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Massri AJ, Fitzpatrick M, Cunny H, Li JL, Harry GJ. Differential gene expression profiling implicates altered network development in rat postnatal day 4 cortex following 4-Methylimidazole (4-MeI) induced maternal seizures. Neurotoxicol Teratol 2023; 100:107301. [PMID: 37783441 PMCID: PMC10843020 DOI: 10.1016/j.ntt.2023.107301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Compromised maternal health leading to maternal seizures can have adverse effects on the healthy development of offspring. This may be the result of inflammation, hypoxia-ischemia, and altered GABA signaling. The current study examined cortical tissue from F2b (2nd litter of the 2nd generation) postnatal day 4 (PND4) offspring of female Harlan SD rats chronically exposed to the seizuregenic compound, 4-Methylimidazole (0, 750, or 2500 ppm 4-MeI). Maternal seizures were evident only at 2500 ppm 4-MeI. GABA related gene expression as examined by qRT-PCR and whole genome microarray showed no indication of disrupted GABA or glutamatergic signaling. Canonical pathway hierarchical clustering and multi-omics combinatory genomic (CNet) plots of differentially expressed genes (DEG) showed alterations in genes associated with regulatory processes of cell development including neuronal differentiation and synaptogenesis. Functional enrichment analysis showed a similarity of cellular processes across the two exposure groups however, the genes comprising each cluster were primarily unique rather than shared and often showed different directionality. A dose-related induction of cytokine signaling was indicated however, pathways associated with individual cytokine signaling were not elevated, suggesting an alternative involvement of cytokine signaling. Pathways related to growth process and cell signaling showed a negative activation supporting an interpretation of disruption or delay in developmental processes at the 2500 ppm 4-MeI exposure level with maternal seizures. Thus, while GABA signaling was not altered as has been observed with maternal seizures, the pattern of DEG suggested a potential for alteration in neuronal network formation.
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Affiliation(s)
- Abdull J Massri
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mackenzie Fitzpatrick
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Helen Cunny
- Office of the Scientific Director, Division of Translational Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - G Jean Harry
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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2
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Challa NVD, Chen S, Yuan H, Duncan MR, Moreno WJ, Bramlett H, Dietrich WD, Benny M, Schmidt AF, Young K, Wu S. GSDMD gene knockout alleviates hyperoxia-induced hippocampal brain injury in neonatal mice. J Neuroinflammation 2023; 20:205. [PMID: 37679766 PMCID: PMC10486051 DOI: 10.1186/s12974-023-02878-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/19/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Neonatal hyperoxia exposure is associated with brain injury and poor neurodevelopment outcomes in preterm infants. Our previous studies in neonatal rodent models have shown that hyperoxia stimulates the brain's inflammasome pathway, leading to the activation of gasdermin D (GSDMD), a key executor of pyroptotic inflammatory cell death. Moreover, we found pharmacological inhibition of caspase-1, which blocks GSDMD activation, attenuates hyperoxia-induced brain injury in neonatal mice. We hypothesized that GSDMD plays a pathogenic role in hyperoxia-induced neonatal brain injury and that GSDMD gene knockout (KO) will alleviate hyperoxia-induced brain injury. METHODS Newborn GSDMD knockout mice and their wildtype (WT) littermates were randomized within 24 h after birth to be exposed to room air or hyperoxia (85% O2) from postnatal days 1 to 14. Hippocampal brain inflammatory injury was assessed in brain sections by immunohistology for allograft inflammatory factor 1 (AIF1) and CD68, markers of microglial activation. Cell proliferation was evaluated by Ki-67 staining, and cell death was determined by TUNEL assay. RNA sequencing of the hippocampus was performed to identify the transcriptional effects of hyperoxia and GSDMD-KO, and qRT-PCR was performed to confirm some of the significantly regulated genes. RESULTS Hyperoxia-exposed WT mice had increased microglia consistent with activation, which was associated with decreased cell proliferation and increased cell death in the hippocampal area. Conversely, hyperoxia-exposed GSDMD-KO mice exhibited considerable resistance to hyperoxia as O2 exposure did not increase AIF1 + , CD68 + , or TUNEL + cell numbers or decrease cell proliferation. Hyperoxia exposure differentially regulated 258 genes in WT and only 16 in GSDMD-KO mice compared to room air-exposed WT and GSDMD-KO, respectively. Gene set enrichment analysis showed that in the WT brain, hyperoxia differentially regulated genes associated with neuronal and vascular development and differentiation, axonogenesis, glial cell differentiation, hypoxia-induced factor 1 pathway, and neuronal growth factor pathways. These changes were prevented by GSDMD-KO. CONCLUSIONS GSDMD-KO alleviates hyperoxia-induced inflammatory injury, cell survival and death, and alterations of transcriptional gene expression of pathways involved in neuronal growth, development, and differentiation in the hippocampus of neonatal mice. This suggests that GSDMD plays a pathogenic role in preterm brain injury, and targeting GSDMD may be beneficial in preventing and treating brain injury and poor neurodevelopmental outcomes in preterm infants.
