99951
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Richard D, Muthuirulan P, Aguiar J, Doxey AC, Banerjee A, Mossman K, Hirota J, Capellini TD. Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways. iScience 2022; 25:104614. [PMID: 35756893 PMCID: PMC9213013 DOI: 10.1016/j.isci.2022.104614] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/30/2021] [Revised: 03/19/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022] Open
Abstract
The angiotensin-converting enzyme 2 (ACE2) protein is a key catalytic regulator of the renin-angiotensin system (RAS), involved in fluid homeostasis and blood pressure modulation. ACE2 also serves as a cell-surface receptor for some coronaviruses such as SARS-CoV and SARS-CoV-2. Improved characterization of ACE2 regulation may help us understand the effects of pre-existing conditions on COVID-19 incidence, as well as pathogenic dysregulation following viral infection. Here, we perform bioinformatic analyses to hypothesize on ACE2 gene regulation in two different physiological contexts, identifying putative regulatory elements of ACE2 expression. We perform functional validation of our computational predictions via targeted CRISPR-Cas9 deletions of these elements in vitro, finding them responsive to immune signaling and oxidative-stress pathways. This contributes to our understanding of ACE2 gene regulation at baseline and immune challenge. Our work supports pursuit of these putative mechanisms in our understanding of infection/disease caused by current, and future, SARS-related viruses such as SARS-CoV-2. Lung expression patterns suggest ACE2 regulation by immune and oxidative signaling CRISPR deletion of intronic regulatory elements (REs) alters ACE2 expression Effects of RE deletion are modified by immune stimulation and oxidative stress Propose two mechanisms for regulating ACE2 at baseline and after immune challenge
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Affiliation(s)
- Daniel Richard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138 USA
| | | | - Jennifer Aguiar
- Department of Biology, University of Waterloo, Waterloo, ON, N2L3G1 Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, N2L3G1 Canada
| | - Arinjay Banerjee
- Department of Biology, University of Waterloo, Waterloo, ON, N2L3G1 Canada.,Vaccine and Infectious Disease Organization, University of Saskatchewan; Saskatoon, SK, S7N 5E3 Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan; Saskatoon, SK, S7N5B4 Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, ON, L8N 3Z5 Canada
| | - Jeremy Hirota
- Department of Biology, University of Waterloo, Waterloo, ON, N2L3G1 Canada.,Department of Medicine, McMaster University, Hamilton, ON, L8N 3Z5 Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, V5Z 1M9 Canada
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138 USA.,Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA
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99952
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Wang K, Peng X, Yang A, Huang Y, Tan Y, Qian Y, Lv F, Si H. Effects of Diets With Different Protein Levels on Lipid Metabolism and Gut Microbes in the Host of Different Genders. Front Nutr 2022; 9:940217. [PMID: 35782952 PMCID: PMC9240812 DOI: 10.3389/fnut.2022.940217] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/30/2022] [Indexed: 12/21/2022] Open
Abstract
The purpose of this experiment was to investigate the effects of different protein levels on lipid metabolism and gut microbes in mice of different genders. A total of 60 mice (30 female and 30 male) were randomly assigned to six groups and fed female mice with low protein diet (FLP), basal protein diet (FBD), and high protein diet (FHP). Similarly, the male mice fed with low protein diet (MLP), basal protein diet (MBD), and high protein diet (MHP). The low protein diet contained 14% CP, the basal diet contained 20% CP, and the high protein diet contained 26% CP. The results of the study showed that both basal and high protein diets significantly reduced the perirenal adipose tissues (PEAT) index in male mice compared to low protein diet (p < 0.05). For the gut, the FHP significantly increased the relative gut weight compared to the FBD and FLP (p < 0.05). At the same time, the FHP also significantly increased the relative gut length compared with the FBD and FLP (p < 0.05). The MHP significantly increased TC concentration compared with the MLP (p < 0.05), and the MBD tended to increase TC concentration compared with the MLP in serum (p = 0.084). The histomorphology result of the jejunum and ileum showed that a low protein diet was beneficial to the digestion and absorption of nutrients in the small intestine of mice. While different protein levels had no effect on the total number of fecal microbial species in mice, different protein levels had a significant effect on certain fecal microbes in mice, the absolute abundance of Verrucomicrobia in the feces of male mice was significantly higher in both high and basal protein diets than in the low protein diet (p < 0.05). The high protein diet significantly reduced the absolute abundance of Patescibacteria in the feces of female mice compared to both the basal and low protein diets (p < 0.05). The absolute abundance of Patescibacteria in male feces was not affected by dietary protein levels (p > 0.05). Taken together, our results suggest that a low protein diet can alter fat deposition and lipid metabolism in mice, and that it benefited small intestinal epithelial structure and microbes.
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Affiliation(s)
- Kaijun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaomin Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Anqi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yiqin Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yuxiao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yajing Qian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Feifei Lv
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hongbin Si
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
- *Correspondence: Hongbin Si,
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99953
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Yang L, Sun J, Chen Z, Liu L, Sun Y, Lin J, Hu X, Zhao M, Ma Y, Lu D, Li Y, Guo Y, Dong E. The LMNA p.R541C mutation causes dilated cardiomyopathy in human and mice. Int J Cardiol 2022; 363:149-158. [PMID: 35714719 DOI: 10.1016/j.ijcard.2022.06.038] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/25/2022]
Abstract
Dilated cardiomyopathy (DCM) is a major cause of heart failure. LMNA variants contribute to 6-10% DCM cases, but the underlying mechanisms remain incompletely understood. Here, we reported two patients carrying the LMNA c.1621C > T/ p.R541C variant and generated a knock-in mouse model (LmnaRC) to study the role of this variant in DCM pathogenesis. We found LmnaRC/RC mice exhibited ventricular dilation and reduced systolic functions at 6 months after birth. The LmnaRC/RC cardiomyocytes increased in size but no nuclear morphology defects were detected. Transcriptomic and microscopic analyses revealed suppressed gene expression and perturbed ultrastructure in LmnaRC/RC mitochondria. These defects were associated with increased heterochromatin structures and epigenetic markers including H3K9me2/3. Together, these data implied that the LMNA c.1621C > T/ p.R541C variant enhanced heterochromatic gene suppression and disrupted mitochondria functions as a cause of DCM.
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Affiliation(s)
- Luzi Yang
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China
| | - Jinhuan Sun
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China
| | - Zhan Chen
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China
| | - Lei Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education (MOE), Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yueshen Sun
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Junsen Lin
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China
| | - Xiaomin Hu
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Mingming Zhao
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; The Institute of Cardiovascular Sciences, Peking University; National Health Commission of China (NHC) Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Key Laboratory of Molecular Cardiovascular Science of Ministry of Education; Beijing Key Laboratory of Cardiovascular Receptors Research. Beijing 100191, China
| | - Yuanwu Ma
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC) and Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Dan Lu
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC) and Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education (MOE), Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Yuxuan Guo
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China.
| | - Erdan Dong
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; The Institute of Cardiovascular Sciences, Peking University; National Health Commission of China (NHC) Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Key Laboratory of Molecular Cardiovascular Science of Ministry of Education; Beijing Key Laboratory of Cardiovascular Receptors Research. Beijing 100191, China
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99954
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Sharma R, Kannourakis G, Prithviraj P, Ahmed N. Precision Medicine: An Optimal Approach to Patient Care in Renal Cell Carcinoma. Front Med (Lausanne) 2022; 9:766869. [PMID: 35775004 PMCID: PMC9237320 DOI: 10.3389/fmed.2022.766869] [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: 08/30/2021] [Accepted: 04/11/2022] [Indexed: 12/24/2022] Open
Abstract
Renal cell cancer (RCC) is a heterogeneous tumor that shows both intra- and inter-heterogeneity. Heterogeneity is displayed not only in different patients but also among RCC cells in the same tumor, which makes treatment difficult because of varying degrees of responses generated in RCC heterogeneous tumor cells even with targeted treatment. In that context, precision medicine (PM), in terms of individualized treatment catered for a specific patient or groups of patients, can shift the paradigm of treatment in the clinical management of RCC. Recent progress in the biochemical, molecular, and histological characteristics of RCC has thrown light on many deregulated pathways involved in the pathogenesis of RCC. As PM-based therapies are rapidly evolving and few are already in current clinical practice in oncology, one can expect that PM will expand its way toward the robust treatment of patients with RCC. This article provides a comprehensive background on recent strategies and breakthroughs of PM in oncology and provides an overview of the potential applicability of PM in RCC. The article also highlights the drawbacks of PM and provides a holistic approach that goes beyond the involvement of clinicians and encompasses appropriate legislative and administrative care imparted by the healthcare system and insurance providers. It is anticipated that combined efforts from all sectors involved will make PM accessible to RCC and other patients with cancer, making a tremendous positive leap on individualized treatment strategies. This will subsequently enhance the quality of life of patients.
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Affiliation(s)
- Revati Sharma
- Fiona Elsey Cancer Research Institute, Ballarat Central Technology Central Park, Ballarat Central, VIC, Australia
- School of Science, Psychology and Sport, Federation University, Mt Helen, VIC, Australia
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Ballarat Central Technology Central Park, Ballarat Central, VIC, Australia
- School of Science, Psychology and Sport, Federation University, Mt Helen, VIC, Australia
| | - Prashanth Prithviraj
- Fiona Elsey Cancer Research Institute, Ballarat Central Technology Central Park, Ballarat Central, VIC, Australia
- School of Science, Psychology and Sport, Federation University, Mt Helen, VIC, Australia
| | - Nuzhat Ahmed
- Fiona Elsey Cancer Research Institute, Ballarat Central Technology Central Park, Ballarat Central, VIC, Australia
- School of Science, Psychology and Sport, Federation University, Mt Helen, VIC, Australia
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Clayton, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia
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99955
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Koh L, Novera W, Lim SW, Chong YK, Pang QY, Low D, Ang BT, Tang C. Integrative multi-omics approach to targeted therapy for glioblastoma. Pharmacol Res 2022; 182:106308. [PMID: 35714825 DOI: 10.1016/j.phrs.2022.106308] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
This review describes recent technological advances applied to glioblastoma (GBM), a brain tumor with dismal prognosis. International consortial efforts suggest the presence of molecular subtypes within histologically identical GBM tumors. This emphasizes that future treatment decisions should no longer be made based solely on morphological analyses, but must now take into consideration such molecular and cellular heterogeneity. The use of single-cell technologies has advanced our understanding and assignation of functional subtypes revealing therapeutic vulnerabilities. Our team has developed stratification approaches in the past few years, and we have been able to identify patient cohorts enriched for various signaling pathways. Importantly, our Glioportal brain tumor resource has been established under the National Neuroscience Institute Tissue Bank in 2021. This resource offers preclinical capability to validate working hypotheses established from patient clinical datasets. This review highlights recent developments with the ultimate goal of assigning functional meaning to molecular subtypes, revealing therapeutic vulnerabilities.
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Affiliation(s)
- Lynnette Koh
- Department of Research, National Neuroscience Institute, Singapore.
| | - Wisna Novera
- Department of Research, National Neuroscience Institute, Singapore
| | - See Wee Lim
- Department of Research, National Neuroscience Institute, Singapore
| | - Yuk Kien Chong
- Department of Research, National Neuroscience Institute, Singapore
| | - Qing You Pang
- Department of Research, National Neuroscience Institute, Singapore
| | - David Low
- Department of Neurosurgery, National Neuroscience Institute, Singapore; Duke-National University of Singapore, Singapore
| | - Beng Ti Ang
- Department of Neurosurgery, National Neuroscience Institute, Singapore; Duke-National University of Singapore, Singapore
| | - Carol Tang
- Department of Research, National Neuroscience Institute, Singapore; Duke-National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore.
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99956
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Davidson RK, Weaver SA, Casey N, Kanojia S, Hogarth E, Aguirre RS, Sims EK, Evans-Molina C, Spaeth JM. The Chd4 subunit of the NuRD complex regulates Pdx1-controlled genes involved in β-cell function. J Mol Endocrinol 2022; 69:329-341. [PMID: 35521759 PMCID: PMC9260723 DOI: 10.1530/jme-22-0011] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/03/2022] [Indexed: 11/08/2022]
Abstract
Type 2 diabetes (T2D) is associated with loss of transcription factors (TFs) from a subset of failing β-cells. Among these TFs is Pdx1, which controls the expression of numerous genes involved in maintaining β-cell function and identity. Pdx1 activity is modulated by transcriptional coregulators and has recently been shown, through an unbiased screen, to interact with the Chd4 ATPase subunit of the nucleosome remodeling and deacetylase complex. Chd4 contributes to the maintenance of cellular identity and functional status of numerous different cell types. Here, we demonstrated that Pdx1 dynamically interacts with Chd4 under physiological and stimulatory conditions within islet β-cells and established a fundamental role for Chd4 in regulating insulin secretion and modulating numerous Pdx1-bound genes in vitro, including the MafA TF, where we discovered Chd4 is bound to the MafA region 3 enhancer. Furthermore, we found that Pdx1:Chd4 interactions are significantly compromised in islet β-cells under metabolically induced stress in vivo and in human donor tissues with T2D. Our findings establish a fundamental role for Chd4 in regulating insulin secretion and modulating Pdx1-bound genes in vitro, and disruption of Pdx1:Chd4 interactions coincides with β-cell dysfunction associated with T2D.
