1
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Zhang X, Pant SM, Ritch CC, Tang HY, Shao H, Dweep H, Gong YY, Brooks R, Brafford P, Wolpaw AJ, Lee Y, Weeraratna A, Sehgal A, Herlyn M, Kossenkov A, Speicher D, Sorger PK, Santagata S, Dang CV. Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity. Nat Commun 2024; 15:633. [PMID: 38245503 PMCID: PMC10799901 DOI: 10.1038/s41467-024-44778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
The circadian clock regulator Bmal1 modulates tumorigenesis, but its reported effects are inconsistent. Here, we show that Bmal1 has a context-dependent role in mouse melanoma tumor growth. Loss of Bmal1 in YUMM2.1 or B16-F10 melanoma cells eliminates clock function and diminishes hypoxic gene expression and tumorigenesis, which could be rescued by ectopic expression of HIF1α in YUMM2.1 cells. By contrast, over-expressed wild-type or a transcriptionally inactive mutant Bmal1 non-canonically sequester myosin heavy chain 9 (Myh9) to increase MRTF-SRF activity and AP-1 transcriptional signature, and shift YUMM2.1 cells from a Sox10high to a Sox9high immune resistant, mesenchymal cell state that is found in human melanomas. Our work describes a link between Bmal1, Myh9, mouse melanoma cell plasticity, and tumor immunity. This connection may underlie cancer therapeutic resistance and underpin the link between the circadian clock, MRTF-SRF and the cytoskeleton.
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Affiliation(s)
- Xue Zhang
- The Wistar Institute, Philadelphia, PA, USA.
- Ludwig Institute for Cancer Research, New York, NY, USA.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Shishir M Pant
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Cecily C Ritch
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Yao-Yu Gong
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Rebekah Brooks
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Patricia Brafford
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Adam J Wolpaw
- The Wistar Institute, Philadelphia, PA, USA
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yool Lee
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Ashani Weeraratna
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Amita Sehgal
- Howard Hughes Medical Institute, Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chi V Dang
- The Wistar Institute, Philadelphia, PA, USA.
- Ludwig Institute for Cancer Research, New York, NY, USA.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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2
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Leung JC, Leu JIJ, Indeglia A, Kannan T, Clarke NL, Kirven NA, Dweep H, Garlick D, Barnoud T, Kossenkov AV, George DL, Murphy ME. Common activities and predictive gene signature identified for genetic hypomorphs of TP53. Proc Natl Acad Sci U S A 2023; 120:e2212940120. [PMID: 36749725 PMCID: PMC9962931 DOI: 10.1073/pnas.2212940120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/05/2023] [Indexed: 02/08/2023] Open
Abstract
Missense mutations that inactivate p53 occur commonly in cancer, and germline mutations in TP53 cause Li Fraumeni syndrome, which is associated with early-onset cancer. In addition, there are over two hundred germline missense variants of p53 that remain uncharacterized. In some cases, these germline variants have been shown to encode lesser-functioning, or hypomorphic, p53 protein, and these alleles are associated with increased cancer risk in humans and mouse models. However, most hypomorphic p53 variants remain un- or mis-classified in clinical genetics databases. There thus exists a significant need to better understand the behavior of p53 hypomorphs and to develop a functional assay that can distinguish hypomorphs from wild-type p53 or benign variants. We report the surprising finding that two different African-centric genetic hypomorphs of p53 that occur in distinct functional domains of the protein share common activities. Specifically, the Pro47Ser variant, located in the transactivation domain, and the Tyr107His variant, located in the DNA binding domain, both share increased propensity to misfold into a conformation specific for mutant, misfolded p53. Additionally, cells and tissues containing these hypomorphic variants show increased NF-κB activity. We identify a common gene expression signature from unstressed lymphocyte cell lines that is shared between multiple germline hypomorphic variants of TP53, and which successfully distinguishes wild-type p53 and a benign variant from lesser-functioning hypomorphic p53 variants. Our findings will allow us to better understand the contribution of p53 hypomorphs to disease risk and should help better inform cancer risk in the carriers of p53 variants.
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Affiliation(s)
- Jessica C. Leung
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA19104
| | - Julia I-Ju Leu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA19104
| | - Alexandra Indeglia
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA19104
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA19104
| | - Toshitha Kannan
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA19104
| | - Nicole L. Clarke
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA19104
| | - Nicole A. Kirven
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA19104
| | - Harsh Dweep
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA19104
| | | | - Thibaut Barnoud
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA19104
| | - Andrew V. Kossenkov
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA19104
| | - Donna L. George
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA19104
| | - Maureen E. Murphy
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA19104
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3
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Gill PS, Dweep H, Rose S, Wickramasinghe PJ, Vyas KK, McCullough S, Porter-Gill PA, Frye RE. Integrated microRNA–mRNA Expression Profiling Identifies Novel Targets and Networks Associated with Autism. J Pers Med 2022; 12:jpm12060920. [PMID: 35743705 PMCID: PMC9225282 DOI: 10.3390/jpm12060920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 01/27/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, with mutations in hundreds of genes contributing to its risk. Herein, we studied lymphoblastoid cell lines (LCLs) from children diagnosed with autistic disorder (n = 10) and controls (n = 7) using RNA and miRNA sequencing profiles. The sequencing analysis identified 1700 genes and 102 miRNAs differentially expressed between the ASD and control LCLs (p ≤ 0.05). The top upregulated genes were GABRA4, AUTS2, and IL27, and the top upregulated miRNAs were hsa-miR-6813-3p, hsa-miR-221-5p, and hsa-miR-21-5p. The RT-qPCR analysis confirmed the sequencing results for randomly selected candidates: AUTS2, FMR1, PTEN, hsa-miR-15a-5p, hsa-miR-92a-3p, and hsa-miR-125b-5p. The functional enrichment analysis showed pathways involved in ASD control proliferation of neuronal cells, cell death of immune cells, epilepsy or neurodevelopmental disorders, WNT and PTEN signaling, apoptosis, and cancer. The integration of mRNA and miRNA sequencing profiles by miRWalk2.0 identified correlated changes in miRNAs and their targets’ expression. The integration analysis found significantly dysregulated miRNA–gene pairs in ASD. Overall, these findings suggest that mRNA and miRNA expression profiles in ASD are greatly altered in LCLs and reveal numerous miRNA–gene interactions that regulate critical pathways involved in the proliferation of neuronal cells, cell death of immune cells, and neuronal development.
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Affiliation(s)
- Pritmohinder S. Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Arkansas Children′s Research Institute, Little Rock, AR 72202, USA; (K.K.V.); (S.M.); (P.A.P.-G.)
- Correspondence: ; Tel.: +1-501-364-2743
| | - Harsh Dweep
- The Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA; (H.D.); (P.J.W.)
| | - Shannon Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Arkansas Children′s Research Institute, Little Rock, AR 72202, USA; (K.K.V.); (S.M.); (P.A.P.-G.)
| | | | - Kanan K. Vyas
- Arkansas Children′s Research Institute, Little Rock, AR 72202, USA; (K.K.V.); (S.M.); (P.A.P.-G.)
| | - Sandra McCullough
- Arkansas Children′s Research Institute, Little Rock, AR 72202, USA; (K.K.V.); (S.M.); (P.A.P.-G.)
| | - Patricia A. Porter-Gill
- Arkansas Children′s Research Institute, Little Rock, AR 72202, USA; (K.K.V.); (S.M.); (P.A.P.-G.)
| | - Richard E. Frye
- Barrow Neurological Institute at Phoenix Children′s Hospital, Phoenix, AZ 85016, USA;
- Department of Child Health, University of Arizona College of Medicine, Phoenix, AZ 85004, USA
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4
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Pieri M, Theori E, Dweep H, Flourentzou M, Kalampalika F, Maniori MA, Papagregoriou G, Papaneophytou C, Felekkis K. A bovine miRNA, bta-miR-154c, withstands in vitro human digestion but does not affect cell viability of colorectal human cell lines after transfection. FEBS Open Bio 2022; 12:925-936. [PMID: 35318810 PMCID: PMC9063428 DOI: 10.1002/2211-5463.13402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/02/2022] [Accepted: 03/21/2022] [Indexed: 11/05/2022] Open
Abstract
Colorectal cancer (CRC) is the third most frequent human cancer with over 1.3 million new cases globally. CRC is a complex disease caused by interactions between genetic and environmental factors; in particular, high consumption of red meat, including beef, is considered a risk factor for CRC initiation and progression. Recent data demonstrate that exogenous microRNAs (miRNAs) entering the body via ingestion could pose an effect on the consumer. In this study, we focused on bovine miRNAs that do not share a seed sequence with humans and mice. We identified bta-miR-154c, a bovine miRNA found in edible parts of beef and predicted via cross-species bioinformatic analysis to affect cancer-related pathways in human cells. When bovine tissue was subjected to cooking and a simulation of human digestion, bta-miR-154c was still detected after all procedures, albeit at reduced concentrations. However, lipofection of bta-miR-154c in three different colorectal human cell lines did not affect their viability as evaluated at various time points and concentrations. These data indicate that bta-miR-154c (a) may affect cancer-related pathways in human cells, (b) can withstand digestion and be detected after all stages of an in vitro digestion protocol, but (c) it does not appear to alter epithelial cell viability after entering human enterocytes, even at supraphysiological amounts. Further experiments will elucidate whether bta-miR-154c exerts a different functional effect on the human gut epithelium, which may cause it to contribute to CRC progression through its consumption.