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Affiliation(s)
- Naga Venkata Divya Challa
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shaoyi Chen
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Huijun Yuan
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Matthew R Duncan
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - William Javier Moreno
- Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Helen Bramlett
- Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - W Dalton Dietrich
- Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Merline Benny
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Augusto F Schmidt
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Karen Young
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shu Wu
- Department of Pediatrics/Division of Neonatology, Batchelor Children's Research Institute, Holtz Children's Hospital, University of Miami Miller School of Medicine, Miami, FL, USA.
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3
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Challa NVD, Chen S, Yun H, Duncan MR, Moreno WJ, Bramlett H, Dietrich WD, Benny M, Schmidt AF, Young K, Wu S. GSDMD gene knockout alleviates hyperoxia-induced hippocampal brain injury in neonatal mice. RESEARCH SQUARE 2023:rs.3.rs-3055085. [PMID: 37398125 PMCID: PMC10312931 DOI: 10.21203/rs.3.rs-3055085/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background: Neonatal hyperoxia exposure is associated with brain injury and poor neurodevelopment outcomes in preterm infants. Our previous studies in neonatal rodent models have shown that hyperoxia stimulates the brain's inflammasome pathway, leading to the activation of gasdermin D (GSDMD), a key executor of pyroptotic inflammatory cell death. Moreover, we found inhibition of GSDMD activation attenuates hyperoxia-induced brain injury in neonatal mice. We hypothesized that GSDMD plays a pathogenic role in hyperoxia-induced neonatal brain injury and that GSDMD gene knockout (KO) will alleviate hyperoxia-induced brain injury. Methods: Newborn GSDMD knockout mice and their wildtype (WT) littermates were randomized within 24 h after birth to be exposed to room air or hyperoxia (85% O2) from postnatal day 1 to 14. Hippocampal brain inflammatory injury was assessed in brain sections by immunohistology for allograft inflammatory factor 1 (AIF1), a marker of microglial activation. Cell proliferation was evaluated by Ki-67 staining, and cell death was determined by TUNEL assay. RNA sequencing of the hippocampus was performed to identify the transcriptional effects of hyperoxia and GSDMD-KO, and qRT-PCR was performed to confirm some of the significantly regulated genes. Results: Hyperoxia-exposed WT mice had increased microglia consistent with activation, which was associated with decreased cell proliferation and increased cell death in the hippocampal area. Conversely, hyperoxia-exposed GSDMD-KO mice exhibited considerable resistance to hyperoxia as O2 exposure failed to increase either AIF1+ or TUNEL+ cell numbers, nor decrease cell proliferation. Hyperoxia exposure differentially regulated 258 genes in WT and only 16 in GSDMD-KO mice compared to room air- exposed WT and GSDMD-KO, respectively. Gene set enrichment analysis showed that in the WT brain, hyperoxia differentially regulated genes associated with neuronal and vascular development and differentiation, axonogenesis, glial cell differentiation, and core development pathways hypoxia-induced factor 1, and neuronal growth factor pathways. These changes were prevented by GSDMD-KO. Conclusion: GSDMD-KO alleviates hyperoxia-induced inflammatory injury, cell survival and death, and alterations of transcriptional gene expression of pathways involved in neuronal growth, development, and differentiation in the hippocampus of neonatal mice. This suggests that GSDMD plays a pathogenic role in preterm brain injury, and targeting GSDMD may be beneficial in preventing and treating brain injury and poor neurodevelopmental outcomes in preterm infants.
