1
|
Castro V, Calvo G, Oliveros JC, Pérez-Del-Pulgar S, Gastaminza P. Hepatitis C virus-induced differential transcriptional traits in host cells after persistent infection elimination by direct-acting antivirals in cell culture. J Med Virol 2024; 96:e29787. [PMID: 38988177 DOI: 10.1002/jmv.29787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/11/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
Chronic hepatitis C virus infection (HCV) causes liver inflammation and fibrosis, leading to the development of severe liver disease, such as cirrhosis or hepatocellular carcinoma (HCC). Approval of direct-acting antiviral drug combinations has revolutionized chronic HCV therapy, with virus eradication in >98% of the treated patients. The efficacy of these treatments is such that it is formally possible for cured patients to carry formerly infected cells that display irreversible transcriptional alterations directly caused by chronic HCV Infection. Combining differential transcriptomes from two different persistent infection models, we observed a major reversion of infection-related transcripts after complete infection elimination. However, a small number of transcripts were abnormally expressed in formerly infected cells. Comparison of the results obtained in proliferating and growth-arrested cell culture models suggest that permanent transcriptional alterations may be established by several mechanisms. Interestingly, some of these alterations were also observed in the liver biopsies of virologically cured patients. Overall, our data suggest a direct and permanent impact of persistent HCV infection on the host cell transcriptome even after virus elimination, possibly contributing to the development of HCC.
Collapse
Affiliation(s)
- Victoria Castro
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gema Calvo
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Juan Carlos Oliveros
- Bioinformatics for Genomics and Proteomics Unit, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Pablo Gastaminza
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| |
Collapse
|
2
|
Nuthikattu S, Milenkovic D, Norman JE, Villablanca AC. Single nuclei transcriptomics in diabetic mice reveals altered brain hippocampal endothelial cell function, permeability, and behavior. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166970. [PMID: 38036105 DOI: 10.1016/j.bbadis.2023.166970] [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: 09/13/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is a metabolic disorder with cerebrovascular and cardiovascular sequelae. Yet, a clear pattern of gene dysregulation by T2DM in dementia has yet to be defined. We used single nuclei RNA sequencing technology to profile the transcriptome of endothelial cells (EC) from anatomically defined hippocampus of db/db mice to identify differentially expressed (DE) genes, gene pathways and networks, predicted regulating transcription factors, and targets of DE long noncoding RNAs. We also applied gadolinium (Gd) enhanced magnetic resonance imaging (MRI) to assess blood brain barrier (BBB) permeability, and functionally assessed cognitive behavior. The murine gene expression profiles were then integrated with those of persons with Alzheimer's disease (AD) and vascular dementia (VaD). We reveal that the transcriptome of the diabetic hippocampal murine brain endothelium differs substantially from control wild types with molecular changes characterized by differential RNA coding and noncoding pathways enriched for EC signaling and for endothelial functions for neuroinflammation, endothelial barrier disruption, and neurodegeneration. Gd enhanced structural brain MRI linked endothelial molecular alterations to BBB dysfunction by neuroimaging. Integrated multiomics of hippocampal endothelial gene dysregulation associated with impairments in cognitive adaptive capacity. In addition, the diabetic transcriptome significantly and positively correlated with that of persons with AD and VaD. Taken together, our results from comprehensive, multilevel, integrated, single nuclei transcriptomics support the hypothesis of T2DM-mediated neuroinflammation and endothelial cell and barrier disruption as key mechanisms in cognitive decline in T2DM, thereby suggesting potential endothelial-specific molecular therapeutic targets.
Collapse
Affiliation(s)
- Saivageethi Nuthikattu
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA 95616, USA.
| | - Dragan Milenkovic
- Department of Nutrition, University of California, Davis, CA 95616, USA
| | - Jennifer E Norman
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA 95616, USA
| | - Amparo C Villablanca
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, CA 95616, USA
| |
Collapse
|
3
|
Ernault AC, de Winter R, Fabrizi B, Bracht JW, Hau C, van Amersfoorth SC, Meulendijks ER, Tijsen AJ, Cócera Ortega L, van der Made I, Gasecka A, Driessen AH, Nieuwland R, Boukens BJ, van der Pol E, de Groot JR, Coronel R. MicroRNAs in extracellular vesicles released from epicardial adipose tissue promote arrhythmogenic conduction slowing. Heart Rhythm O2 2023; 4:805-814. [PMID: 38204457 PMCID: PMC10774655 DOI: 10.1016/j.hroo.2023.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Abstract
Background Patients with excess epicardial adipose tissue (EAT) are at increased risk of developing cardiac arrhythmias. EAT promotes arrhythmias by depolarizing the resting membrane of cardiomyocytes, which slows down conduction and facilitates re-entrant arrhythmias. We hypothesized that EAT slows conduction by secreting extracellular vesicles (EVs) and their microRNA (miRNA) cargo. Objective We aimed to determine the role of EAT-derived EVs and their miRNA cargo in conduction slowing. Methods EAT and subcutaneous adipose tissue (SAT) were collected from patients with atrial fibrillation. Adipose tissue explants were incubated in culture medium and secretome was collected. The numbers of EVs in the EAT and SAT secretome were measured by calibrated flow cytometry. EVs in the EAT secretome were isolated by size exclusion chromatography and miRNAs were sequenced. Pathway analysis was performed to predict candidates involved in cardiac electrophysiology. The candidates were validated in the EAT and SAT by quantitative real-time polymerase chain reaction. Finally, miRNA candidates were overexpressed in neonatal rat ventricular myocytes. Results The EV concentration was higher in the EAT secretome than in the SAT and control secretomes. miRNA sequencing of EAT-derived EVs detected a total of 824 miRNAs. Pathway analysis led to the identification of 7 miRNAs potentially involved in regulation of cardiac resting membrane potential. Validation of those miRNA candidates showed that they were all expressed in EAT, and that miR-1-3p and miR-133a-3p were upregulated in EAT in comparison with SAT. Overexpression of miR-1-3p and miR-133a-3p in neonatal rat ventricular myocytes led to conduction slowing and reduced Kcnj2 and Kcnj12 expression. Conclusion miR-1-3p and miR-133a-3p are potential mediators of EAT arrhythmogenicity.
Collapse
Affiliation(s)
- Auriane C. Ernault
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Rosan de Winter
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Benedetta Fabrizi
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Jillian W.P. Bracht
- Laboratory of Experimental Clinical Chemistry, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
- Vesicle Observation Center, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | - Chi Hau
- Laboratory of Experimental Clinical Chemistry, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
- Vesicle Observation Center, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | - Shirley C.M. van Amersfoorth
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Eva R. Meulendijks
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Anke J. Tijsen
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Lucía Cócera Ortega
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Ingeborg van der Made
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Aleksandra Gasecka
- Laboratory of Experimental Clinical Chemistry, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
- Vesicle Observation Center, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
- Department of Cardiology, Medical University of Warsaw, Warsaw, Poland
| | - Antoine H. Driessen
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Rienk Nieuwland
- Laboratory of Experimental Clinical Chemistry, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
- Vesicle Observation Center, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | - Bastiaan J. Boukens
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
- Department of Medical Biology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
| | - Edwin van der Pol
- Laboratory of Experimental Clinical Chemistry, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
- Vesicle Observation Center, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
- Biomedical Engineering and Physics, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | - Joris R. de Groot
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Ruben Coronel
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, location University of Amsterdam, Amsterdam, the Netherlands
- Heart Failure and Arrhythmias, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| |
Collapse
|
4
|
Mamrosh JL, Sherman DJ, Cohen JR, Johnston JA, Joubert MK, Li J, Lipford JR, Lomenick B, Moradian A, Prabhu S, Sweredoski MJ, Vander Lugt B, Verma R, Deshaies RJ. Quantitative measurement of the requirement of diverse protein degradation pathways in MHC class I peptide presentation. SCIENCE ADVANCES 2023; 9:eade7890. [PMID: 37352349 PMCID: PMC10289651 DOI: 10.1126/sciadv.ade7890] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/17/2023] [Indexed: 06/25/2023]
Abstract
Peptides from degradation of intracellular proteins are continuously displayed by major histocompatibility complex (MHC) class I. To better understand origins of these peptides, we performed a comprehensive census of the class I peptide repertoire in the presence and absence of ubiquitin-proteasome system (UPS) activity upon developing optimized methodology to enrich for and quantify these peptides. Whereas most class I peptides are dependent on the UPS for their generation, a surprising 30%, enriched in peptides of mitochondrial origin, appears independent of the UPS. A further ~10% of peptides were found to be dependent on the proteasome but independent of ubiquitination for their generation. Notably, clinically achievable partial inhibition of the proteasome resulted in display of atypical peptides. Our results suggest that generation of MHC class I•peptide complexes is more complex than previously recognized, with UPS-dependent and UPS-independent components; paradoxically, alternative protein degradation pathways also generate class I peptides when canonical pathways are impaired.
Collapse
Affiliation(s)
- Jennifer L. Mamrosh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - David J. Sherman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - Joseph R. Cohen
- Process Development, Amgen Inc., Thousand Oaks, CA 91320, USA
| | | | | | - Jing Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | | | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Michael J. Sweredoski
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Rati Verma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - Raymond J. Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| |
Collapse
|
5
|
Mariano V, Kanellopoulos AK, Aiello G, Lo AC, Legius E, Achsel T, Bagni C. SREBP modulates the NADP +/NADPH cycle to control night sleep in Drosophila. Nat Commun 2023; 14:763. [PMID: 36808152 PMCID: PMC9941135 DOI: 10.1038/s41467-022-35577-8] [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: 11/20/2021] [Accepted: 12/12/2022] [Indexed: 02/22/2023] Open
Abstract
Sleep behavior is conserved throughout evolution, and sleep disturbances are a frequent comorbidity of neuropsychiatric disorders. However, the molecular basis underlying sleep dysfunctions in neurological diseases remains elusive. Using a model for neurodevelopmental disorders (NDDs), the Drosophila Cytoplasmic FMR1 interacting protein haploinsufficiency (Cyfip85.1/+), we identify a mechanism modulating sleep homeostasis. We show that increased activity of the sterol regulatory element-binding protein (SREBP) in Cyfip85.1/+ flies induces an increase in the transcription of wakefulness-associated genes, such as the malic enzyme (Men), causing a disturbance in the daily NADP+/NADPH ratio oscillations and reducing sleep pressure at the night-time onset. Reduction in SREBP or Men activity in Cyfip85.1/+ flies enhances the NADP+/NADPH ratio and rescues the sleep deficits, indicating that SREBP and Men are causative for the sleep deficits in Cyfip heterozygous flies. This work suggests modulation of the SREBP metabolic axis as a new avenue worth exploring for its therapeutic potential in sleep disorders.
Collapse
Affiliation(s)
- Vittoria Mariano
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland.,Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | | | - Giuseppe Aiello
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
| | - Adrian C Lo
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
| | - Eric Legius
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, 1005, Switzerland. .,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, 00133, Italy.
| |
Collapse
|
6
|
Sabharwal A, Wishman MD, Cervera RL, Serres MR, Anderson JL, Holmberg SR, Kar B, Treichel AJ, Ichino N, Liu W, Yang J, Ding Y, Deng Y, Lacey JM, Laxen WJ, Loken PR, Oglesbee D, Farber SA, Clark KJ, Xu X, Ekker SC. Genetic therapy in a mitochondrial disease model suggests a critical role for liver dysfunction in mortality. eLife 2022; 11:e65488. [PMID: 36408801 PMCID: PMC9859037 DOI: 10.7554/elife.65488] [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: 12/15/2020] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
The clinical and largely unpredictable heterogeneity of phenotypes in patients with mitochondrial disorders demonstrates the ongoing challenges in the understanding of this semi-autonomous organelle in biology and disease. Previously, we used the gene-breaking transposon to create 1200 transgenic zebrafish strains tagging protein-coding genes (Ichino et al., 2020), including the lrpprc locus. Here, we present and characterize a new genetic revertible animal model that recapitulates components of Leigh Syndrome French Canadian Type (LSFC), a mitochondrial disorder that includes diagnostic liver dysfunction. LSFC is caused by allelic variations in the LRPPRC gene, involved in mitochondrial mRNA polyadenylation and translation. lrpprc zebrafish homozygous mutants displayed biochemical and mitochondrial phenotypes similar to clinical manifestations observed in patients, including dysfunction in lipid homeostasis. We were able to rescue these phenotypes in the disease model using a liver-specific genetic model therapy, functionally demonstrating a previously under-recognized critical role for the liver in the pathophysiology of this disease.
