] [Indexed: 05/17/2023] Open
Abstract
Despite decades of genetic studies on late-onset Alzheimer's disease, the underlying molecular mechanisms remain unclear. To better comprehend its complex etiology, we use an integrative approach to build robust predictive (causal) network models using two large human multi-omics datasets. We delineate bulk-tissue gene expression into single cell-type gene expression and integrate clinical and pathologic traits, single nucleotide variation, and deconvoluted gene expression for the construction of cell type-specific predictive network models. Here, we focus on neuron-specific network models and prioritize 19 predicted key drivers modulating Alzheimer's pathology, which we then validate by knockdown in human induced pluripotent stem cell-derived neurons. We find that neuronal knockdown of 10 of the 19 targets significantly modulates levels of amyloid-beta and/or phosphorylated tau peptides, most notably JMJD6. We also confirm our network structure by RNA sequencing in the neurons following knockdown of each of the 10 targets, which additionally predicts that they are upstream regulators of REST and VGF. Our work thus identifies robust neuronal key drivers of the Alzheimer's-associated network state which may represent therapeutic targets with relevance to both amyloid and tau pathology in Alzheimer's disease.
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Affiliation(s)
- Julie P Merchant
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kuixi Zhu
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Marc Y R Henrion
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, Pembroke Place, L3 5QA, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi
| | - Syed S A Zaidi
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Branden Lau
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
- Arizona Research Labs, Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Sara Moein
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Melissa L Alamprese
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Boston, MA, USA.
| | - Rui Chang
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA.
- Department of Neurology, University of Arizona, Tucson, AZ, USA.
- INTelico Therapeutics LLC, Tucson, AZ, USA.
- PATH Biotech LLC, Tucson, AZ, USA.
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Lopez-Ibañez J, Pazos F, Chagoyen M. MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis. Nucleic Acids Res 2023:7161529. [PMID: 37178003 DOI: 10.1093/nar/gkad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/17/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
MBROLE (Metabolites Biological Role) facilitates the biological interpretation of metabolomics experiments. It performs enrichment analysis of a set of chemical compounds through statistical analysis of annotations from several databases. The original MBROLE server was released in 2011 and, since then, different groups worldwide have used it to analyze metabolomics experiments from a variety of organisms. Here we present the latest version of the system, MBROLE3, accessible at http://csbg.cnb.csic.es/mbrole3. This new version contains updated annotations from previously included databases as well as a wide variety of new functional annotations, such as additional pathway databases and Gene Ontology terms. Of special relevance is the inclusion of a new category of annotations, 'indirect annotations', extracted from the scientific literature and from curated chemical-protein associations. The latter allows to analyze enriched annotations of the proteins known to interact with the set of chemical compounds of interest. Results are provided in the form of interactive tables, formatted data to download, and graphical plots.
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Affiliation(s)
- Javier Lopez-Ibañez
- Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), 28049 Madrid, Spain
| | - Florencio Pazos
- Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), 28049 Madrid, Spain
| | - Monica Chagoyen
- Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), 28049 Madrid, Spain
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Gomari D, Achkar IW, Benedetti E, Tabling J, Halama A, Krumsiek J. piTracer - Automatic reconstruction of molecular cascades for the identification of synergistic drug targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.08.535933. [PMID: 37066188 PMCID: PMC10104160 DOI: 10.1101/2023.04.08.535933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Cancer cells frequently undergo metabolic reprogramming as a mechanism of resistance against chemotherapeutic drugs. Metabolomic profiling provides a direct readout of metabolic changes and can thus be used to identify these tumor escape mechanisms. Here, we introduce piTracer, a computational tool that uses multi-scale molecular networks to identify potential combination therapies from pre- and post-treatment metabolomics data. We first demonstrate piTracer’s core ability to reconstruct cellular cascades by inspecting well-characterized molecular pathways and previously studied associations between genetic variants and metabolite levels. We then apply a new gene ranking algorithm on differential metabolomic profiles from human breast cancer cells after glutaminase inhibition. Four of the automatically identified gene targets were experimentally tested by simultaneous inhibition of the respective targets and glutaminase. Of these combination treatments, two were be confirmed to induce synthetic lethality in the cell line. In summary, piTracer integrates the molecular monitoring of escape mechanisms into comprehensive pathway networks to accelerate drug target identification. The tool is open source and can be accessed at https://github.com/krumsieklab/pitracer .
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Kori M, Arga KY. HPV16 status predicts potential protein biomarkers and therapeutics in head and neck squamous cell carcinoma. Virology 2023; 582:90-99. [PMID: 37031657 DOI: 10.1016/j.virol.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/11/2023]
Abstract
Human papillomavirus (HPV) infection, especially HPV16, is one of the causative factors for the development of head and neck squamous cell (HNSC) carcinoma. HPV-positive and HPV-negative HNSC patients differ significantly in their molecular profiles and clinical features, so they should be evaluated differently depending on their HPV status. Given the tremendous variation in HNSC cancers depending on HPV, our goal in this study was to present biomarkers and treatment options tailored to the patient's HPV status. Gene expression levels of HPV16-positive and -negative patients were used as proxies, and the differential interactome algorithm was employed to identify the differential interacting proteins (DIPs). By assessing the prognostic capabilities and druggabilities of DIPs and their interacting partners (DIP-centered modules), we introduce eight modules as potential biomarkers specialized for either positive or negative phenotype. Finally, raloxifene was repositioned for the first time as a drug candidate for the treatment of HPV16-positive HNSC patients.