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Affiliation(s)
- Myrtani Pieri
- Department of Life and Health Sciences, University of Nicosia, Cyprus
| | - Elena Theori
- Department of Life and Health Sciences, University of Nicosia, Cyprus
| | - Harsh Dweep
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | | | | | | | | | - Kyriacos Felekkis
- Department of Life and Health Sciences, University of Nicosia, Cyprus
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5
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Dweep H, Showe LC, Kossenkov AV. Functional Annotation of MicroRNAs Using Existing Resources. Methods Mol Biol 2022; 2257:57-77. [PMID: 34432273 DOI: 10.1007/978-1-0716-1170-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are endogenous small noncoding RNAs that are involved in most biological signaling pathways, including the cell cycle, apoptosis, proliferation, immune response, metabolism as well as in biological processes including organ development and in human diseases like cancers. During the past two decades, high-throughput transcriptomic profiling using next generation sequencing and microarrays have been extensively utilized to identify differentially expressed miRNAs across different conditions and diseases. A natural extension of miRNA identification is to the process of functionally annotating known or predicted gene targets of those miRNAs and, by inference, revealing their potential influences on diverse biological pathways and functions. In this chapter, we provide a stepwise guideline on how to perform functional enrichment analyses on miRNAs of interest using publicly available resources such as miRWalk2.0.
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Affiliation(s)
- Harsh Dweep
- The Wistar Institute, Philadelphia, PA, USA.
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6
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Giron LB, Dweep H, Yin X, Wang H, Damra M, Goldman AR, Gorman N, Palmer CS, Tang HY, Shaikh MW, Forsyth CB, Balk RA, Zilberstein NF, Liu Q, Kossenkov A, Keshavarzian A, Landay A, Abdel-Mohsen M. Corrigendum: Plasma Markers of Disrupted Gut Permeability in Severe COVID-19 Patients. Front Immunol 2021; 12:779064. [PMID: 34671365 PMCID: PMC8522493 DOI: 10.3389/fimmu.2021.779064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 12/23/2022] Open
Affiliation(s)
- Leila B Giron
- The Wistar Institute, Philadelphia, PA, United States
| | - Harsh Dweep
- The Wistar Institute, Philadelphia, PA, United States
| | - Xiangfan Yin
- The Wistar Institute, Philadelphia, PA, United States
| | - Han Wang
- The Wistar Institute, Philadelphia, PA, United States
| | | | | | - Nicole Gorman
- The Wistar Institute, Philadelphia, PA, United States
| | - Clovis S Palmer
- The Burnet Institute, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Hsin-Yao Tang
- The Wistar Institute, Philadelphia, PA, United States
| | - Maliha W Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, United States
| | - Christopher B Forsyth
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, United States.,Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Robert A Balk
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Netanel F Zilberstein
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Qin Liu
- The Wistar Institute, Philadelphia, PA, United States
| | | | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, United States.,Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Alan Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
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7
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Gill PS, Clothier JL, Veerapandiyan A, Dweep H, Porter-Gill PA, Schaefer GB. Molecular Dysregulation in Autism Spectrum Disorder. J Pers Med 2021; 11:848. [PMID: 34575625 PMCID: PMC8466026 DOI: 10.3390/jpm11090848] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Autism Spectrum Disorder (ASD) comprises a heterogeneous group of neurodevelopmental disorders with a strong heritable genetic component. At present, ASD is diagnosed solely by behavioral criteria. Advances in genomic analysis have contributed to numerous candidate genes for the risk of ASD, where rare mutations and s common variants contribute to its susceptibility. Moreover, studies show rare de novo variants, copy number variation and single nucleotide polymorphisms (SNPs) also impact neurodevelopment signaling. Exploration of rare and common variants involved in common dysregulated pathways can provide new diagnostic and therapeutic strategies for ASD. Contributions of current innovative molecular strategies to understand etiology of ASD will be explored which are focused on whole exome sequencing (WES), whole genome sequencing (WGS), microRNA, long non-coding RNAs and CRISPR/Cas9 models. Some promising areas of pharmacogenomic and endophenotype directed therapies as novel personalized treatment and prevention will be discussed.
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Affiliation(s)
- Pritmohinder S. Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA;
| | - Jeffery L. Clothier
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Aravindhan Veerapandiyan
- Pediatric Neurology, Arkansas Children’s Hospital, 1 Children’s Way, Little Rock, AR 72202, USA;
| | - Harsh Dweep
- The Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA;
| | | | - G. Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Genetics and Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Hospital NW, Springdale, AR 72762, USA
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8
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Giron LB, Dweep H, Yin X, Wang H, Damra M, Goldman AR, Gorman N, Palmer CS, Tang HY, Shaikh MW, Forsyth CB, Balk RA, Zilberstein NF, Liu Q, Kossenkov A, Keshavarzian A, Landay A, Abdel-Mohsen M. Plasma Markers of Disrupted Gut Permeability in Severe COVID-19 Patients. Front Immunol 2021; 12:686240. [PMID: 34177935 PMCID: PMC8219958 DOI: 10.3389/fimmu.2021.686240] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
A disruption of the crosstalk between the gut and the lung has been implicated as a driver of severity during respiratory-related diseases. Lung injury causes systemic inflammation, which disrupts gut barrier integrity, increasing the permeability to gut microbes and their products. This exacerbates inflammation, resulting in positive feedback. We aimed to test whether severe Coronavirus disease 2019 (COVID-19) is associated with markers of disrupted gut permeability. We applied a multi-omic systems biology approach to analyze plasma samples from COVID-19 patients with varying disease severity and SARS-CoV-2 negative controls. We investigated the potential links between plasma markers of gut barrier integrity, microbial translocation, systemic inflammation, metabolome, lipidome, and glycome, and COVID-19 severity. We found that severe COVID-19 is associated with high levels of markers of tight junction permeability and translocation of bacterial and fungal products into the blood. These markers of disrupted intestinal barrier integrity and microbial translocation correlate strongly with higher levels of markers of systemic inflammation and immune activation, lower levels of markers of intestinal function, disrupted plasma metabolome and glycome, and higher mortality rate. Our study highlights an underappreciated factor with significant clinical implications, disruption in gut functions, as a potential force that may contribute to COVID-19 severity.
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Affiliation(s)
- Leila B Giron
- The Wistar Institute, Philadelphia, PA, United States
| | - Harsh Dweep
- The Wistar Institute, Philadelphia, PA, United States
| | - Xiangfan Yin
- The Wistar Institute, Philadelphia, PA, United States
| | - Han Wang
- The Wistar Institute, Philadelphia, PA, United States
| | | | | | - Nicole Gorman
- The Wistar Institute, Philadelphia, PA, United States
| | - Clovis S Palmer
- The Burnet Institute, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Hsin-Yao Tang
- The Wistar Institute, Philadelphia, PA, United States
| | - Maliha W Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, United States
| | - Christopher B Forsyth
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, United States.,Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Robert A Balk
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Netanel F Zilberstein
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Qin Liu
- The Wistar Institute, Philadelphia, PA, United States
| | | | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, United States.,Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Alan Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
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9
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Veglia F, Hashimoto A, Dweep H, Sanseviero E, De Leo A, Tcyganov E, Kossenkov A, Mulligan C, Nam B, Masters G, Patel J, Bhargava V, Wilkinson P, Smirnov D, Sepulveda MA, Singhal S, Eruslanov EB, Cristescu R, Loboda A, Nefedova Y, Gabrilovich DI. Analysis of classical neutrophils and polymorphonuclear myeloid-derived suppressor cells in cancer patients and tumor-bearing mice. J Exp Med 2021; 218:211778. [PMID: 33566112 PMCID: PMC7879582 DOI: 10.1084/jem.20201803] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/28/2020] [Accepted: 01/07/2021] [Indexed: 01/08/2023] Open
Abstract
In this study, using single-cell RNA-seq, cell mass spectrometry, flow cytometry, and functional analysis, we characterized the heterogeneity of polymorphonuclear neutrophils (PMNs) in cancer. We describe three populations of PMNs in tumor-bearing mice: classical PMNs, polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs), and activated PMN-MDSCs with potent immune suppressive activity. In spleens of mice, PMN-MDSCs gradually replaced PMNs during tumor progression. Activated PMN-MDSCs were found only in tumors, where they were present at the very early stages of the disease. These populations of PMNs in mice could be separated based on the expression of CD14. In peripheral blood of cancer patients, we identified two distinct populations of PMNs with characteristics of classical PMNs and PMN-MDSCs. The gene signature of tumor PMN-MDSCs was similar to that in mouse activated PMN-MDSCs and was closely associated with negative clinical outcome in cancer patients. Thus, we provide evidence that PMN-MDSCs are a distinct population of PMNs with unique features and potential for selective targeting opportunities.