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Affiliation(s)
- Rebecca K. Davidson
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Staci A. Weaver
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nolan Casey
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sukrati Kanojia
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Elise Hogarth
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rebecca Schneider Aguirre
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Emily K. Sims
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Carmella Evans-Molina
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Richard L. Roudebush VA Medical Center, Indianapolis, Indiana, USA
| | - Jason M. Spaeth
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Corresponding Author: Address: 635 Barnhill Drive, MS 2021, Indianapolis, IN 46202 (JMS), (JMS)
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99957
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Omoto T, Yimiti D, Sanada Y, Toriyama M, Ding C, Hayashi Y, Ikuta Y, Nakasa T, Ishikawa M, Sano M, Lee M, Akimoto T, Shukunami C, Miyaki S, Adachi N. Tendon-Specific Dicer Deficient Mice Exhibit Hypoplastic Tendon Through the Downregulation of Tendon-Related Genes and MicroRNAs. Front Cell Dev Biol 2022; 10:898428. [PMID: 35784484 PMCID: PMC9241168 DOI: 10.3389/fcell.2022.898428] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/23/2022] [Indexed: 12/17/2022] Open
Abstract
Tendon is a fibrous connective tissue, that is, transmitting the forces that permit body movement. However, tendon/ligament biology is still not fully understood and especially, the role of miRNAs in tendon/ligament is sparse and uncharacterized in in vivo models. The objectives of this study were to address the function of DICER using mice with tendon/ligament-specific deletion of Dicer (Dicer conditional knockout; cKO), and to identify key miRNAs in tendon/ligament. Dicer cKO mice exhibited hypoplastic tendons through structurally abnormal collagen fibrils with downregulation of tendon-related genes. The fragility of tendon did not significantly affect the tensile strength of tendon in Dicer cKO mice, but they showed larger dorsiflexion angle in gait compared with Control mice. We identified two miRNAs, miR-135a and miR-1247, which were highly expressed in the Achilles tendon of Control mice and were downregulated in the Achilles tendon of Dicer cKO mice compared with Control mice. miR-135a mimic increased the expression of tendon-related genes in injured Achilles tendon-derived fibroblasts. In this study, Dicer cKO mice exhibited immature tendons in which collagen fibrils have small diameter with the downregulation of tendon-related genes such as transcriptional factor, extracellular matrix, and miRNAs. Thus, DICER plays an important role in tendon maturation, and miR-135a may have the potential to become key miRNA for tendon maturation and healing.
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Affiliation(s)
- Takenori Omoto
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Dilimulati Yimiti
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yohei Sanada
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima, Japan
| | - Minoru Toriyama
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Chenyang Ding
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yuta Hayashi
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Department of Musculoskeletal Traumatology and Reconstructive Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasunari Ikuta
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoyuki Nakasa
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima, Japan
| | - Masakazu Ishikawa
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Department of Artificial Joints and Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masayuki Sano
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Minjung Lee
- Faculty of Sport Sciences, Waseda University, Saitama, Japan
| | | | - Chisa Shukunami
- Department of Molecular Biology and Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shigeru Miyaki
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima, Japan
- *Correspondence: Shigeru Miyaki,
| | - Nobuo Adachi
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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99958
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Mousavi SM, Amin Mahdian SM, Ebrahimi MS, Taghizadieh M, Vosough M, Sadri Nahand J, Hosseindoost S, Vousooghi N, Javar HA, Larijani B, Hadjighassem MR, Rahimian N, Hamblin MR, Mirzaei H. Microfluidics for detection of exosomes and microRNAs in cancer: State of the art. Mol Ther Nucleic Acids 2022; 28:758-791. [PMID: 35664698 PMCID: PMC9130092 DOI: 10.1016/j.omtn.2022.04.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exosomes are small extracellular vesicles with sizes ranging from 30-150 nanometers that contain proteins, lipids, mRNAs, microRNAs, and double-stranded DNA derived from the cells of origin. Exosomes can be taken up by target cells, acting as a means of cell-to-cell communication. The discovery of these vesicles in body fluids and their participation in cell communication has led to major breakthroughs in diagnosis, prognosis, and treatment of several conditions (e.g., cancer). However, conventional isolation and evaluation of exosomes and their microRNA content suffers from high cost, lengthy processes, difficult standardization, low purity, and poor yield. The emergence of microfluidics devices with increased efficiency in sieving, trapping, and immunological separation of small volumes could provide improved detection and monitoring of exosomes involved in cancer. Microfluidics techniques hold promise for advances in development of diagnostic and prognostic devices. This review covers ongoing research on microfluidics devices for detection of microRNAs and exosomes as biomarkers and their translation to point-of-care and clinical applications.
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Affiliation(s)
- Seyed Mojtaba Mousavi
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Amin Mahdian
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Saeid Ebrahimi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Taghizadieh
- Department of Pathology, School of Medicine, Center for Women’s Health Research Zahra, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saereh Hosseindoost
- Pain Research Center, Neuroscience Institute, Tehran University of Medical Science, Tehran, Iran
| | - Nasim Vousooghi
- Department of Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Cognitive and Behavioral Sciences, Tehran University of Medical Sciences, Tehran, Iran
- Iranian National Center for Addiction Studies (INCAS), Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Akbari Javar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Reza Hadjighassem
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Brain and Spinal Cord Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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99959
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Shammas MK, Huang X, Wu BP, Fessler E, Song I, Randolph NP, Li Y, Bleck CK, Springer DA, Fratter C, Barbosa IA, Powers AF, Quirós PM, Lopez-Otin C, Jae LT, Poulton J, Narendra DP. OMA1 mediates local and global stress responses against protein misfolding in CHCHD10 mitochondrial myopathy. J Clin Invest 2022; 132:157504. [PMID: 35700042 PMCID: PMC9282932 DOI: 10.1172/jci157504] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 12/13/2021] [Accepted: 06/07/2022] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial stress triggers a response in the cell’s mitochondria and nucleus, but how these stress responses are coordinated in vivo is poorly understood. Here, we characterize a family with myopathy caused by a dominant p.G58R mutation in the mitochondrial protein CHCHD10. To understand the disease etiology, we developed a knockin (KI) mouse model and found that mutant CHCHD10 aggregated in affected tissues, applying a toxic protein stress to the inner mitochondrial membrane. Unexpectedly, the survival of CHCHD10-KI mice depended on a protective stress response mediated by the mitochondrial metalloendopeptidase OMA1. The OMA1 stress response acted both locally within mitochondria, causing mitochondrial fragmentation, and signaled outside the mitochondria, activating the integrated stress response through cleavage of DAP3-binding cell death enhancer 1 (DELE1). We additionally identified an isoform switch in the terminal complex of the electron transport chain as a component of this response. Our results demonstrate that OMA1 was critical for neonatal survival conditionally in the setting of inner mitochondrial membrane stress, coordinating local and global stress responses to reshape the mitochondrial network and proteome.
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Affiliation(s)
- Mario K Shammas
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, United States of America
| | - Xiaoping Huang
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, United States of America
| | - Beverly P Wu
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, United States of America
| | - Evelyn Fessler
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Insung Song
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, United States of America
| | - Nicholas P Randolph
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, United States of America
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, United States of America
| | - Christopher Ke Bleck
- Electron Microscopy Core Facility, National Heart, Lung, and Blood Institute, Bethesda, United States of America
| | - Danielle A Springer
- Mouse Phenotyping Core, National Heart, Lung, and Blood Institute, Bethesda, United States of America
| | - Carl Fratter
- Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Ines A Barbosa
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | | | - Pedro M Quirós
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Carlos Lopez-Otin
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - Lucas T Jae
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Joanna Poulton
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Derek P Narendra
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, United States of America
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99960
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Xu J, Xu J, Liu X, Jiang J. The role of lncRNA-mediated ceRNA regulatory networks in pancreatic cancer. Cell Death Dis 2022; 8:287. [PMID: 35697671 DOI: 10.1038/s41420-022-01061-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Non-coding RNAs (ncRNAs), which occupy the vast majority of human transcripts are known for their inability to encode proteins. NcRNAs consist of a diverse range of RNA species, including long non-coding RNAs (lncRNAs), which have significant meaning for epigenetic modification, post-transcriptional regulation of target genes, molecular interference, etc. The dysregulation of ncRNAs will mediate the pathogenesis of diverse human diseases, like cancer. Pancreatic cancer, as one of the most lethal malignancies in the digestive system that is hard to make a definite diagnosis at an early clinicopathological stage with a miserable prognosis. Therefore, the identification of potential and clinically applicable biomarker is momentous to improve the overall survival rate and positively ameliorate the prognosis of patients with pancreatic carcinoma. LncRNAs as one kind of ncRNAs exert multitudinous biological functions, and act as molecular sponges, relying on microRNA response elements (MREs) to competitively target microRNAs (miRNAs), thereby attenuating the degradation or inhibition of miRNAs to their own downstream protein-coding target genes, also thus regulating the initiation and progression of neoplasms. LncRNAs, which emerge aforementioned function are called competing endogenous RNAs (ceRNAs). Consequently, abundant research of lncRNAs as potential biomarkers is of critical significance for the molecular diagnosis, targeted therapy, as well as prognosis monitoring of pancreatic cancer.
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99961
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Manevski M, Devadoss D, Long C, Singh SP, Nasser MW, Borchert GM, Nair MN, Rahman I, Sopori M, Chand HS. Increased Expression of LASI lncRNA Regulates the Cigarette Smoke and COPD Associated Airway Inflammation and Mucous Cell Hyperplasia. Front Immunol 2022; 13:803362. [PMID: 35774797 PMCID: PMC9237255 DOI: 10.3389/fimmu.2022.803362] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 10/27/2021] [Accepted: 05/09/2022] [Indexed: 12/04/2022] Open
Abstract
Research Impact Cigarette smoke (CS) exposure is strongly associated with chronic obstructive pulmonary disease (COPD). In respiratory airways, CS exposure disrupts airway barrier functions, mucous/phlegm production, and basic immune responses of airway epithelial cells. Based on our recent identification of a specific immunomodulatory long noncoding RNA (lncRNA), we investigated its role in CS-induced responses in bronchial airways of cynomolgus macaque model of CS-induced COPD and in former smokers with and without COPD. The lncRNA was significantly upregulated in CS-induced macaque airways and in COPD airways that exhibited higher mucus expression and goblet cell hyperplasia. Experimental models of cells derived from COPD subjects recapitulated the augmented inflammation and mucus expression following the smoke challenge. Blocking of lncRNA expression in cell culture setting suppressed the smoke-induced and COPD-associated dysregulated mucoinflammatory response suggesting that this airway specific immunomodulatory lncRNA may represent a novel target to mitigate the smoke-mediated inflammation and mucus hyperexpression. Rationale In conducting airways, CS disrupts airway epithelial functions, mucociliary clearances, and innate immune responses that are primarily orchestrated by human bronchial epithelial cells (HBECs). Mucus hypersecretion and dysregulated immune response are the hallmarks of chronic bronchitis (CB) that is often exacerbated by CS. Notably, we recently identified a long noncoding RNA (lncRNA) antisense to ICAM-1 (LASI) that mediates airway epithelial responses. Objective To investigate the role of LASI lncRNA in CS-induced airway inflammation and mucin hyperexpression in an animal model of COPD, and in HBECs and lung tissues from former smokers with and without COPD. To interrogate LASI lncRNA role in CS-mediated airway mucoinflammatory responses by targeted gene editing. Methods Small airway tissue sections from cynomolgus macaques exposed to long-term mainstream CS, and those from former smokers with and without COPD were analyzed. The structured-illumination imaging, RNA fluorescence in-situ hybridization (FISH), and qRT-PCR were used to characterize lncRNA expression and the expression of inflammatory factors and airway mucins in a cell culture model of CS extract (CSE) exposure using HBECs from COPD (CHBEs) in comparison with cells from normal control (NHBEs) subjects. The protein levels of mucin MUC5AC, and inflammatory factors ICAM-1, and IL-6 were determined using specific ELISAs. RNA silencing was used to block LASI lncRNA expression and lentivirus encoding LASI lncRNA was used to achieve LASI overexpression (LASI-OE). Results Compared to controls, LASI lncRNA was upregulated in CS-exposed macaques and in COPD smoker airways, correlating with mucus hyperexpression and mucus cell hyperplasia in severe COPD airways. At baseline, the unstimulated CHBEs showed increased LASI lncRNA expression with higher expression of secretory mucin MUC5AC, and inflammatory factors, ICAM-1, and IL-6 compared to NHBEs. CSE exposure of CHBEs resulted in augmented inflammation and mucus expression compared to controls. While RNA silencing-mediated LASI knockdown suppressed the mucoinflammatory response, cells overexpressing LASI lncRNA showed elevated mRNA levels of inflammatory factors. Conclusions Altogether, LASI lncRNA may represent a novel target to control the smoke-mediated dysregulation in airway responses and COPD exacerbations.