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Affiliation(s)
- Medi Kori
- Department of Bioengineering, Marmara University, Istanbul, Turkey.
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Istanbul, Turkey; Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey.
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36
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Aydin B, Beklen H, Arga KY, Bayrakli F, Turanli B. Epigenomic and transcriptomic landscaping unraveled candidate repositioned therapeutics for non-functioning pituitary neuroendocrine tumors. J Endocrinol Invest 2023; 46:727-747. [PMID: 36306107 DOI: 10.1007/s40618-022-01923-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 09/12/2022] [Indexed: 10/31/2022]
Abstract
PURPOSE Non-functioning pituitary neuroendocrine tumors are challengingly diagnosed tumors in the clinic. Transsphenoidal surgery remains the first-line treatment. Despite the development of state-of-the-art techniques, no drug therapy is currently approved for the treatment. There are also no randomized controlled trials comparing therapeutic strategies or drug therapy for the management after surgery. Therefore, novel therapeutic interventions for the therapeutically challenging NF-PitNETs are urgently needed. METHODS We integrated epigenome and transcriptome data (both coding and non-coding) that elucidate disease-specific signatures, in addition to biological and pharmacological data, to utilize rational pathway and drug prioritization in NF-PitNETs. We constructed an epigenome- and transcriptome-based PPI network and proposed hub genes. The signature-based drug repositioning based on the integration of multi-omics data was performed. RESULTS The construction of a disease-specific network based on three different biological levels revealed DCC, DLG5, ETS2, FOXO1, HBP1, HMGA2, PCGF3, PSME4, RBPMS, RREB1, SMAD1, SOCS1, SOX2, YAP1, ZFHX3 as hub proteins. Signature-based drug repositioning using hub proteins yielded repositioned drug candidates that were confirmed in silico via molecular docking. As a result of molecular docking simulations, palbociclib, linifanib, trametinib, eplerenone, niguldipine, and zuclopenthixol showed higher binding affinities with hub genes compared to their inhibitors and were proposed as potential repositioned therapeutics for the management of NF-PitNETs. CONCLUSION The proposed systems' biomedicine-oriented multi-omics data integration for drug repurposing to provide promising results for the construction of effective clinical therapeutics. To the best of our knowledge, this is the first study reporting epigenome- and transcriptome-based drug repositioning for NF-PitNETs using in silico confirmations.
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Affiliation(s)
- B Aydin
- Department of Bioengineering, Faculty of Engineering and Architecture, Konya Food and Agriculture University, Konya, Turkey
| | - H Beklen
- Department of Bioengineering, Faculty of Engineering, Marmara University, RTE Basibuyuk Campus, 34720, Istanbul, Turkey
| | - K Y Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, RTE Basibuyuk Campus, 34720, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, Istanbul, Turkey
| | - F Bayrakli
- Department of Neurosurgery, Faculty of Medicine, Marmara University, Istanbul, Turkey
- Institute of Neurological Sciences, Marmara University, Istanbul, Turkey
| | - B Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, RTE Basibuyuk Campus, 34720, Istanbul, Turkey.
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Grandt CL, Brackmann LK, Foraita R, Schwarz H, Hummel-Bartenschlager W, Hankeln T, Kraemer C, Zahnreich S, Drees P, Mirsch J, Spix C, Blettner M, Schmidberger H, Binder H, Hess M, Galetzka D, Marini F, Poplawski A, Marron M. Gene expression variability in long-term survivors of childhood cancer and cancer-free controls in response to ionizing irradiation. Mol Med 2023; 29:41. [PMID: 36997855 PMCID: PMC10061869 DOI: 10.1186/s10020-023-00629-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/20/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Differential expression analysis is usually adjusted for variation. However, most studies that examined the expression variability (EV) have used computations affected by low expression levels and did not examine healthy tissue. This study aims to calculate and characterize an unbiased EV in primary fibroblasts of childhood cancer survivors and cancer-free controls (N0) in response to ionizing radiation. METHODS Human skin fibroblasts of 52 donors with a first primary neoplasm in childhood (N1), 52 donors with at least one second primary neoplasm (N2 +), as well as 52 N0 were obtained from the KiKme case-control study and exposed to a high (2 Gray) and a low dose (0.05 Gray) of X-rays and sham- irradiation (0 Gray). Genes were then classified as hypo-, non-, or hyper-variable per donor group and radiation treatment, and then examined for over-represented functional signatures. RESULTS We found 22 genes with considerable EV differences between donor groups, of which 11 genes were associated with response to ionizing radiation, stress, and DNA repair. The largest number of genes exclusive to one donor group and variability classification combination were all detected in N0: hypo-variable genes after 0 Gray (n = 49), 0.05 Gray (n = 41), and 2 Gray (n = 38), as well as hyper-variable genes after any dose (n = 43). While after 2 Gray positive regulation of cell cycle was hypo-variable in N0, (regulation of) fibroblast proliferation was over-represented in hyper-variable genes of N1 and N2+. In N2+, 30 genes were uniquely classified as hyper-variable after the low dose and were associated with the ERK1/ERK2 cascade. For N1, no exclusive gene sets with functions related to the radiation response were detected in our data. CONCLUSION N2+ showed high degrees of variability in pathways for the cell fate decision after genotoxic insults that may lead to the transfer and multiplication of DNA-damage via proliferation, where apoptosis and removal of the damaged genome would have been appropriate. Such a deficiency could potentially lead to a higher vulnerability towards side effects of exposure to high doses of ionizing radiation, but following low-dose applications employed in diagnostics, as well.