Collapse
Affiliation(s)
- Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Mark D Wishman
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Roberto Lopez Cervera
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - MaKayla R Serres
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Jennifer L Anderson
- Department of Embryology, Carnegie Institution for ScienceBaltimoreUnited States
| | - Shannon R Holmberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Anthony J Treichel
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Noriko Ichino
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Weibin Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Jingchun Yang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Yun Deng
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Jean M Lacey
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of MedicineRochesterUnited States
| | - William J Laxen
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of MedicineRochesterUnited States
| | - Perry R Loken
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of MedicineRochesterUnited States
| | - Devin Oglesbee
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of MedicineRochesterUnited States
| | - Steven A Farber
- Department of Embryology, Carnegie Institution for ScienceBaltimoreUnited States
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| |
Collapse
|
7
|
Loss of the Nuclear Envelope Protein LAP1B Disrupts the Myogenic Differentiation of Patient-Derived Fibroblasts. Int J Mol Sci 2022; 23:ijms232113615. [PMID: 36362402 PMCID: PMC9656778 DOI: 10.3390/ijms232113615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/10/2022] Open
Abstract
Lamina-associated polypeptide 1 (LAP1) is a ubiquitously expressed inner nuclear membrane protein encoded by TOR1AIP1, and presents as two isoforms in humans, LAP1B and LAP1C. While loss of both isoforms results in a multisystemic progeroid-like syndrome, specific loss of LAP1B causes muscular dystrophy and cardiomyopathy, suggesting that LAP1B has a critical role in striated muscle. To gain more insight into the molecular pathophysiology underlying muscular dystrophy caused by LAP1B, we established a patient-derived fibroblast line that was transdifferentiated into myogenic cells using inducible MyoD expression. Compared to the controls, we observed strongly reduced myogenic differentiation and fusion potentials. Similar defects were observed in the C2C12 murine myoblasts carrying loss-of-function LAP1A/B mutations. Using RNA sequencing, we found that, despite MyoD overexpression and efficient cell cycle exit, transcriptional reprogramming of the LAP1B-deficient cells into the myogenic lineage is impaired with delayed activation of MYOG and muscle-specific genes. Gene set enrichment analyses suggested dysregulations of protein metabolism, extracellular matrix, and chromosome organization. Finally, we found that the LAP1B-deficient cells exhibit nuclear deformations, such as an increased number of micronuclei and altered morphometric parameters. This study uncovers the phenotypic and transcriptomic changes occurring during myoconversion of patient-derived LAP1B-deficient fibroblasts and provides a useful resource to gain insights into the mechanisms implicated in LAP1B-associated nuclear envelopathies.
Collapse
|
8
|
Carecho R, Figueira I, Terrasso AP, Godinho‐Pereira J, de Oliveira Sequeira C, Pereira SA, Milenkovic D, Leist M, Brito C, Nunes dos Santos C. Circulating (Poly)phenol Metabolites: Neuroprotection in a 3D Cell Model of Parkinson's Disease. Mol Nutr Food Res 2022; 66:e2100959. [PMID: 34964254 PMCID: PMC9788306 DOI: 10.1002/mnfr.202100959] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/10/2021] [Indexed: 12/30/2022]
Abstract
SCOPE Diets rich in (poly)phenols have been associated with positive effects on neurodegenerative disorders, such as Parkinson's disease (PD). Several low-molecular weight (poly)phenol metabolites (LMWPM) are found in the plasma after consumption of (poly)phenol-rich food. It is expected that LMWPM, upon reaching the brain, may have beneficial effects against both oxidative stress and neuroinflammation, and possibly attenuate cell death mechanisms relate to the loss of dopaminergic neurons in PD. METHODS AND RESULTS This study investigates the neuroprotective potential of two blood-brain barrier permeant LMWPM, catechol-O-sulfate (cat-sulf), and pyrogallol-O-sulfate (pyr-sulf), in a human 3D cell model of PD. Neurospheroids were generated from LUHMES neuronal precursor cells and challenged by 1-methyl-4-phenylpyridinium (MPP+ ) to induce neuronal stress. LMWPM pretreatments were differently neuroprotective towards MPP+ insult, presenting distinct effects on the neuronal transcriptome. Particularly, cat-sulf pretreatment appeared to boost counter-regulatory defense mechanisms (preconditioning). When MPP+ is applied, both LMWPM positively modulated glutathione metabolism and heat-shock response, as also favorably shifting the balance of pro/anti-apoptotic proteins. CONCLUSIONS Our findings point to the potential of LMWPM to trigger molecular mechanisms that help dopaminergic neurons to cope with a subsequent toxic insult. They are promising molecules to be further explored in the context of preventing and attenuating parkinsonian neurodegeneration.
Collapse
Affiliation(s)
- Rafael Carecho
- CEDOCNOVA Medical SchoolFaculdade de Ciências MédicasUniversidade NOVA de Lisboa1150‐082LisboaPortugal
- ITQBInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa2780‐157OeirasPortugal
| | - Inês Figueira
- CEDOCNOVA Medical SchoolFaculdade de Ciências MédicasUniversidade NOVA de Lisboa1150‐082LisboaPortugal
| | - Ana Paula Terrasso
- ITQBInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa2780‐157OeirasPortugal
- iBETInstituto de Biologia Experimental e Tecnológica2781–901OeirasPortugal
| | - Joana Godinho‐Pereira
- ITQBInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa2780‐157OeirasPortugal
- iBETInstituto de Biologia Experimental e Tecnológica2781–901OeirasPortugal
| | | | - Sofia Azeredo Pereira
- CEDOCNOVA Medical SchoolFaculdade de Ciências MédicasUniversidade NOVA de Lisboa1150‐082LisboaPortugal
| | - Dragan Milenkovic
- INRAEUNHUniversité Clermont Auvergne63122St Genes ChampanelleFrance
- Department of NutritionUniversity of California Davis95616DavisCAUSA
| | - Marcel Leist
- In‐vitro Toxicology and BiomedicineUniversity of Konstanz78457ConstanceGermany
| | - Catarina Brito
- ITQBInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa2780‐157OeirasPortugal
- iBETInstituto de Biologia Experimental e Tecnológica2781–901OeirasPortugal
| | - Cláudia Nunes dos Santos
- CEDOCNOVA Medical SchoolFaculdade de Ciências MédicasUniversidade NOVA de Lisboa1150‐082LisboaPortugal
- ITQBInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa2780‐157OeirasPortugal
- iBETInstituto de Biologia Experimental e Tecnológica2781–901OeirasPortugal
| |
Collapse
|
9
|
Nuthikattu S, Milenkovic D, Norman JE, Rutledge J, Villablanca A. High Glycemia and Soluble Epoxide Hydrolase in Females: Differential Multiomics in Murine Brain Microvasculature. Int J Mol Sci 2022; 23:13044. [PMID: 36361847 PMCID: PMC9655872 DOI: 10.3390/ijms232113044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 12/02/2023] Open
Abstract
The effect of a high glycemic diet (HGD) on brain microvasculature is a crucial, yet understudied research topic, especially in females. This study aimed to determine the transcriptomic changes in female brain hippocampal microvasculature induced by a HGD and characterize the response to a soluble epoxide hydrolase inhibitor (sEHI) as a mechanism for increased epoxyeicosatrienoic acids (EETs) levels shown to be protective in prior models of brain injury. We fed mice a HGD or a low glycemic diet (LGD), with/without the sEHI (t-AUCB), for 12 weeks. Using microarray, we assessed differentially expressed protein-coding and noncoding genes, functional pathways, and transcription factors from laser-captured hippocampal microvessels. We demonstrated for the first time in females that the HGD had an opposite gene expression profile compared to the LGD and differentially expressed 506 genes, primarily downregulated, with functions related to cell signaling, cell adhesion, cellular metabolism, and neurodegenerative diseases. The sEHI modified the transcriptome of female mice consuming the LGD more than the HGD by modulating genes involved in metabolic pathways that synthesize neuroprotective EETs and associated with a higher EETs/dihydroxyeicosatrienoic acids (DHETs) ratio. Our findings have implications for sEHIs as promising therapeutic targets for the microvascular dysfunction that accompanies vascular dementia.
Collapse
Affiliation(s)
| | - Dragan Milenkovic
- Department of Nutrition, University of California, Davis, CA 95616, USA
| | - Jennifer E. Norman
- Division of Cardiovascular Medicine, University of California, Davis, CA 95616, USA
| | - John Rutledge
- Division of Cardiovascular Medicine, University of California, Davis, CA 95616, USA
| | - Amparo Villablanca
- Division of Cardiovascular Medicine, University of California, Davis, CA 95616, USA
| |
Collapse
|
10
|
Maghsoudi Z, Nguyen H, Tavakkoli A, Nguyen T. A comprehensive survey of the approaches for pathway analysis using multi-omics data integration. Brief Bioinform 2022; 23:6761962. [PMID: 36252928 PMCID: PMC9677478 DOI: 10.1093/bib/bbac435] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/26/2022] [Accepted: 09/08/2022] [Indexed: 02/07/2023] Open
Abstract
Pathway analysis has been widely used to detect pathways and functions associated with complex disease phenotypes. The proliferation of this approach is due to better interpretability of its results and its higher statistical power compared with the gene-level statistics. A plethora of pathway analysis methods that utilize multi-omics setup, rather than just transcriptomics or proteomics, have recently been developed to discover novel pathways and biomarkers. Since multi-omics gives multiple views into the same problem, different approaches are employed in aggregating these views into a comprehensive biological context. As a result, a variety of novel hypotheses regarding disease ideation and treatment targets can be formulated. In this article, we review 32 such pathway analysis methods developed for multi-omics and multi-cohort data. We discuss their availability and implementation, assumptions, supported omics types and databases, pathway analysis techniques and integration strategies. A comprehensive assessment of each method's practicality, and a thorough discussion of the strengths and drawbacks of each technique will be provided. The main objective of this survey is to provide a thorough examination of existing methods to assist potential users and researchers in selecting suitable tools for their data and analysis purposes, while highlighting outstanding challenges in the field that remain to be addressed for future development.
Collapse
Affiliation(s)
- Zeynab Maghsoudi
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, Nevada, USA
| | - Ha Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, Nevada, USA
| | - Alireza Tavakkoli
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, Nevada, USA
| | - Tin Nguyen
- Corresponding author: Tin Nguyen, Department of Computer Science and Engineering, University of Nevada, Reno, NV, USA. Tel.: +1-775-784-6619;
| |
Collapse
|
11
|
Kijima Y, Wantong W, Igarashi Y, Yoshitake K, Asakawa S, Suzuki Y, Watabe S, Kinoshita S. Age-Associated Different Transcriptome Profiling in Zebrafish and Rats: an Insight into the Diversity of Vertebrate Aging. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:895-910. [PMID: 36063238 DOI: 10.1007/s10126-022-10153-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish can be attractive models to study senescence because of their unique aging characteristics. The lifespan of fish varies widely, and several species can live for over 200 years. Moreover, some fish show anti-aging features and indeterminate growth throughout their life. Therefore, exploring the aging mechanism in fish could provide new insights into vertebrate aging. To this end, we conducted RNA sequencing (RNA-seq) assays for various organs and growth stages of zebrafish and compared the data with previously published RNA-seq data of rats. Age-associated differentially expressed genes (DEGs) for all zebrafish tissue samples reveal the upregulation of circadian genes and downregulation of hmgb3a. On one hand, a comparative analysis of DEG profiles associated with aging between zebrafish and rats identifies upregulation of circadian genes and downregulation of collagen genes as conserved transcriptome changes. On the other hand, in zebrafish, upregulation of autophagy-related genes in muscles and AP-1 transcription factor genes in various tissues is observed, which may imply fish-specific anti-aging characteristics. Consistent with our knowledge of mammalian aging, DEG profiles related to tissue senescence are observed in rats. We also detect age-associated downregulation of muscle homeostasis and differentiation-related genes in zebrafish gills, indicating a fish-specific senescence phenotype. Our results indicate both common and different aging profiles between fish and mammals, which could be used for future translational research.
Collapse
Affiliation(s)
- Yusuke Kijima
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Wang Wantong
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Yoji Igarashi
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
- Graduate School of Bioresources, Mie University, Mie, 514-8507, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, 272-8562, Japan
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan.
| |
Collapse
|
12
|
Non-coding RNA network associated with obesity and rheumatoid arthritis. Immunobiology 2022; 227:152281. [DOI: 10.1016/j.imbio.2022.152281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022]
|
13
|
Nuthikattu S, Milenkovic D, Norman JE, Rutledge J, Villablanca A. The Brain’s Microvascular Response to High Glycemia and to the Inhibition of Soluble Epoxide Hydrolase Is Sexually Dimorphic. Nutrients 2022; 14:nu14173451. [PMID: 36079709 PMCID: PMC9460226 DOI: 10.3390/nu14173451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/09/2022] [Accepted: 08/18/2022] [Indexed: 12/13/2022] Open
Abstract
Biological sex and a high glycemic diet (HGD) contribute to dementia, yet little is known about the operative molecular mechanisms. Our goal was to understand the differences between males and females in the multi-genomic response of the hippocampal microvasculature to the HGD, and whether there was vasculoprotection via the inhibition of soluble epoxide hydrolase (sEHI). Adult wild type mice fed high or low glycemic diets for 12 weeks, with or without an sEHI inhibitor (t-AUCB), had hippocampal microvessels isolated by laser-capture microdissection. Differential gene expression was determined by microarray and integrated multi-omic bioinformatic analyses. The HGD induced opposite effects in males and females: the HGD-upregulated genes were involved in neurodegeneration or neuroinflammation in males, whereas in females they downregulated the same pathways, favoring neuroprotection. In males, the HGD was associated with a greater number of clinical diseases than in females, the sEHI downregulated genes involved in neurodegenerative diseases to a greater extent with the HGD and compared to females. In females, the sEHI downregulated genes involved in endothelial cell functions to a greater extent with the LGD and compared to males. Our work has potentially important implications for sex-specific therapeutic targets for vascular dementia and cardiovascular diseases in males and females.