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Affiliation(s)
- Naga Venkata Divya Challa
- Department of Pediatrics/Division of Neonatology, Batchelor Children’s Research Institute and Holtz Children’s Hospital, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Shaoyi Chen
- Department of Pediatrics/Division of Neonatology, Batchelor Children’s Research Institute and Holtz Children’s Hospital, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Huijun Yun
- Department of Pediatrics/Division of Neonatology, Batchelor Children’s Research Institute and Holtz Children’s Hospital, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Matthew R Duncan
- Department of Pediatrics/Division of Neonatology, Batchelor Children’s Research Institute and Holtz Children’s Hospital, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Williams Javier Moreno
- Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Helen Bramlett
- Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - W Dalton Dietrich
- Miami Project to Cure Paralysis and Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Merline Benny
- Department of Pediatrics/Division of Neonatology, Batchelor Children’s Research Institute and Holtz Children’s Hospital, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Augusto F Schmidt
- Department of Pediatrics/Division of Neonatology, Batchelor Children’s Research Institute and Holtz Children’s Hospital, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Karen Young
- Department of Pediatrics/Division of Neonatology, Batchelor Children’s Research Institute and Holtz Children’s Hospital, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Shu Wu
- Department of Pediatrics/Division of Neonatology, Batchelor Children’s Research Institute and Holtz Children’s Hospital, University of Miami Miller School of Medicine, Miami, FL, United States
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4
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Yin Y, Xin Y, Zhang F, An D, Fan H, Qin M, Xia J, Xi T, Xiong J. Overcoming ABCB1-mediated multidrug resistance by transcription factor BHLHE40. Neoplasia 2023; 39:100891. [PMID: 36931039 PMCID: PMC10025992 DOI: 10.1016/j.neo.2023.100891] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 03/17/2023]
Abstract
Multidrug resistance (MDR) hinders treatment efficacy in cancer therapy. One typical mechanism contributing to MDR is the overexpression of permeability-glycoprotein (P-gp) encoded by ATP-binding cassette subfamily B member 1 (ABCB1). Basic helix-loop-helix family member e40 (BHLHE40) is a well-known transcription factor that has pleiotropic effects including the regulation of cancer-related processes. However, whether BHLHE40 regulates MDR is still unknown. Chromatin immunoprecipitation-seq study revealed BHLHE40 occupancy in the promoter of ABCB1 gene. Adriamycin (ADM)-resistant human chronic myeloid leukemia cells (K562/A) and human breast cancer cells (MCF-7/A) were established. BHLHE40 expression was downregulated in the ADM-resistant cell lines. Overexpression of BHLHE40 resensitized resistant cells to ADM, promoted cell apoptosis in vitro and suppressed tumor growth in vivo, whereas BHLHE40 knockdown induced resistance to ADM in parental cells. Moreover, we found that BHLHE40 regulated drug resistance by directly binding to the ABCB1 promoter (-1605 to -1597) and inactivating its transcription. In consistence, the expression of BHLHE40 was negatively correlated with ABCB1 in various cancer cells, while positively with cancer cell chemosensitivity and better prognosis of patients with breast cancer. The study reveals the role of BHLHE40 as a transcriptional suppressor on the expression of ABCB1, major ABC transporter in chemoresistance. The findings extend the function of BHLHE40 in tumor progression and provides a novel mechanism for the reversal of multidrug resistance.