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Affiliation(s)
- Caine Lucas Grandt
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany.
- Faculty of Human and Health Sciences, University of Bremen, Bremen, Germany.
| | - Lara Kim Brackmann
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany
| | - Ronja Foraita
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany
| | - Heike Schwarz
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany
| | | | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christiane Kraemer
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian Zahnreich
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Philipp Drees
- Department of Orthopaedics and Traumatology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Johanna Mirsch
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Claudia Spix
- Division of Childhood Cancer Epidemiology, German Childhood Cancer Registry, Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maria Blettner
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Center of the Johannes, University Medical, Gutenberg University, Mainz, Germany
| | - Heinz Schmidberger
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Harald Binder
- Institute of Medical Biometry and Statistics, University Medical Center, Freiburg, Germany
| | - Moritz Hess
- Institute of Medical Biometry and Statistics, University Medical Center, Freiburg, Germany
| | - Danuta Galetzka
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Center of the Johannes, University Medical, Gutenberg University, Mainz, Germany
| | - Alicia Poplawski
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Center of the Johannes, University Medical, Gutenberg University, Mainz, Germany
| | - Manuela Marron
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Achterstr. 30, 28359, Bremen, Germany
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Raja R, Khanum S, Aboulmouna L, Maurya MR, Gupta S, Subramaniam S, Ramkrishna D. Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533676. [PMID: 36993235 PMCID: PMC10055344 DOI: 10.1101/2023.03.21.533676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Quantitative understanding of cellular processes, such as cell cycle and differentiation, is impeded by various forms of complexity ranging from myriad molecular players and their multilevel regulatory interactions, cellular evolution with multiple intermediate stages, lack of elucidation of cause-effect relationships among the many system players, and the computational complexity associated with the profusion of variables and parameters. In this paper, we present an elegant modeling framework based on the cybernetic concept that biological regulation is inspired by objectives embedding entirely novel strategies for dimension reduction, process stage specification through the system dynamics, and innovative causal association of regulatory events with the ability to predict the evolution of the dynamical system. The elementary step of the modeling strategy involves stage-specific objective functions that are computationally-determined from experiments, augmented with dynamical network computations involving end point objective functions, mutual information, change point detection, and maximal clique centrality. We demonstrate the power of the method through application to the mammalian cell cycle, which involves thousands of biomolecules engaged in signaling, transcription, and regulation. Starting with a fine-grained transcriptional description obtained from RNA sequencing measurements, we develop an initial model, which is then dynamically modeled using the cybernetic-inspired method (CIM), utilizing the strategies described above. The CIM is able to distill the most significant interactions from a multitude of possibilities. In addition to capturing the complexity of regulatory processes in a mechanistically causal and stage-specific manner, we identify the functional network modules, including novel cell cycle stages. Our model is able to predict future cell cycles consistent with experimental measurements. We posit that this state-of-the-art framework has the promise to extend to the dynamics of other biological processes, with a potential to provide novel mechanistic insights. STATEMENT OF SIGNIFICANCE Cellular processes like cell cycle are overly complex, involving multiple players interacting at multiple levels, and explicit modeling of such systems is challenging. The availability of longitudinal RNA measurements provides an opportunity to "reverse-engineer" for novel regulatory models. We develop a novel framework, inspired using goal-oriented cybernetic model, to implicitly model transcriptional regulation by constraining the system using inferred temporal goals. A preliminary causal network based on information-theory is used as a starting point, and our framework is used to distill the network to temporally-based networks containing essential molecular players. The strength of this approach is its ability to dynamically model the RNA temporal measurements. The approach developed paves the way for inferring regulatory processes in many complex cellular processes.
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Identifying multiscale translational safety biomarkers using a network-based systems approach. iScience 2023; 26:106094. [PMID: 36895646 PMCID: PMC9988559 DOI: 10.1016/j.isci.2023.106094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/30/2022] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Animal testing is the current standard for drug and chemicals safety assessment, but hazards translation to human is uncertain. Human in vitro models can address the species translation but might not replicate in vivo complexity. Herein, we propose a network-based method addressing these translational multiscale problems that derives in vivo liver injury biomarkers applicable to in vitro human early safety screening. We applied weighted correlation network analysis (WGCNA) to a large rat liver transcriptomic dataset to obtain co-regulated gene clusters (modules). We identified modules statistically associated with liver pathologies, including a module enriched for ATF4-regulated genes as associated with the occurrence of hepatocellular single-cell necrosis, and as preserved in human liver in vitro models. Within the module, we identified TRIB3 and MTHFD2 as a novel candidate stress biomarkers, and developed and used BAC-eGFPHepG2 reporters in a compound screening, identifying compounds showing ATF4-dependent stress response and potential early safety signals.