Collapse
Affiliation(s)
| | - Dragan Milenkovic
- Department of Nutrition, University of California, Davis, CA 95616, USA
| | - Jennifer E. Norman
- Division of Cardiovascular Medicine, University of California, Davis, CA 95616, USA
| | - John Rutledge
- Division of Cardiovascular Medicine, University of California, Davis, CA 95616, USA
| | - Amparo Villablanca
- Division of Cardiovascular Medicine, University of California, Davis, CA 95616, USA
- Correspondence: mail:; Tel.: +1-530-752-0718; Fax: +1-530-752-3264
| |
Collapse
|
14
|
Abstract
Pathway enrichment analysis (PEA) is a computational biology method that identifies biological functions that are overrepresented in a group of genes more than would be expected by chance and ranks these functions by relevance. The relative abundance of genes pertinent to specific pathways is measured through statistical methods, and associated functional pathways are retrieved from online bioinformatics databases. In the last decade, along with the spread of the internet, higher availability of computational resources made PEA software tools easy to access and to use for bioinformatics practitioners worldwide. Although it became easier to use these tools, it also became easier to make mistakes that could generate inflated or misleading results, especially for beginners and inexperienced computational biologists. With this article, we propose nine quick tips to avoid common mistakes and to out a complete, sound, thorough PEA, which can produce relevant and robust results. We describe our nine guidelines in a simple way, so that they can be understood and used by anyone, including students and beginners. Some tips explain what to do before starting a PEA, others are suggestions of how to correctly generate meaningful results, and some final guidelines indicate some useful steps to properly interpret PEA results. Our nine tips can help users perform better pathway enrichment analyses and eventually contribute to a better understanding of current biology.
Collapse
|
15
|
Yellapragada V, Eskici N, Wang Y, Madhusudan S, Vaaralahti K, Tuuri T, Raivio T. Time and dose-dependent effects of FGF8-FGFR1 signaling in GnRH neurons derived from human pluripotent stem cells. Dis Model Mech 2022; 15:276003. [PMID: 35833364 PMCID: PMC9403748 DOI: 10.1242/dmm.049436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/24/2022] [Indexed: 11/25/2022] Open
Abstract
Fibroblast growth factor 8 (FGF8), acting through the fibroblast growth factor receptor 1 (FGFR1), has an important role in the development of gonadotropin-releasing hormone-expressing neurons (GnRH neurons). We hypothesized that FGF8 regulates differentiation of human GnRH neurons in a time- and dose-dependent manner via FGFR1. To investigate this further, human pluripotent stem cells were differentiated during 10 days of dual-SMAD inhibition into neural progenitor cells, followed either by treatment with FGF8 at different concentrations (25 ng/ml, 50 ng/ml or 100 ng/ml) for 10 days or by treatment with 100 ng/ml FGF8 for different durations (2, 4, 6 or 10 days); cells were then matured through DAPT-induced inhibition of Notch signaling for 5 days into GnRH neurons. FGF8 induced expression of GNRH1 in a dose-dependent fashion and the duration of FGF8 exposure correlated positively with gene expression of GNRH1 (P<0.05, Rs=0.49). However, cells treated with 100 ng/ml FGF8 for 2 days induced the expression of genes, such as FOXG1, ETV5 and SPRY2, and continued FGF8 treatment induced the dynamic expression of several other genes. Moreover, during exposure to FGF8, FGFR1 localized to the cell surface and its specific inhibition with the FGFR1 inhibitor PD166866 reduced expression of GNRH1 (P<0.05). In neurons, FGFR1 also localized to the nucleus. Our results suggest that dose- and time-dependent FGF8 signaling via FGFR1 is indispensable for human GnRH neuron ontogeny. This article has an associated First Person interview with the first author of the paper. Summary: This article demonstrates the essential role FGF8–FGFR1 signaling has in the development of gonadotropin-releasing hormone (GnRH)-expressing neurons by using a human stem cell model.
Collapse
Affiliation(s)
- Venkatram Yellapragada
- Stem Cells and Metabolism Research Program (STEMM), Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland.,Medicum, Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland
| | - Nazli Eskici
- Stem Cells and Metabolism Research Program (STEMM), Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland.,Medicum, Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland
| | - Yafei Wang
- Stem Cells and Metabolism Research Program (STEMM), Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland.,Medicum, Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland
| | - Shrinidhi Madhusudan
- Stem Cells and Metabolism Research Program (STEMM), Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland.,Medicum, Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland
| | - Kirsi Vaaralahti
- Stem Cells and Metabolism Research Program (STEMM), Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland.,Medicum, Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, 00029 Helsinki University Hospital, Helsinki, Finland
| | - Taneli Raivio
- Stem Cells and Metabolism Research Program (STEMM), Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland.,Medicum, Faculty of Medicine, 00014 University of Helsinki, Helsinki, Finland.,New Children's Hospital, Pediatric Research Center, 00029 Helsinki University Central Hospital, Helsinki, Finland
| |
Collapse
|
16
|
Benkner A, Rüdebusch J, Nath N, Hammer E, Grube K, Gross S, Dhople VM, Eckstein G, Meitinger T, Kaderali L, Völker U, Fielitz J, Felix SB. Riociguat attenuates left ventricular proteome and microRNA profile changes after experimental aortic stenosis in mice. Br J Pharmacol 2022; 179:4575-4592. [PMID: 35751875 DOI: 10.1111/bph.15910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 04/15/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND PURPOSE Development and progression of heart failure (HF) involve endothelial and myocardial dysfunction as well as a dysregulation of the nitric oxide - soluble guanylyl cyclase - cyclic guanosine monophosphate (NO-sGC-cGMP) signalling pathway. Recently, we reported that the sGC stimulator riociguat (RIO) has beneficial effects on cardiac remodelling and progression of HF in response to chronic pressure overload. Here, we examined if these favourable RIO effects are also reflected in alterations of the myocardial proteome and microRNA profiles. EXPERIMENTAL APPROACH Male C57BL/6N mice underwent transverse aortic constriction (TAC) and sham operated mice served as controls. TAC and sham animals were randomised and treated with either RIO or vehicle for five weeks, starting three weeks post-surgery when cardiac hypertrophy was established. Afterwards we performed mass spectrometric proteome analyses and microRNA sequencing of proteins and RNAs, respectively, isolated from left ventricles (LV). KEY RESULTS TAC-induced changes of the LV proteome were significantly reduced by RIO treatment. Bioinformatics analyses revealed that RIO improved TAC-induced cardiovascular disease related pathways, metabolism and energy production, e.g. reversed alterations in the levels of myosin heavy chain 7 (MYH7), cardiac phospholamban (PLN), and ankyrin repeat domain-containing protein 1 (ANKRD1). RIO also attenuated TAC-induced changes of microRNA levels in the LV. CONCLUSION AND IMPLICATIONS The sGC stimulator RIO has beneficial effects on cardiac structure and function during pressure overload, which is accompanied by a reversal of TAC-induced changes of the cardiac proteome and microRNA profile. Our data support the potential of RIO as a novel HF therapeutic.
Collapse
Affiliation(s)
- Alexander Benkner
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Julia Rüdebusch
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Neetika Nath
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Karina Grube
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Gross
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Vishnu M Dhople
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Gertrud Eckstein
- Institute of Human Genetics, Helmholtz Centre Munich, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Centre Munich, Neuherberg, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Lars Kaderali
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jens Fielitz
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Stephan B Felix
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
17
|
Sabina S, Panico A, Mincarone P, Leo CG, Garbarino S, Grassi T, Bagordo F, De Donno A, Scoditti E, Tumolo MR. Expression and Biological Functions of miRNAs in Chronic Pain: A Review on Human Studies. Int J Mol Sci 2022; 23:ijms23116016. [PMID: 35682695 PMCID: PMC9181121 DOI: 10.3390/ijms23116016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023] Open
Abstract
Chronic pain is a major public health problem and an economic burden worldwide. However, its underlying pathological mechanisms remain unclear. MicroRNAs (miRNAs) are a class of small noncoding RNAs that post-transcriptionally regulate gene expression and serve key roles in physiological and pathological processes. This review aims to synthesize the human studies examining miRNA expression in the pathogenesis of chronic primary pain and chronic secondary pain. Additionally, to understand the potential pathophysiological impact of miRNAs in these conditions, an in silico analysis was performed to reveal the target genes and pathways involved in primary and secondary pain and their differential regulation in the different types of chronic pain. The findings, methodological issues and challenges of miRNA research in the pathophysiology of chronic pain are discussed. The available evidence suggests the potential role of miRNA in disease pathogenesis and possibly the pain process, eventually enabling this role to be exploited for pain monitoring and management.
Collapse
Affiliation(s)
- Saverio Sabina
- Institute of Clinical Physiology, National Research Council, Via Monteroni, 73100 Lecce, Italy; (S.S.); (C.G.L.); (M.R.T.)
| | - Alessandra Panico
- Department of Biological and Environmental Sciences and Technology, University of Salento, Via Monteroni, 73100 Lecce, Italy; (A.P.); (T.G.); (A.D.D.)
| | - Pierpaolo Mincarone
- Institute for Research on Population and Social Policies, National Research Council, c/o ex Osp. Di Summa, Piazza Di Summa, 72100 Brindisi, Italy;
| | - Carlo Giacomo Leo
- Institute of Clinical Physiology, National Research Council, Via Monteroni, 73100 Lecce, Italy; (S.S.); (C.G.L.); (M.R.T.)
| | - Sergio Garbarino
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal/Child Sciences, University of Genoa, 16132 Genoa, Italy;
| | - Tiziana Grassi
- Department of Biological and Environmental Sciences and Technology, University of Salento, Via Monteroni, 73100 Lecce, Italy; (A.P.); (T.G.); (A.D.D.)
| | - Francesco Bagordo
- Department of Pharmacy-Pharmaceutical Science, University of Bari Aldo Moro, Via Edoardo Orabona, 70126 Bari, Italy;
| | - Antonella De Donno
- Department of Biological and Environmental Sciences and Technology, University of Salento, Via Monteroni, 73100 Lecce, Italy; (A.P.); (T.G.); (A.D.D.)
| | - Egeria Scoditti
- Institute of Clinical Physiology, National Research Council, Via Monteroni, 73100 Lecce, Italy; (S.S.); (C.G.L.); (M.R.T.)
- Correspondence: ; Tel.: +39-(08)-3229-8860
| | - Maria Rosaria Tumolo
- Institute of Clinical Physiology, National Research Council, Via Monteroni, 73100 Lecce, Italy; (S.S.); (C.G.L.); (M.R.T.)
- Department of Biological and Environmental Sciences and Technology, University of Salento, Via Monteroni, 73100 Lecce, Italy; (A.P.); (T.G.); (A.D.D.)
| |
Collapse
|
18
|
Krga I, Corral-Jara KF, Barber-Chamoux N, Dubray C, Morand C, Milenkovic D. Grapefruit Juice Flavanones Modulate the Expression of Genes Regulating Inflammation, Cell Interactions and Vascular Function in Peripheral Blood Mononuclear Cells of Postmenopausal Women. Front Nutr 2022; 9:907595. [PMID: 35694160 PMCID: PMC9178201 DOI: 10.3389/fnut.2022.907595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/26/2022] [Indexed: 12/04/2022] Open
Abstract
Grapefruit is a rich source of flavanones, phytochemicals suggested excreting vasculoprotective effects. We previously showed that flavanones in grapefruit juice (GFJ) reduced postmenopausal women’s pulse-wave velocity (PWV), a measure of arterial stiffness. However, mechanisms of flavanone action in humans are largely unknown. This study aimed to decipher molecular mechanisms of flavanones by multi-omics analysis in PBMCs of volunteers consuming GFJ and flavanone-free control drink for 6 months. Modulated genes and microRNAs (miRNAs) were identified using microarrays. Bioinformatics analyses assessed their functions, interactions and correlations with previously observed changes in PWV. GFJ modified gene and miRNA expressions. Integrated analysis of modulated genes and miRNA-target genes suggests regulation of inflammation, immune response, cell interaction and mobility. Bioinformatics identified putative mediators of the observed nutrigenomic effect (STAT3, NF-κB) and molecular docking demonstrated potential binding of flavanone metabolites to transcription factors and cell-signaling proteins. We also observed 34 significant correlations between changes in gene expression and PWV. Moreover, global gene expression was negatively correlated with gene expression profiles in arterial stiffness and hypertension. This study revealed molecular mechanisms underlying vasculoprotective effects of flavanones, including interactions with transcription factors and gene and miRNA expression changes that inversely correlate with gene expression profiles associated with cardiovascular risk factors.
Collapse
Affiliation(s)
- Irena Krga
- Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | | | - Claude Dubray
- Institut National de la Santé et de la Recherche Médicale (INSERM), CIC 501, UMR 766, Clermont-Ferrand, France
| | - Christine Morand
- Université Clermont Auvergne, INRAE, UNH, Clermont-Ferrand, France
| | - Dragan Milenkovic
- Université Clermont Auvergne, INRAE, UNH, Clermont-Ferrand, France
- Department of Nutrition, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
- *Correspondence: Dragan Milenkovic,
| |
Collapse
|
19
|
Cerulo L, Pagnotta SM. massiveGST: A Mann-Whitney-Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis. ENTROPY 2022; 24:e24050739. [PMID: 35626622 PMCID: PMC9140214 DOI: 10.3390/e24050739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 01/27/2023]
Abstract
Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space’s statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wider range of application. Great attention has been devoted to global tests, in contrast to competitive methods that have been largely ignored, although they appear more flexible because they are independent from the source of gene-profiles. We analyzed the properties of the Mann–Whitney–Wilcoxon test, a competitive method, and adapted its interpretation in the context of enrichment analysis by introducing a Normalized Enrichment Score that summarize two interpretations: a probability estimate and a location index. Two implementations are presented and compared with relevant literature methods: an R package and an online web tool. Both allow for obtaining tabular and graphical results with attention to reproducible research.