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Affiliation(s)
- Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Christopher Long
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Shashi P. Singh
- Respiratory Immunology Program, Lovelace Respiratory Research Institute, Albuquerque, NM, United States
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL, United States
| | - Madhavan N. Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Mohan Sopori
- Respiratory Immunology Program, Lovelace Respiratory Research Institute, Albuquerque, NM, United States
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
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99962
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Liang X, Li L, Fan Y. Diagnostic, Prognostic, and Immunological Roles of HELLS in Pan-Cancer: A Bioinformatics Analysis. Front Immunol 2022; 13:870726. [PMID: 35774795 PMCID: PMC9237247 DOI: 10.3389/fimmu.2022.870726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/07/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background Inappropriate repair of DNA damage drives carcinogenesis. Lymphoid-specific helicase (HELLS) is an important component of the chromatin remodeling complex that helps repair DNA through various mechanisms such as DNA methylation, histone posttranslational modification, and nucleosome remodeling. Its role in human cancer initiation and progression has garnered recent attention. Our study aims to provide a more systematic and comprehensive understanding of the role of HELLS in the development and progression of multiple malignancies through analysis of HELLS in cancers. Methods We explored the role of HELLS in cancers using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database. Multiple web platforms and software were used for data analysis, including R, Cytoscape, HPA, Archs4, TISIDB, cBioPortal, STRING, GSCALite, and CancerSEA. Results High HELLS expression was found in a variety of cancers and differentially expressed across molecular and immune subtypes. HELLS was involved in many cancer pathways. Its expression positively correlated with Th2 and Tcm cells in most cancers. It also correlated with genetic markers of immunomodulators in various cancers. Conclusions Our study elucidates the role HELLS plays in promotion, inhibition, and treatment of different cancers. HELLS is a potential cancer diagnostic and prognostic biomarker with immune, targeted, or cytotoxic therapeutic value. This work is a prerequisite to clinical validation and treatment of HELLS in cancers.
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Affiliation(s)
- Xiao Liang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Linji Li
- Department of Anesthesiology, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, China
| | - Yuchao Fan
- Department of Anesthesiology, Sichuan Cancer Center, Sichuan Cancer Hospital & Institute, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Yuchao Fan,
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99963
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Bhattacharjee S, Rehman I, Basu S, Nandy S, Richardson JM, Das BB. Interplay between symmetric arginine dimethylation and ubiquitylation regulates TDP1 proteostasis for the repair of topoisomerase I-DNA adducts. Cell Rep 2022; 39:110940. [PMID: 35705029 DOI: 10.1016/j.celrep.2022.110940] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 04/05/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase (TDP1) hydrolyzes the phosphodiester bond between a DNA 3' end and a tyrosyl moiety and is implicated in the repair of trapped topoisomerase I (Top1)-DNA covalent complexes (Top1cc). Protein arginine methyltransferase 5 (PRMT5) catalyzes arginine methylation of TDP1 at the residues R361 and R586. Here, we establish mechanistic crosstalk between TDP1 arginine methylation and ubiquitylation, which is critical for TDP1 homeostasis and cellular responses to Top1 poisons. We show that R586 methylation promotes TDP1 ubiquitylation, which facilitates ubiquitin/proteasome-dependent TDP1 turnover by impeding the binding of UCHL3 (deubiquitylase enzyme) with TDP1. TDP1-R586 also promotes TDP1-XRCC1 binding and XRCC1 foci formation at Top1cc-damage sites. Intriguingly, R361 methylation enhances the 3'-phosphodiesterase activity of TDP1 in real-time fluorescence-based cleavage assays, and this was rationalized using structural modeling. Together, our findings establish arginine methylation as a co-regulator of TDP1 proteostasis and activity, which modulates the repair of trapped Top1cc.
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Affiliation(s)
- Sangheeta Bhattacharjee
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ishita Rehman
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Saini Basu
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Souvik Nandy
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Benu Brata Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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99964
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Nguyen LT, Lau LY, Fortes MRS. Proteomic Analysis of Hypothalamus and Pituitary Gland in Pre and Postpubertal Brahman Heifers. Front Genet 2022; 13:935433. [PMID: 35774501 PMCID: PMC9237413 DOI: 10.3389/fgene.2022.935433] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/03/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022] Open
Abstract
The hypothalamus and the pituitary gland are directly involved in the complex systemic changes that drive the onset of puberty in cattle. Here, we applied integrated bioinformatics to elucidate the critical proteins underlying puberty and uncover potential molecular mechanisms from the hypothalamus and pituitary gland of prepubertal (n = 6) and postpubertal (n = 6) cattle. Proteomic analysis in the hypothalamus and pituitary gland revealed 275 and 186 differentially abundant (DA) proteins, respectively (adjusted p-value < 0.01). The proteome profiles found herein were integrated with previously acquired transcriptome profiles. These transcriptomic studies used the same tissues harvested from the same heifers at pre- and post-puberty. This comparison detected a small number of matched transcripts and protein changes at puberty in each tissue, suggesting the need for multiple omics analyses for interpreting complex biological systems. In the hypothalamus, upregulated DA proteins at post-puberty were enriched in pathways related to puberty, including GnRH, calcium and oxytocin signalling pathways, whereas downregulated proteins were observed in the estrogen signalling pathway, axon guidance and GABAergic synapse. Additionally, this study revealed that ribosomal pathway proteins in the pituitary were involved in the pubertal development of mammals. The reported molecules and derived protein-protein networks are a starting point for future experimental approaches that might dissect with more detail the role of each molecule to provide new insights into the mechanisms of puberty onset in cattle.
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Affiliation(s)
- Loan To Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
- *Correspondence: Loan To Nguyen,
| | - Li Yieng Lau
- Agency of Science, Technology and Research, Singapore, Singapore
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99965
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Lu X, Miao J, Shen D, Dou D. Proteinaceous Effector Discovery and Characterization in Plant Pathogenic Colletotrichum Fungi. Front Microbiol 2022; 13:914035. [PMID: 35694285 PMCID: PMC9184758 DOI: 10.3389/fmicb.2022.914035] [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: 04/06/2022] [Accepted: 05/10/2022] [Indexed: 02/05/2023] Open
Abstract
Anthracnose caused by plant pathogenic Colletotrichum fungi results in large economic losses in field crop production worldwide. To aid the establishment of plant host infection, Colletotrichum pathogens secrete numerous effector proteins either in apoplastic space or inside of host cells for effective colonization. Understanding these effector repertoires is critical for developing new strategies for resistance breeding and disease management. With the advance of genomics and bioinformatics tools, a large repertoire of putative effectors has been identified in Colletotrichum genomes, and the biological functions and molecular mechanisms of some studied effectors have been summarized. Here, we review recent advances in genomic identification, understanding of evolutional characteristics, transcriptional profiling, and functional characterization of Colletotrichum effectors. We also offer a perspective on future research.
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Affiliation(s)
- Xinyu Lu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Jinlu Miao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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99966
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Sahoo S, Padhy AA, Kumari V, Mishra P. Role of Ubiquitin-Proteasome and Autophagy-Lysosome Pathways in α-Synuclein Aggregate Clearance. Mol Neurobiol 2022; 59:5379-5407. [PMID: 35699874 DOI: 10.1007/s12035-022-02897-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/21/2022] [Indexed: 11/26/2022]
Abstract
Synuclein aggregation in neuronal cells is the primary underlying cause of synucleinopathies. Changes in gene expression patterns, structural modifications, and altered interactions with other cellular proteins often trigger aggregation of α-synuclein, which accumulates as oligomers or fibrils in Lewy bodies. Although fibrillar forms of α-synuclein are primarily considered pathological, recent studies have revealed that even the intermediate states of aggregates are neurotoxic, complicating the development of therapeutic interventions. Autophagy and ubiquitin-proteasome pathways play a significant role in maintaining the soluble levels of α-synuclein inside cells; however, the heterogeneous nature of the aggregates presents a significant bottleneck to its degradation by these cellular pathways. With studies focused on identifying the proteins that modulate synuclein aggregation and clearance, detailed mechanistic insights are emerging about the individual and synergistic effects of these degradation pathways in regulating soluble α-synuclein levels. In this article, we discuss the impact of α-synuclein aggregation on autophagy-lysosome and ubiquitin-proteasome pathways and the therapeutic strategies that target various aspects of synuclein aggregation or degradation via these pathways. Additionally, we also highlight the natural and synthetic compounds that have shown promise in alleviating the cellular damage caused due to synuclein aggregation.
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Affiliation(s)
- Subhashree Sahoo
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Amrita Arpita Padhy
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Varsha Kumari
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Parul Mishra
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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99967
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Dave A, Nekritz E, Charytonowicz D, Beaumont M, Smith M, Beaumont K, Silva J, Sebra R. Integration of Single-Cell Transcriptomics With a High Throughput Functional Screening Assay to Resolve Cell Type, Growth Kinetics, and Stemness Heterogeneity Within the Comma-1D Cell Line. Front Genet 2022; 13:894597. [PMID: 36630696 PMCID: PMC9237515 DOI: 10.3389/fgene.2022.894597] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/20/2022] [Indexed: 01/14/2023] Open
Abstract
Cell lines are one of the most frequently implemented model systems in life sciences research as they provide reproducible high throughput testing. Differentiation of cell cultures varies by line and, in some cases, can result in functional modifications within a population. Although research is increasingly dependent on these in vitro model systems, the heterogeneity within cell lines has not been thoroughly investigated. Here, we have leveraged high throughput single-cell assays to investigate the Comma-1D mouse cell line that is known to differentiate in culture. Using scRNASeq and custom single-cell phenotype assays, we resolve the clonal heterogeneity within the referenced cell line on the genomic and functional level. We performed a cohesive analysis of the transcriptome of 5,195 sequenced cells, of which 85.3% of the total reads successfully mapped to the mm10-3.0.0 reference genome. Across multiple gene expression analysis pipelines, both luminal and myoepithelial lineages were observed. Deep differential gene expression analysis revealed eight subclusters identified as luminal progenitor, luminal differentiated, myoepithelial differentiated, and fibroblast subpopulations-suggesting functional clustering within each lineage. Gene expression of published mammary stem cell (MaSC) markers Epcam, Cd49f, and Sca-1 was detected across the population, with 116 (2.23%) sequenced cells expressing all three markers. To gain insight into functional heterogeneity, cells with patterned MaSC marker expression were isolated and phenotypically investigated through a custom single-cell high throughput assay. The comparison of growth kinetics demonstrates functional heterogeneity within each cell cluster while also illustrating significant limitations in current cell isolation methods. We outlined the upstream use of our novel automated cell identification platform-to be used prior to single-cell culture-for reduced cell stress and improved rare cell identification and capture. Through compounding single-cell pipelines, we better reveal the heterogeneity within Comma-1D to identify subpopulations with specific functional characteristics.
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Affiliation(s)
- Arpit Dave
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Erin Nekritz
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
| | - Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Michael Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Melissa Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States
| | - Kristin Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jose Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States,Sema4, A Mount Sinai Venture, Stamford, CT, United States,*Correspondence: Robert Sebra,
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99968
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Li T, Li J, Wang H, Zhao J, Yan M, He H, Yu S. Exosomes: Potential Biomarkers and Functions in Head and Neck Squamous Cell Carcinoma. Front Mol Biosci 2022; 9:881794. [PMID: 35775082 PMCID: PMC9237451 DOI: 10.3389/fmolb.2022.881794] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 02/23/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC), originating from the mucosal epithelial cells of the oral cavity, pharynx, and larynx, is a lethal malignancy of the head and neck. Patients with advanced and recurrent HNSCC have poor outcomes due to limited therapeutic options. Exosomes have active roles in the pathophysiology of tumors and are suggested as a potential therapeutic target of HNSCC. Exosomes in HNSCC have been intensively studied for disease activity, tumor staging, immunosuppression, and therapeutic monitoring. In this review, the biological mechanisms and the recent clinical application of exosomes are highlighted to reveal the potential of exosomes as biomarkers and therapeutic targets for HNSCC.