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Affiliation(s)
| | | | | | | | | | | | | | - Charles Mulligan
- Helen F. Graham Cancer Center and Research Institute, Christiana Care, Newark, DE
| | - Brian Nam
- Helen F. Graham Cancer Center and Research Institute, Christiana Care, Newark, DE
| | - Gregory Masters
- Helen F. Graham Cancer Center and Research Institute, Christiana Care, Newark, DE
| | - Jaymala Patel
- Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson, Spring House, PA
| | - Vipul Bhargava
- Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson, Spring House, PA
| | - Patrick Wilkinson
- Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson, Spring House, PA
| | - Denis Smirnov
- Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson, Spring House, PA
| | - Manuel A Sepulveda
- Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson, Spring House, PA
| | - Sunil Singhal
- Division of Thoracic Surgery, Department of Surgery, University of Pennsylvania, Philadelphia, PA
| | - Evgeniy B Eruslanov
- Division of Thoracic Surgery, Department of Surgery, University of Pennsylvania, Philadelphia, PA
| | - Razvan Cristescu
- Department of Genetics and Pharmacogenomics, Merck Research Laboratories, Merck & Co., Inc., Boston, MA
| | - Andrey Loboda
- Department of Genetics and Pharmacogenomics, Merck Research Laboratories, Merck & Co., Inc., Boston, MA
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10
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Somasundaram R, Connelly T, Choi R, Choi H, Samarkina A, Li L, Gregorio E, Chen Y, Thakur R, Abdel-Mohsen M, Beqiri M, Kiernan M, Perego M, Wang F, Xiao M, Brafford P, Yang X, Xu X, Secreto A, Danet-Desnoyers G, Traum D, Kaestner KH, Huang AC, Hristova D, Wang J, Fukunaga-Kalabis M, Krepler C, Ping-Chen F, Zhou X, Gutierrez A, Rebecca VW, Vonteddu P, Dotiwala F, Bala S, Majumdar S, Dweep H, Wickramasinghe J, Kossenkov AV, Reyes-Arbujas J, Santiago K, Nguyen T, Griss J, Keeney F, Hayden J, Gavin BJ, Weiner D, Montaner LJ, Liu Q, Peiffer L, Becker J, Burton EM, Davies MA, Tetzlaff MT, Muthumani K, Wargo JA, Gabrilovich D, Herlyn M. Tumor-infiltrating mast cells are associated with resistance to anti-PD-1 therapy. Nat Commun 2021; 12:346. [PMID: 33436641 PMCID: PMC7804257 DOI: 10.1038/s41467-020-20600-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
Anti-PD-1 therapy is used as a front-line treatment for many cancers, but mechanistic insight into this therapy resistance is still lacking. Here we generate a humanized (Hu)-mouse melanoma model by injecting fetal liver-derived CD34+ cells and implanting autologous thymus in immune-deficient NOD-scid IL2Rγnull (NSG) mice. Reconstituted Hu-mice are challenged with HLA-matched melanomas and treated with anti-PD-1, which results in restricted tumor growth but not complete regression. Tumor RNA-seq, multiplexed imaging and immunohistology staining show high expression of chemokines, as well as recruitment of FOXP3+ Treg and mast cells, in selective tumor regions. Reduced HLA-class I expression and CD8+/Granz B+ T cells homeostasis are observed in tumor regions where FOXP3+ Treg and mast cells co-localize, with such features associated with resistance to anti-PD-1 treatment. Combining anti-PD-1 with sunitinib or imatinib results in the depletion of mast cells and complete regression of tumors. Our results thus implicate mast cell depletion for improving the efficacy of anti-PD-1 therapy. Immune checkpoint therapies (ICT) are promising for treating various cancers, but response rates vary. Here the authors show, in mouse models, that tumor-infiltrating mast cells colocalize with regulatory T cells, coincide with local reduction of MHC-I and CD8 T cells, and is associated with resistance to ICT, which can be reversed by c-kit inhibitor treatment.
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Affiliation(s)
| | | | - Robin Choi
- The Wistar Institute, Philadelphia, PA, USA
| | | | | | - Ling Li
- The Wistar Institute, Philadelphia, PA, USA
| | | | | | - Rohit Thakur
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | - Fang Wang
- The Wistar Institute, Philadelphia, PA, USA
| | - Min Xiao
- The Wistar Institute, Philadelphia, PA, USA
| | | | - Xue Yang
- The Wistar Institute, Philadelphia, PA, USA
| | - Xiaowei Xu
- Department of Pathology and Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anthony Secreto
- Department of Medicine, Stem Cell and Xenograft Core, University of Pennsylvania, Philadelphia, PA, USA
| | - Gwenn Danet-Desnoyers
- Department of Medicine, Stem Cell and Xenograft Core, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Traum
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander C Huang
- Department of Pathology and Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Johannes Griss
- Division of Immunology, Allergy and Infectious Diseases (DIAID), Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | | | | | | | | | - Qin Liu
- The Wistar Institute, Philadelphia, PA, USA
| | | | | | - Elizabeth M Burton
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, University of California, San Francisco, CA, USA
| | - Michael T Tetzlaff
- Department of Pathology and Dermatology, University of California, San Francisco, CA, USA
| | - Kar Muthumani
- The Wistar Institute, Philadelphia, PA, USA.,GeneOne Life Science Inc., Fort Washington, PA, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
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11
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Colomb F, Giron LB, Kuri-Cervantes L, Adeniji OS, Ma T, Dweep H, Battivelli E, Verdin E, Palmer CS, Tateno H, Kossenkov AV, Roan NR, Betts MR, Abdel-Mohsen M. Sialyl-Lewis X Glycoantigen Is Enriched on Cells with Persistent HIV Transcription during Therapy. Cell Rep 2020; 32:107991. [PMID: 32755584 PMCID: PMC7432956 DOI: 10.1016/j.celrep.2020.107991] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/30/2020] [Accepted: 07/14/2020] [Indexed: 12/30/2022] Open
Abstract
A comprehensive understanding of the phenotype of persistent HIV-infected cells, transcriptionally active and/or transcriptionally inactive, is imperative for developing a cure. The relevance of cell-surface glycosylation to HIV persistence has never been explored. We characterize the relationship between cell-surface glycomic signatures and persistent HIV transcription in vivo. We find that the cell surface of CD4+ T cells actively transcribing HIV, despite suppressive therapy, harbors high levels of fucosylated carbohydrate ligands, including the cell extravasation mediator Sialyl-LewisX (SLeX), compared with HIV-infected transcriptionally inactive cells. These high levels of SLeX are induced by HIV transcription in vitro and are maintained after therapy in vivo. Cells with high-SLeX are enriched with markers associated with HIV susceptibility, signaling pathways that drive HIV transcription, and pathways involved in leukocyte extravasation. We describe a glycomic feature of HIV-infected transcriptionally active cells that not only differentiates them from their transcriptionally inactive counterparts but also may affect their trafficking abilities.