Collapse
Affiliation(s)
- Luigi Cerulo
- Department of Science and Technology, Università degli Studi del Sannio, 82100 Benevento, Italy;
- Bioinformatics Lab, Biogem, Molecular Biology and Genetics Research Institute, 83031 Ariano Irpino, Italy
| | - Stefano Maria Pagnotta
- Department of Science and Technology, Università degli Studi del Sannio, 82100 Benevento, Italy;
- Correspondence:
| |
Collapse
|
20
|
Orben F, Lankes K, Schneeweis C, Hassan Z, Jakubowsky H, Krauß L, Boniolo F, Schneider C, Schäfer A, Murr J, Schlag C, Kong B, Öllinger R, Wang C, Beyer G, Mahajan UM, Xue Y, Mayerle J, Schmid RM, Kuster B, Rad R, Braun CJ, Wirth M, Reichert M, Saur D, Schneider G. Epigenetic drug screening defines a PRMT5 inhibitor-sensitive pancreatic cancer subtype. JCI Insight 2022; 7:e151353. [PMID: 35439169 PMCID: PMC9220834 DOI: 10.1172/jci.insight.151353] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 04/12/2022] [Indexed: 11/17/2022] Open
Abstract
Systemic therapies for pancreatic ductal adenocarcinoma (PDAC) remain unsatisfactory. Clinical prognosis is particularly poor for tumor subtypes with activating aberrations in the MYC pathway, creating an urgent need for novel therapeutic targets. To unbiasedly find MYC-associated epigenetic dependencies, we conducted a drug screen in pancreatic cancer cell lines. Here, we found that protein arginine N-methyltransferase 5 (PRMT5) inhibitors triggered an MYC-associated dependency. In human and murine PDACs, a robust connection of MYC and PRMT5 was detected. By the use of gain- and loss-of-function models, we confirmed the increased efficacy of PRMT5 inhibitors in MYC-deregulated PDACs. Although inhibition of PRMT5 was inducing DNA damage and arresting PDAC cells in the G2/M phase of the cell cycle, apoptotic cell death was executed predominantly in cells with high MYC expression. Experiments in primary patient-derived PDAC models demonstrated the existence of a highly PRMT5 inhibitor-sensitive subtype. Our work suggests developing PRMT5 inhibitor-based therapies for PDAC.
Collapse
Affiliation(s)
- Felix Orben
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
| | | | - Christian Schneeweis
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich (TUM), Munich, Germany
| | - Zonera Hassan
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
| | - Hannah Jakubowsky
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich (TUM), Munich, Germany
| | - Lukas Krauß
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, Göttingen, Germany
| | - Fabio Boniolo
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich (TUM), Munich, Germany
| | - Carolin Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, Göttingen, Germany
| | - Arlett Schäfer
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
| | - Janine Murr
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
| | | | - Bo Kong
- Department of Surgery, Klinikum rechts der Isar, TUM, Munich, Germany
- Department of General Surgery, University of Ulm, Ulm, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine and
| | - Chengdong Wang
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, TUM, Freising, Germany
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Department of Surgery, Children’s Hospital of Soochow University, Suzhou, China
| | - Georg Beyer
- Department of Medicine II, LMU University Hospital, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Ujjwal M. Mahajan
- Department of Medicine II, LMU University Hospital, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Yonggan Xue
- Department of Medicine II, LMU University Hospital, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, LMU University Hospital, Ludwig-Maximilians-Universität München (LMU Munich), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Roland M. Schmid
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, TUM, Freising, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM, Freising, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine and
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christian J. Braun
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Maximilian Reichert
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Center for Protein Assemblies (CPA), TUM, Garching, Germany
- Translational Pancreatic Research Cancer Center, Medical Clinic and Polyclinic II, Klinikum rechts der Isar, TUM, Munich, Germany
| | - Dieter Saur
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich (TUM), Munich, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Günter Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar and
- University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, Göttingen, Germany
| |
Collapse
|
21
|
Systematic analysis of nutrigenomic effects of polyphenols related to cardiometabolic health in humans - Evidence from untargeted mRNA and miRNA studies. Ageing Res Rev 2022; 79:101649. [PMID: 35595185 DOI: 10.1016/j.arr.2022.101649] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 04/15/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022]
Abstract
Cardiovascular and metabolic disorders present major causes of mortality in the ageing population. Polyphenols present in human diets possess cardiometabolic protective properties, however their underlying molecular mechanisms in humans are still not well identified. Even though preclinical and in vitro studies advocate that these bioactives can modulate gene expression, most studies were performed using targeted approaches. With the objective to decipher the molecular mechanisms underlying polyphenols cardiometabolic preventive properties in humans, we performed integrative multi-omic bioinformatic analyses of published studies which reported improvements of cardiometabolic risk factors following polyphenol intake, together with genomic analyses performed using untargeted approach. We identified 5 studies within our criteria and nearly 5000 differentially expressed genes, both mRNAs and miRNAs, in peripheral blood cells. Integrative bioinformatic analyses (e.g. pathway and gene network analyses, identification of transcription factors, correlation of gene expression profiles with those associated with diseases and drug intake) revealed that these genes are involved in the processes such as cell adhesion and mobility, immune system, metabolism, or cell signaling. We also identified 27 miRNAs known to regulate processes such as cell cytoskeleton, chemotaxis, cell signaling, or cell metabolism. Gene expression profiles negatively correlated with expression profiles of cardiovascular disease patients, while a positive correlation was observed with gene expression profiles following intake of drugs against cardiometabolic disorders. These analyses further advocate for health protective effects of these bioactives against age-associated diseases. In conclusion, polyphenols can exert multi-genomic modifications in humans and use of untargeted methods coupled with bioinformatic analyses represent the best approach to decipher molecular mechanisms underlying healthy-ageing effects of these bioactives.
Collapse
|
22
|
Corral-Jara KF, Nuthikattu S, Rutledge J, Villablanca A, Fong R, Heiss C, Ottaviani JI, Milenkovic D. Structurally related (-)-epicatechin metabolites and gut microbiota derived metabolites exert genomic modifications via VEGF signaling pathways in brain microvascular endothelial cells under lipotoxic conditions: Integrated multi-omic study. J Proteomics 2022; 263:104603. [PMID: 35568144 DOI: 10.1016/j.jprot.2022.104603] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/04/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022]
Abstract
Dysfunction of blood-brain barrier formed by endothelial cells of cerebral blood vessels, plays a key role in development of neurodegenerative disorders. Epicatechin exerts vasculo-protective effects through genomic modifications, however molecular mechanisms of action, particularly on brain endothelial cells, are largely unknow. This study aimed to use a multi-omic approach (transcriptomics of mRNA, miRNAs and lncRNAs, and proteomics), to provide novel in-depth insights into molecular mechanisms of how metabolites affect brain endothelial cells under lipid-stressed (as a model of BBB dysfunction) at physiological concentrations. We showed that metabolites can simultaneously modulate expression of protein-coding, non-coding genes and proteins. Integrative analysis revealed interactions between different types of RNAs and form functional groups of genes involved in regulation of processing like VEGF-related functions, cell signaling, cell adhesion and permeability. Molecular modeling of genomics data predicted that metabolites decrease endothelial cell permeability, increased by lipotoxic stress. Correlation analysis between genomic modifications observed and genomic signature of patients with vascular dementia and Alzheimer's diseases showed opposite gene expression changes. Taken together, this study describes for the first time a multi-omic mechanism of action by which (-)-epicatechin metabolites could preserve brain vascular endothelial cell integrity and reduce the risk of neurodegenerative diseases. SIGNIFICANCE: Dysfunction of the blood-brain barrier (BBB), characterized by dysfunction of endothelial cells of cerebral blood vessels, result in an increase in permeability and neuroinflammation which constitute a key factor in the development neurodegenerative disorders. Even though it is suggested that polyphenols can prevent or delay the development of these disorders, their impact on brain endothelial cells and underlying mechanisms of actions are unknow. This study aimed to use a multi-omic approach including analysis of expression of mRNA, microRNA, long non-coding RNAs, and proteins to provide novel global in-depth insights into molecular mechanisms of how (-)-epicatechin metabolites affect brain microvascular endothelial cells under lipid-stressed (as a model of BBB dysfunction) at physiological relevant conditions. The results provide basis of knowledge on the capacity of polyphenols to prevent brain endothelial dysfunction and consequently neurodegenerative disorders.
Collapse
Affiliation(s)
| | - Saivageethi Nuthikattu
- Division of Cardiovascular Medicine, University of California Davis, 95616 Davis, CA, USA
| | - John Rutledge
- Division of Cardiovascular Medicine, University of California Davis, 95616 Davis, CA, USA
| | - Amparo Villablanca
- Division of Cardiovascular Medicine, University of California Davis, 95616 Davis, CA, USA
| | - Reedmond Fong
- Department of Nutrition, University of California Davis, 95616 Davis, CA, USA
| | - Christian Heiss
- Clinical Medicine Section, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom; Vascular Department, Surrey and Sussex NHS Healthcare Trust, East Surrey Hospital, Redhill, United Kingdom
| | | | - Dragan Milenkovic
- Department of Nutrition, University of California Davis, 95616 Davis, CA, USA; Université Clermont Auvergne, INRAE, UNH, F-63000 Clermont-Ferrand, France.
| |
Collapse
|
23
|
Iram T, Kern F, Kaur A, Myneni S, Morningstar AR, Shin H, Garcia MA, Yerra L, Palovics R, Yang AC, Hahn O, Lu N, Shuken SR, Haney MS, Lehallier B, Iyer M, Luo J, Zetterberg H, Keller A, Zuchero JB, Wyss-Coray T. Young CSF restores oligodendrogenesis and memory in aged mice via Fgf17. Nature 2022; 605:509-515. [PMID: 35545674 PMCID: PMC9377328 DOI: 10.1038/s41586-022-04722-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 04/04/2022] [Indexed: 12/15/2022]
Abstract
Recent understanding of how the systemic environment shapes the brain throughout life has led to numerous intervention strategies to slow brain ageing1-3. Cerebrospinal fluid (CSF) makes up the immediate environment of brain cells, providing them with nourishing compounds4,5. We discovered that infusing young CSF directly into aged brains improves memory function. Unbiased transcriptome analysis of the hippocampus identified oligodendrocytes to be most responsive to this rejuvenated CSF environment. We further showed that young CSF boosts oligodendrocyte progenitor cell (OPC) proliferation and differentiation in the aged hippocampus and in primary OPC cultures. Using SLAMseq to metabolically label nascent mRNA, we identified serum response factor (SRF), a transcription factor that drives actin cytoskeleton rearrangement, as a mediator of OPC proliferation following exposure to young CSF. With age, SRF expression decreases in hippocampal OPCs, and the pathway is induced by acute injection with young CSF. We screened for potential SRF activators in CSF and found that fibroblast growth factor 17 (Fgf17) infusion is sufficient to induce OPC proliferation and long-term memory consolidation in aged mice while Fgf17 blockade impairs cognition in young mice. These findings demonstrate the rejuvenating power of young CSF and identify Fgf17 as a key target to restore oligodendrocyte function in the ageing brain.
Collapse
Affiliation(s)
- Tal Iram
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA,Correspondence to or
| | - Fabian Kern
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University Campus E8.1, Saarbrücken, Germany
| | - Achint Kaur
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Saket Myneni
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Allison R. Morningstar
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Heather Shin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Miguel A. Garcia
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Lakshmi Yerra
- Palo Alto Veterans Institute for Research, Palo Alto, CA 94304
| | - Robert Palovics
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Andrew C. Yang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Nannan Lu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Steven R. Shuken
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA,Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Michael s. Haney
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Manasi Iyer
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Jian Luo
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Palo Alto Veterans Institute for Research, Palo Alto, CA 94304
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Andreas Keller
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - J. Bradley Zuchero
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA,Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, California, USA.,Correspondence to or
| |
Collapse
|
24
|
A Single Bout of Ultra-Endurance Exercise Reveals Early Signs of Muscle Aging in Master Athletes. Int J Mol Sci 2022; 23:ijms23073713. [PMID: 35409073 PMCID: PMC8998696 DOI: 10.3390/ijms23073713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/22/2022] [Accepted: 03/26/2022] [Indexed: 01/27/2023] Open
Abstract
Middle-aged and master endurance athletes exhibit similar physical performance and long-term muscle adaptation to aerobic exercise. Nevertheless, we hypothesized that the short-term plasticity of the skeletal muscle might be distinctly altered for master athletes when they are challenged by a single bout of prolonged moderate-intensity exercise. Six middle-aged (37Y) and five older (50Y) master highly-trained athletes performed a 24-h treadmill run (24TR). Vastus lateralis muscle biopsies were collected before and after the run and assessed for proteomics, fiber morphometry, intramyocellular lipid droplets (LD), mitochondrial oxidative activity, extracellular matrix (ECM), and micro-vascularisation. Before 24TR, muscle fiber type morphometry, intramyocellular LD, oxidative activity, ECM and micro-vascularisation were similar between master and middle-aged runners. For 37Y runners, 24TR was associated with ECM thickening, increased capillary-to-fiber interface, and an 89% depletion of LD in type-I fibers. In contrast, for 50Y runners, 24TR did not alter ECM and capillarization and poorly depleted LDs. Moreover, an impaired succinate dehydrogenase activity and functional class scoring of proteomes suggested reduced oxidative phosphorylation post-24TR exclusively in 50Y muscle. Collectively, our data support that middle-aged and master endurance athletes exhibit distinct transient plasticity in response to a single bout of ultra-endurance exercise, which may constitute early signs of muscle aging for master athletes.