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Affiliation(s)
- Ting Li
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Juan Li
- Department of Pathology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Haitao Wang
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jiayu Zhao
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Mingze Yan
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hongjiang He
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Hongjiang He, ; Shan Yu,
| | - Shan Yu
- Department of Pathology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Hongjiang He, ; Shan Yu,
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99969
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Ai K, Li X, Zhang P, Pan J, Li H, He Z, Zhang H, Yi L, Kang Y, Wang Y, Chen J, Li Y, Xiang X, Chai X, Zhang D. Genetic or siRNA inhibition of MBD2 attenuates the UUO- and I/R-induced renal fibrosis via downregulation of EGR1. Mol Ther Nucleic Acids 2022; 28:77-86. [PMID: 35356685 PMCID: PMC8933641 DOI: 10.1016/j.omtn.2022.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 02/25/2022] [Indexed: 12/20/2022]
Abstract
DNA methylation plays a pivotal role in the progression of renal fibrosis. Methyl-CpG–binding domain protein 2 (MBD2), a protein reader of methylation, is involved in the development of acute kidney injury (AKI) caused by vancomycin. However, the role and mechanism of action of MBD2 in renal remain unclear. In this study, MBD2 mediated extracellular matrix (ECM) production induced by TGF-β1 in Boston University mouse proximal tubule (BUMPT) cells,and upregulated the expression EGR1 to promote ECM production in murine embryonic NIH 3T3 fibroblasts. ChIP analysis demonstrated that MBD2 physically interacted with the promoter region of the CpG islands of EGR1 genes and then activated their expression by inducing hypomethylation of the promoter region. In vivo, PT-MBD2-KO attenuated unilateral ureteral obstruction (UUO)-induced renal tubulointerstitial fibrosis via downregulation of EGR1, which was demonstrated by the downregulation of fibronectin (FN), collagen I and IV, α-SMA, and EGR1. Injection of MBD2-siRNA attenuated the UUO- and I/R-induced renal fibrosis. Those molecular changes were verified by biopsies from patients with obstructive nephropathy (OB). These data collectively demonstrated that inhibition of MBD2 reduces renal fibrosis via downregulating EGR1, which could be a target for treatment of fibrotic kidney disease.
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Affiliation(s)
- Kai Ai
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Xiaozhou Li
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Pan Zhang
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Jian Pan
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Huiling Li
- Department of Ophthalmology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Zhibiao He
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Hongliang Zhang
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Lei Yi
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Ye Kang
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Yinhuai Wang
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Junxiang Chen
- Department of Nephrology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Yijian Li
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Xudong Xiang
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Xiangping Chai
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Dongshan Zhang
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
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99970
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Laporte E, Hermans F, De Vriendt S, Vennekens A, Lambrechts D, Nys C, Cox B, Vankelecom H. Decoding the activated stem cell phenotype of the neonatally maturing pituitary. eLife 2022; 11:75742. [PMID: 35699412 PMCID: PMC9333987 DOI: 10.7554/elife.75742] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 11/22/2021] [Accepted: 06/13/2022] [Indexed: 12/02/2022] Open
Abstract
The pituitary represents the endocrine master regulator. In mouse, the gland undergoes active maturation immediately after birth. Here, we in detail portrayed the stem cell compartment of neonatal pituitary. Single-cell RNA-sequencing pictured an active gland, revealing proliferative stem as well as hormonal (progenitor) cell populations. The stem cell pool displayed a hybrid epithelial/mesenchymal phenotype, characteristic of development-involved tissue stem cells. Organoid culturing recapitulated the stem cells’ phenotype, interestingly also reproducing their paracrine activity. The pituitary stem cell-activating interleukin-6 advanced organoid growth, although the neonatal stem cell compartment was not visibly affected in Il6−/− mice, likely due to cytokine family redundancy. Further transcriptomic analysis exposed a pronounced WNT pathway in the neonatal gland, shown to be involved in stem cell activation and to overlap with the (fetal) human pituitary transcriptome. Following local damage, the neonatal gland efficiently regenerates, despite absence of additional stem cell proliferation, or upregulated IL-6 or WNT expression, all in line with the already high stem cell activation status, thereby exposing striking differences with adult pituitary. Together, our study decodes the stem cell compartment of neonatal pituitary, exposing an activated state in the maturing gland. Understanding stem cell activation is key to potential pituitary regenerative prospects. The pituitary gland is a pea-sized structure found just below the brain that produces hormones controlling everything from growth and stress to reproduction and immunity. To perform its role, the pituitary gland needs specialised hormone-producing cells, but it also contains stem cells. These stem cells can divide to produce more cells like themselves, or differentiate into cells of different types, including hormone-producing cells. In mice, the stem cells of the pituitary gland appear to be activated in the first few weeks after birth, and later become ‘quiescent’ (or lazy) in the adult pituitary gland. However, it remains unclear how the activated state found in the maturing gland is established and regulated. To answer this question, Laporte et al. used single-cell RNA sequencing, a technique that allows researchers to profile which genes are active in individual cells, which can provide vital information about the state and activity of a tissue. The researchers compared the cells of the maturing pituitary gland of newborn mice to the cells in the established gland of adult mice. This analysis revealed that the maturing pituitary gland is a dynamic tissue, with populations of cells that are actively dividing (including the stem cells), which the mature pituitary gland lacks. Additionally, Laporte et al. established the molecular basis for the activated state of the stem cells in the maturing pituitary gland, which relies on the activation of a cell signalling pathway called WNT. To confirm these findings, Laporte et al. used an organoid system that allowed them to recapitulate the stem cell compartment of the maturing pituitary gland in a dish. When Laporte et al. blocked WNT signalling in these organoids, the organoids failed to form or divide. Furthermore, blocking the pathway directly in newborn mice reduced the number of dividing stem cells in the pituitary gland. Both findings support the notion that WNT signalling is required to establish the activated state of the maturing pituitary gland in newborn mice. Laporte et al. also wanted to know whether the newborn pituitary gland responded to injury differently than the adult gland. It had already been established that the adult pituitary stem cells become activated upon injury, and that the gland has some regenerative capacity. However, when Laporte et al. injured the newborn pituitary gland, the gland was able to fully regenerate, despite the stem cells not becoming more activated. This is likely because these cells are already activated (or ‘primed’), and do not require further activation to divide and repair the gland with the help of other proliferating cells. With these results, Laporte et al. shed light on the activated state of the stem cells in the pituitary gland of newborn mice. This provides insight into the role of these stem cells, as well as unveiling possible routes towards regenerating pituitary tissue. This could eventually prove useful in medicine, in cases when the pituitary gland is damaged or removed.
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Affiliation(s)
- Emma Laporte
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Florian Hermans
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Silke De Vriendt
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | | | | | - Charlotte Nys
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Benoit Cox
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Hugo Vankelecom
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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99971
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Fu LY, Zhu T, Zhou X, Yu R, He Z, Zhang P, Wu Z, Chen M, Kaufmann K, Chen D. ChIP-Hub provides an integrative platform for exploring plant regulome. Nat Commun 2022; 13:3413. [PMID: 35701419 PMCID: PMC9197862 DOI: 10.1038/s41467-022-30770-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 08/14/2021] [Accepted: 05/18/2022] [Indexed: 11/18/2022] Open
Abstract
Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms the basis for most life on earth. A wealth of regulome and epigenome data have been generated in various plant species, but no common, standardized resource is available so far for biologists. Here, we present ChIP-Hub, an integrative web-based platform in the ENCODE standards that bundles >10,000 publicly available datasets reanalyzed from >40 plant species, allowing visualization and meta-analysis. We manually curate the datasets through assessing ~540 original publications and comprehensively evaluate their data quality. As a proof of concept, we extensively survey the co-association of different regulators and construct a hierarchical regulatory network under a broad developmental context. Furthermore, we show how our annotation allows to investigate the dynamic activity of tissue-specific regulatory elements (promoters and enhancers) and their underlying sequence grammar. Finally, we analyze the function and conservation of tissue-specific promoters, enhancers and chromatin states using comparative genomics approaches. Taken together, the ChIP-Hub platform and the analysis results provide rich resources for deep exploration of plant ENCODE. ChIP-Hub is available at https://biobigdata.nju.edu.cn/ChIPHub/. A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue-specific chromatin dynamics, putative enhancers and chromatin states.
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Affiliation(s)
- Liang-Yu Fu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.,Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhaohui He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Peijing Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhigui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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99972
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Harris AJ, Foley NM, Williams TL, Murphy WJ. Tree House Explorer: A Novel Genome Browser for Phylogenomics. Mol Biol Evol 2022; 39:msac130. [PMID: 35700217 PMCID: PMC9246335 DOI: 10.1093/molbev/msac130] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/09/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations (GFF/GTF), recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.
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Affiliation(s)
- Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Tiffani L Williams
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
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99973
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Konstantinidis E, Molisak A, Perrin F, Streubel-Gallasch L, Fayad S, Kim DY, Petri K, Aryee MJ, Aguilar X, György B, Giedraitis V, Joung JK, Pattanayak V, Essand M, Erlandsson A, Berezovska O, Ingelsson M. CRISPR-Cas9 treatment partially restores amyloid-β 42/40 in human fibroblasts with the Alzheimer's disease PSEN 1 M146L mutation. Mol Ther Nucleic Acids 2022; 28:450-461. [PMID: 35505961 PMCID: PMC9043867 DOI: 10.1016/j.omtn.2022.03.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/27/2022] [Indexed: 11/29/2022]
Abstract
Presenilin 1 (PS1) is a central component of γ-secretase, an enzymatic complex involved in the generation of the amyloid-β (Aβ) peptide that deposits as plaques in the Alzheimer’s disease (AD) brain. The M146L mutation in the PS1 gene (PSEN1) leads to an autosomal dominant form of early-onset AD by promoting a relative increase in the generation of the more aggregation-prone Aβ42. This change is evident not only in the brain but also in peripheral cells of mutation carriers. In this study we used the CRISPR-Cas9 system from Streptococcus pyogenes to selectively disrupt the PSEN1M146L allele in human fibroblasts. A disruption of more than 50% of mutant alleles was observed in all CRISPR-Cas9-treated samples, resulting in reduced extracellular Aβ42/40 ratios. Fluorescence resonance energy transfer-based conformation and western blot analyses indicated that CRISPR-Cas9 treatment also affects the overall PS1 conformation and reduces PS1 levels. Moreover, our guide RNA did not lead to any detectable editing at the highest-ranking candidate off-target sites identified by ONE-seq and CIRCLE-seq. Overall, our data support the effectiveness of CRISPR-Cas9 in selectively targeting the PSEN1M146L allele and counteracting the AD-associated phenotype. We believe that this system could be developed into a therapeutic strategy for patients with this and other dominant mutations leading to early-onset AD.