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Affiliation(s)
- Florent Colomb
- The Wistar Institute, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leila B Giron
- The Wistar Institute, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Opeyemi S Adeniji
- The Wistar Institute, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tongcui Ma
- University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Harsh Dweep
- The Wistar Institute, Philadelphia, PA 19104, USA
| | | | - Eric Verdin
- The Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Clovis S Palmer
- The Burnet Institute, Melbourne, VIC 3004, Australia; Department of Infectious Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Hiroaki Tateno
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | | | - Nadia R Roan
- University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mohamed Abdel-Mohsen
- The Wistar Institute, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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McCullough S, Dweep H, McGill MR, Bhattacharyya S, James L, Frankowski S, Woodall A, Kearns G, Gill P. Granzyme B and miR-378a Interaction in Acetaminophen Toxicity in Children. Microrna 2020; 9:121-132. [PMID: 31393259 PMCID: PMC10507677 DOI: 10.2174/2211536608666190808144456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 07/23/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND AND AIM Hepatic phase I drug-metabolizing enzymes CYP2E1, CYP1A2 and CYP3A4 catalyze the biotransformation of Acetaminophen (APAP) and are important in the mediation of toxicity. The potential role of other hepatic and non-hepatic Phase I enzymes in APAP toxicity has not been established. METHODS PCR array containing 84 genes involved in phase I drug metabolism was examined in subgroups of hospitalized children for APAP overdose, categorized as no toxicity (ALT ≤ 45 IU/L, n=5) and moderate toxicity (ALT ≥ 500 IU/L, n=5). RESULTS Significant downregulation was observed for ALDH6A1, CYP4F12 and GZMB in the no toxicity subgroup and ALDH1A1, CYP27A1 and GZMB in the moderate toxicity subgroup. qRTPCR confirmed significant downregulation for ALDH1A1, CYP4F12, and GZMB. In-silico analysis identified GZMB 3'UTR to be a target of miR-378a-5p. Overexpression of miR-378a-5p reduced the luciferase activity of GZMB 3'UTR reporter plasmid reportedly by 50%. NK-92 cells transfected with the miR-378a-5p mimic extended the effect of APAP on GZMB protein expression compared to mimic controls. In addition, miR-378a-5p was significantly upregulated in blood samples of children with APAP overdose undergoing NAC treatment. CONCLUSION Overall, our study suggests the presence of a novel signaling pathway, whereby miR- 378a-5p inhibits GZMB expression in children with APAP overdose.
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Affiliation(s)
- Sandra McCullough
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202, USA
| | - Harsh Dweep
- The Wistar Institute, 3601 Spruce St, Philadelphia, PA, 19104, USA
| | - Mitchell R. McGill
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sudeepa Bhattacharyya
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202, USA
| | - Laura James
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202, USA
| | - Sara Frankowski
- Arkansas Children’s Research Institute, Little Rock, AR 72202, USA
| | - Aaron Woodall
- Arkansas Children’s Research Institute, Little Rock, AR 72202, USA
| | - Gregory Kearns
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202, USA
| | - Pritmohinder Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202, USA
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13
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Schleimann MH, Kobberø ML, Vibholm LK, Kjær K, Giron LB, Busman-Sahay K, Chan CN, Nekorchuk M, Schmidt M, Wittig B, Damsgaard TE, Ahlburg P, Hellfritzsch MB, Zuwala K, Rothemejer FH, Olesen R, Schommers P, Klein F, Dweep H, Kossenkov A, Nyengaard JR, Estes JD, Abdel-Mohsen M, Østergaard L, Tolstrup M, Søgaard OS, Denton PW. TLR9 agonist MGN1703 enhances B cell differentiation and function in lymph nodes. EBioMedicine 2019; 45:328-340. [PMID: 31300344 PMCID: PMC6642412 DOI: 10.1016/j.ebiom.2019.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/28/2022] Open
Abstract
Background TLR9 agonists are being developed as immunotherapy against malignancies and infections. TLR9 is primarily expressed in B cells and plasmacytoid dendritic cells (pDCs). TLR9 signalling may be critically important for B cell activity in lymph nodes but little is known about the in vivo impact of TLR9 agonism on human lymph node B cells. As a pre-defined sub-study within our clinical trial investigating TLR9 agonist MGN1703 (lefitolimod) treatment in the context of developing HIV cure strategies (NCT02443935), we assessed TLR9 agonist-mediated effects in lymph nodes. Methods Participants received MGN1703 for 24 weeks concurrent with antiretroviral therapy. Seven participants completed the sub-study including lymph node resection at baseline and after 24 weeks of treatment. A variety of tissue-based immunologic and virologic parameters were assessed. Findings MGN1703 dosing increased B cell differentiation; activated pDCs, NK cells, and T cells; and induced a robust interferon response in lymph nodes. Expression of Activation-Induced cytidine Deaminase, an essential regulator of B cell diversification and somatic hypermutation, was highly elevated. During MGN1703 treatment IgG production increased and antibody glycosylation patterns were changed. Interpretation Our data present novel evidence that the TLR9 agonist MGN1703 modulates human lymph node B cells in vivo. These findings warrant further considerations in the development of TLR9 agonists as immunotherapy against cancers and infectious diseases. Fund This work was supported by Aarhus University Research Foundation, the Danish Council for Independent Research and the NovoNordisk Foundation. Mologen AG provided study drug free of charge.
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Affiliation(s)
- Mariane H Schleimann
- Department of Infectious Diseases, Aarhus University Hospital, Denmark; Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, OR, USA.
| | | | - Line K Vibholm
- Department of Infectious Diseases, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Kathrine Kjær
- Department of Infectious Diseases, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Leila B Giron
- Vaccine & Immunotherapy Center, The Wistar Institute, Philadelphia, PA, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, OR, USA
| | - Chi Ngai Chan
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, OR, USA
| | - Michael Nekorchuk
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, OR, USA
| | | | - Burghardt Wittig
- Mologen AG, Berlin, Germany; MolBio2Math - Molecular Biology & Integral Biomathics, a non-profit Foundation Institute, Berlin, Germany
| | - Tine E Damsgaard
- Department of Clinical Medicine, Aarhus University, Denmark; Department of Plastic and Breast Surgery, Plastic Surgery Research Unit, Aarhus University Hospital, Denmark
| | - Peter Ahlburg
- Department of Anesthesiology, Aarhus University Hospital, Denmark
| | - Michel B Hellfritzsch
- Department of Clinical Medicine, Aarhus University, Denmark; Department of Radiology, Aarhus University Hospital, Denmark
| | - Kaja Zuwala
- Department of Infectious Diseases, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | | | - Rikke Olesen
- Department of Clinical Medicine, Aarhus University, Denmark
| | - Phillipp Schommers
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Harsh Dweep
- Bioinformatics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Andrew Kossenkov
- Bioinformatics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Jens R Nyengaard
- Department of Clinical Medicine, Aarhus University, Denmark; Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Centre for Stochastic Geometry and Advanced Bioimaging, Aarhus University Hospital, Aarhus, Denmark
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, OR, USA
| | | | - Lars Østergaard
- Department of Infectious Diseases, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Ole S Søgaard
- Department of Infectious Diseases, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark
| | - Paul W Denton
- Department of Infectious Diseases, Aarhus University Hospital, Denmark; Department of Clinical Medicine, Aarhus University, Denmark.
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14
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Voskarides K, Dweep H, Chrysostomou C. Correction to: Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes. Hum Genomics 2019; 13:29. [PMID: 31266543 PMCID: PMC6604313 DOI: 10.1186/s40246-019-0214-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the original publication of this article [1], the Figure 1 and Figure 2 were wrong. The Figure 1 "Heat map showing the quantity of DNA repair genes, from red to blue in ascending order, per species' genome (numbers at the top of the figure represent the species code that is found in Table 1). Each DNA repair gene pathway was analyzed separately in rows. Radiated species' genomes are richer in DNA repair genes. Analytical data can be found in Additional file 2: Table S2. M mammals, B&R birds and reptiles, BF bony fishes" should be the picture of Figure 2. The figure 2 "Linear regression analysis. The number of DNA repair genes is linearly related to genome size and protein number. As a negative control, we show that genome size is not linearly related with protein number" should be the picture of figure 1.
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15
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Voskarides K, Dweep H, Chrysostomou C. Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes. Hum Genomics 2019; 13:26. [PMID: 31174607 PMCID: PMC6555970 DOI: 10.1186/s40246-019-0210-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/20/2019] [Indexed: 01/05/2023] Open
Abstract
Adaptive radiation and evolutionary stasis are characterized by very different evolution rates. The main aim of this study was to investigate if any genes have a special role to a high or low evolution rate. The availability of animal genomes permitted comparison of gene content of genomes of 24 vertebrate species that evolved through adaptive radiation (representing high evolutionary rate) and of 20 vertebrate species that are considered as living fossils (representing a slow evolutionary rate or evolutionary stasis). Mammals, birds, reptiles, and bony fishes were included in the analysis. Pathway analysis was performed for genes found to be specific in adaptive radiation or evolutionary stasis respectively. Pathway analysis revealed that DNA repair and cellular response to DNA damage are important (false discovery rate = 8.35 × 10−5; 7.15 × 10−6, respectively) for species evolved through adaptive radiation. This was confirmed by further genetic in silico analysis (p = 5.30 × 10−3). Nucleotide excision repair and base excision repair were the most significant pathways. Additionally, the number of DNA repair genes was found to be linearly related to the genome size and the protein number (proteome) of the 44 animals analyzed (p < 1.00 × 10−4), this being compatible with Drake’s rule. This is the first study where radiated and living fossil species have been genetically compared. Evidence has been found that cancer-related genes have a special role in radiated species. Linear association of the number of DNA repair genes with the species genome size has also been revealed. These comparative genetics results can support the idea of punctuated equilibrium evolution.