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Weaver DT, Scott JG. Crosstalkr: An open-source R package to facilitate drug target identification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531526. [PMID: 36945602 PMCID: PMC10028947 DOI: 10.1101/2023.03.07.531526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In the last few decades, interest in graph-based analysis of biological networks has grown substantially. Protein-protein interaction networks are one of the most common biological networks, and represent the molecular relationships between every known protein and every other known protein. Integration of these interactomic data into bioinformatic pipelines may increase the translational potential of discoveries made through analysis of multi-omic datasets. Crosstalkr provides a unified toolkit for drug target and disease subnetwork identification, two of the most common uses of protein protein interaction networks. First, crosstalkr enables users to download and leverage high-quality protein-protein interaction networks from online repositories. Users can then filter these large networks into manageable subnetworks using a variety of methods. For example, network filtration can be done using random walks with restarts, starting at the user-provided seed proteins. Affinity scores from a given random walk with restarts are compared to a bootstrapped null distribution to assess statistical significance. Random walks are implemented using sparse matrix multiplication to facilitate fast execution. Next, users can perform in-silico repression experiments to assess the relative importance of nodes in their network. At this step, users can supply protein or gene expression data to make node rankings more meaningful. The default behavior evaluates the human interactome. However, users can evaluate more than 1000 non-human protein-protein interaction networks as a result of integration with StringDB. It is a free, open-source R package designed to allow users to integrate functional analysis using the protein-protein interaction network into existing bioinformatic pipelines. A beta version of crosstalkr available on CRAN (https://cran.rstudio.com/web/packages/crosstalkr/index.html).
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Affiliation(s)
- Davis T. Weaver
- Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Translational Hematology Oncology Research, Cleveland Clinic, Cleveland OH, 44106, USA
| | - Jacob G. Scott
- Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Translational Hematology Oncology Research, Cleveland Clinic, Cleveland OH, 44106, USA
- Department of Physics, Case Western Reserve University, Cleveland, OH, 44106, USA
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Klimentidis YC, Chen Z, Gonzalez-Garay ML, Grigoriadis D, Sackey E, Pittman A, Ostergaard P, Herbst KL. Genome-wide association study of a lipedema phenotype among women in the UK Biobank identifies multiple genetic risk factors. Eur J Hum Genet 2023; 31:338-344. [PMID: 36385154 PMCID: PMC9995497 DOI: 10.1038/s41431-022-01231-6] [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: 06/22/2021] [Revised: 09/27/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
Lipedema is a common disorder characterized by excessive deposition of subcutaneous adipose tissue (SAT) in the legs, hips, and buttocks, mainly occurring in adult women. Although it appears to be heritable, no specific genes have yet been identified. To identify potential genetic risk factors for lipedema, we used bioelectrical impedance analysis and anthropometric data from the UK Biobank to identify women with and without a lipedema phenotype. Specifically, we identified women with both a high percentage of fat in the lower limbs and a relatively small waist, adjusting for hip circumference. We performed a genome-wide association study (GWAS) for this phenotype, and performed multiple sensitivity GWAS. In an independent case/control study of lipedema based on strict clinical criteria, we attempted to replicate our top hits. We identified 18 significant loci (p < 5 × 10-9), several of which have previously been identified in GWAS of waist-to-hip ratio with larger effects in women. Two loci (VEGFA and GRB14-COBLL1) were significantly associated with lipedema in the independent replication study. Follow-up analyses suggest an enrichment of genes expressed in blood vessels and adipose tissue, among other tissues. Our findings provide a starting point towards better understanding the genetic and physiological basis of lipedema.
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Affiliation(s)
- Yann C Klimentidis
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA.
- BIO5 Institute, University of Arizona, Arizona, AZ, USA.
| | - Zhao Chen
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | | | - Dionysios Grigoriadis
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Ege Sackey
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Alan Pittman
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Pia Ostergaard
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, London, UK
| | - Karen L Herbst
- TREAT Program, College of Medicine, University of Arizona, Tucson, AZ, USA
- Total Lipedema Care, Beverly Hills, CA, USA
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Song X, Li R, Wang K, Bai Y, Xiao Y, Wang YP. Joint Sparse Collaborative Regression on Imaging Genetics Study of Schizophrenia. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1137-1146. [PMID: 35503837 PMCID: PMC10321021 DOI: 10.1109/tcbb.2022.3172289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The imaging genetics approach generates large amount of high dimensional and multi-modal data, providing complementary information for comprehensive study of Schizophrenia, a complex mental disease. However, at the same time, the variety of these data in structures, resolutions, and formats makes their integrative study a forbidding task. In this paper, we propose a novel model called Joint Sparse Collaborative Regression (JSCoReg), which can extract class-specific features from different health conditions/disease classes. We first evaluate the performance of feature selection in terms of Receiver operating characteristic curve and the area under the ROC curve in the simulation experiment. We demonstrate that the JSCoReg model can achieve higher accuracy compared with similar models including Joint Sparse Canonical Correlation Analysis and Sparse Collaborative Regression. We then applied the JSCoReg model to the analysis of schizophrenia dataset collected from the Mind Clinical Imaging Consortium. The JSCoReg enables us to better identify biomarkers associated with schizophrenia, which are verified to be both biologically and statistically significant.