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Affiliation(s)
- Evangelos Konstantinidis
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Agnieszka Molisak
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Florian Perrin
- Department of Neurology, Massachusetts General Hospital, Memory Disorders Unit, Harvard Medical School, Charlestown, MA, USA
| | - Linn Streubel-Gallasch
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Sarah Fayad
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Daniel Y Kim
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Karl Petri
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Martin J Aryee
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ximena Aguilar
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Bence György
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Vikram Pattanayak
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Magnus Essand
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anna Erlandsson
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Oksana Berezovska
- Department of Neurology, Massachusetts General Hospital, Memory Disorders Unit, Harvard Medical School, Charlestown, MA, USA
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.,Krembil Brain Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine and Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
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99974
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Aleman TS, Huckfeldt RM, Serrano LW, Pearson DJ, Vergilio GK, McCague S, Marshall KA, Ashtari M, Doan TM, Weigel-DiFranco CA, Biron BS, Wen XH, Chung DC, Liu E, Ferenchak K, Morgan JIW, Pierce EA, Eliott D, Bennett J, Comander J, Maguire AM. AAV2-hCHM Subretinal Delivery to the Macula in Choroideremia: Two Year Interim Results of an Ongoing Phase I/II Gene Therapy Trial. Ophthalmology 2022:S0161-6420(22)00438-9. [PMID: 35714735 DOI: 10.1016/j.ophtha.2022.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/22/2022] Open
Abstract
PURPOSE To assess the safety of the subretinal delivery of a recombinant adeno-associated virus serotype 2 (AAV2) vector carrying a human CHM-encoding cDNA in choroideremia (CHM). DESIGN Prospective, open-label, non-randomized, dose-escalation, phase 1/2 clinical trial. SUBJECTS, PARTICIPANTS, AND/OR CONTROLS Fifteen CHM patients (ages 20-57 years at dosing). METHODS, INTERVENTION, OR TESTING Patients received uniocular subfoveal injections of low dose (up to 5x1010 vector genome (vg) per eye, n=5) or high dose (up to 1x1011 vg per eye, n=10) AAV2-hCHM. Patients were evaluated pre- and post-operatively for two years with ophthalmic examinations, multimodal retinal imaging and psychophysical testing. MAIN OUTCOME Measures: visual acuity (VA), perimetry (10-2 protocol), spectral-domain optical coherence tomography (SD-OCT) and short-wavelength fundus autofluorescence (SW-FAF). RESULTS We detected no vector-related or systemic toxicities. VA returned to within 15 letters of baseline in all but two patients (one developed acute foveal thinning, another patient, a macular hole); the rest showed no gross changes in foveal structure at two years. There were no significant differences between intervention and control eyes in mean light-adapted sensitivity by perimetry, or in the lateral extent of retinal pigment epithelium (RPE) relative preservation by SD-OCT and SW-FAF. Microperimetry showed non-significant (<3SD of the intervisit variability) gains in sensitivity in some locations and participants in the intervention eye. There were no obvious dose-dependent relationships. CONCLUSIONS VA was within 15 letters of baseline after the subfoveal AAV2-hCHM injections in 13/15 (87%) of the patients. Acute foveal thinning with unchanged perifoveal function in one patient and macular hole in a second suggests foveal vulnerability to the subretinal injections. Longer observation intervals will help establish the significance of the minor differences in sensitivities and rate of disease progression observed between intervention and control eyes.
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99975
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Pérez-Antón M, Schneider I, Kroll P, Hofhuis H, Metzger S, Pauly M, Hay A. Explosive seed dispersal depends on SPL7 to ensure sufficient copper for localized lignin deposition via laccases. Proc Natl Acad Sci U S A 2022; 119:e2202287119. [PMID: 35666865 DOI: 10.1073/pnas.2202287119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The sudden explosion of seed pods in popping cress (Cardamine hirsuta) takes less than 3 ms to accelerate seeds away from the plant. This explosive mechanism relies on polar deposition of the cell-wall polymer lignin. To investigate the genetic basis for polar lignin deposition, we conducted a mutant screen and identified SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 7 (SPL7)—a transcriptional regulator of copper homeostasis. We discovered three multicopper laccases, LAC4, 11, and 17, that precisely colocalize with, and are required for, the polar deposition of lignin in explosive seed pods. Activity of these three laccases depends on SPL7 to acclimate to copper deficiency. Our findings demonstrate how mineral nutrition is integrated with polar lignin deposition to facilitate dispersal. Exploding seed pods evolved in the Arabidopsis relative Cardamine hirsuta via morphomechanical innovations that allow the storage and rapid release of elastic energy. Asymmetric lignin deposition within endocarpb cell walls is one such innovation that is required for explosive seed dispersal and evolved in association with the trait. However, the genetic control of this novel lignin pattern is unknown. Here, we identify three lignin-polymerizing laccases, LAC4, 11, and 17, that precisely colocalize with, and are redundantly required for, asymmetric lignification of endocarpb cells. By screening for C. hirsuta mutants with less lignified fruit valves, we found that loss of function of the transcription factor gene SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 7 (SPL7) caused a reduction in endocarpb cell-wall lignification and a consequent reduction in seed dispersal range. SPL7 is a conserved regulator of copper homeostasis and is both necessary and sufficient for copper to accumulate in the fruit. Laccases are copper-requiring enzymes. We discovered that laccase activity in endocarpb cell walls depends on the SPL7 pathway to acclimate to copper deficiency and provide sufficient copper for lignin polymerization. Hence, SPL7 links mineral nutrition to efficient dispersal of the next generation.
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99976
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Zhang H, Du X, Dong C, Zheng Z, Mu W, Zhu M, Yang Y, Li X, Hu H, Shrestha N, Li M, Yang Y. Genomes and demographic histories of the endangered Bretschneidera sinensis (Akaniaceae). Gigascience 2022; 11:6608505. [PMID: 35701375 PMCID: PMC9197684 DOI: 10.1093/gigascience/giac050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/14/2021] [Revised: 03/02/2022] [Accepted: 04/23/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Bretschneidera sinensis is an endangered relic tree species in the Akaniaceae family and is sporadically distributed in eastern Asia. As opposed to its current narrow and rare distribution, the fossil pollen of B. sinensis has been found to be frequent and widespread in the Northern Hemisphere during the Late Miocene. B. sinensis is also a typical mycorrhizal plant, and its annual seedlings exhibit high mortality rates in absence of mycorrhizal development. The chromosome-level high-quality genome of B. sinensis will help us to more deeply understand the survival and demographic histories of this relic species. RESULTS A total of 25.39 Gb HiFi reads and 109.17 Gb Hi-C reads were used to construct the chromosome-level genome of B. sinensis, which is 1.21 Gb in length with the contig N50 of 64.13 Mb and chromosome N50 of 146.54 Mb. The identified transposable elements account for 55.21% of the genome. A total of 45,839 protein-coding genes were predicted in B. sinensis. A lineage-specific whole-genome duplication was detected, and 7,283 lineage-specific expanded gene families with functions related to the specialized endotrophic mycorrhizal adaptation were identified. The historical effective population size (Ne) of B. sinensis was found to oscillate greatly in response to Quaternary climatic changes. The Ne of B. sinensis has decreased rapidly in the recent past, making its extant Ne extremely lower. Our additional evolutionary genomic analyses suggested that the developed mycorrhizal adaption might have been repeatedly disrupted by environmental changes caused by Quaternary climatic oscillations. The environmental changes and an already decreased population size during the Holocene may have led to the current rarity of B. sinensis. CONCLUSION This is a detailed report of the genome sequences for the family Akaniaceae distributed in evergreen forests in eastern Asia. Such a high-quality genomic resource may provide critical clues for comparative genomics studies of this family in the future.
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Affiliation(s)
- Han Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Congcong Dong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Wenjie Mu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yingbo Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaojie Li
- Emeishan Biological Resources Experimental Station, Emei 511181, Sichuan, China
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology & School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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99977
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Li T, Lu L, Pember E, Li X, Zhang B, Zhu Z. New Insights into Neuroinflammation Involved in Pathogenic Mechanism of Alzheimer's Disease and Its Potential for Therapeutic Intervention. Cells 2022; 11:cells11121925. [PMID: 35741054 PMCID: PMC9221885 DOI: 10.3390/cells11121925] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/05/2022] [Accepted: 06/11/2022] [Indexed: 02/04/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, affecting more than 50 million people worldwide with an estimated increase to 139 million people by 2050. The exact pathogenic mechanisms of AD remain elusive, resulting in the fact that the current therapeutics solely focus on symptomatic management instead of preventative or curative strategies. The two most widely accepted pathogenic mechanisms of AD include the amyloid and tau hypotheses. However, it is evident that these hypotheses cannot fully explain neuronal degeneration shown in AD. Substantial evidence is growing for the vital role of neuroinflammation in AD pathology. The neuroinflammatory hypothesis provides a new, exciting lead in uncovering the underlying mechanisms contributing to AD. This review aims to highlight new insights into the role of neuroinflammation in the pathogenesis of AD, mainly including the involvement of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), nucleotide-binding oligomerization domain, leucine-rich repeat-containing protein 3 (NLRP3)/caspase-1 axis, triggering receptor expressed on myeloid cells 2 (TREM2) and cGAS-STING as key influencers in augmenting AD development. The inflammasomes related to the pathways of NF-κB, NLRP3, TREM2, and cGAS-STING as biomarkers of the neuroinflammation associated with AD, as well as an overview of novel AD treatments based on these biomarkers as potential drug targets reported in the literature or under clinical trials, are explored.
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Affiliation(s)
- Tiantian Li
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK; (T.L.); (L.L.); (E.P.); (B.Z.)
| | - Li Lu
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK; (T.L.); (L.L.); (E.P.); (B.Z.)
| | - Eloise Pember
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK; (T.L.); (L.L.); (E.P.); (B.Z.)
| | - Xinuo Li
- School of Pharmacy, China Pharmaceutical University, Nanjing 211112, China;
| | - Bocheng Zhang
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK; (T.L.); (L.L.); (E.P.); (B.Z.)
| | - Zheying Zhu
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK; (T.L.); (L.L.); (E.P.); (B.Z.)
- Correspondence:
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99978
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Garza NM, Zulkifli M, Gohil VM. Elesclomol elevates cellular and mitochondrial iron levels by delivering copper to the iron import machinery. J Biol Chem 2022; 298:102139. [PMID: 35714767 PMCID: PMC9270252 DOI: 10.1016/j.jbc.2022.102139] [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: 12/29/2021] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 01/16/2023] Open
Abstract
Copper (Cu) and iron (Fe) are redox-active metals that serve as cofactors for many essential cellular enzymes. Disruption in the intracellular homeostasis of these metals results in debilitating and frequently fatal human disorders, such as Menkes disease and Friedreich's ataxia. Recently, we reported that an investigational anticancer drug, elesclomol (ES), can deliver Cu to critical mitochondrial cuproenzymes and has the potential to be repurposed for treatment of Cu deficiency disorders. Here, we sought to determine the specificity of ES and the ES-Cu complex in delivering Cu to cuproenzymes in different intracellular compartments. Using a combination of yeast genetics, subcellular fractionation, and inductively coupled plasma-mass spectrometry-based metal measurements, we showed that ES and ES-Cu treatment results in an increase in cellular and mitochondrial Fe content, along with the expected increase in Cu. Utilizing yeast mutants of Cu and Fe transporters, we demonstrate that ES-based elevation in cellular Fe levels is independent of the major cellular Cu importer, but is dependent on the Fe importer Ftr1 and its partner Fet3, a multicopper-oxidase. As Fet3 is metallated in the Golgi lumen, we sought to uncover the mechanism by which Fet3 receives Cu from ES. Using yeast knockouts of genes involved in Cu delivery to Fet3, we determined that ES can bypass Atx1, a metallochaperone involved in Cu delivery to the Golgi membrane Cu pump, Ccc2, but not Ccc2 itself. Taken together, our study provides a mechanism by which ES distributes Cu in cells and impacts cellular and mitochondrial Fe homeostasis.
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Affiliation(s)
- Natalie M Garza
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Mohammad Zulkifli
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Vishal M Gohil
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA.
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99979
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Sluysmans S, Salmaso A, Rouaud F, Méan I, Brini M, Citi S. The PLEKHA7-PDZD11 complex regulates the localization of the calcium pump PMCA and calcium handling in cultured cells. J Biol Chem 2022; 298:102138. [PMID: 35714771 PMCID: PMC9307954 DOI: 10.1016/j.jbc.2022.102138] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 01/11/2023] Open
Abstract
The plasma membrane calcium ATPase (PMCA) extrudes calcium from the cytosol to the extracellular space to terminate calcium-dependent signaling. Although the distribution of PMCA is crucial for its function, the molecular mechanisms that regulate the localization of PMCA isoforms are not well understood. PLEKHA7 is implicated by genetic studies in hypertension and the regulation of calcium handling. PLEKHA7 recruits the small adapter protein PDZD11 to adherens junctions, and together they control the trafficking and localization of plasma membrane associated proteins, including the Menkes copper ATPase. Since PDZD11 binds to the C-terminal domain of b-isoforms of PMCA, PDZD11 and its interactor PLEKHA7 could control the localization and activity of PMCA. Here, we test this hypothesis using cultured cell model systems. We show using immunofluorescence microscopy and a surface biotinylation assay that KO of either PLEKHA7 or PDZD11 in mouse kidney collecting duct epithelial cells results in increased accumulation of endogenous PMCA at lateral cell–cell contacts and PDZ-dependent ectopic apical localization of exogenous PMCA4x/b isoform. In HeLa cells, coexpression of PDZD11 reduces membrane accumulation of overexpressed PMCA4x/b, and analysis of cytosolic calcium transients shows that PDZD11 counteracts calcium extrusion activity of overexpressed PMCA4x/b, but not PMCA4x/a, which lacks the PDZ-binding motif. Moreover, KO of PDZD11 in either endothelial (bEnd.3) or epithelial (mouse kidney collecting duct) cells increases the rate of calcium extrusion. Collectively, these results suggest that the PLEKHA7–PDZD11 complex modulates calcium homeostasis by regulating the localization of PMCA.