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16
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Affiliation(s)
- Alisha Parveen
- Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg Mannheim Germany
| | - Norbert Gretz
- Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg Mannheim Germany
| | - Harsh Dweep
- Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg Mannheim Germany
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17
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Wohlfarth C, Schmitteckert S, Härtle JD, Houghton LA, Dweep H, Fortea M, Assadi G, Braun A, Mederer T, Pöhner S, Becker PP, Fischer C, Granzow M, Mönnikes H, Mayer EA, Sayuk G, Boeckxstaens G, Wouters MM, Simrén M, Lindberg G, Ohlsson B, Schmidt PT, Dlugosz A, Agreus L, Andreasson A, D'Amato M, Burwinkel B, Bermejo JL, Röth R, Lasitschka F, Vicario M, Metzger M, Santos J, Rappold GA, Martinez C, Niesler B. miR-16 and miR-103 impact 5-HT 4 receptor signalling and correlate with symptom profile in irritable bowel syndrome. Sci Rep 2017; 7:14680. [PMID: 29089619 PMCID: PMC5665867 DOI: 10.1038/s41598-017-13982-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/04/2017] [Indexed: 12/19/2022] Open
Abstract
Irritable bowel syndrome (IBS) is a gut-brain disorder involving alterations in intestinal sensitivity and motility. Serotonin 5-HT4 receptors are promising candidates in IBS pathophysiology since they regulate gut motor function and stool consistency, and targeted 5-HT4R selective drug intervention has been proven beneficial in subgroups of patients. We identified a single nucleotide polymorphism (SNP) (rs201253747) c.*61 T > C within the 5-HT4 receptor gene HTR4 to be predominantly present in diarrhoea-IBS patients (IBS-D). It affects a binding site for the miR-16 family and miR-103/miR-107 within the isoforms HTR4b/i and putatively impairs HTR4 expression. Subsequent miRNA-profiling revealed downregulation of miR-16 and miR-103 in the jejunum of IBS-D patients correlating with symptoms. In vitro assays confirmed expression regulation via three 3'UTR binding sites. The novel isoform HTR4b_2 lacking two of the three miRNA binding sites escapes miR-16/103/107 regulation in SNP carriers. We provide the first evidence that HTR4 expression is fine-tuned by miRNAs, and that this regulation is impaired either by the SNP c.*61 T > C or by diminished levels of miR-16 and miR-103 suggesting that HTR4 might be involved in the development of IBS-D.
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Affiliation(s)
- Carolin Wohlfarth
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Stefanie Schmitteckert
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Janina D Härtle
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Lesley A Houghton
- University of Leeds, St. James's University Hospital, LS97TF, Leeds, UK
- Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Harsh Dweep
- Medical Research Centre, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, 68167, Germany
- Division of Bioinformatics and Biostatistics, National Centre for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, USA
| | - Marina Fortea
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), 08035, Barcelona, Spain
| | - Ghazaleh Assadi
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Alexander Braun
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Tanja Mederer
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Sarina Pöhner
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Philip P Becker
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Christine Fischer
- Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | | | - Emeran A Mayer
- Oppenheimer Centre for Neurobiology of Stress, Division of Digestive Diseases, University of California, Los Angeles, CA 90095-7378, USA
| | - Gregory Sayuk
- Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Mira M Wouters
- TARGID, University Hospital Leuven, 3000, Leuven, Belgium
| | - Magnus Simrén
- Department of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 41345, Gothenburg, Sweden
| | - Greger Lindberg
- Department of Medicine, Division of Gastroenterology and Hepatology, Karolinska University Hospital, Karolinska Institutet, Huddinge, 17176, Stockholm, Sweden
| | - Bodil Ohlsson
- Department of Clinical Sciences, Division of Internal Medicine, Skåne University Hospital, Malmö, Lund University, 22241, Lund, Sweden
| | - Peter Thelin Schmidt
- Department of Medicine, Division of Gastroenterology and Hepatology, Karolinska University Hospital, Karolinska Institutet, 14186, Stockholm, Sweden
| | - Aldona Dlugosz
- Department of Medicine, Division of Gastroenterology and Hepatology, Karolinska University Hospital, Karolinska Institutet, Huddinge, 17176, Stockholm, Sweden
| | - Lars Agreus
- Division for Family Medicine and Primary Care, Karolinska Institutet, 14183, Huddinge, Sweden
| | - Anna Andreasson
- Department of Medicine, Solna, Karolinska Institutet, 171 76, Solna, Sweden
- Stress Research Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Mauro D'Amato
- Unit of Clinical Epidemiology, Department of Medicine, Karolinska Institutet, 171 76, Stockholm, Sweden
- BioDonostia Health Research Institute, San Sebastian and Ikerbasque, Basque Science Foundation, 48013, Bilbao, Spain
| | - Barbara Burwinkel
- Molecular Epidemiology Group, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Division of Molecular Biology of Breast Cancer, Department of Gynaecology and Obstetrics, University Women's Clinic, University of Heidelberg, 69120, Heidelberg, Germany
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Ralph Röth
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
- nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Maria Vicario
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), 08035, Barcelona, Spain
| | - Marco Metzger
- Department Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, 97082, Wuerzburg, Germany
- Translational Centre 'Regenerative Therapies for Oncology and Musculoskeletal Diseases' (TZKME), Branch of the Fraunhofer Institute Interfacial Engineering and Biotechnology (IGB) Wuerzburg, 97082, Wuerzburg, Germany
| | - Javier Santos
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), 08035, Barcelona, Spain
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Cristina Martinez
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), 08035, Barcelona, Spain
| | - Beate Niesler
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany.
- nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany.
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18
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Gill P, Bhattacharyya S, McCullough S, Letzig L, Mishra PJ, Luo C, Dweep H, James L. MicroRNA regulation of CYP 1A2, CYP3A4 and CYP2E1 expression in acetaminophen toxicity. Sci Rep 2017; 7:12331. [PMID: 28951593 PMCID: PMC5614957 DOI: 10.1038/s41598-017-11811-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/30/2017] [Indexed: 01/29/2023] Open
Abstract
MicroRNAs (miRNAs) that regulate the cytochrome P-450 isoforms involved in acetaminophen (APAP) toxicity were examined in HepaRG cells treated with APAP (20 mM). In-vitro studies found that APAP protein adducts were increased at 1 h, followed by ALT increases at 12 and 24 h. CYP1A2, CYP3A4 and CYP2E1 mRNA levels were decreased, while miRNAs were increased for miR-122-5p, miR-378a-5p, miR-27b-3p at 6 h and miR-125b-5p at 12 h and miR-27b-3p at 24 h. Putative miRNA binding sites on the 3′UTRs of the CYPs were identified in-silico. Overexpression of miR-122-5p and miR-378a-5p in cells suppressed protein expression of CYP1A2, CYP3A4 and CYP2E1. Luciferase reporter assays confirmed the interaction between miR-122 and the 3′UTR of the CYP1A2 and CYP3A4. Thus, the in-vitro experiments showed that miR-122-5p and miR-378a-5p upregulation were associated with translational repression of CYPs. Serum samples of children with APAP overdose had significant elevation of miR-122-5p, miR-378a-5p, miR-125b-5p and miR-27b-3p, compared to healthy controls and receiver operator curves of the miRNAs had AUCs of 91 to 100%. Collectively, the data suggest that miRNA elevations in APAP toxicity represent a regulatory response to modify CYP1A2, CYP3A4 and CYP2E1 translation due to cellular stress and injury.