Collapse
|
25
|
Przanowska RK, Weidmann CA, Saha S, Cichewicz MA, Jensen KN, Przanowski P, Irving PS, Janes KA, Guertin MJ, Weeks KM, Dutta A. Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors. Cell Rep 2022; 38:110361. [PMID: 35172143 PMCID: PMC8937029 DOI: 10.1016/j.celrep.2022.110361] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/03/2021] [Accepted: 01/19/2022] [Indexed: 12/27/2022] Open
Abstract
Many lncRNAs have been discovered using transcriptomic data; however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as DRReRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information. We show that these specific and structurally distinct domains are required for induction of promyogenic genes, for binding genomic sites and gene expression regulation, and for binding the cohesin complex. Myod1 induction and cohesin interaction comprise only a subset of MUNC phenotype. Our study reveals unexpectedly complex, structure-driven functions for the MUNC lncRNA and emphasizes the importance of experimentally determined structures for understanding structure-function relationships in lncRNAs.
Collapse
Affiliation(s)
- Roza K Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biological Chemistry and Center for RNA Biomedicine, University of Michigan Medical School, Ann Arbor, MI 48103, USA
| | - Shekhar Saha
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Magdalena A Cichewicz
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Kate N Jensen
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Piotr Przanowski
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin A Janes
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Virginia School of Engineering, Charlottesville, VA 22908, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT 06030, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Genetics, University of Alabama, Birmingham, AL 35233, USA.
| |
Collapse
|
26
|
Genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma. Nat Commun 2022; 13:281. [PMID: 35022408 PMCID: PMC8755833 DOI: 10.1038/s41467-021-27704-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/07/2021] [Indexed: 02/08/2023] Open
Abstract
SUMOylation is a post-translational modification of proteins that regulates these proteins’ localization, turnover or function. Aberrant SUMOylation is frequently found in cancers but its origin remains elusive. Using a genome-wide transposon mutagenesis screen in a MYC-driven B-cell lymphoma model, we here identify the SUMO isopeptidase (or deconjugase) SENP6 as a tumor suppressor that links unrestricted SUMOylation to tumor development and progression. Notably, SENP6 is recurrently deleted in human lymphomas and SENP6 deficiency results in unrestricted SUMOylation. Mechanistically, SENP6 loss triggers release of DNA repair- and genome maintenance-associated protein complexes from chromatin thereby impairing DNA repair in response to DNA damages and ultimately promoting genomic instability. In line with this hypothesis, SENP6 deficiency drives synthetic lethality to Poly-ADP-Ribose-Polymerase (PARP) inhibition. Together, our results link SENP6 loss to defective genome maintenance and reveal the potential therapeutic application of PARP inhibitors in B-cell lymphoma. SUMOylation is a post-translational modification that has been shown to be altered in cancer. Here, the authors show that loss of the SUMO isopeptidase SENP6 leads to unrestricted SUMOylation and genomic instability promoting lymphomagenesis and generating vulnerability to PARP inhibition.
Collapse
|
27
|
Vardapour R, Kehl T, Kneitz S, Ludwig N, Meese E, Lenhof HP, Gessler M. The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression patterns and biological processes. Carcinogenesis 2021; 43:82-93. [PMID: 34919667 DOI: 10.1093/carcin/bgab110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/01/2021] [Accepted: 11/25/2021] [Indexed: 11/14/2022] Open
Abstract
Wilms tumor (WT) is the most common renal tumor in childhood. We and others have previously identified oncogenic driver mutations affecting the microprocessor genes DROSHA and DGCR8 that lead to altered miRNA expression patterns. In the case of DGCR8, a single recurrent hotspot mutation (E518K) was found in the RNA binding domain. To functionally assess this mutation in vitro, we generated mouse Dgcr8-KO embryonic stem cell (mESC) lines with an inducible expression of wild-type or mutant DGCR8, mirroring the hemizygous mutant expression seen in WT. RNA-seq analysis revealed significant differences of miRNA expression profiles in DGCR8-E518K compared to DGCR8-wild-type mESCs. The E518K mutation only led to a partial rescue of the reported miRNA processing defect in Dgcr8-KO, with selectively reduced expression of numerous canonical miRNAs. Nevertheless, DGCR8-E518K retained significant activity given its ability to still process many miRNAs. Subsequent to altered miRNA levels, the expression of mRNA targets was likewise changed. Functional assays showed that DGCR8-E518K cells still have a partial proliferation and differentiation defect but were able to rescue critical biological processes in embryoid body development. The stem cell program could be shut down and all three germ layers were formed. These findings suggest that the E518K mutation leads to a partial reduction of microprocessor activity and altered specificity with selective impairment only in certain developmental contexts, apparently including nephrogenesis.
Collapse
Affiliation(s)
- Romina Vardapour
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Susanne Kneitz
- Theodor-Boveri-Institute/Biocenter, Physiological Chemistry, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, 97074 Wuerzburg, Germany.,Comprehensive Cancer Center Mainfranken, 97078 Wuerzburg, Germany
| |
Collapse
|
28
|
Adipose Tissue Dysfunctions in Response to an Obesogenic Diet Are Reduced in Mice after Transgenerational Supplementation with Omega 3 Fatty Acids. Metabolites 2021; 11:metabo11120838. [PMID: 34940596 PMCID: PMC8706165 DOI: 10.3390/metabo11120838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/23/2022] Open
Abstract
Obesity is characterized by profound alterations in adipose tissue (AT) biology, leading to whole body metabolic disturbances such as insulin resistance and cardiovascular diseases. These alterations are related to the development of a local inflammation, fibrosis, hypertrophy of adipocytes, and dysregulation in energy homeostasis, notably in visceral adipose tissue (VAT). Omega 3 (n-3) fatty acids (FA) have been described to possess beneficial effects against obesity-related disorders, including in the AT; however, the long-term effect across generations remains unknown. The current study was conducted to identify if supplementation with n-3 polyunsaturated FA (PUFA) for three generations could protect from the consequences of an obesogenic diet in VAT. Young mice from the third generation of a lineage receiving a daily supplementation (1% of the diet) with fish oil rich in eicosapentaenoic acid (EPA) or an isocaloric amount of sunflower oil, were fed a high-fat, high-sugar content diet for 4 months. We explore the transcriptomic adaptations in each lineage using DNA microarray in VAT and bioinformatic exploration of biological regulations using online databases. Transgenerational intake of EPA led to a reduced activation of inflammatory processes, perturbation in metabolic homeostasis, cholesterol metabolism, and mitochondrial functions in response to the obesogenic diet as compared to control mice from a control lineage. This suggests that the continuous intake of long chain n-3 PUFA could be preventive in situations of oversupply of energy-dense, nutrient-poor foods.
Collapse
|
29
|
Inhibition of Soluble Epoxide Hydrolase Is Protective against the Multiomic Effects of a High Glycemic Diet on Brain Microvascular Inflammation and Cognitive Dysfunction. Nutrients 2021; 13:nu13113913. [PMID: 34836168 PMCID: PMC8622784 DOI: 10.3390/nu13113913] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/22/2022] Open
Abstract
Diet is a modifiable risk factor for cardiovascular disease (CVD) and dementia, yet relatively little is known about the effect of a high glycemic diet (HGD) on the brain’s microvasculature. The objective of our study was to determine the molecular effects of an HGD on hippocampal microvessels and cognitive function and determine if a soluble epoxide hydrolase (sEH) inhibitor (sEHI), known to be vasculoprotective and anti-inflammatory, modulates these effects. Wild type male mice were fed a low glycemic diet (LGD, 12% sucrose/weight) or an HGD (34% sucrose/weight) with/without the sEHI, trans-4-[4-(3-adamantan-1-yl-ureido)-cyclohexyloxy]-benzoic acid (t-AUCB), for 12 weeks. Brain hippocampal microvascular gene expression was assessed by microarray and data analyzed using a multi-omic approach for differential expression of protein and non-protein-coding genes, gene networks, functional pathways, and transcription factors. Global hippocampal microvascular gene expression was fundamentally different for mice fed the HGD vs. the LGD. The HGD response was characterized by differential expression of 608 genes involved in cell signaling, neurodegeneration, metabolism, and cell adhesion/inflammation/oxidation effects reversible by t-AUCB and hence sEH inhibitor correlated with protection against Alzheimer’s dementia. Ours is the first study to demonstrate that high dietary glycemia contributes to brain hippocampal microvascular inflammation through sEH.
Collapse
|
30
|
Milenkovic D, Krga I, Dinel AL, Morand C, Laye S, Castanon N. Nutrigenomic modification induced by anthocyanin-rich bilberry extract in the hippocampus of ApoE-/- mice. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
31
|
Gerstner N, Kehl T, Lenhof K, Eckhart L, Schneider L, Stöckel D, Backes C, Meese E, Keller A, Lenhof HP. GeneTrail: A Framework for the Analysis of High-Throughput Profiles. Front Mol Biosci 2021; 8:716544. [PMID: 34604304 PMCID: PMC8481803 DOI: 10.3389/fmolb.2021.716544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/01/2021] [Indexed: 12/05/2022] Open
Abstract
Experimental high-throughput techniques, like next-generation sequencing or microarrays, are nowadays routinely applied to create detailed molecular profiles of cells. In general, these platforms generate high-dimensional and noisy data sets. For their analysis, powerful bioinformatics tools are required to gain novel insights into the biological processes under investigation. Here, we present an overview of the GeneTrail tool suite that offers rich functionality for the analysis and visualization of (epi-)genomic, transcriptomic, miRNomic, and proteomic profiles. Our framework enables the analysis of standard bulk, time-series, and single-cell measurements and includes various state-of-the-art methods to identify potentially deregulated biological processes and to detect driving factors within those deregulated processes. We highlight the capabilities of our web service with an analysis of a single-cell COVID-19 data set that demonstrates its potential for uncovering complex molecular mechanisms. GeneTrail can be accessed freely and without login requirements at http://genetrail.bioinf.uni-sb.de.
Collapse
Affiliation(s)
- Nico Gerstner
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Kerstin Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Lea Eckhart
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Lara Schneider
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Daniel Stöckel
- Healthcare Digital & Data, Merck Healthcare KGaA, Darmstadt, Germany
| | - Christina Backes
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, United States
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| |
Collapse
|
32
|
Theobald L, Stroeder R, Melchior P, Iordache II, Tänzer T, Port M, Glombitza B, Marx S, Schub D, Herr C, Hart M, Ludwig N, Meese E, Kim YJ, Bohle RM, Smola S, Rübe C, Solomayer EF, Walch-Rückheim B. Chemoradiotherapy-induced increase in Th17 cell frequency in cervical cancer patients is associated with therapy resistance and early relapse. Mol Oncol 2021; 15:3559-3577. [PMID: 34469022 PMCID: PMC8637579 DOI: 10.1002/1878-0261.13095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/22/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022] Open
Abstract
Cervical cancer therapy is still a major clinical challenge, as patients substantially differ in their response to standard treatments, including chemoradiotherapy (CRT). During cervical carcinogenesis, T-helper (Th)-17 cells accumulate in the peripheral blood and tumor tissues of cancer patients and are associated with poor prognosis. In this prospective study, we find increased Th17 frequencies in the blood of patients after chemoradiotherapy and a post-therapeutic ratio of Th17/CD4+ T cells > 8% was associated with early recurrence. Furthermore, Th17 cells promote resistance of cervical cancer cells toward CRT, which was dependent on the AKT signaling pathway. Consistently, patients with high Th17 frequencies in pretherapeutic biopsies exhibit lower response to primary CRT. This work reveals a key role of Th17 cells in CRT resistance and elevated Th17 frequencies in the blood after CRT correspond with early recurrence. Our results may help to explain individual treatment responses of cervical cancer patients and suggest evaluation of Th17 cells as a novel predictive biomarker for chemoradiotherapy responses and as a potential target for immunotherapy in cervical cancer.
Collapse
Affiliation(s)
- Laura Theobald
- Institute of Virology and Center of Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Russalina Stroeder
- Department of Obstetrics and Gynecology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Patrick Melchior
- Department of Radiation Oncology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Ioan Iulian Iordache
- Department of Obstetrics and Gynecology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Tanja Tänzer
- Institute of Virology and Center of Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Meike Port
- Institute of Virology and Center of Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Birgit Glombitza
- Institute of Virology and Center of Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Stefanie Marx
- Department of Transplant and Infection Immunology, Saarland University, Homburg/Saar, Germany
| | - David Schub
- Department of Transplant and Infection Immunology, Saarland University, Homburg/Saar, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology and Critical Care Medicine, Saarland University Medical Center, Homburg/Saar, Germany
| | - Martin Hart
- Institute of Human Genetics, Saarland University, Homburg/Saar, Germany
| | - Nicole Ludwig
- Institute of Human Genetics and Center of Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, Homburg/Saar, Germany
| | - Yoo-Jin Kim
- Institute of Pathology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Rainer Maria Bohle
- Institute of Pathology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Sigrun Smola
- Institute of Virology and Center of Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Christian Rübe
- Department of Radiation Oncology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Erich Franz Solomayer
- Department of Obstetrics and Gynecology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Barbara Walch-Rückheim
- Institute of Virology and Center of Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| |
Collapse
|
33
|
Nguyen H, Tran D, Galazka JM, Costes SV, Beheshti A, Petereit J, Draghici S, Nguyen T. CPA: a web-based platform for consensus pathway analysis and interactive visualization. Nucleic Acids Res 2021; 49:W114-W124. [PMID: 34037798 PMCID: PMC8262702 DOI: 10.1093/nar/gkab421] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/16/2021] [Accepted: 05/05/2021] [Indexed: 01/06/2023] Open
Abstract
In molecular biology and genetics, there is a large gap between the ease of data collection and our ability to extract knowledge from these data. Contributing to this gap is the fact that living organisms are complex systems whose emerging phenotypes are the results of multiple complex interactions taking place on various pathways. This demands powerful yet user-friendly pathway analysis tools to translate the now abundant high-throughput data into a better understanding of the underlying biological phenomena. Here we introduce Consensus Pathway Analysis (CPA), a web-based platform that allows researchers to (i) perform pathway analysis using eight established methods (GSEA, GSA, FGSEA, PADOG, Impact Analysis, ORA/Webgestalt, KS-test, Wilcox-test), (ii) perform meta-analysis of multiple datasets, (iii) combine methods and datasets to accurately identify the impacted pathways underlying the studied condition and (iv) interactively explore impacted pathways, and browse relationships between pathways and genes. The platform supports three types of input: (i) a list of differentially expressed genes, (ii) genes and fold changes and (iii) an expression matrix. It also allows users to import data from NCBI GEO. The CPA platform currently supports the analysis of multiple organisms using KEGG and Gene Ontology, and it is freely available at http://cpa.tinnguyen-lab.com.