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Affiliation(s)
- Sophie Sluysmans
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Andrea Salmaso
- Department of Biology, University of Padua, Padua, Italy
| | - Florian Rouaud
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Isabelle Méan
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Marisa Brini
- Department of Biology, University of Padua, Padua, Italy.
| | - Sandra Citi
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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99980
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Pawlina-Tyszko K, Semik-Gurgul E, Ząbek T, Witkowski M. Methylation Status of Gene Bodies of Selected microRNA Genes Associated with Neoplastic Transformation in Equine Sarcoids. Cells 2022; 11:1917. [PMID: 35741046 DOI: 10.3390/cells11121917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 02/04/2023] Open
Abstract
Horses are of great importance in recreation, livestock production, as working animals in poorly developed countries, and for equine-assisted therapy. Equine sarcoids belong to the most commonly diagnosed tumors in this species. They may cause discomfort, pain, and can lead to the permanent impairment of motor function. The molecular bases of their formation are still under investigation. Our previous studies revealed altered microRNA (miRNA) expression and DNA methylation levels in sarcoid tumors. Abnormal patterns of methylation may be responsible for changes in gene expression levels, including microRNAs. Recently, the DNA methylation of gene bodies has also been shown to have an impact on gene expression. Thus, the aim of the study was to investigate the methylation pattern of gene bodies of chosen miRNAs identified in sarcoid tissue (miR-101, miR-10b, miR-200a, and miR-338-3p), which have also been established to play roles in neoplastic transformation. To this end, we applied qRT-PCR, Bisulfite Sequencing PCR (BSP), and Mquant methods. As a result, we identified the statistically significant downregulation of pri-mir-101-1, pri-mir-10b, and pri-mir-200a in the sarcoid samples in comparison to the control. The DNA methylation analysis revealed their hypermethylation. This suggests that DNA methylation may be one mechanism responsible for the downregulation of theses miRNAs. However, the identified differences in the methylation levels are not very high, which implies that other mechanisms may also underlie the downregulation of the expression of these miRNAs in equine sarcoids. For the first time, the results obtained shed light on microRNA expression regulation by gene body methylation in equine sarcoids and provide bases for further deeper studies on other mechanisms influencing the miRNA repertoire.
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99981
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Avramovic D, Archaimbault SA, Kemble AM, Gruener S, Lazendic M, Westenskow PD. TGFβ1 Induces Senescence and Attenuated VEGF Production in Retinal Pericytes. Biomedicines 2022; 10:biomedicines10061404. [PMID: 35740425 PMCID: PMC9219633 DOI: 10.3390/biomedicines10061404] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/23/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/24/2022] Open
Abstract
Diabetic retinopathy (DR) is a microvascular disease of the retina and a serious complication of type I and type II diabetes mellitus. DR affects working-age populations and can cause permanent vision loss if left untreated. The standard of care for proliferative DR is inhibiting VEGF. However, the mechanisms that induce excessive VEGF production in the retina remain elusive, although some evidence links elevated VEGF in the diabetic retina with local and systemic TGFβ1 upexpression. Here, we present evidence from animal models of disease suggesting that excessive TGFβ1 production in the early DR is correlated with VEGF mRNA and protein production by senescent pericytes and other retinal cells. Collectively, these results confirm that TGFβ1 is strongly implicated in the vascular complications of DR.
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Affiliation(s)
- Dragana Avramovic
- Ocular Technologies, Immunology, Infectious Diseases and Ophthalmology, Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland; (S.A.A.); (S.G.); (M.L.)
- Correspondence: (D.A.); (P.D.W.)
| | - Sébastien A. Archaimbault
- Ocular Technologies, Immunology, Infectious Diseases and Ophthalmology, Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland; (S.A.A.); (S.G.); (M.L.)
| | - Alicia M. Kemble
- Neuroscience and Rare Disease, Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland;
| | - Sabine Gruener
- Ocular Technologies, Immunology, Infectious Diseases and Ophthalmology, Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland; (S.A.A.); (S.G.); (M.L.)
| | - Mirjana Lazendic
- Ocular Technologies, Immunology, Infectious Diseases and Ophthalmology, Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland; (S.A.A.); (S.G.); (M.L.)
| | - Peter D. Westenskow
- Ocular Technologies, Immunology, Infectious Diseases and Ophthalmology, Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland; (S.A.A.); (S.G.); (M.L.)
- Correspondence: (D.A.); (P.D.W.)
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99982
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Labadie J, Swafford B, DePena M, Tietje K, Page R, Patterson-Kane J. Cohort profile: The Golden Retriever Lifetime Study (GRLS). PLoS One 2022; 17:e0269425. [PMID: 35679242 PMCID: PMC9182714 DOI: 10.1371/journal.pone.0269425] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
The aim of this article is to provide a detailed description of the Golden Retriever Lifetime Study (GRLS), a prospective cohort study investigating nutritional, environmental, lifestyle, and genetic risk factors for cancer and other common diseases in dogs. Primary outcomes of interest include hemangiosarcoma, lymphoma, osteosarcoma, and high-grade mast cell tumors. Secondary outcomes of interest include other cancers, hypothyroidism, epilepsy, atopy, otitis externa, hip dysplasia, heart failure, and renal failure. A total of 3,044 United States Golden Retrievers aged 6 months to 2 years completed baseline enrollment from June 2012 to April 2015. As of May 31, 2021, 2,251 dogs remain engaged in the study, 352 have died, and 441 are lost to follow-up. Extensive annual questionnaires completed by owners and veterinarians gather information about lifestyle, environmental exposures, physical activity, reproductive history, behavior, diet, medications, and diagnoses. Dogs also have annual veterinary examinations and biospecimen collection (blood, serum, hair, nails, feces, urine) for biobanking. Additional reporting, including histology and tumor biobanking, is conducted for any malignancies or deaths. When an animal dies, full medical records are obtained, and necropsies are requested at owner discretion. Full or partial necropsies have been performed on 218 dogs. Questionnaire data are freely available to researchers with approved credentials who agree to a data use agreement. In addition, researchers can submit proposals to utilize biospecimens or obtain additional data.
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Affiliation(s)
- Julia Labadie
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
- * E-mail:
| | - Brenna Swafford
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
| | - Mara DePena
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
| | - Kathy Tietje
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
| | - Rodney Page
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, United States of America
| | - Janet Patterson-Kane
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
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99983
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Chen L, Li J, Yuan R, Wang Y, Zhang J, Lin Y, Wang L, Zhu X, Zhu W, Bai J, Kong F, Zeng B, Lu L, Ma J, Long K, Jin L, Huang Z, Huo J, Gu Y, Wang D, Mo D, Li D, Tang Q, Li X, Wu J, Chen Y, Li M. Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver. Cell Discov 2022; 8:56. [PMID: 35701393 PMCID: PMC9197842 DOI: 10.1038/s41421-022-00416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/07/2021] [Accepted: 04/28/2022] [Indexed: 11/28/2022] Open
Abstract
Liver development is a complex process that is regulated by a series of signaling pathways. Three-dimensional (3D) chromatin architecture plays an important role in transcriptional regulation; nonetheless, its dynamics and role in the rapid transition of core liver functions during development and obesity-induced metabolic stress remain largely unexplored. To investigate the dynamic chromatin architecture during liver development and under metabolic stress, we generated high-resolution maps of chromatin architecture for porcine livers across six major developmental stages (from embryonic day 38 to the adult stage) and under a high-fat diet-induced obesity. The characteristically loose chromatin architecture supports a highly plastic genome organization during early liver development, which fundamentally contributes to the rapid functional transitions in the liver after birth. We reveal the multi-scale reorganization of chromatin architecture and its influence on transcriptional regulation of critical signaling processes during liver development, and show its close association with transition in hepatic functions (i.e., from hematopoiesis in the fetus to metabolism and immunity after birth). The limited changes in chromatin structure help explain the observed metabolic adaptation to excessive energy intake in pigs. These results provide a global overview of chromatin architecture dynamics associated with the transition of physiological liver functions between prenatal development and postnatal maturation, and a foundational resource that allows for future in-depth functional characterization.
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Affiliation(s)
- Luxi Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renqiang Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lina Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.,Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xingxing Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wei Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jingyi Bai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fanli Kong
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zeng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lu Lu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jinlong Huo
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Danyang Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiangwei Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
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99984
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Zhang P, Chen L, Wu S, Ye B, Chen C, Shi L. Construction of a Metabolism-Related Long Non-Coding RNAs-Based Risk Score Model of Hepatocellular Carcinoma for Prognosis and Personalized Treatment Prediction. Pathol Oncol Res 2022; 28:1610066. [PMID: 35685867 PMCID: PMC9171512 DOI: 10.3389/pore.2022.1610066] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022]
Abstract
Background: Long non-coding RNAs (lncRNAs) play a key regulatory role in tumor metabolism. Although hepatocellular carcinoma (HCC) is a metabolic disease, there have been few systematic reports on the association between lncRNA expression and metabolism in HCC. Results: In this study, we screened 557 metabolism-related lncRNAs in HCC. A risk score model based on 13 metabolism-related lncRNA pairs was constructed to predict the outcome and drug response in HCC. The risk score model presented a better prediction of the outcomes than that with common clinicopathological characteristics, such as tumor stage, grade, and status and aneuploidy score in both training and testing cohorts. In addition, patients in the high-risk group exhibited higher responses to gemcitabine and epothilone, whereas those in the low-risk group were more sensitive to metformin and nilotinib. Conclusion: The metabolism-related lncRNAs-based risk score model and the other findings of this study may be helpful for HCC prognosis and personalized treatment prediction.
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Affiliation(s)
- Peichen Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liping Chen
- Department of Pharmacy, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shengjie Wu
- Department of Pharmacy, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Bailiang Ye
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chao Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lingyan Shi
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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99985
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Kobayashi S, Nagafuchi Y, Shoda H, Fujio K. The Pathophysiological Roles of Regulatory T Cells in the Early Phase of Systemic Sclerosis. Front Immunol 2022; 13:900638. [PMID: 35686127 PMCID: PMC9172592 DOI: 10.3389/fimmu.2022.900638] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Systemic sclerosis (SSc) is an autoimmune disease that is characterized by vascular damage and fibrosis. Both clinical manifestations and immunological disturbances are diverse according to the disease duration. Particularly, changes in immunological processes are prominent in the early phase of SSc. The orchestration of several subsets of immune cells promotes autoimmune responses and inflammation, and eventually stimulates pro-fibrotic processes. Many reports have indicated that CD4+ T cells play pivotal roles in pathogenesis in the early phase of SSc. In particular, the pathogenic roles of regulatory T (Treg) cells have been investigated. Although the results were controversial, recent reports suggested an increase of Treg cells in the early phase of SSc patients. Treg cells secrete transforming growth factor-β (TGF-β), which promotes myofibroblast activation and fibrosis. In addition, the dysfunction of Treg cells in the early phase of SSc was reported, which results in the development of autoimmunity and inflammation. Notably, Treg cells have the plasticity to convert to T-helper17 (Th17) cells under pro-inflammatory conditions. Th17 cells secrete IL-17A, which could also promote myofibroblast transformation and fibrosis and contributes to vasculopathy, although the issue is still controversial. Our recent transcriptomic comparison between the early and late phases of SSc revealed a clear difference of gene expression patterns only in Treg cells. The gene signature of an activated Treg cell subpopulation was expanded in the early phase of SSc and the oxidative phosphorylation pathway was enhanced, which can promote Th17 differentiation. And this result was accompanied by the increase in Th17 cells frequency. Therefore, an imbalance between Treg and Th17 cells could also have an important role in the pathogenesis of the early phase of SSc. In this review, we outlined the roles of Treg cells in the early phase of SSc, summarizing the data of both human and mouse models. The contributions of Treg cells to autoimmunity, vasculopathy, and fibrosis were revealed, based on the dysfunction and imbalance of Treg cells. We also referred to the potential development in treatment strategies in SSc.