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Affiliation(s)
- Pritmohinder Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA. .,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA.
| | - Sudeepa Bhattacharyya
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Sandra McCullough
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Lynda Letzig
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Prasun J Mishra
- Department of Biochemical and Cellular Pharmacology, Genentech, 1, DNA Way, South San Francisco, California, 94080, USA
| | - Chunqiao Luo
- Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Harsh Dweep
- The Wistar Institute, 3601 Spruce St, Philadelphia, Pennsylvania, 19104, USA
| | - Laura James
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
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19
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Zhao J, Qi X, Dai Q, He X, Dweep H, Guo M, Luo Y, Gretz N, Luo H, Huang K, Xu W. Toxicity study of ochratoxin A using HEK293 and HepG2 cell lines based on microRNA profiling. Hum Exp Toxicol 2016; 36:8-22. [PMID: 26893291 DOI: 10.1177/0960327116632048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ochratoxin A (OTA) induced DNA damage, cytotoxicity, and apoptosis in mammalian cell lines. Micro RNAs (miRNAs) are involved in physiological and developmental processes and contribute to cancer development and progression. In our study, high-throughput miRNA profiling and Kyoto Encyclopedia of Genes and Genomes analysis were applied to comparatively study the toxicity of OTA in HEK293 cells and HepG2 cells treated with 25 μM OTA for 24 h. In these two cells, the same changing miRNAs were mostly related to signal transduction pathways, whereas the different changing miRNAs were mostly related to human cancer pathways. DGCR8, Dicer1, and Drosha were significantly suppressed in HEK293 cells, indicating an impairment of miRNA biogenesis. The damage seemed more extensive in HEK293 cells. Cell models and in vivo models were also compared. Many miRNAs in vitro were markedly different from those in vivo; however, OTA toxicity was observed both in vitro and in vivo. The classification of deregulated pathways is similar. The biogenesis of miRNA was impaired in both lines. In conclusion, deregulated miRNAs in vitro are mostly related to human cancer and signal transduction pathways. The deregulated pathways in vivo are similar to those in vitro.
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Affiliation(s)
- J Zhao
- 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - X Qi
- 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Q Dai
- 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - X He
- 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - H Dweep
- 2 Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - M Guo
- 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Y Luo
- 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - N Gretz
- 2 Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - H Luo
- 3 State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - K Huang
- 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - W Xu
- 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,4 Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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20
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Herrera-Pérez Z, Gretz N, Dweep H. A Comprehensive Review on the Genetic Regulation of Cisplatin-induced Nephrotoxicity. Curr Genomics 2016; 17:279-93. [PMID: 27252593 PMCID: PMC4869013 DOI: 10.2174/1389202917666160202220555] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 09/10/2015] [Accepted: 09/28/2015] [Indexed: 12/16/2022] Open
Abstract
Cisplatin (CDDP) is a well-known antineoplastic drug which has been extensively utilized over the last decades in the treatment of numerous kinds of tumors. However, CDDP induces a wide range of toxicities in a dose-dependent manner, among which nephrotoxicity is of particular importance. Still, the mechanism of CDDP-induced renal damage is not completely understood; moreover, the knowledge about the role of microRNAs (miRNAs) in the nephrotoxic response is still unknown. miRNAs are known to interact with the representative members of a diverse range of regulatory pathways (including postnatal development, proliferation, inflammation and fibrosis) and pathological conditions, including kidney diseases: polycystic kidney diseases (PKDs), diabetic nephropathy (DN), kidney cancer, and drug-induced kidney injury. In this review, we shed light on the following important aspects: (i) information on genes/proteins and their interactions with previously known pathways engaged with CDDP-induced nephrotoxicity, (ii) information on newly discovered biomarkers, especially, miRNAs for detecting CDDP-induced nephrotoxicity and (iii) information to improve our understanding on CDDP. This information will not only help the researchers belonging to nephrotoxicity field, but also supply an indisputable help for oncologists to better understand and manage the side effects induced by CDDP during cancer treatment. Moreover, we provide up-to-date information about different in vivo and in vitro models that have been utilized over the last decades to study CDDP-induced renal injury. Taken together, this review offers a comprehensive network on genes, miRNAs, pathways and animal models which will serve as a useful resource to understand the molecular mechanism of CDDP-induced nephrotoxicity.
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Affiliation(s)
- Zeneida Herrera-Pérez
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Norbert Gretz
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Harsh Dweep
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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21
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Affiliation(s)
- Harsh Dweep
- Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
| | - Norbert Gretz
- Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
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22
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Gaynullina D, Dweep H, Gloe T, Tarasova OS, Sticht C, Gretz N, Schubert R. Alteration of mRNA and microRNA expression profiles in rat muscular type vasculature in early postnatal development. Sci Rep 2015; 5:11106. [PMID: 26073182 PMCID: PMC4466593 DOI: 10.1038/srep11106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 05/15/2015] [Indexed: 12/23/2022] Open
Abstract
The vascular system is characterized by a high degree of plasticity. In particular, functional and structural remodeling of the arterial system takes place during early postnatal development. However, the mechanisms providing such alterations in the rapidly growing organisms are poorly understood, especially for the peripheral vasculature. To explore this, we performed mRNA- and miRNA microarray analysis on muscular type saphenous arteries of young (10-12 days) and adult (2-3 months) rats. Thirty-eight significant pathways (such as oxidative phosphorylation, MAPK signaling, metabolism, cell cycle, DNA replication and focal adhesion) were obtained on differentially regulated genes during postnatal development. Many differentially regulated genes were determined as target- and miRNA-hubs. We also found 92 miRNAs differentially expressed in arteries of young and adult rats. Several significantly regulated pathways were found on these regulated miRNAs. Interestingly, these biological cascades also contain those significantly enriched pathways that were previously identified based on the differently expressed genes. Our data indicate that the expression of many genes involved in the regulation of pathways that are relevant for different functions in arteries may be under the control of miRNAs and these miRNAs regulate the functional, and structural remodeling occurring in the vascular system during early postnatal development.
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Affiliation(s)
- Dina Gaynullina
- 1] Cardiovascular Physiology, Centre for Biomedicine and Medical Technology Mannheim, Ruprecht-Karls-University Heidelberg, 68167 Mannheim, Germany [2] Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia [3] Department of Physiology, Russian National Research Medical University, Ostrovityanova str. 1, 117997 Moscow, Russia
| | - Harsh Dweep
- Medical Research Center, University of Heidelberg, D-68167 Mannheim, Germany
| | - Torsten Gloe
- Cardiovascular Physiology, Centre for Biomedicine and Medical Technology Mannheim, Ruprecht-Karls-University Heidelberg, 68167 Mannheim, Germany
| | - Olga S Tarasova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Carsten Sticht
- Medical Research Center, University of Heidelberg, D-68167 Mannheim, Germany
| | - Norbert Gretz
- Medical Research Center, University of Heidelberg, D-68167 Mannheim, Germany
| | - Rudolf Schubert
- Cardiovascular Physiology, Centre for Biomedicine and Medical Technology Mannheim, Ruprecht-Karls-University Heidelberg, 68167 Mannheim, Germany
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23
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Dai Q, Zhao J, Qi X, Xu W, He X, Guo M, Dweep H, Cheng WH, Luo Y, Xia K, Gretz N, Huang K. MicroRNA profiling of rats with ochratoxin A nephrotoxicity. BMC Genomics 2014; 15:333. [PMID: 24885635 PMCID: PMC4035064 DOI: 10.1186/1471-2164-15-333] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 04/30/2014] [Indexed: 12/31/2022] Open
Abstract
Background Nephrotoxicity is the most prominent one among the various toxicities of ochratoxin A (OTA). MicroRNAs (miRNAs) are small non-coding RNAs that have an impact on a wide range of biological processes by regulating gene expression at post-transcriptional level or protein systhesis level. The objective of this study is to analyze miRNA profiling in the kidneys of rats gavaged with OTA. Results To profile miRNAs in the kidneys of rats with OTA nephrotoxicity, high-throughput sequencing and bioinformatics approaches were applied to analyze the miRNAs in the kidney of rats following OTA treatment. A total of 409 known miRNAs and 8 novel miRNAs were identified in the kidney and the levels of the novel miRNAs were varied in response to different doses of OTA. Expression of miR-129, miR-130a, miR-130b, miR-141, miR-218b and miR-3588 were uniquely suppressed in mid dose but then elevated in high dose, with opposite expression to their target genes. The expression pattern was closely related with the “MAPK signaling pathway”. Dicer1 and Drosha were significantly suppressed, indicating an impairment of miRNA biogenesis in response to OTA. Conclusions The abrogation of miRNA maturation process suggests a new target of OTA toxicity. Moreover, the identification of the differentially expressed miRNAs provides us a molecular insight into the nephrtoxicity of OTA. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-333) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Wentao Xu
- Laboratory of food safety and molecular biology, College of Food Science and Nutritional Engineering, China Agricultural University, 302 box, No,17, Qinghua East Rd, Beijing, Haidian District 100083, P R China.