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Affiliation(s)
- Yongmei Yin
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China; Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yu Xin
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China
| | - Feng Zhang
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China
| | - Donghao An
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China
| | - Hui Fan
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China
| | - Mengyao Qin
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China
| | - Jinxin Xia
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China
| | - Tao Xi
- Research Center of Biotechnology, School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China
| | - Jing Xiong
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China.
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5
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Perone I, Ghena N, Wang J, Mackey C, Wan R, Malla S, Gorospe M, Cheng A, Mattson MP. Mitochondrial SIRT3 Deficiency Results in Neuronal Network Hyperexcitability, Accelerates Age-Related Aβ Pathology, and Renders Neurons Vulnerable to Aβ Toxicity. Neuromolecular Med 2023; 25:27-39. [PMID: 35749057 PMCID: PMC9810471 DOI: 10.1007/s12017-022-08713-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 01/05/2023]
Abstract
Aging is the major risk factor for Alzheimer's disease (AD). Mitochondrial dysfunction and neuronal network hyperexcitability are two age-related alterations implicated in AD pathogenesis. We found that levels of the mitochondrial protein deacetylase sirtuin-3 (SIRT3) are significantly reduced, and consequently mitochondria protein acetylation is increased in brain cells during aging. SIRT3-deficient mice exhibit robust mitochondrial protein hyperacetylation and reduced mitochondrial mass during aging. Moreover, SIRT3-deficient mice exhibit epileptiform and burst-firing electroencephalogram activity indicating neuronal network hyperexcitability. Both aging and SIRT3 deficiency result in increased sensitivity to kainic acid-induced seizures. Exposure of cultured cerebral cortical neurons to amyloid β-peptide (Aβ) results in a reduction in SIRT3 levels and SIRT3-deficient neurons exhibit heightened sensitivity to Aβ toxicity. Finally, SIRT3 haploinsufficiency in middle-aged App/Ps1 double mutant transgenic mice results in a significant increase in Aβ load compared with App/Ps1 double mutant mice with normal SIRT3 levels. Collectively, our findings suggest that SIRT3 plays an important role in protecting neurons against Aβ pathology and excitotoxicity.
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Affiliation(s)
- Isabella Perone
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA
| | - Nathaniel Ghena
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA
| | - Jing Wang
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA
- Department of Integrative Medicine and Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chelsea Mackey
- Department of Integrative Medicine and Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
- Laboratory of Cardiovascular Science, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA
| | - Ruiqian Wan
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA
| | - Sulochan Malla
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA
| | - Aiwu Cheng
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA.
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA.
| | - Mark P Mattson
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, Baltimore, MD, 21224, USA.
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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6
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Sui Y, Jiang H, Kellogg CM, Oh S, Janknecht R. Promotion of colorectal cancer by transcription factor BHLHE40 involves upregulation of ADAM19 and KLF7. Front Oncol 2023; 13:1122238. [PMID: 36890812 PMCID: PMC9986587 DOI: 10.3389/fonc.2023.1122238] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
BHLHE40 is a transcription factor, whose role in colorectal cancer has remained elusive. We demonstrate that the BHLHE40 gene is upregulated in colorectal tumors. Transcription of BHLHE40 was jointly stimulated by the DNA-binding ETV1 protein and two associated histone demethylases, JMJD1A/KDM3A and JMJD2A/KDM4A, which were shown to also form complexes on their own and whose enzymatic activity was required for BHLHE40 upregulation. Chromatin immunoprecipitation assays revealed that ETV1, JMJD1A and JMJD2A interacted with several regions within the BHLHE40 gene promoter, suggesting that these three factors directly control BHLHE40 transcription. BHLHE40 downregulation suppressed both growth and clonogenic activity of human HCT116 colorectal cancer cells, strongly hinting at a pro-tumorigenic role of BHLHE40. Through RNA sequencing, the transcription factor KLF7 and the metalloproteinase ADAM19 were identified as putative BHLHE40 downstream effectors. Bioinformatic analyses showed that both KLF7 and ADAM19 are upregulated in colorectal tumors as well as associated with worse survival and their downregulation impaired HCT116 clonogenic activity. In addition, ADAM19, but not KLF7, downregulation reduced HCT116 cell growth. Overall, these data have revealed a ETV1/JMJD1A/JMJD2A→BHLHE40 axis that may stimulate colorectal tumorigenesis through upregulation of genes such as KLF7 and ADAM19, suggesting that targeting this axis represents a potential novel therapeutic avenue.