Collapse
Affiliation(s)
- Hung Nguyen
- University of Nevada Reno, Department of Computer Science and Engineering, Reno, NV 89557, USA
| | - Duc Tran
- University of Nevada Reno, Department of Computer Science and Engineering, Reno, NV 89557, USA
| | - Jonathan M Galazka
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA
| | - Sylvain V Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA
| | - Afshin Beheshti
- KBR, NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA
| | - Juli Petereit
- University of Nevada Reno, Nevada Bioinformatics Center, Reno, NV 89557, USA
| | - Sorin Draghici
- Wayne State University, Department of Computer Science, Detroit, MI 48202, USA
| | - Tin Nguyen
- University of Nevada Reno, Department of Computer Science and Engineering, Reno, NV 89557, USA
| |
Collapse
|
34
|
Ruskovska T, Budić-Leto I, Corral-Jara KF, Ajdžanović V, Arola-Arnal A, Bravo FI, Deligiannidou GE, Havlik J, Janeva M, Kistanova E, Kontogiorgis C, Krga I, Massaro M, Miler M, Milosevic V, Morand C, Scoditti E, Suárez M, Vauzour D, Milenkovic D. Systematic Bioinformatic Analyses of Nutrigenomic Modifications by Polyphenols Associated with Cardiometabolic Health in Humans-Evidence from Targeted Nutrigenomic Studies. Nutrients 2021; 13:nu13072326. [PMID: 34371836 PMCID: PMC8308901 DOI: 10.3390/nu13072326] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/14/2022] Open
Abstract
Cardiometabolic disorders are among the leading causes of mortality in the human population. Dietary polyphenols exert beneficial effects on cardiometabolic health in humans. Molecular mechanisms, however, are not completely understood. Aiming to conduct in-depth integrative bioinformatic analyses to elucidate molecular mechanisms underlying the protective effects of polyphenols on cardiometabolic health, we first conducted a systematic literature search to identify human intervention studies with polyphenols that demonstrate improvement of cardiometabolic risk factors in parallel with significant nutrigenomic effects. Applying the predefined inclusion criteria, we identified 58 differentially expressed genes at mRNA level and 5 miRNAs, analyzed in peripheral blood cells with RT-PCR methods. Subsequent integrative bioinformatic analyses demonstrated that polyphenols modulate genes that are mainly involved in the processes such as inflammation, lipid metabolism, and endothelial function. We also identified 37 transcription factors that are involved in the regulation of polyphenol modulated genes, including RELA/NFKB1, STAT1, JUN, or SIRT1. Integrative bioinformatic analysis of mRNA and miRNA-target pathways demonstrated several common enriched pathways that include MAPK signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway, focal adhesion, or PPAR signaling pathway. These bioinformatic analyses represent a valuable source of information for the identification of molecular mechanisms underlying the beneficial health effects of polyphenols and potential target genes for future nutrigenetic studies.
Collapse
Affiliation(s)
- Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, 2000 Stip, North Macedonia; (T.R.); (M.J.)
| | - Irena Budić-Leto
- Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia;
| | - Karla Fabiola Corral-Jara
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
| | - Vladimir Ajdžanović
- Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia; (V.A.); (M.M.); (V.M.)
| | - Anna Arola-Arnal
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.A.-A.); (F.I.B.); (M.S.)
| | - Francisca Isabel Bravo
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.A.-A.); (F.I.B.); (M.S.)
| | - Georgia-Eirini Deligiannidou
- Department of Medicine, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece; (G.-E.D.); (C.K.)
| | - Jaroslav Havlik
- Department of Food Science, Czech University of Life Sciences, 16521 Prague, Czech Republic;
| | - Milkica Janeva
- Faculty of Medical Sciences, Goce Delcev University, 2000 Stip, North Macedonia; (T.R.); (M.J.)
| | - Elena Kistanova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Christos Kontogiorgis
- Department of Medicine, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece; (G.-E.D.); (C.K.)
| | - Irena Krga
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
- Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia
| | - Marika Massaro
- National Research Council (CNR) Institute of Clinical Physiology (IFC), 73100 Lecce, Italy; (M.M.); (E.S.)
| | - Marko Miler
- Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia; (V.A.); (M.M.); (V.M.)
| | - Verica Milosevic
- Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia; (V.A.); (M.M.); (V.M.)
| | - Christine Morand
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
| | - Egeria Scoditti
- National Research Council (CNR) Institute of Clinical Physiology (IFC), 73100 Lecce, Italy; (M.M.); (E.S.)
| | - Manuel Suárez
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.A.-A.); (F.I.B.); (M.S.)
| | - David Vauzour
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK;
| | - Dragan Milenkovic
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
- Department of Internal Medicine, Division of Cardiovascular Medicine, School of Medicine, University of California Davis, Davis, CA 95616, USA
- Correspondence:
| |
Collapse
|
35
|
Hu Y, Yu L, Fan H, Huang G, Wu Q, Nie Y, Liu S, Yan L, Wei F. Genomic Signatures of Coevolution between Nonmodel Mammals and Parasitic Roundworms. Mol Biol Evol 2021; 38:531-544. [PMID: 32960966 PMCID: PMC7826172 DOI: 10.1093/molbev/msaa243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antagonistic coevolution between host and parasite drives species evolution. However, most of the studies only focus on parasitism adaptation and do not explore the coevolution mechanisms from the perspective of both host and parasite. Here, through the de novo sequencing and assembly of the genomes of giant panda roundworm, red panda roundworm, and lion roundworm parasitic on tiger, we investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms and those of roundworm parasitism in general. The genome-wide phylogeny revealed that these parasitic roundworms have not phylogenetically coevolved with their hosts. The CTSZ and prolyl 4-hydroxylase subunit beta (P4HB) immunoregulatory proteins played a central role in protein interaction between mammals and parasitic roundworms. The gene tree comparison identified that seven pairs of interactive proteins had consistent phylogenetic topology, suggesting their coevolution during host–parasite interaction. These coevolutionary proteins were particularly relevant to immune response. In addition, we found that the roundworms of both pandas exhibited higher proportions of metallopeptidase genes, and some positively selected genes were highly related to their larvae’s fast development. Our findings provide novel insights into the genetic mechanisms of coevolution between nonmodel mammals and parasites and offer the valuable genomic resources for scientific ascariasis prevention in both pandas.
Collapse
Affiliation(s)
- Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Lijun Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yonggang Nie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Shuai Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
36
|
Kitao T, Taguchi K, Seto S, Arasaki K, Ando H, Nagai H, Kubori T. Legionella Manipulates Non-canonical SNARE Pairing Using a Bacterial Deubiquitinase. Cell Rep 2021; 32:108107. [PMID: 32905772 DOI: 10.1016/j.celrep.2020.108107] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 05/30/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila uses many effector proteins delivered by the bacterial type IV secretion system (T4SS) to hijack the early secretory pathway to establish its replicative niche, known as the Legionella-containing vacuole (LCV). On LCV biogenesis, the endoplasmic reticulum (ER) vesicular soluble N-ethylmaleimide-sensitive factor attachment protein receptors (v-SNARE) Sec22b is recruited to the bacterial phagosome and forms non-canonical pairings with target membrane SNAREs (t-SNAREs) from the plasma membrane. Here, we identify a Legionella deubiquitinase (DUB), LotB, that can modulate the early secretory pathway by interacting with coatomer protein complex I (COPI) vesicles when ectopically expressed. We show that Sec22b is ubiquitinated upon L. pneumophila infection in a T4SS-dependent manner and that, subsequently, LotB deconjugates K63-linked ubiquitins from Sec22b. The DUB activity of LotB stimulates dissociation of the t-SNARE syntaxin 3 (Stx3) from Sec22b, which resides on the LCV. Our study highlights a bacterial strategy manipulating the dynamics of infection-induced SNARE pairing using a bacterial DUB.
Collapse
Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Kyoichiro Taguchi
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan; Laboratory of Veterinary Microbiology, Faculty of Applied Biological Science, Gifu University, Gifu, Gifu 501-1193, Japan
| | - Shintaro Seto
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo 204-8533, Japan
| | - Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Hiroki Ando
- G-CHAIN, Gifu University, Gifu, Gifu 501-1194, Japan; Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan; G-CHAIN, Gifu University, Gifu, Gifu 501-1194, Japan.
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan; G-CHAIN, Gifu University, Gifu, Gifu 501-1194, Japan.
| |
Collapse
|
37
|
Ruskovska T, Massaro M, Carluccio MA, Arola-Arnal A, Muguerza B, Vanden Berghe W, Declerck K, Bravo FI, Calabriso N, Combet E, Gibney ER, Gomes A, Gonthier MP, Kistanova E, Krga I, Mena P, Morand C, Nunes Dos Santos C, de Pascual-Teresa S, Rodriguez-Mateos A, Scoditti E, Suárez M, Milenkovic D. Systematic bioinformatic analysis of nutrigenomic data of flavanols in cell models of cardiometabolic disease. Food Funct 2021; 11:5040-5064. [PMID: 32537624 DOI: 10.1039/d0fo00701c] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Flavanol intake positively influences several cardiometabolic risk factors in humans. However, the specific molecular mechanisms of action of flavanols, in terms of gene regulation, in the cell types relevant to cardiometabolic disease have never been systematically addressed. On this basis, we conducted a systematic literature review and a comprehensive bioinformatic analysis of genes whose expression is affected by flavanols in cells defining cardiometabolic health: hepatocytes, adipocytes, endothelial cells, smooth muscle cells and immune cells. A systematic literature search was performed using the following pre-defined criteria: treatment with pure compounds and metabolites (no extracts) at low concentrations that are close to their plasma concentrations. Differentially expressed genes were analyzed using bioinformatics tools to identify gene ontologies, networks, cellular pathways and interactions, as well as transcriptional and post-transcriptional regulators. The systematic literature search identified 54 differentially expressed genes at the mRNA level in in vitro models of cardiometabolic disease exposed to flavanols and their metabolites. Global bioinformatic analysis revealed that these genes are predominantly involved in inflammation, leukocyte adhesion and transendothelial migration, and lipid metabolism. We observed that, although the investigated cells responded differentially to flavanol exposure, the involvement of anti-inflammatory responses is a common mechanism of flavanol action. We also identified potential transcriptional regulators of gene expression: transcriptional factors, such as GATA2, NFKB1, FOXC1 or PPARG, and post-transcriptional regulators: miRNAs, such as mir-335-5p, let-7b-5p, mir-26b-5p or mir-16-5p. In parallel, we analyzed the nutrigenomic effects of flavanols in intestinal cells and demonstrated their predominant involvement in the metabolism of circulating lipoproteins. In conclusion, the results of this systematic analysis of the nutrigenomic effects of flavanols provide a more comprehensive picture of their molecular mechanisms of action and will support the future setup of genetic studies to pave the way for individualized dietary recommendations.