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24
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Abstract
miRWalk (http://mirwalk.uni-hd.de/) is a publicly available comprehensive resource, hosting the predicted as well as the experimentally validated microRNA (miRNA)-target interaction pairs. This database allows obtaining the possible miRNA-binding site predictions within the complete sequence of all known genes of three genomes (human, mouse, and rat). Moreover, it also integrates many novel features such as a comparative platform of miRNA-binding sites resulting from ten different prediction datasets, a holistic view of genetic networks of miRNA-gene pathway, and miRNA-gene-Online Mendelian Inheritance in Man disorder interactions, and unique experimentally validated information (e.g., cell lines, diseases, miRNA processing proteins). In this chapter, we describe a schematic workflow on how one can access the stored information from miRWalk and subsequently summarize its applications.
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Affiliation(s)
- Harsh Dweep
- Medical Faculty Mannheim, Medical Research Center, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, D-68167, Mannheim, Germany,
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25
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Dweep H, Gretz N, Felekkis K. A schematic workflow for collecting information about the interaction between copy number variants and microRNAs using existing resources. Methods Mol Biol 2014; 1182:307-320. [PMID: 25055921 DOI: 10.1007/978-1-4939-1062-5_26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
MicroRNAs (miRNAs) and copy number variations (CNVs) are two extensively studied genomic components in the field of modern biology-as they have been found to be associated with many disorders such as cancer, Alzheimer, pancreatitis, HIV susceptibility, beta-thalassemia, and glomerulonephritis. Several studies suggested that an alteration in CNV-miRNA interaction could result in some human diseases such as cancer. Therefore, the possible miRNA-binding site information within the CNV genes opens new avenues in understanding such disorders. In this chapter, we present a schematic approach for collecting the information on CNV-miRNA interactions using miRWalk and TargetScan databases.
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Affiliation(s)
- Harsh Dweep
- Medical Faculty Mannheim, Medical Research Center, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, Mannheim, D-68167, Germany,
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26
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Pieri M, Stefanou C, Zaravinos A, Erguler K, Stylianou K, Lapathitis G, Karaiskos C, Savva I, Paraskeva R, Dweep H, Sticht C, Anastasiadou N, Zouvani I, Goumenos D, Felekkis K, Saleem M, Voskarides K, Gretz N, Deltas C. Evidence for activation of the unfolded protein response in collagen IV nephropathies. J Am Soc Nephrol 2013; 25:260-75. [PMID: 24262798 DOI: 10.1681/asn.2012121217] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Thin-basement-membrane nephropathy (TBMN) and Alport syndrome (AS) are progressive collagen IV nephropathies caused by mutations in COL4A3/A4/A5 genes. These nephropathies invariably present with microscopic hematuria and frequently progress to proteinuria and CKD or ESRD during long-term follow-up. Nonetheless, the exact molecular mechanisms by which these mutations exert their deleterious effects on the glomerulus remain elusive. We hypothesized that defective trafficking of the COL4A3 chain causes a strong intracellular effect on the cell responsible for COL4A3 expression, the podocyte. To this end, we overexpressed normal and mutant COL4A3 chains (G1334E mutation) in human undifferentiated podocytes and tested their effects in various intracellular pathways using a microarray approach. COL4A3 overexpression in the podocyte caused chain retention in the endoplasmic reticulum (ER) that was associated with activation of unfolded protein response (UPR)-related markers of ER stress. Notably, the overexpression of normal or mutant COL4A3 chains differentially activated the UPR pathway. Similar results were observed in a novel knockin mouse carrying the Col4a3-G1332E mutation, which produced a phenotype consistent with AS, and in biopsy specimens from patients with TBMN carrying a heterozygous COL4A3-G1334E mutation. These results suggest that ER stress arising from defective localization of collagen IV chains in human podocytes contributes to the pathogenesis of TBMN and AS through activation of the UPR, a finding that may pave the way for novel therapeutic interventions for a variety of collagenopathies.
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Affiliation(s)
- Myrtani Pieri
- Molecular Medicine Research Center, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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27
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Dweep H, Sticht C, Gretz N. In-Silico Algorithms for the Screening of Possible microRNA Binding Sites and Their Interactions. Curr Genomics 2013; 14:127-36. [PMID: 24082822 PMCID: PMC3637677 DOI: 10.2174/1389202911314020005] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) comprise a recently discovered class of small, non-coding RNA molecules of 21-25 nucleotides in length that regulate the gene expression by base-pairing with the transcripts of their targets i.e. protein-coding genes, leading to down-regulation or repression of the target genes. However, target gene activation has also been described. miRNAs are involved in diverse regulatory pathways, including control of developmental timing, apoptosis, cell proliferation, cell differentiation, modulation of immune response to macrophages, and organ development and are associated with many diseases, such as cancer. Computational prediction of miRNA targets is much more challenging in animals than in plants, because animal miRNAs often perform imperfect base-pairing with their target sites, unlike plant miRNAs which almost always bind their targets with near perfect complementarity. In the past years, a large number of target prediction programs and databases on experimentally validated information have been developed for animal miRNAs to fulfil the need of experimental scientists conducting miRNA research. In this review we first succinctly describe the prediction criteria (rules or principles) adapted by prediction algorithms to generate possible miRNA binding site interactions and introduce most relevant algorithms, and databases. We then summarize their applications with the help of some previously published studies. We further provide experimentally validated functional binding sites outside 3’-UTR region of target mRNAs and the resources which offer such predictions. Finally, the issue of experimental validation of miRNA binding sites will be briefly discussed.
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Affiliation(s)
- Harsh Dweep
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, D-68167 Mannheim, Germany
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28
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Legendre C, Cohen D, Delmas Y, Feldkamp T, Fouque D, Furman R, Gaber O, Greenbaum L, Goodship T, Haller H, Herthelius M, Hourmant M, Licht C, Moulin B, Sheerin N, Trivelli A, Bedrosian CL, Loirat C, Legendre C, Babu S, Cohen D, Delmas Y, Furman R, Gaber O, Greenbaum L, Hourmant M, Jungraithmayr T, Lebranchu Y, Riedl M, Sheerin N, Bedrosian CL, Loirat C, Sheerin N, Legendre C, Greenbaum L, Furman R, Cohen D, Gaber AO, Bedrosian C, Loirat C, Haller H, Licht C, Muus P, Legendre C, Douglas K, Hourmant M, Herthelius M, Trivelli A, Goodship T, Remuzzi G, Bedrosian C, Loirat C, Kourouklaris A, Ioannou K, Athanasiou I, Demetriou K, Panagidou A, Zavros M, Rodriguez C NY, Blasco M, Arcal C, Quintana LF, Rodriguez de Cordoba S, Campistol JM, Bachmann N, Eisenberger T, Decker C, Bolz HJ, Bergmann C, Pesce F, Cox SN, Serino G, De Palma G, Sallustio FP, Schena F, Falchi M, Pieri M, Stefanou C, Zaravinos A, Erguler K, Lapathitis G, Dweep H, Sticht C, Anastasiadou N, Zouvani I, Voskarides K, Gretz N, Deltas CC, Ruiz A, Bonny O, Sallustio F, Serino G, Curci C, Cox S, De Palma G, Schena F, Kemter E, Sklenak S, Aigner B, Wanke R, Kitzler TM, Moskowitz JL, Piret SE, Lhotta K, Tashman A, Velez E, Thakker RV, Kotanko P, Leierer J, Rudnicki M, Perco P, Koppelstaetter C, Mayer G, Sa MJN, Alves S, Storey H, Flinter F, Willems PJ, Carvalho F, Oliveira J, Arsali M, Papazachariou L, Demosthenous P, Lazarou A, Hadjigavriel M, Stavrou C, Yioukkas L, Voskarides K, Deltas C, Zavros M, Pierides A, Arsali M, Demosthenous P, Papazachariou L, Voskarides K, Kkolou M, Hadjigavriel M, Zavros M, Deltas C, Pierides A, Toka HR, Dibartolo S, Lanske B, Brown EM, Pollak MR, Familiari A, Zavan B, Sanna Cherchi S, Fabris A, Cristofaro R, Gambaro G, D'Angelo A, Anglani F, Toka H, Mount D, Pollak M, Curhan G, Sengoge G, Bajari T, Kupczok A, von Haeseler A, Schuster M, Pfaller W, Jennings P, Weltermann A, Blake S, Sunder-Plassmann G, Kerti A, Csohany