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Affiliation(s)
- Yuan Sui
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Hanlin Jiang
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Collyn M Kellogg
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Stephenson Cancer Center, Oklahoma City, OK, United States
| | - Ralf Janknecht
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Stephenson Cancer Center, Oklahoma City, OK, United States
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7
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Huseby CJ, Delvaux E, Brokaw DL, Coleman PD. Blood RNA transcripts reveal similar and differential alterations in fundamental cellular processes in Alzheimer's disease and other neurodegenerative diseases. Alzheimers Dement 2022. [DOI: 10.1002/alz.12880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Carol J. Huseby
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
| | - Elaine Delvaux
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
| | - Danielle L. Brokaw
- University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
| | - Paul D. Coleman
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
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8
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Papale LA, Madrid A, Zhang Q, Chen K, Sak L, Keleş S, Alisch RS. Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders. Genome Res 2022; 32:266-279. [PMID: 34949667 PMCID: PMC8805724 DOI: 10.1101/gr.276137.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/22/2021] [Indexed: 11/25/2022]
Abstract
Mouse knockouts of Cntnap2 show altered neurodevelopmental behavior, deficits in striatal GABAergic signaling, and a genome-wide disruption of an environmentally sensitive DNA methylation modification (5-hydroxymethylcytosine [5hmC]) in the orthologs of a significant number of genes implicated in human neurodevelopmental disorders. We tested adult Cntnap2 heterozygous mice (Cntnap2 +/-; lacking behavioral or neuropathological abnormalities) subjected to a prenatal stress and found that prenatally stressed Cntnap2 +/- female mice show repetitive behaviors and altered sociability, similar to the homozygote phenotype. Genomic profiling revealed disruptions in hippocampal and striatal 5hmC levels that are correlated to altered transcript levels of genes linked to these phenotypes (e.g., Reln, Dst, Trio, and Epha5). Chromatin immunoprecipitation coupled with high-throughput sequencing and hippocampal nuclear lysate pull-down data indicated that 5hmC abundance alters the binding of the transcription factor CLOCK near the promoters of these genes (e.g., Palld, Gigyf1, and Fry), providing a mechanistic role for 5hmC in gene regulation. Together, these data support gene-by-environment hypotheses for the origins of mental illness and provide a means to identify the elusive factors contributing to complex human diseases.
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Affiliation(s)
- Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
- Neuroscience Training Program, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Qi Zhang
- Department Mathematics and Statistics, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Kailei Chen
- Department of Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Lara Sak
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Sündüz Keleş
- Department of Statistics, Biostatistics, and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53719, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, Wisconsin 53719, USA
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9
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Ribeiro MM, Okawa S, Del Sol A. TransSynW: A single-cell RNA-sequencing based web application to guide cell conversion experiments. Stem Cells Transl Med 2020; 10:230-238. [PMID: 33125830 PMCID: PMC7848352 DOI: 10.1002/sctm.20-0227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/03/2020] [Accepted: 08/16/2020] [Indexed: 12/16/2022] Open
Abstract
Generation of desired cell types by cell conversion remains a challenge. In particular, derivation of novel cell subtypes identified by single‐cell technologies will open up new strategies for cell therapies. The recent increase in the generation of single‐cell RNA‐sequencing (scRNA‐seq) data and the concomitant increase in the interest expressed by researchers in generating a wide range of functional cells prompted us to develop a computational tool for tackling this challenge. Here we introduce a web application, TransSynW, which uses scRNA‐seq data for predicting cell conversion transcription factors (TFs) for user‐specified cell populations. TransSynW prioritizes pioneer factors among predicted conversion TFs to facilitate chromatin opening often required for cell conversion. In addition, it predicts marker genes for assessing the performance of cell conversion experiments. Furthermore, TransSynW does not require users' knowledge of computer programming and computational resources. We applied TransSynW to different levels of cell conversion specificity, which recapitulated known conversion TFs at each level. We foresee that TransSynW will be a valuable tool for guiding experimentalists to design novel protocols for cell conversion in stem cell research and regenerative medicine.