Collapse
Affiliation(s)
- Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, Stip, North Macedonia
| | - Marika Massaro
- National Research Council (CNR) Institute of Clinical Physiology (IFC), 73100 Lecce, Italy
| | | | - Anna Arola-Arnal
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Nutrigenomics Research Group, 43007, Tarragona, Spain
| | - Begoña Muguerza
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Nutrigenomics Research Group, 43007, Tarragona, Spain
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Francisca Isabel Bravo
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Nutrigenomics Research Group, 43007, Tarragona, Spain
| | - Nadia Calabriso
- National Research Council (CNR) Institute of Clinical Physiology (IFC), 73100 Lecce, Italy
| | - Emilie Combet
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Eileen R Gibney
- UCD Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, Ireland
| | - Andreia Gomes
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901, Oeiras, Portugal and Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Marie-Paule Gonthier
- Université de La Réunion, INSERM, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), Saint-Denis de La Réunion, France
| | - Elena Kistanova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Irena Krga
- Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, University of Belgrade, Belgrade, Serbia and Université Clermont Auvergne, INRAe, UNH, F-63000 Clermont-Ferrand, France.
| | - Pedro Mena
- The Laboratory of Phytochemicals in Physiology, Human Nutrition Unit, Department of Food and Drug, University of Parma, Via Volturno 39, 43125 Parma, Italy
| | - Christine Morand
- Université Clermont Auvergne, INRAe, UNH, F-63000 Clermont-Ferrand, France.
| | - Claudia Nunes Dos Santos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901, Oeiras, Portugal and Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal and CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
| | - Sonia de Pascual-Teresa
- Department of Metabolism and Nutrition, Institute of Food Science, Technology and Nutrition (ICTAN-CSIC), Jose Antonio Novais 10, 28040 Madrid, Spain
| | - Ana Rodriguez-Mateos
- Department of Nutritional Sciences, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Egeria Scoditti
- National Research Council (CNR) Institute of Clinical Physiology (IFC), 73100 Lecce, Italy
| | - Manuel Suárez
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Nutrigenomics Research Group, 43007, Tarragona, Spain
| | - Dragan Milenkovic
- Université Clermont Auvergne, INRAe, UNH, F-63000 Clermont-Ferrand, France. and Department of Internal Medicine, Division of Cardiovascular Medicine, School of Medicine, University of California Davis, Davis, California 95616, USA
| |
Collapse
|
38
|
Gueugneau M, Coudy-Gandilhon C, Chambon C, Verney J, Taillandier D, Combaret L, Polge C, Walrand S, Roche F, Barthélémy JC, Féasson L, Béchet D. Muscle Proteomic and Transcriptomic Profiling of Healthy Aging and Metabolic Syndrome in Men. Int J Mol Sci 2021; 22:4205. [PMID: 33921590 PMCID: PMC8074053 DOI: 10.3390/ijms22084205] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
(1) Background: Aging is associated with a progressive decline in muscle mass and function. Aging is also a primary risk factor for metabolic syndrome, which further alters muscle metabolism. However, the molecular mechanisms involved remain to be clarified. Herein we performed omic profiling to decipher in muscle which dominating processes are associated with healthy aging and metabolic syndrome in old men. (2) Methods: This study included 15 healthy young, 15 healthy old, and 9 old men with metabolic syndrome. Old men were selected from a well-characterized cohort, and each vastus lateralis biopsy was used to combine global transcriptomic and proteomic analyses. (3) Results: Over-representation analysis of differentially expressed genes (ORA) and functional class scoring of pathways (FCS) indicated that healthy aging was mainly associated with upregulations of apoptosis and immune function and downregulations of glycolysis and protein catabolism. ORA and FCS indicated that with metabolic syndrome the dominating biological processes were upregulation of proteolysis and downregulation of oxidative phosphorylation. Proteomic profiling matched 586 muscle proteins between individuals. The proteome of healthy aging revealed modifications consistent with a fast-to-slow transition and downregulation of glycolysis. These transitions were reduced with metabolic syndrome, which was more associated with alterations in NADH/NAD+ shuttle and β-oxidation. Proteomic profiling further showed that all old muscles overexpressed protein chaperones to preserve proteostasis and myofiber integrity. There was also evidence of aging-related increases in reactive oxygen species but better detoxifications of cytotoxic aldehydes and membrane protection in healthy than in metabolic syndrome muscles. (4) Conclusions: Most candidate proteins and mRNAs identified herein constitute putative muscle biomarkers of healthy aging and metabolic syndrome in old men.
Collapse
Affiliation(s)
- Marine Gueugneau
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Cécile Coudy-Gandilhon
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Christophe Chambon
- Metabolomic and Proteomic Exploration Facility, Université Clermont Auvergne, INRAE, 63000 Clermont-Ferrand, France;
| | - Julien Verney
- Laboratoire AME2P, Université Clermont Auvergne, 3533 Clermont-Ferrand, France;
| | - Daniel Taillandier
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Lydie Combaret
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Cécile Polge
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Stéphane Walrand
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Frédéric Roche
- Service de Physiologie Clinique et de l’Exercice, CHU Saint Etienne, 42055 Saint Etienne, France; (F.R.); (J.-C.B.)
- INSERM, SAINBIOSE, U1059, Dysfonction Vasculaire et Hémostase, Université Jean-Monnet, 42055 Saint-Etienne, France
| | - Jean-Claude Barthélémy
- Service de Physiologie Clinique et de l’Exercice, CHU Saint Etienne, 42055 Saint Etienne, France; (F.R.); (J.-C.B.)
- INSERM, SAINBIOSE, U1059, Dysfonction Vasculaire et Hémostase, Université Jean-Monnet, 42055 Saint-Etienne, France
| | - Léonard Féasson
- Unité de Myologie, Service de Physiologie Clinique et de l’Exercice, Centre Référent Maladies Neuromusculaires Euro-NmD, 42000 CHU de Saint-Etienne, France;
- Laboratoire Interuniversitaire de Biologie de la Motricité, Université de Lyon, Université Jean Monnet Saint-Etienne, 69000 Lyon, France
| | - Daniel Béchet
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| |
Collapse
|
39
|
Aimo A, Egea OI, Emdin M, Bayes-Genis A. Overlapping Effects of miR-21 Inhibition and Drugs for Idiopathic Pulmonary Fibrosis: Rationale for Repurposing Nintedanib as a Novel Treatment for Ischemia/Reperfusion Injury. J Cardiovasc Pharmacol 2021; 77:332-333. [PMID: 33394826 DOI: 10.1097/fjc.0000000000000978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/03/2020] [Indexed: 11/26/2022]
Abstract
ABSTRACT A specific anti-miR-21 has emerged as an effective treatment for ischemia/reperfusion injury in a pig model of myocardial infarction (MI), but the perspectives for clinical translation are limited. Anti-miR-21 blunts profibrotic pathways, whose excessive activation is detrimental in the post-MI setting. Repurposing antifibrotic drugs approved for other indications is a possible strategy. We compared the molecular effects of anti-miR-21 and the 2 drugs approved for idiopathic pulmonary fibrosis (nintedanib and pirfenidone) through a bioinformatic approach. We report that nintedanib and anti-miR-21 share many targets, including the proto-oncogene Rous sarcoma oncogene cellular homolog. Conversely, pirfenidone and anti-miR-21 do not have common mechanisms of action. In summary, the molecular mechanisms activated by nintedanib are partially overlapping with those elicited by anti-miR-21. Nintedanib could be evaluated in animal studies or clinical trials on MI.
Collapse
Affiliation(s)
- Alberto Aimo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- Cardiology Division, University Hospital of Pisa, Italy
| | - Oriol I Egea
- ICREC (Heart Failure and Cardiac Regeneration) Research Programme, Health Sciences Research Institute Germans Trias i Pujol (IGTP)
- Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona
| | - Michele Emdin
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- Cardiology Division, Fondazione Toscana Gabriele Monasterio, Pisa, Italy; and
| | - Antoni Bayes-Genis
- ICREC (Heart Failure and Cardiac Regeneration) Research Programme, Health Sciences Research Institute Germans Trias i Pujol (IGTP)
- Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona
- CIBER Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
40
|
Pinel A, Rigaudière JP, Jouve C, Montaurier C, Jousse C, LHomme M, Morio B, Capel F. Transgenerational supplementation with eicosapentaenoic acid reduced the metabolic consequences on the whole body and skeletal muscle in mice receiving an obesogenic diet. Eur J Nutr 2021; 60:3143-3157. [PMID: 33543364 DOI: 10.1007/s00394-021-02502-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/22/2021] [Indexed: 11/29/2022]
Abstract
PURPOSE The effect of manipulating the fatty acid profile of the diet over generations could affect the susceptibility to develop obesity and metabolic disorders. Although some acute effects were described, the impact of transgenerational continuous supplementation with omega 3 fatty acids on metabolic homeostasis and skeletal muscle metabolic flexibility during a nutritional stress is unknown. METHODS We analyzed the effect of an obesogenic diet in mice after transgenerational supplementation with an omega-3 rich oil (mainly EPA) or a control oil. Young F3 animals received a high fat and high sucrose diet for 4 months. Whole-body biometric data were recorded and lipidomic/transcriptomic adaptations were explored in the skeletal muscle. RESULTS F3 mice from the lineage supplemented with EPA gained less weight, fat mass, and exhibited better metabolic parameters after the obesogenic diet compared to mice from the control lineage. Transcriptomic exploration of skeletal muscle showed differential regulation of biological processes such as fibrosis, fatty acid catabolism, and inflammation between lineages. These adaptations were associated to subtle lipid remodeling of cellular membranes with an enrichment in phospholipids with omega 3 fatty acid in mice from the EPA lineage. CONCLUSION Transgenerational and continuous intake of EPA could help to reduce cardiovascular and metabolic risks related to an unbalanced diet by the modulation of insulin sensitivity, fatty acid metabolism, and fibrosis in skeletal muscle.
Collapse
Affiliation(s)
- Alexandre Pinel
- Unité de Nutrition Humaine (UNH), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université Clermont Auvergne, CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Jean Paul Rigaudière
- Unité de Nutrition Humaine (UNH), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université Clermont Auvergne, CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Chrystèle Jouve
- Unité de Nutrition Humaine (UNH), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université Clermont Auvergne, CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Christophe Montaurier
- Unité de Nutrition Humaine (UNH), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université Clermont Auvergne, CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Céline Jousse
- Unité de Nutrition Humaine (UNH), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université Clermont Auvergne, CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Marie LHomme
- ICANalytics Lipidomic, Institute of Cardiometabolism and Nutrition (ICAN), Paris, France
| | - Béatrice Morio
- CarMeN Laboratory, INSERM U1060, INRAE U1397, University Lyon 1, 69310, Pierre-Bénite, France
| | - Frédéric Capel
- Unité de Nutrition Humaine (UNH), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université Clermont Auvergne, CRNH Auvergne, 63000, Clermont-Ferrand, France. .,UFR de Medecine, UMR1019, Equipe ASMS, 28 Place Henri Dunant, BP 38, Clermont-Ferrand Cedex 1, 63001, Clermont-Ferrand, France.
| |
Collapse
|
41
|
Vavougios GD. Human coronaviruses in idiopathic Parkinson's disease: Implications of SARS-CoV-2's modulation of the host's transcriptome. INFECTION GENETICS AND EVOLUTION 2021; 89:104733. [PMID: 33516970 PMCID: PMC7844365 DOI: 10.1016/j.meegid.2021.104733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/04/2021] [Accepted: 01/22/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVE A recent study on the effects of SARS-CoV-2 infection on the host's transcriptome indicated the perturbation of several pathways associated with neurodegeneration, including but not limited to Parkinson's and Huntington's diseases. The purpose of this study was to determine overlapping pathways between iPD vs. Controls and those associated with SARS-CoV-2 infection. METHODS Gene set enrichment analyses (GSEA) were performed on gene expression data from tissues donated by idiopathic Parkinson's disease patients (iPD). These included dorsal motor nucleus of the vagus (DMNV), substantia nigra (SN), whole blood (WB) and peripheral blood mononuclear cell samples (PBMC). Enriched pathways detected by GSEA results were subsequently compared to (a) those retrieved by two independently constructed SARS-CoV-2 - host interactomes, as well as (b) previously published pathway data. For all analyses, a false discovery rate (FDR) <0.05 was considered statistically significant. RESULTS Analysis of iPD data revealed multiple immune response and viral parasitism -related pathways (FDR < 0.05). Head-to-head comparisons as well as confirmatory analyses revealed several pathways and gene ontology (GO) terms overlapping between iPD tissues and SARS-CoV-2 induced transcriptomic changes: "Parkinson's Disease" and "Huntington's Disease" (overlapping in DMNV, ION, SN, and WB; FDR < 0.05), "NAFLD" (overlapping in DMNV, SN, PBMC and WB; FDR < 0.05), mRNA surveillance and proteostasis pathways (All datasets; FDR < 0.5), among others. CONCLUSION The overlap noted in this comparative transcriptomic study outlines the potential contribution of human coronaviruses in the pathogenesis of iPD. Furthermore, given SARS-CoV-2's neuroinvasive potential, closer scrutiny is warranted towards its contribution in the long-term development of neurodegenerative disease.
Collapse
Affiliation(s)
- George D Vavougios
- Neuroimmunology Laboratory, Department of Neurology, Athens Naval Hospital, Athens, Greece; Department of Respiratory Medicine, University of Thessaly, Larisa, Greece; Department of Computer and Telecommunications, Lamia, Greece.
| |
Collapse
|
42
|
Kehoe S, Jewgenow K, Johnston PR, Mbedi S, Braun BC. Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat. Sci Rep 2021; 11:2683. [PMID: 33514822 PMCID: PMC7846758 DOI: 10.1038/s41598-021-82051-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
In vitro growth (IVG) of dormant primordial ovarian follicles aims to produce mature competent oocytes for assisted reproduction. Success is dependent on optimal in vitro conditions complemented with an understanding of oocyte and ovarian follicle development in vivo. Complete IVG has not been achieved in any other mammalian species besides mice. Furthermore, ovarian folliculogenesis remains sparsely understood overall. Here, gene expression patterns were characterised by RNA-sequencing in primordial (PrF), primary (PF), and secondary (SF) ovarian follicles from Felis catus (domestic cat) ovaries. Two major transitions were investigated: PrF-PF and PF-SF. Transcriptional analysis revealed a higher proportion in gene expression changes during the PrF-PF transition. Key influencing factors during this transition included the interaction between the extracellular matrix (ECM) and matrix metalloproteinase (MMPs) along with nuclear components such as, histone HIST1H1T (H1.6). Conserved signalling factors and expression patterns previously described during mammalian ovarian folliculogenesis were observed. Species-specific features during domestic cat ovarian folliculogenesis were also found. The signalling pathway terms "PI3K-Akt", "transforming growth factor-β receptor", "ErbB", and "HIF-1" from the functional annotation analysis were studied. Some results highlighted mechanistic cues potentially involved in PrF development in the domestic cat. Overall, this study provides an insight into regulatory factors and pathways during preantral ovarian folliculogenesis in domestic cat.