R, Wagner L, Javorszky E, Maka E, Tulassay T, Tory K, Kingswood J, Nikolskaya N, Mbundi J, Kingswood J, Jozwiak S, Belousova E, Frost M, Kuperman R, Bebin M, Korf B, Flamini R, Kohrman M, Sparagana S, Wu J, Brechenmacher T, Stein K, Bissler J, Franz D, Kingswood J, Zonnenberg B, Frost M, Cheung W, Wang J, Brechenmacher T, Lam D, Bissler J, Budde K, Ivanitskiy L, Sowershaewa E, Krasnova T, Samokhodskaya L, Safarikova M, Jana R, Jitka S, Obeidova L, Kohoutova M, Tesar V, Evrengul H, Ertan P, Serdaroglu E, Yuksel S, Mir S, Yang n Ergon E, Berdeli A, Zawada A, Rogacev K, Rotter B, Winter P, Fliser D, Heine G, Bataille S, Moal V, Berland Y, Daniel L, Rosado C, Bueno E, Fraile P, Lucas C, Garcoa-Cosmes P, Tabernero JM, Gonzalez R, Rosado C, Bueno E, Fraile P, Lucas C, Garcia-Cosmes P, Tabernero JM, Gonzalez R, Silska-Dittmar M, Zaorska K, Malke A, Musielak A, Ostalska-Nowicka D, Zachwieja J, K d r V, Uz E, Yigit A, Altuntas A, Yigit B, Inal S, Uz E, Sezer M, Yilmaz R, Visciano B, Porto C, Acampora E, Russo R, Riccio E, Capuano I, Parenti G, Pisani A, Feriozzi S, Perrin A, West M, Nicholls K, Sunder-Plassmann G, Torras J, Cybulla M, Conti M, Angioi A, Floris M, Melis P, Asunis AM, Piras D, Pani A, Warnock D, Guasch A, Thomas C, Wanner C, Campbell R, Vujkovac B, Okur I, Biberoglu G, Ezgu F, Tumer L, Hasanoglu A, Bicik Z, Akin Y, Mumcuoglu M, Ecder T, Paliouras C, Mattas G, Papagiannis N, Ntetskas G, Lamprianou F, Karvouniaris N, Alivanis P. Genetic diseases and molecular genetics. Nephrol Dial Transplant 2013. [DOI: 10.1093/ndt/gft126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Papagregoriou G, Erguler K, Dweep H, Voskarides K, Koupepidou P, Athanasiou Y, Pierides A, Gretz N, Felekkis KN, Deltas C. A miR-1207-5p binding site polymorphism abolishes regulation of HBEGF and is associated with disease severity in CFHR5 nephropathy. PLoS One 2012; 7:e31021. [PMID: 22319602 PMCID: PMC3271095 DOI: 10.1371/journal.pone.0031021] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 12/31/2011] [Indexed: 01/08/2023] Open
Abstract
Heparin binding epidermal growth factor (HBEGF) is expressed in podocytes and was shown to play a role in glomerular physiology. MicroRNA binding sites on the 3′UTR of HBEGF were predicted using miRWalk algorithm and followed by DNA sequencing in 103 patients diagnosed with mild or severe glomerulopathy. A single nucleotide polymorphism, miRSNP C1936T (rs13385), was identified at the 3′UTR of HBEGF that corresponds to the second base of the hsa-miR-1207-5p seed region. When AB8/13 undifferentiated podocytes were transfected with miRNA mimics of hsa-miR-1207-5p, the HBEGF protein levels were reduced by about 50%. A DNA fragment containing the miRSNP allele-1936C was cloned into the pMIR-Report Luciferase vector and co-transfected with miRNA mimics of hsa-miR-1207-5p into AB8/13 podocytes. In agreement with western blot data, this resulted in reduced luciferase expression demonstrating the ability of hsa-miR-1207-5p to directly regulate HBEGF expression. On the contrary, in the presence of the miRSNP 1936T allele, this regulation was abolished. Collectively, these results demonstrate that variant 1936T of this miRSNP prevents hsa-miR-1207-5p from down-regulating HBEGF in podocytes. We hypothesized that this variant has a functional role as a genetic modifier. To this end, we showed that in a cohort of 78 patients diagnosed with CFHR5 nephropathy (also known as C3-glomerulopathy), inheritance of miRSNP 1936T allele was significantly increased in the group demonstrating progression to chronic renal failure on long follow-up. No similar association was detected in a cohort of patients with thin basement membrane nephropathy. This is the first report associating a miRSNP as genetic modifier to a monogenic renal disorder.
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Affiliation(s)
- Gregory Papagregoriou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Kamil Erguler
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Harsh Dweep
- Medical Research Center, University of Heidelberg, Mannheim, Germany
| | - Konstantinos Voskarides
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Panayiota Koupepidou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Alkis Pierides
- Department of Nephrology, Hippocrateon Hospital, Nicosia, Cyprus
| | - Norbert Gretz
- Medical Research Center, University of Heidelberg, Mannheim, Germany
| | - Kyriacos N. Felekkis
- Department of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
- * E-mail: (KNF); (CD)
| | - Constantinos Deltas
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- * E-mail: (KNF); (CD)
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Dweep H, Sticht C, Pandey P, Gretz N. miRWalk--database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform 2011; 44:839-47. [PMID: 21605702 DOI: 10.1016/j.jbi.2011.05.002] [Citation(s) in RCA: 1329] [Impact Index Per Article: 102.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 04/08/2011] [Accepted: 05/06/2011] [Indexed: 12/16/2022]
Abstract
MicroRNAs are small, non-coding RNA molecules that can complementarily bind to the mRNA 3'-UTR region to regulate the gene expression by transcriptional repression or induction of mRNA degradation. Increasing evidence suggests a new mechanism by which miRNAs may regulate target gene expression by binding in promoter and amino acid coding regions. Most of the existing databases on miRNAs are restricted to mRNA 3'-UTR region. To address this issue, we present miRWalk, a comprehensive database on miRNAs, which hosts predicted as well as validated miRNA binding sites, information on all known genes of human, mouse and rat. All mRNAs, mitochondrial genes and 10 kb upstream flanking regions of all known genes of human, mouse and rat were analyzed by using a newly developed algorithm named 'miRWalk' as well as with eight already established programs for putative miRNA binding sites. An automated and extensive text-mining search was performed on PubMed database to extract validated information on miRNAs. Combined information was put into a MySQL database. miRWalk presents predicted and validated information on miRNA-target interaction. Such a resource enables researchers to validate new targets of miRNA not only on 3'-UTR, but also on the other regions of all known genes. The 'Validated Target module' is updated every month and the 'Predicted Target module' is updated every 6 months. miRWalk is freely available at http://mirwalk.uni-hd.de/.
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Affiliation(s)
- Harsh Dweep
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, D-68167 Mannheim, Germany.
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Felekkis K, Voskarides K, Dweep H, Sticht C, Gretz N, Deltas C. Increased Number of MicroRNA Target Sites in Genes Encoded in CNV Regions. Evidence for an Evolutionary Genomic Interaction. Mol Biol Evol 2011; 28:2421-4. [DOI: 10.1093/molbev/msr078] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Durand C, Roeth R, Dweep H, Vlatkovic I, Decker E, Schneider KU, Rappold G. Alternative splicing and nonsense-mediated RNA decay contribute to the regulation of SHOX expression. PLoS One 2011; 6:e18115. [PMID: 21448463 PMCID: PMC3063249 DOI: 10.1371/journal.pone.0018115] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 02/24/2011] [Indexed: 11/18/2022] Open
Abstract
The human SHOX gene is composed of seven exons and encodes a paired-related homeodomain transcription factor. SHOX mutations or deletions have been associated with different short stature syndromes implying a role in growth and bone formation. During development, SHOX is expressed in a highly specific spatiotemporal expression pattern, the underlying regulatory mechanisms of which remain largely unknown. We have analysed SHOX expression in diverse embryonic, fetal and adult human tissues and detected expression in many tissues that were not known to express SHOX before, e.g. distinct brain regions. By using RT-PCR and comparing the results with RNA-Seq data, we have identified four novel exons (exon 2a, 7-1, 7-2 and 7-3) contributing to different SHOX isoforms, and also established an expression profile for the emerging new SHOX isoforms. Interestingly, we found the exon 7 variants to be exclusively expressed in fetal neural tissues, which could argue for a specific role of these variants during brain development. A bioinformatical analysis of the three novel 3′UTR exons yielded insights into the putative role of the different 3′UTRs as targets for miRNA binding. Functional analysis revealed that inclusion of exon 2a leads to nonsense-mediated RNA decay altering SHOX expression in a tissue and time specific manner. In conclusion, SHOX expression is regulated by different mechanisms and alternative splicing coupled with nonsense-mediated RNA decay constitutes a further component that can be used to fine tune the SHOX expression level.
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Affiliation(s)
- Claudia Durand
- Department of Human Molecular Genetics, University of Heidelberg, Heidelberg, Germany
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