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Affiliation(s)
- Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan.,Department of Medicine and Rheumatology, Tokyo Metropolitan Geriatric Hospital, Itabashi-ku, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
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99986
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Choi S, Lee HS, Cho N, Kim I, Cheon S, Park C, Kim EM, Kim W, Kim KK. RBFOX2-regulated TEAD1 alternative splicing plays a pivotal role in Hippo-YAP signaling. Nucleic Acids Res 2022; 50:8658-8673. [PMID: 35699208 PMCID: PMC9410899 DOI: 10.1093/nar/gkac509] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/15/2021] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/14/2022] Open
Abstract
Alternative pre-mRNA splicing is key to proteome diversity; however, the biological roles of alternative splicing (AS) in signaling pathways remain elusive. Here, we focus on TEA domain transcription factor 1 (TEAD1), a YAP binding factor in the Hippo signaling pathway. Public database analyses showed that expression of YAP-TEAD target genes negatively correlated with the expression of a TEAD1 isoform lacking exon 6 (TEAD1ΔE6) but did not correlate with overall TEAD1 expression. We confirmed that the transcriptional activity and oncogenic properties of the full-length TEAD1 isoform were greater than those of TEAD1ΔE6, with the difference in transcription related to YAP interaction. Furthermore, we showed that RNA-binding Fox-1 homolog 2 (RBFOX2) promoted the inclusion of TEAD1 exon 6 via binding to the conserved GCAUG element in the downstream intron. These results suggest a regulatory mechanism of RBFOX2-mediated TEAD1 AS and provide insight into AS-specific modulation of signaling pathways.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hyo Seong Lee
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Inyoung Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seongmin Cheon
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea.,Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Wantae Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
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99987
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Zhou Q. Progress in modern reproductive biology research in China. Biol Reprod 2022; 107:3-11. [PMID: 35699410 DOI: 10.1093/biolre/ioac122] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Reproductive biology is closely associated with human health and social progress. Modern reproductive biology research in China began in the 1930s. Advances in science, technology, government support and international collaborations spawned the rapid growth of reproductive biology research in China. While the development of reproductive biology has provided both theoretical knowledge and applicable technologies, it has also generated new social and ethical concerns. This review summarizes and highlights the contributions of modern reproductive biology research in China, with a specific focus on aspects that are most related to human reproduction and health.
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Affiliation(s)
- Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
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99988
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Khantakova D, Brioschi S, Molgora M. Exploring the Impact of TREM2 in Tumor-Associated Macrophages. Vaccines (Basel) 2022; 10:vaccines10060943. [PMID: 35746551 PMCID: PMC9227554 DOI: 10.3390/vaccines10060943] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 04/30/2022] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary TREM2+ macrophages were recently reported to be highly enriched and associated with immunosuppression in various cancer types. Hence, TREM2 targeting represents a new promising approach for cancer treatment that is based on reprogramming of tumor-associated macrophages to reshape anti-tumor immunity and overcome resistance to current therapies. Abstract Tumor-associated macrophages (TAMs) represent a key component of the tumor microenvironment and are generally associated with immunosuppression and poor prognosis. TREM2 is a transmembrane receptor of the immunoglobulin superfamily expressed in myeloid cells. TREM2 has been extensively studied in microglia and neurodegenerative diseases and recently emerged as a marker of pro-tumorigenic macrophages. The accumulation of TREM2-expressing TAMs was reported across numerous cancer patients and tumor models. TREM2 genetic blockade or TREM2 targeting with antibodies resulted in improved tumor control, enhanced response to anti-PD1, and significant changes in the tumor immune landscape. Preclinical studies paved the way for an ongoing clinical trial with a TREM2 depleting antibody and inspired further exploration of TREM2 targeting therapies. Here, we review the current knowledge about the impact of TREM2 in cancer, with an emphasis on the TREM2+ macrophage signature across different cancer types, the contribution of TREM2 to TAM phenotype and function, and the promising effects of TREM2 modulation.
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99989
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Chrisman B, He C, Jung JY, Stockham N, Paskov K, Washington P, Wall DP. The human "contaminome": bacterial, viral, and computational contamination in whole genome sequences from 1000 families. Sci Rep 2022; 12:9863. [PMID: 35701436 DOI: 10.1038/s41598-022-13269-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/18/2022] [Indexed: 01/11/2023] Open
Abstract
The unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1000 families and nearly 5000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies. We present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes. Both experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.
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99990
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Sapkota Y, Ehrhardt MJ, Qin N, Wang Z, Liu Q, Qiu W, Shelton K, Shao Y, Plyler E, Mulder HL, Easton J, Michael JR, Burridge PW, Wang X, Wilson CL, Jefferies JL, Chow EJ, Oeffinger KC, Morton LM, Li C, Yang JJ, Zhang J, Bhatia S, Mulrooney DA, Hudson MM, Robison LL, Armstrong GT, Yasui Y. A novel locus on 6p21.2 for cancer treatment-induced cardiac dysfunction among childhood cancer survivors. J Natl Cancer Inst 2022; 114:1109-1116. [PMID: 35698272 DOI: 10.1093/jnci/djac115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Adult survivors of childhood cancer are at increased risk of cardiac late effects. METHODS Using whole-genome sequencing data from 1,870 survivors of European ancestry in the St. Jude Lifetime Cohort (SJLIFE) study, genetic variants were examined for association with ejection fraction (EF) and clinically assessed cancer therapy-induced cardiac dysfunction (CCD). Significant findings were validated in 301 SJLIFE survivors of African ancestry and 4,020 survivors of European ancestry from the Childhood Cancer Survivor Study (CCSS). All statistical tests were 2-sided. RESULTS A variant near KCNK17 showed genome-wide significant association with EF (rs2815063-A: EF reduction = 1.6%; P = 2.1 × 10-8) in SJLIFE survivors of European ancestry, which replicated in SJLIFE survivors of African ancestry (EF reduction: 1.5%; P = .004). The rs2815063-A also showed a 1.80-fold (P = .008) risk of severe/disabling or life-threatening CCD and replicated in 4,020 CCSS survivors of European ancestry (OR = 1.40; P = .039). Notably, rs2815063-A was specifically associated among survivors exposed to doxorubicin only, with a stronger effect on EF (3.3% EF reduction) and CCD (2.97-fold). Whole blood DNA methylation data in 1,651 SJLIFE survivors of European ancestry showed significant correlation of rs2815063-A with dysregulation of KCNK17 enhancers (false discovery rate <5%), which replicated in 263 survivors of African ancestry. Consistently, the rs2815063-A was associated with KCNK17 downregulation based on RNA-sequencing of 75 survivors. CONCLUSIONS Leveraging the two largest cohorts of childhood cancer survivors in North America and survivor-specific polygenomic functional data, we identified a novel risk locus for CCD which showed specificity with doxorubicin-induced cardiac dysfunction and highlighted dysregulation of KCNK17 as the likely molecular mechanism underlying this genetic association.
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Affiliation(s)
- Yadav Sapkota
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Na Qin
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaoming Wang
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qi Liu
- University of Alberta, Edmonton, AB, Canada
| | - Weiyu Qiu
- University of Alberta, Edmonton, AB, Canada
| | - Kyla Shelton
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ying Shao
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Emily Plyler
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - John Easton
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | | | | | - John L Jefferies
- The University of Tennessee Heath Science Center, Memphis, TN, USA
| | - Eric J Chow
- Fred Hutchinson Cancer Research Center, WA, USA
| | | | | | - Chunliang Li
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Smita Bhatia
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | - Yutaka Yasui
- St. Jude Children's Research Hospital, Memphis, TN, USA
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99991
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Inoue R, Tsuno T, Togashi Y, Okuyama T, Sato A, Nishiyama K, Kyohara M, Li J, Fukushima S, Kin T, Miyashita D, Shiba Y, Atobe Y, Kiyonari H, Bando K, Shapiro AJ, Funakoshi K, Kulkarni RN, Terauchi Y, Shirakawa J. Uncoupling protein 2 and aldolase B impact insulin release by modulating mitochondrial function and Ca 2+ release from the ER. iScience 2022; 25:104603. [PMID: 35800776 PMCID: PMC9253497 DOI: 10.1016/j.isci.2022.104603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 07/22/2021] [Revised: 03/25/2022] [Accepted: 06/08/2022] [Indexed: 02/02/2023] Open
Abstract
Uncoupling protein 2 (UCP2), a mitochondrial protein, is known to be upregulated in pancreatic islets of patients with type 2 diabetes (T2DM); however, the pathological significance of this increase in UCP2 expression is unclear. In this study, we highlight the molecular link between the increase in UCP2 expression in β-cells and β-cell failure by using genetically engineered mice and human islets. β-cell-specific UCP2-overexpressing transgenic mice (βUCP2Tg) exhibited glucose intolerance and a reduction in insulin secretion. Decreased mitochondrial function and increased aldolase B (AldB) expression through oxidative-stress-mediated pathway were observed in βUCP2Tg islets. AldB, a glycolytic enzyme, was associated with reduced insulin secretion via mitochondrial dysfunction and impaired calcium release from the endoplasmic reticulum (ER). Taken together, our findings provide a new mechanism of β-cell dysfunction by UCP2 and AldB. Targeting the UCP2/AldB axis is a promising approach for the recovery of β-cell function.
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Affiliation(s)
- Ryota Inoue
- Laboratory of Diabetes and Metabolic Disorders, Institute for Molecular and Cellular Regulation (IMCR), Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan,Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Takahiro Tsuno
- Laboratory of Diabetes and Metabolic Disorders, Institute for Molecular and Cellular Regulation (IMCR), Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan,Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Yu Togashi
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Tomoko Okuyama
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Aoi Sato
- Laboratory of Diabetes and Metabolic Disorders, Institute for Molecular and Cellular Regulation (IMCR), Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan
| | - Kuniyuki Nishiyama
- Laboratory of Diabetes and Metabolic Disorders, Institute for Molecular and Cellular Regulation (IMCR), Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan,Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Mayu Kyohara
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Jinghe Li
- Laboratory of Diabetes and Metabolic Disorders, Institute for Molecular and Cellular Regulation (IMCR), Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan,Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Setsuko Fukushima
- Laboratory of Diabetes and Metabolic Disorders, Institute for Molecular and Cellular Regulation (IMCR), Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan
| | - Tatsuya Kin
- Clinical Islet Laboratory and Clinical Islet Transplant Program, University of Alberta, Edmonton, AB T6G2C8, Canada
| | - Daisuke Miyashita
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Yusuke Shiba
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Yoshitoshi Atobe
- Department of Neuroanatomy, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Kana Bando
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - A.M. James Shapiro
- Clinical Islet Laboratory and Clinical Islet Transplant Program, University of Alberta, Edmonton, AB T6G2C8, Canada
| | - Kengo Funakoshi
- Department of Neuroanatomy, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Rohit N. Kulkarni
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Yasuo Terauchi
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Jun Shirakawa
- Laboratory of Diabetes and Metabolic Disorders, Institute for Molecular and Cellular Regulation (IMCR), Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan,Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan,Corresponding author
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99992
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Abstract
Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead to genetic instability. Most of these rearrangements arise from recombination, repair, or replication mechanisms that occur after a double-strand break or the stalling/breakage of a replication fork. Here, we review the mechanisms of formation of structural rearrangements, highlighting their main features and differences. The most important mechanisms of constitutional chromosomal alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling and Template Switching (FoSTeS), and Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis and in the formation of complex chromosomal rearrangements, inverted duplications associated with terminal deletions, and ring chromosomes is also outlined. We reinforce the importance of high-resolution analysis to determine the DNA sequence at, and near, their breakpoints in order to infer the mechanisms of formation of structural rearrangements and to reveal how cells respond to DNA damage and repair broken ends.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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99993
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Kiani Shabestari S, Morabito S, Danhash EP, McQuade A, Sanchez JR, Miyoshi E, Chadarevian JP, Claes C, Coburn MA, Hasselmann J, Hidalgo J, Tran KN, Martini AC, Chang Rothermich W, Pascual J, Head E, Hume DA, Pridans C, Davtyan H, Swarup V, Blurton-Jones M. Absence of microglia promotes diverse pathologies and early lethality in Alzheimer's disease mice. Cell Rep 2022; 39:110961. [PMID: 35705056 PMCID: PMC9285116 DOI: 10.1016/j.celrep.2022.110961] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [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: 11/02/2021] [Revised: 04/13/2022] [Accepted: 05/24/2022] [Indexed: 11/03/2022] Open
Abstract
Microglia are strongly implicated in the development and progression of Alzheimer's disease (AD), yet their impact on pathology and lifespan remains unclear. Here we utilize a CSF1R hypomorphic mouse to generate a model of AD that genetically lacks microglia. The resulting microglial-deficient mice exhibit a profound shift from parenchymal amyloid plaques to cerebral amyloid angiopathy (CAA), which is accompanied by numerous transcriptional changes, greatly increased brain calcification and hemorrhages, and premature lethality. Remarkably, a single injection of wild-type microglia into adult mice repopulates the microglial niche and prevents each of these pathological changes. Taken together, these results indicate the protective functions of microglia in reducing CAA, blood-brain barrier dysfunction, and brain calcification. To further understand the clinical implications of these findings, human AD tissue and iPSC-microglia were examined, providing evidence that microglia phagocytose calcium crystals, and this process is impaired by loss of the AD risk gene, TREM2.