Collapse
Affiliation(s)
- Shauna Kehoe
- Reproduction Biology Department, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
| | - Katarina Jewgenow
- Reproduction Biology Department, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Paul R Johnston
- Berlin Center for Genomics in Biodiversity Research BeGenDiv, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
- Freie Universität Berlin, Institut für Biologie, Königin-Luise-Straße 1-3, 14195, Berlin, Germany
| | - Susan Mbedi
- Berlin Center for Genomics in Biodiversity Research BeGenDiv, Königin-Luise-Straße 6-8, D-14195, Berlin, Germany
- Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
| | - Beate C Braun
- Reproduction Biology Department, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| |
Collapse
|
43
|
Kern F, Krammes L, Danz K, Diener C, Kehl T, Küchler O, Fehlmann T, Kahraman M, Rheinheimer S, Aparicio-Puerta E, Wagner S, Ludwig N, Backes C, Lenhof HP, von Briesen H, Hart M, Keller A, Meese E. Validation of human microRNA target pathways enables evaluation of target prediction tools. Nucleic Acids Res 2021; 49:127-144. [PMID: 33305319 PMCID: PMC7797041 DOI: 10.1093/nar/gkaa1161] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 10/20/2020] [Accepted: 11/13/2020] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.
Collapse
Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Lena Krammes
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Karin Danz
- Department of Bioprocessing & Bioanalytics, Fraunhofer Institute for Biomedical Engineering, 66280 Sulzbach, Germany
| | - Caroline Diener
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Oliver Küchler
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | - Ernesto Aparicio-Puerta
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain.,Instituto de Investigación Biosanitaria ibs. Granada, University of Granada, 18071 Granada, Spain
| | - Sylvia Wagner
- Department of Bioprocessing & Bioanalytics, Fraunhofer Institute for Biomedical Engineering, 66280 Sulzbach, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany.,Center of Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Hagen von Briesen
- Department of Bioprocessing & Bioanalytics, Fraunhofer Institute for Biomedical Engineering, 66280 Sulzbach, Germany
| | - Martin Hart
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| |
Collapse
|
44
|
Amirmahani F, Ebrahimi N, Molaei F, Faghihkhorasani F, Jamshidi Goharrizi K, Mirtaghi SM, Borjian‐Boroujeni M, Hamblin MR. Approaches for the integration of big data in translational medicine: single‐cell and computational methods. Ann N Y Acad Sci 2021; 1493:3-28. [DOI: 10.1111/nyas.14544] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/31/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Farzane Amirmahani
- Genetics Division, Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology University of Isfahan Isfahan Iran
| | - Nasim Ebrahimi
- Genetics Division, Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology University of Isfahan Isfahan Iran
| | - Fatemeh Molaei
- Department of Anesthesiology, Faculty of Paramedical Jahrom University of Medical Sciences Jahrom Iran
| | | | | | | | | | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science University of Johannesburg South Africa
| |
Collapse
|
45
|
Corral-Jara KF, Cantini L, Poupin N, Ye T, Rigaudière JP, Vincent SDS, Pinel A, Morio B, Capel F. An Integrated Analysis of miRNA and Gene Expression Changes in Response to an Obesogenic Diet to Explore the Impact of Transgenerational Supplementation with Omega 3 Fatty Acids. Nutrients 2020; 12:E3864. [PMID: 33348802 PMCID: PMC7765958 DOI: 10.3390/nu12123864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
Insulin resistance decreases the ability of insulin to inhibit hepatic gluconeogenesis, a key step in the development of metabolic syndrome. Metabolic alterations, fat accumulation, and fibrosis in the liver are closely related and contribute to the progression of comorbidities, such as hypertension, type 2 diabetes, or cancer. Omega 3 (n-3) polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA), were identified as potent positive regulators of insulin sensitivity in vitro and in animal models. In the current study, we explored the effects of a transgenerational supplementation with EPA in mice exposed to an obesogenic diet on the regulation of microRNAs (miRNAs) and gene expression in the liver using high-throughput techniques. We implemented a comprehensive molecular systems biology approach, combining statistical tools, such as MicroRNA Master Regulator Analysis pipeline and Boolean modeling to integrate these biochemical processes. We demonstrated that EPA mediated molecular adaptations, leading to the inhibition of miR-34a-5p, a negative regulator of Irs2 as a master regulatory event leading to the inhibition of gluconeogenesis by insulin during the fasting-feeding transition. Omics data integration provided greater biological insight and a better understanding of the relationships between biological variables. Such an approach may be useful for deriving innovative data-driven hypotheses and for the discovery of molecular-biochemical mechanistic links.
Collapse
Affiliation(s)
- Karla Fabiola Corral-Jara
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Laura Cantini
- Computational Systems Biology Team, Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France;
| | - Nathalie Poupin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France;
| | - Tao Ye
- GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries/BP 10142/, 67404 Illkirch, France;
| | - Jean Paul Rigaudière
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Sarah De Saint Vincent
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Alexandre Pinel
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| | - Béatrice Morio
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Lyon 1, 69310 Pierre Bénite, France;
| | - Frédéric Capel
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (J.P.R.); (S.D.S.V.); (A.P.)
| |
Collapse
|
46
|
Chen Q, Huang Y, Wang Z, Teng S, Hanif Q, Lei C, Sun J. Whole-genome resequencing reveals diversity and selective signals in Longlin goat. Gene 2020; 771:145371. [PMID: 33346103 DOI: 10.1016/j.gene.2020.145371] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 11/30/2022]
Abstract
The Longlin goat is one of the most valuable livestock species in Guangxi Autonomous Region of China, but its genomic diversity and selective signals are not clearly elucidated. Here we compared 20 genomes of Longlin goat to 66 genomes of other seven goat breeds worldwide to analyze patterns of Longlin goat genetic variation. We found the lowest linkage disequilibrium at the large distances between SNPs associated with the highest effective population size in the recent generations ago in Longlin goat. The eight goat breeds could be divided into Euro-African and East Asian goat population. Interestingly, like East Asian taurine, the same two migration phases might have occurred in the history of East Asian goat. More importantly, we identified selective signals implicated in immune resistance to disease, especially for skin disease, in Longlin goat. Our findings will not only help understand the evolutionary history and breed characteristic but can provide valuable resources for conservation of germplasm resources and implementation of crossbreeding programs.
Collapse
Affiliation(s)
- Qiuming Chen
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yingfei Huang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China
| | - Zihao Wang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China
| | - Shaohua Teng
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad 577, Pakistan; Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan
| | - Chuzhao Lei
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China
| | - Junli Sun
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China.
| |
Collapse
|
47
|
Hiller M, Geissler M, Janssen G, van Veelen P, Aartsma-Rus A, Spitali P. The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:384-396. [PMID: 33338663 PMCID: PMC8242265 DOI: 10.1016/j.gpb.2020.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/29/2020] [Accepted: 06/04/2020] [Indexed: 01/24/2023]
Abstract
Muscle formation is a coordinated process driven by extensive gene expression changes where single cells fuse together to form multinucleated muscle fibers. Newly synthesized mRNAs are then regulated by RNA binding proteins (RBPs), affecting post-transcriptional transcript metabolism. Here, we determined how large-scale gene expression changes affect the catalog of RBPs by studying proliferating and differentiated muscle cells in healthy and dystrophic conditions. Transcriptomic analysis showed that the expression of more than 7000 genes was affected during myogenesis. We identified 769 RBPs, of which 294 were muscle-specific and 49 were uniquely shared with cardiomyocytes. A subset of 32 RBPs (half of which were muscle-specific) was found to be preferentially associated with target mRNAs in either myoblasts (MBs) or myotubes (MTs). A large proportion of catalytic proteins were bound to mRNAs even though they lack classical RNA binding domains. Finally, we showed how the identification of cell-specific RBPs enabled the identification of biomarkers that can separate healthy individuals from dystrophic patients. Our data show how interactome data can shed light on new basic RNA biology as well as provide cell-specific data that can be used for diagnostic purposes.
Collapse
Affiliation(s)
- Monika Hiller
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Miriam Geissler
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - George Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Peter van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands.
| |
Collapse
|
48
|
Gerstner N, Kehl T, Lenhof K, Müller A, Mayer C, Eckhart L, Grammes NL, Diener C, Hart M, Hahn O, Walter J, Wyss-Coray T, Meese E, Keller A, Lenhof HP. GeneTrail 3: advanced high-throughput enrichment analysis. Nucleic Acids Res 2020; 48:W515-W520. [PMID: 32379325 PMCID: PMC7319559 DOI: 10.1093/nar/gkaa306] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/31/2020] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
We present GeneTrail 3, a major extension of our web service GeneTrail that offers rich functionality for the identification, analysis, and visualization of deregulated biological processes. Our web service provides a comprehensive collection of biological processes and signaling pathways for 12 model organisms that can be analyzed with a powerful framework for enrichment and network analysis of transcriptomic, miRNomic, proteomic, and genomic data sets. Moreover, GeneTrail offers novel workflows for the analysis of epigenetic marks, time series experiments, and single cell data. We demonstrate the capabilities of our web service in two case-studies, which highlight that GeneTrail is well equipped for uncovering complex molecular mechanisms. GeneTrail is freely accessible at: http://genetrail.bioinf.uni-sb.de.
Collapse
Affiliation(s)
- Nico Gerstner
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Kerstin Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Anne Müller
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Carolin Mayer
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Lea Eckhart
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Nadja Liddy Grammes
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany.,Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Caroline Diener
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Martin Hart
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Oliver Hahn
- School of Medicine Office, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken D-66041, Germany
| | - Tony Wyss-Coray
- School of Medicine Office, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany.,Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,School of Medicine Office, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| |
Collapse
|
49
|
Kern F, Fehlmann T, Solomon J, Schwed L, Grammes N, Backes C, Van Keuren-Jensen K, Craig DW, Meese E, Keller A. miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems. Nucleic Acids Res 2020; 48:W521-W528. [PMID: 32374865 PMCID: PMC7319446 DOI: 10.1093/nar/gkaa309] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/06/2020] [Accepted: 04/22/2020] [Indexed: 01/01/2023] Open
Abstract
Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from ten frequently investigated organisms. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miRBase miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualizations such as heatmaps and running sum curves with background distributions. We demonstrate the new features with case studies for human kidney cancer, a biomarker study on Parkinson’s disease from the PPMI cohort, and a mouse model for breast cancer. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.
Collapse
Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jeffrey Solomon
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Louisa Schwed
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nadja Grammes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | - David Wesley Craig
- Institute of Translational Genomics, University of Southern California, Los Angeles, CA 90033, USA
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,School of Medicine Office, Stanford University, Stanford, CA 94305, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94304, USA
| |
Collapse
|
50
|
Lankes K, Hassan Z, Doffo MJ, Schneeweis C, Lier S, Öllinger R, Rad R, Krämer OH, Keller U, Saur D, Reichert M, Schneider G, Wirth M. Targeting the ubiquitin-proteasome system in a pancreatic cancer subtype with hyperactive MYC. Mol Oncol 2020; 14:3048-3064. [PMID: 33099868 PMCID: PMC7718946 DOI: 10.1002/1878-0261.12835] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/11/2020] [Accepted: 10/04/2020] [Indexed: 12/12/2022] Open
Abstract
The myelocytomatosis oncogene (MYC) is an important driver in a subtype of pancreatic ductal adenocarcinoma (PDAC). However, MYC remains a challenging therapeutic target; therefore, identifying druggable synthetic lethal interactions in MYC‐active PDAC may lead to novel precise therapies. First, to identify networks with hyperactive MYC, we profiled transcriptomes of established human cell lines, murine primary PDAC cell lines, and accessed publicly available repositories to analyze transcriptomes of primary human PDAC. Networks active in MYC‐hyperactive subtypes were analyzed by gene set enrichment analysis. Next, we performed an unbiased pharmacological screen to define MYC‐associated vulnerabilities. Hits were validated by analysis of drug response repositories and genetic gain‐ and loss‐of‐function experiments. In these experiments, we discovered that the proteasome inhibitor bortezomib triggers a MYC‐associated vulnerability. In addition, by integrating publicly available data, we found the unfolded protein response as a signature connected to MYC. Furthermore, increased sensitivity of MYC‐hyperactive PDACs to bortezomib was validated in genetically modified PDAC cells. In sum, we provide evidence that perturbing the ubiquitin–proteasome system (UPS) might be an option to target MYC‐hyperactive PDAC cells. Our data provide the rationale to further develop precise targeting of the UPS as a subtype‐specific therapeutic approach.
Collapse
Affiliation(s)
- Katharina Lankes
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany
| | - Zonera Hassan
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany
| | - María Josefina Doffo
- Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Campus Benjamin Franklin, Berlin, Germany
| | - Christian Schneeweis
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany
| | - Svenja Lier
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, Munich, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, Munich, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Oliver H Krämer
- Department of Toxicology, University Medical Center, Mainz, Germany
| | - Ulrich Keller
- Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Campus Benjamin Franklin, Berlin, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dieter Saur
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, Munich, Germany
| | - Maximilian Reichert
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Günter Schneider
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Munich, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthias Wirth
- Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Campus Benjamin Franklin, Berlin, Germany
| |
Collapse
|