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Affiliation(s)
- Mariana Messias Ribeiro
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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10
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Hentrich T, Wassouf Z, Riess O, Schulze-Hentrich JM. SNCA overexpression disturbs hippocampal gene expression trajectories in midlife. Aging (Albany NY) 2019; 10:4024-4041. [PMID: 30543522 PMCID: PMC6326667 DOI: 10.18632/aging.101691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
Synucleinopathies like Parkinson's disease and dementia with Lewy bodies originate from a complex and still largely enigmatic interplay of genetic predisposition, age, and environmental factors. While progressively declining motor functions hallmark late-life symptoms, first signs of the disease often surface already decades earlier during midlife. To better understand early disease stages with respect to the genetic, temporal, and environmental dimension, we interrogated hippocampal transcriptome data obtained during midlife for a mouse model overexpressing human SNCA, a pivotal gene in synucleinopathies, under different environments. To relate differentially expressed genes to human, we integrated expression signatures for aging and Parkinson's disease. We identified two distinctive modes of age-dependent disturbances: First, cellular processes seemingly activated too early that reflected advanced stages of age and, second, typical longitudinal adaptations of the system that no longer occurred during midlife. Environmental enrichment prevented both disturbances modes despite persistent SNCA overload. Together, our results caution the view that expression changes characterising early stages of SNCA-related pathology reflect accelerated aging alone. Instead, we provide evidence that failure to undergo healthy adaptions during midlife represents a second origin of disturbances. This bimodal disturbance principle could inform therapeutic efforts to distinguish between preventive and restorative attempts to target the disease.
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Affiliation(s)
- Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Zinah Wassouf
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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SIRT3 Haploinsufficiency Aggravates Loss of GABAergic Interneurons and Neuronal Network Hyperexcitability in an Alzheimer's Disease Model. J Neurosci 2019; 40:694-709. [PMID: 31818974 DOI: 10.1523/jneurosci.1446-19.2019] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/26/2019] [Accepted: 11/05/2019] [Indexed: 01/17/2023] Open
Abstract
Impaired mitochondrial function and aberrant neuronal network activity are believed to be early events in the pathogenesis of Alzheimer's disease (AD), but how mitochondrial alterations contribute to aberrant activity in neuronal circuits is unknown. In this study, we examined the function of mitochondrial protein deacetylase sirtuin 3 (SIRT3) in the pathogenesis of AD. Compared with AppPs1 mice, Sirt3-haploinsufficient AppPs1 mice (Sirt3+/-AppPs1) exhibit early epileptiform EEG activity and seizure. Both male and female Sirt3+/-AppPs1 mice were observed to die prematurely before 5 months of age. When comparing male mice among different genotypes, Sirt3 haploinsufficiency renders GABAergic interneurons in the cerebral cortex vulnerable to degeneration and associated neuronal network hyperexcitability. Feeding Sirt3+/-AppPs1 AD mice with a ketone ester-rich diet increases SIRT3 expression and prevents seizure-related death and the degeneration of GABAergic neurons, indicating that the aggravated GABAergic neuron loss and neuronal network hyperexcitability in Sirt3+/-AppPs1 mice are caused by SIRT3 reduction and can be rescued by increase of SIRT3 expression. Consistent with a protective role in AD, SIRT3 levels are reduced in association with cerebral cortical Aβ pathology in AD patients. In summary, SIRT3 preserves GABAergic interneurons and protects cerebral circuits against hyperexcitability, and this neuroprotective mechanism can be bolstered by dietary ketone esters.SIGNIFICANCE STATEMENT GABAergic neurons provide the main inhibitory control of neuronal activity in the brain. By preserving mitochondrial function, SIRT3 protects parvalbumin and calretinin interneurons against Aβ-associated dysfunction and degeneration in AppPs1 Alzheimer's disease mice, thus restraining neuronal network hyperactivity. The neuronal network dysfunction that occurs in Alzheimer's disease can be partially reversed by physiological, dietary, and pharmacological interventions to increase SIRT3 expression and enhance the functionality of GABAergic interneurons.