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Affiliation(s)
- Xueli Song
- School of Sciences, Chang’an University, Xi’an, 710064, China
| | - Rongpeng Li
- School of Sciences, Chang’an University, Xi’an, 710064, China
| | - Kaiming Wang
- School of Sciences, Chang’an University, Xi’an, 710064, China
| | - Yuntong Bai
- Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA
| | - Yuzhu Xiao
- School of Sciences, Chang’an University, Xi’an, 710064, China
| | - Yu-ping Wang
- Biomedical Engineering Department, Tulane University, New Orleans, LA 70118, USA
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Sinha I, Fogle RL, Gulfidan G, Stanley AE, Walter V, Hollenbeak CS, Arga KY, Sinha R. Potential Early Markers for Breast Cancer: A Proteomic Approach Comparing Saliva and Serum Samples in a Pilot Study. Int J Mol Sci 2023; 24:ijms24044164. [PMID: 36835577 PMCID: PMC9966955 DOI: 10.3390/ijms24044164] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/04/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Breast cancer is the second leading cause of death for women in the United States, and early detection could offer patients the opportunity to receive early intervention. The current methods of diagnosis rely on mammograms and have relatively high rates of false positivity, causing anxiety in patients. We sought to identify protein markers in saliva and serum for early detection of breast cancer. A rigorous analysis was performed for individual saliva and serum samples from women without breast disease, and women diagnosed with benign or malignant breast disease, using isobaric tags for relative and absolute quantitation (iTRAQ) technique, and employing a random effects model. A total of 591 and 371 proteins were identified in saliva and serum samples from the same individuals, respectively. The differentially expressed proteins were mainly involved in exocytosis, secretion, immune response, neutrophil-mediated immunity and cytokine-mediated signaling pathway. Using a network biology approach, significantly expressed proteins in both biological fluids were evaluated for protein-protein interaction networks and further analyzed for these being potential biomarkers in breast cancer diagnosis and prognosis. Our systems approach illustrates a feasible platform for investigating the responsive proteomic profile in benign and malignant breast disease using saliva and serum from the same women.
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Affiliation(s)
- Indu Sinha
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Rachel L. Fogle
- Environmental Science and Sustainability Program, Harrisburg University of Science and Technology, Harrisburg, PA 17101, USA
| | - Gizem Gulfidan
- Department of Bioengineering, Marmara University, Istanbul 34854, Turkey
| | - Anne E. Stanley
- Mass Spectrometry Core, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Vonn Walter
- Department of Public Health Sciences, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Christopher S. Hollenbeak
- Department of Health Policy and Administration, The Pennsylvania State University, University Park, State College, PA 16801, USA
| | - Kazim Y. Arga
- Department of Bioengineering, Marmara University, Istanbul 34854, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul 34854, Turkey
| | - Raghu Sinha
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
- Correspondence: ; Tel.: +1-(717)-531-4663
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Cui TX, Brady AE, Zhang YJ, Fulton CT, Goldsmith AM, Popova AP. Early-life hyperoxia-induced Flt3L drives neonatal lung dendritic cell expansion and proinflammatory responses. Front Immunol 2023; 14:1116675. [PMID: 36845082 PMCID: PMC9950736 DOI: 10.3389/fimmu.2023.1116675] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
Premature infants with chronic lung disease, bronchopulmonary dysplasia (BPD), develop recurrent cough and wheezing following respiratory viral infections. The mechanisms driving the chronic respiratory symptoms are ill-defined. We have shown that hyperoxic exposure of neonatal mice (a model of BPD) increases the activated lung CD103+ dendritic cells (DCs) and these DCs are required for exaggerated proinflammatory responses to rhinovirus (RV) infection. Since CD103+ DC are essential for specific antiviral responses and their development depends on the growth factor Flt3L, we hypothesized that early-life hyperoxia stimulates Flt3L expression leading to expansion and activation of lung CD103+ DCs and this mediates inflammation. We found that hyperoxia numerically increased and induced proinflammatory transcriptional signatures in neonatal lung CD103+ DCs, as well as CD11bhi DCs. Hyperoxia also increased Flt3L expression. Anti-Flt3L antibody blocked CD103+ DC development in normoxic and hyperoxic conditions, and while it did not affect the baseline number of CD11bhi DCs, it neutralized the effect of hyperoxia on these cells. Anti-Flt3L also inhibited hyperoxia-induced proinflammatory responses to RV. In tracheal aspirates from preterm infants mechanically-ventilated for respiratory distress in the first week of life levels of FLT3L, IL-12p40, IL-12p70 and IFN-γ were higher in infants who went on to develop BPD and FLT3L levels positively correlated with proinflammatory cytokines levels. This work highlights the priming effect of early-life hyperoxia on lung DC development and function and the contribution of Flt3L in driving these effects.
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Affiliation(s)
| | | | | | | | | | - Antonia P. Popova
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, United States
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Eptaminitaki GC, Zaravinos A, Stellas D, Panagopoulou M, Karaliota S, Baltsavia I, Iliopoulos I, Chatzaki E, Iliopoulos D, Baritaki S. Genome-Wide Analysis of lncRNA-mRNA Co-Expression Networks in CD133+/CD44+ Stem-like PDAC Cells. Cancers (Basel) 2023; 15:cancers15041053. [PMID: 36831395 PMCID: PMC9954787 DOI: 10.3390/cancers15041053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), the second most prevalent gastrointestinal malignancy and the most common type of pancreatic cancer is linked with poor prognosis and, eventually, with high mortality rates. Early detection is seldom, while tumor heterogeneity and microarchitectural alterations benefit PDAC resistance to conventional therapeutics. Although emerging evidence suggest the core role of cancer stem cells (CSCs) in PDAC aggressiveness, unique stem signatures are poorly available, thus limiting the efforts of anti-CSC-targeted therapy. Herein, we report the findings of the first genome-wide analyses of mRNA/lncRNA transcriptome profiling and co-expression networks in PDAC cell line-derived CD133+/CD44+ cells, which were shown to bear a CSC-like phenotype in vitro and in vivo. Compared to CD133-/CD44- cells, the CD133+/CD44+ population demonstrated significant expression differences in both transcript pools. Using emerging bioinformatic tools, we performed lncRNA target coding gene prediction analysis, which revealed significant Gene Ontology (GO), pathway, and network enrichments in many dyregulated lncRNA nearby (cis or trans) mRNAs, with reported involvement in the regulation of CSC phenotype and functions. In this context, the construction of lncRNA/mRNA networks by ingenuity platforms identified the lncRNAs ATF2, CHEK1, DCAF8, and PAX8 to interact with "hub" SC-associated mRNAs. In addition, the expressions of the above lncRNAs retrieved by TCGA-normalized RNAseq gene expression data of PAAD were significantly correlated with clinicopathological features of PDAC, including tumor grade and stage, nodal metastasis, and overall survival. Overall, our findings shed light on the identification of CSC-specific lncRNA signatures with potential prognostic and therapeutic significance in PDAC.
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Affiliation(s)
- Giasemi C. Eptaminitaki
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Apostolos Zaravinos
- Basic and Translational Cancer Research Center (BTCRC), Genomics and Systems Biology Laboratory, Cancer Genetics, Nicosia 1516, Cyprus
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus
| | - Dimitris Stellas
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Maria Panagopoulou
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Institute of Agri-Food and Life Sciences, Hellenic Mediterranean University Research Centre, 71410 Heraklion, Greece
| | - Sevasti Karaliota
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Ismini Baltsavia
- Laboratory of Computational Biology, Division of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Ioannis Iliopoulos
- Laboratory of Computational Biology, Division of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Ekaterini Chatzaki
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Institute of Agri-Food and Life Sciences, Hellenic Mediterranean University Research Centre, 71410 Heraklion, Greece
| | | | - Stavroula Baritaki
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Correspondence: ; Tel.: +30-281-039-4727
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Karthikeyan R, Gayathri P, Ramasamy S, Suvekbala V, Jagannadham MV, Rajendhran J. Transcriptome responses of intestinal epithelial cells induced by membrane vesicles of Listeria monocytogenes. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 4:100185. [PMID: 36942003 PMCID: PMC10023947 DOI: 10.1016/j.crmicr.2023.100185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Membrane vesicles (MVs) serve as an essential virulence factor in several pathogenic bacteria. The release of MVs by Listeria monocytogenes is only recently recognized; still, the enigmatic role of MVs in pathogenesis is yet to be established. We report the transcriptome response of Caco-2 cells upon exposure to MVs and the L. monocytogenes that leads to observe the up-regulation of autophagy-related genes in the early phase of exposure to MVs. Transcription of inflammatory cytokines is to the peak at the fourth hour of exposure. An array of differentially expressed genes was associated with actin cytoskeleton rearrangement, autophagy, cell cycle arrest, and induction of oxidative stress. At a later time point, transcriptional programs are generated upon interaction with MVs to evade innate immune signals, by modulating the expression of anti-inflammatory genes. KEGG pathway analysis is palpably confirming that MVs appear principally responsible for the induction of immune signaling pathways. Besides, MVs induced the expression of cell cycle regulatory genes, likely responsible for the ability to prolong host cell survival, thus protecting the replicative niche for L. monocytogenes. Notably, we identified several non-coding RNAs (ncRNAs), possibly involved in the regulation of early manipulation of the host gene expression, essential for the persistence of L. monocytogenes.
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Affiliation(s)
- Raman Karthikeyan
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
| | - Pratapa Gayathri
- CSIR - Centre for Cellular and Molecular Biology, Tarnaka, Hyderabad 500007, India
| | - Subbiah Ramasamy
- Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
| | - Vemparthan Suvekbala
- EDII-Anna Business Incubation Research Foundation, University College of Engineering, BIT Campus, Anna University, Tiruchirappalli 620024, India
| | - Medicharla V. Jagannadham
- CSIR - Centre for Cellular and Molecular Biology, Tarnaka, Hyderabad 500007, India
- Corresponding authors.
| | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
- Corresponding authors.