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Taguchi YH, Turki T. Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis. Front Genet 2019; 10:864. [PMID: 31608111 PMCID: PMC6761323 DOI: 10.3389/fgene.2019.00864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/19/2019] [Indexed: 12/14/2022] Open
Abstract
Although single-cell RNA sequencing (scRNA-seq) technology is newly invented and a promising one, but because of lack of enough information that labels individual cells, it is hard to interpret the obtained gene expression of each cell. Because of insufficient information available, unsupervised clustering, for example, t-distributed stochastic neighbor embedding and uniform manifold approximation and projection, is usually employed to obtain low-dimensional embedding that can help to understand cell–cell relationship. One possible drawback of this strategy is that the outcome is highly dependent upon genes selected for the usage of clustering. In order to fulfill this requirement, there are many methods that performed unsupervised gene selection. In this study, a tensor decomposition (TD)-based unsupervised feature extraction (FE) was applied to the integration of two scRNA-seq expression profiles that measure human and mouse midbrain development. TD-based unsupervised FE could select not only coincident genes between human and mouse but also biologically reliable genes. Coincidence between two species as well as biological reliability of selected genes is increased compared with that using principal component analysis (PCA)-based FE applied to the same data set in the previous study. Since PCA-based unsupervised FE outperformed the other three popular unsupervised gene selection methods, highly variable genes, bimodal genes, and dpFeature, TD-based unsupervised FE can do so as well. In addition to this, 10 transcription factors (TFs) that might regulate selected genes and might contribute to midbrain development were identified. These 10 TFs, BHLHE40, EGR1, GABPA, IRF3, PPARG, REST, RFX5, STAT3, TCF7L2, and ZBTB33, were previously reported to be related to brain functions and diseases. TD-based unsupervised FE is a promising method to integrate two scRNA-seq profiles effectively.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, Tokyo, Japan
| | - Turki Turki
- Department of Computer Science, King Abdulaziz University, Jeddah, Saudi Arabia
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DeltaNp63-dependent super enhancers define molecular identity in pancreatic cancer by an interconnected transcription factor network. Proc Natl Acad Sci U S A 2018; 115:E12343-E12352. [PMID: 30541891 DOI: 10.1073/pnas.1812915116] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Molecular subtyping of cancer offers tremendous promise for the optimization of a precision oncology approach to anticancer therapy. Recent advances in pancreatic cancer research uncovered various molecular subtypes with tumors expressing a squamous/basal-like gene expression signature displaying a worse prognosis. Through unbiased epigenome mapping, we identified deltaNp63 as a major driver of a gene signature in pancreatic cancer cell lines, which we report to faithfully represent the highly aggressive pancreatic squamous subtype observed in vivo, and display the specific epigenetic marking of genes associated with decreased survival. Importantly, depletion of deltaNp63 in these systems significantly decreased cell proliferation and gene expression patterns associated with a squamous subtype and transcriptionally mimicked a subtype switch. Using genomic localization data of deltaNp63 in pancreatic cancer cell lines coupled with epigenome mapping data from patient-derived xenografts, we uncovered that deltaNp63 mainly exerts its effects by activating subtype-specific super enhancers. Furthermore, we identified a group of 45 subtype-specific super enhancers that are associated with poorer prognosis and are highly dependent on deltaNp63. Genes associated with these enhancers included a network of transcription factors, including HIF1A, BHLHE40, and RXRA, which form a highly intertwined transcriptional regulatory network with deltaNp63 to further activate downstream genes associated with poor survival.
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