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Oxytocin Exposure in Labor and its Relationship with Cognitive Impairment and the Genetic Architecture of Autism. J Autism Dev Disord 2023; 53:66-79. [PMID: 34982326 DOI: 10.1007/s10803-021-05409-7] [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] [Accepted: 12/14/2021] [Indexed: 02/03/2023]
Abstract
Whether there is a relationship between oxytocin (OXT) use in labor and the risk of autism (ASD), and the nature of such relationship, is unclear. By integrating genetic and clinical data in a sample of 176 ASD participants, we tested the hypothesis that OXT is a marker for abnormal prenatal development which leads to impairments in the process of labor. OXT-exposed ASD had more obstetric complications (P = 0.031), earlier onset of symptoms (P = 0.027), poorer cognitive development (P = 0.011), higher mutation burden across neurodevelopment genes (P = 0.020; OR = 5.33) and lower transmission of polygenic risk for ASD (P = 0.0319), than non-exposed ASD. OXT seems to constitute a risk indicator rather than a risk factor for ASD, which is relevant for diagnostic and genetic counselling.
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Grandt CL, Brackmann LK, Poplawski A, Schwarz H, Marini F, Hankeln T, Galetzka D, Zahnreich S, Mirsch J, Spix C, Blettner M, Schmidberger H, Marron M. Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls. Front Oncol 2023; 13:1158176. [PMID: 37182169 PMCID: PMC10174438 DOI: 10.3389/fonc.2023.1158176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction Long non-coding ribonucleic acids (lncRNAs) are involved in the cellular damage response following exposure to ionizing radiation as applied in radiotherapy. However, the role of lncRNAs in radiation response concerning intrinsic susceptibility to late effects of radiation exposure has not been examined in general or in long-term survivors of childhood cancer with and without potentially radiotherapy-related second primary cancers, in particular. Methods Primary skin fibroblasts (n=52 each) of long-term childhood cancer survivors with a first primary cancer only (N1), at least one second primary neoplasm (N2+), as well as tumor-free controls (N0) from the KiKme case-control study were matched by sex, age, and additionally by year of diagnosis and entity of the first primary cancer. Fibroblasts were exposed to 0.05 and 2 Gray (Gy) X-rays. Differentially expressed lncRNAs were identified with and without interaction terms for donor group and dose. Weighted co-expression networks of lncRNA and mRNA were constructed using WGCNA. Resulting gene sets (modules) were correlated to the radiation doses and analyzed for biological function. Results After irradiation with 0.05Gy, few lncRNAs were differentially expressed (N0: AC004801.4; N1: PCCA-DT, AF129075.3, LINC00691, AL158206.1; N2+: LINC02315). In reaction to 2 Gy, the number of differentially expressed lncRNAs was higher (N0: 152, N1: 169, N2+: 146). After 2 Gy, AL109976.1 and AL158206.1 were prominently upregulated in all donor groups. The co-expression analysis identified two modules containing lncRNAs that were associated with 2 Gy (module1: 102 mRNAs and 4 lncRNAs: AL158206.1, AL109976.1, AC092171.5, TYMSOS, associated with p53-mediated reaction to DNA damage; module2: 390 mRNAs, 7 lncRNAs: AC004943.2, AC012073.1, AC026401.3, AC092718.4, MIR31HG, STXBP5-AS1, TMPO-AS1, associated with cell cycle regulation). Discussion For the first time, we identified the lncRNAs AL158206.1 and AL109976.1 as involved in the radiation response in primary fibroblasts by differential expression analysis. The co-expression analysis revealed a role of these lncRNAs in the DNA damage response and cell cycle regulation post-IR. These transcripts may be targets in cancer therapy against radiosensitivity, as well as provide grounds for the identification of at-risk patients for immediate adverse reactions in healthy tissues. With this work we deliver a broad basis and new leads for the examination of lncRNAs in the radiation response.
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Affiliation(s)
- Caine Lucas Grandt
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
- Faculty of Human and Health Sciences, University of Bremen, Bremen, Germany
- *Correspondence: Caine Lucas Grandt,
| | - Lara Kim Brackmann
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
| | - Alicia Poplawski
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Heike Schwarz
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Danuta Galetzka
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian Zahnreich
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Johanna Mirsch
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Claudia Spix
- Division of Childhood Cancer Epidemiology, German Childhood Cancer Registry, Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maria Blettner
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Heinz Schmidberger
- Department of Radiation Oncology and Radiation Therapy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Manuela Marron
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
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Tumurkhuu G, Casanova NG, Kempf CL, Ercan Laguna D, Camp SM, Dagvadorj J, Song JH, Reyes Hernon V, Travelli C, Montano EN, Yu JM, Ishimori M, Wallace DJ, Sammani S, Jefferies C, Garcia JG. eNAMPT/TLR4 inflammatory cascade activation is a key contributor to SLE Lung vasculitis and alveolar hemorrhage. J Transl Autoimmun 2022; 6:100181. [PMID: 36619655 PMCID: PMC9816774 DOI: 10.1016/j.jtauto.2022.100181] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Rationale Effective therapies to reduce the severity and high mortality of pulmonary vasculitis and diffuse alveolar hemorrhage (DAH) in patients with systemic lupus erythematosus (SLE) is a serious unmet need. We explored whether biologic neutralization of eNAMPT (extracellular nicotinamide phosphoribosyl-transferase), a novel DAMP and Toll-like receptor 4 ligand, represents a viable therapeutic strategy in lupus vasculitis. Methods Serum was collected from SLE subjects (n = 37) for eNAMPT protein measurements. In the preclinical pristane-induced murine model of lung vasculitis/hemorrhage, C57BL/6 J mice (n = 5-10/group) were treated with PBS, IgG (1 mg/kg), or the eNAMPT-neutralizing ALT-100 mAb (1 mg/kg, IP or subcutaneously (SQ). Lung injury evaluation (Day 10) included histology/immuno-histochemistry, BAL protein/cellularity, tissue biochemistry, RNA sequencing, and plasma biomarker assessment. Results SLE subjects showed highly significant increases in blood NAMPT mRNA expression and eNAMPT protein levels compared to healthy controls. Preclinical pristane-exposed mice studies showed significantly increased NAMPT lung tissue expression and increased plasma eNAMPT levels accompanied by marked increases in alveolar hemorrhage and lung inflammation (BAL protein, PMNs, activated monocytes). In contrast, ALT-100 mAb-treated mice showed significant attenuation of inflammatory lung injury, alveolar hemorrhage, BAL protein, tissue leukocytes, and plasma inflammatory cytokines (eNAMPT, IL-6, IL-8). Lung RNA sequencing showed pristane-induced activation of inflammatory genes/pathways including NFkB, cytokine/chemokine, IL-1β, and MMP signaling pathways, each rectified in ALT-100 mAb-treated mice. Conclusions These findings highlight the role of eNAMPT/TLR4-mediated inflammatory signaling in the pathobiology of SLE pulmonary vasculitis and alveolar hemorrhage. Biologic neutralization of this novel DAMP appears to serve as a viable strategy to reduce the severity of SLE lung vasculitis.
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Affiliation(s)
- Gantsetseg Tumurkhuu
- Department of Medicine, Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Nancy G. Casanova
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Carrie L. Kempf
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Duygu Ercan Laguna
- Department of Medicine, Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sara M. Camp
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | | | - Jin H. Song
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Vivian Reyes Hernon
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | | | - Erica N. Montano
- Department of Medicine, Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jeong Min Yu
- Department of Medicine, Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mariko Ishimori
- Department of Medicine, Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine at University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Daniel J. Wallace
- Department of Medicine, Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine at University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Saad Sammani
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Caroline Jefferies
- Department of Medicine, Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joe G.N. Garcia
- Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
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Onderwater GLJ, van Dongen RM, Harms AC, Zielman R, van Oosterhout WPJ, van Klinken JB, Goeman JJ, Terwindt GM, van den Maagdenberg AMJM, Hankemeier T, Ferrari MD. Cerebrospinal Fluid and Plasma Amine Profiles in Interictal Migraine. Ann Neurol 2022; 93:715-728. [PMID: 36511835 DOI: 10.1002/ana.26576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 11/18/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Impaired amine metabolism has been associated with the etiology of migraine, that is, why patients continue to get migraine attacks. However, evidence from cerebrospinal fluid (CSF) is lacking. Here, we evaluated individual amine levels, global amine profiles, and amine pathways in CSF and plasma of interictal migraine patients and healthy controls. METHODS CSF and plasma were sampled between 8:30 am and 1:00 pm, randomly and interchangeably over the time span to avoid any diurnal and seasonal influences, from healthy volunteers and interictal migraine patients, matched for age, sex, and sampling time. The study was approved by the local medical ethics committee. Individual amines (n = 31), global amine profiles, and specific amine pathways were analyzed using a validated ultraperformance liquid chromatography mass spectrometry platform. RESULTS We analyzed n = 99 participants with migraine with aura, n = 98 with migraine without aura, and n = 96 healthy volunteers. Univariate analysis with Bonferroni correction indicated that CSF L-arginine was reduced in migraine with aura (10.4%, p < 0.001) and without aura (5.0%, p = 0.03). False discovery rate-corrected CSF L-phenylalanine was also lower in migraine with aura (6.9%, p = 0.011) and without aura (8.1%, p = 0.001), p = 0.088 after Bonferroni correction. Multivariate analysis revealed that CSF global amine profiles were similar for both types of migraine (p = 0.64), but distinct from controls (p = 0.009). Global profile analyses were similar in plasma. The strongest associated pathways with migraine were related to L-arginine metabolism. INTERPRETATION L-Arginine was decreased in the CSF (but not in plasma) of interictal patients with migraine with or without aura, and associated pathways were altered. This suggests that dysfunction of nitric oxide signaling is involved in susceptibility to getting migraine attacks. ANN NEUROL 2023.
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Affiliation(s)
| | - Robin M van Dongen
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Amy C Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden, the Netherlands
| | - Ronald Zielman
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Jan B van Klinken
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jelle J Goeman
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Gisela M Terwindt
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arn M J M van den Maagdenberg
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden, the Netherlands
| | - Michel D Ferrari
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
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