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Affiliation(s)
- Sepideh Kiani Shabestari
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Samuel Morabito
- Mathematical, Computational and System Biology (MCSB) Program, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Emma Pascal Danhash
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Amanda McQuade
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Jessica Ramirez Sanchez
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Emily Miyoshi
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA
| | - Jean Paul Chadarevian
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Christel Claes
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Morgan Alexandra Coburn
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Jonathan Hasselmann
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Jorge Hidalgo
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Kayla Nhi Tran
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA
| | - Alessandra C Martini
- Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA; Department of Pathology & Laboratory Medicine, UC Irvine, Irvine, CA 92697, USA
| | | | - Jesse Pascual
- Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA; Department of Pathology & Laboratory Medicine, UC Irvine, Irvine, CA 92697, USA
| | - Elizabeth Head
- Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA; Department of Pathology & Laboratory Medicine, UC Irvine, Irvine, CA 92697, USA
| | - David A Hume
- Mater Research Institute-University of Queensland, Brisbane, Australia
| | - Clare Pridans
- University of Edinburgh Centre for Inflammation Research, Edinburgh, UK; Simons Initiative for the Developing Brain Centre, University of Edinburgh, Edinburgh, UK; The Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK
| | - Hayk Davtyan
- Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology & Behavior, UC Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA.
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99994
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Roman AJ, Cideciyan AV, Wu V, Mascio AA, Krishnan AK, Garafalo AV, Jacobson SG. Mobility test to assess functional vision in dark-adapted patients with Leber congenital amaurosis. BMC Ophthalmol 2022; 22:266. [PMID: 35701753 DOI: 10.1186/s12886-022-02475-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/01/2022] [Indexed: 11/30/2022] Open
Abstract
Background Inherited retinal degenerations (IRDs) affect daylight and night vision to different degrees. In the current work, we devise a method to quantify mobility under dark-adapted conditions in patients with severe childhood blindness due to Leber congenital amaurosis (LCA). Mobility thresholds from two different LCA genotypes are compared to dark-adapted vision measurements using the full-field stimulus test (FST), a conventional desktop outcome measure of rod vision. Methods A device consisting of vertical LED strips on a plane resembling a beaded curtain was programmed to produce a rectangular pattern target defining a ‘door’ of varying luminance that could appear at one of three positions. Mobility performance was evaluated by letting the subject walk from a fixed starting position ~ 4 m away from the device with instructions to touch the door. Success was defined as the subject touching within the ‘door’ area. Ten runs were performed and the process was repeated for different levels of luminance. Tests were performed monocularly in dark-adapted and dilated eyes. Results from LCA patients with the GUCY2D and CEP290 genotypes and normal subjects were analyzed using logistic regression to estimate the mobility threshold for successful navigation. The relation of thresholds for mobility, FST and visual acuity were quantified using linear regression. Results Normal subjects had mobility thresholds near limits of dark-adapted rod vision. GUCY2D-LCA patients had a wide range of mobility thresholds from within 1 log of normal to greater than 8 log abnormal. CEP290-LCA patients had abnormal mobility thresholds that were between 5 and 6 log from normal. Sensitivity loss estimates using FST related linearly to the mobility thresholds which were not correlated with visual acuity. Conclusions The mobility task we developed can quantify functional vision in severely disabled patients with LCA. Taken together with other outcome measures of rod and cone photoreceptor-mediated vision, dark-adapted functional vision should provide a more complete understanding of the natural history and effects of treatment in patients with LCA. Supplementary Information The online version contains supplementary material available at 10.1186/s12886-022-02475-y.
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99995
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Moaeen-Ud-Din M, Danish Muner R, Khan MS. Genome wide association study identifies novel candidate genes for growth and body conformation traits in goats. Sci Rep 2022; 12:9891. [PMID: 35701479 DOI: 10.1038/s41598-022-14018-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Pakistan is third largest country in term of goat population with distinct characteristics of breeds and estimated population of 78.2 million. Punjab province has 37% of country's total population with seven important documented goat breeds namely Beetal, Daira Din Pannah, Nachi, Barbari, Teddi, Pahari and Pothwari. There is paucity of literature on GWAS for economically important traits i.e., body weight and morphometric measurements. Therefore, we performed GWAS using 50 K SNP Chip for growth in term of age adjusted body weight and morphometric measurements in order to identify genomic regions influencing these traits among Punjab goat breeds. Blood samples were collected from 879 unrelated animals of seven goat breeds along with data for body weight and morphometric measurements including body length, body height, pubic bone length, heart girth and chest length. Genomic DNA was extracted and genotyped using 50 K SNP bead chip. Association of genotypic data with the phenotypic data was performed using Plink 1.9 software. Linear mixed model was used for the association study. Genes were annotated from Capra hircus genome using assembly ARS1. We have identified a number of highly significant SNPs and respective candidate genes associated with growth and body conformation traits. The functional aspects of these candidate genes suggested their potential role in body growth. Moreover, pleiotropic effects were observed for some SNPs for body weight and conformation traits. The results of current study contributed to a better understanding of genes influencing growth and body conformation traits in goat.
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99996
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Di Miceli M, Martinat M, Rossitto M, Aubert A, Alashmali S, Bosch-Bouju C, Fioramonti X, Joffre C, Bazinet RP, Layé S. Dietary Long-Chain n-3 Polyunsaturated Fatty Acid Supplementation Alters Electrophysiological Properties in the Nucleus Accumbens and Emotional Behavior in Naïve and Chronically Stressed Mice. Int J Mol Sci 2022; 23:ijms23126650. [PMID: 35743093 PMCID: PMC9224532 DOI: 10.3390/ijms23126650] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 02/01/2023] Open
Abstract
Long-chain (LC) n-3 polyunsaturated fatty acids (PUFAs) have drawn attention in the field of neuropsychiatric disorders, in particular depression. However, whether dietary supplementation with LC n-3 PUFA protects from the development of mood disorders is still a matter of debate. In the present study, we studied the effect of a two-month exposure to isocaloric diets containing n-3 PUFAs in the form of relatively short-chain (SC) (6% of rapeseed oil, enriched in α-linolenic acid (ALA)) or LC (6% of tuna oil, enriched in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)) PUFAs on behavior and synaptic plasticity of mice submitted or not to a chronic social defeat stress (CSDS), previously reported to alter emotional and social behavior, as well as synaptic plasticity in the nucleus accumbens (NAc). First, fatty acid content and lipid metabolism gene expression were measured in the NAc of mice fed a SC (control) or LC n-3 (supplemented) PUFA diet. Our results indicate that LC n-3 supplementation significantly increased some n-3 PUFAs, while decreasing some n-6 PUFAs. Then, in another cohort, control and n-3 PUFA-supplemented mice were subjected to CSDS, and social and emotional behaviors were assessed, together with long-term depression plasticity in accumbal medium spiny neurons. Overall, mice fed with n-3 PUFA supplementation displayed an emotional behavior profile and electrophysiological properties of medium spiny neurons which was distinct from the ones displayed by mice fed with the control diet, and this, independently of CSDS. Using the social interaction index to discriminate resilient and susceptible mice in the CSDS groups, n-3 supplementation promoted resiliency. Altogether, our results pinpoint that exposure to a diet rich in LC n-3 PUFA, as compared to a diet rich in SC n-3 PUFA, influences the NAc fatty acid profile. In addition, electrophysiological properties and emotional behavior were altered in LC n-3 PUFA mice, independently of CSDS. Our results bring new insights about the effect of LC n-3 PUFA on emotional behavior and synaptic plasticity.
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Affiliation(s)
- Mathieu Di Miceli
- Laboratoire NutriNeuro, UMR INRAE 1286, Bordeaux INP, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (M.D.M.); (M.M.); (M.R.); (A.A.); (C.B.-B.); (X.F.); (C.J.)
- Worcester Biomedical Research Group, School of Science and the Environment, University of Worcester, Worcester WR2 6AJ, UK
- International Research Network Food4BrainHealth;
| | - Maud Martinat
- Laboratoire NutriNeuro, UMR INRAE 1286, Bordeaux INP, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (M.D.M.); (M.M.); (M.R.); (A.A.); (C.B.-B.); (X.F.); (C.J.)
- International Research Network Food4BrainHealth;
| | - Moïra Rossitto
- Laboratoire NutriNeuro, UMR INRAE 1286, Bordeaux INP, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (M.D.M.); (M.M.); (M.R.); (A.A.); (C.B.-B.); (X.F.); (C.J.)
- International Research Network Food4BrainHealth;
| | - Agnès Aubert
- Laboratoire NutriNeuro, UMR INRAE 1286, Bordeaux INP, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (M.D.M.); (M.M.); (M.R.); (A.A.); (C.B.-B.); (X.F.); (C.J.)
- International Research Network Food4BrainHealth;
| | - Shoug Alashmali
- Department of Clinical Nutrition, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 22254, Saudi Arabia;
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Clémentine Bosch-Bouju
- Laboratoire NutriNeuro, UMR INRAE 1286, Bordeaux INP, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (M.D.M.); (M.M.); (M.R.); (A.A.); (C.B.-B.); (X.F.); (C.J.)
- International Research Network Food4BrainHealth;
| | - Xavier Fioramonti
- Laboratoire NutriNeuro, UMR INRAE 1286, Bordeaux INP, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (M.D.M.); (M.M.); (M.R.); (A.A.); (C.B.-B.); (X.F.); (C.J.)
- International Research Network Food4BrainHealth;
| | - Corinne Joffre
- Laboratoire NutriNeuro, UMR INRAE 1286, Bordeaux INP, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (M.D.M.); (M.M.); (M.R.); (A.A.); (C.B.-B.); (X.F.); (C.J.)
- International Research Network Food4BrainHealth;
| | - Richard P. Bazinet
- International Research Network Food4BrainHealth;
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Sophie Layé
- Laboratoire NutriNeuro, UMR INRAE 1286, Bordeaux INP, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France; (M.D.M.); (M.M.); (M.R.); (A.A.); (C.B.-B.); (X.F.); (C.J.)
- International Research Network Food4BrainHealth;
- Correspondence:
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He J, Bao S, Deng J, Li Q, Ma S, Liu Y, Cui Y, Zhu Y, Wei X, Ding X, Ke K, Chen C. A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree. Gigascience 2022; 11:6608506. [PMID: 35701376 PMCID: PMC9197682 DOI: 10.1093/gigascience/giac042] [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: 05/24/2021] [Revised: 10/31/2021] [Accepted: 03/29/2022] [Indexed: 12/30/2022] Open
Abstract
Artocarpus nanchuanensis (Moraceae), which is naturally distributed in China, is a representative and extremely endangered tree species. In this study, we obtained a high-quality chromosome-scale genome assembly and annotation information for A. nanchuanensis using integrated approaches, including Illumina, Nanopore sequencing platform, and Hi-C. A total of 128.71 Gb of raw Nanopore reads were generated from 20-kb libraries, and 123.38 Gb of clean reads were obtained after filtration with 160.34× coverage depth and a 17.48-kb average read length. The final assembled A. nanchuanensis genome was 769.44 Mb with a 2.09 Mb contig N50, and 99.62% (766.50 Mb) of the assembled data was assigned to 28 pseudochromosomes. In total, 39,596 genes (95.10%, 39,596/41,636) were successfully annotated, and 129 metabolic pathways were detected. Plants disease resistance/insect resistance genes, plant–pathogen interaction metabolic pathways, and abundant biosynthesis pathways of vitamins, flavonoid, and gingerol were detected. Unigene reveals the basis of species-specific functions, and gene family in contraction and expansion generally implies strong functional differences in the evolution. Compared with other related species, a total of 512 unigenes, 309 gene families in contraction, and 559 gene families in expansion were detected in A. nanchuanensis. This A. nanchuanensis genome information provides an important resource to expand our understanding of the unique biological processes, nutritional and medicinal benefits, and evolutionary relationship of this species. The study of gene function and metabolic pathway in A. nanchuanensis may reveal the theoretical basis of a special trait in A. nanchuanensis and promote the study and utilization of its rare medicinal value.
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Affiliation(s)
- Jiaoyu He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China
| | - Shanfei Bao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China
| | - Junhang Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China
| | - Qiufu Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China
| | - Shiyu Ma
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China
| | - Yiran Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China
| | - Yanru Cui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China
| | - Yuqi Zhu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China.,Wood Comprehensive Factory of Chengdu, Sichuan 610081, P.R. China
| | - Xia Wei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China
| | - Xianping Ding
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,Chongqing Jinfo Shan Advanced Research Institute, Chongqing 408400, P.R. China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing 408400, P.R. China
| | - Kehui Ke
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Chaojie Chen
- Biomarker Technologies Corporation, Beijing 101300, China
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Dunn PJ, Harvey NR, Maksemous N, Smith RA, Sutherland HG, Haupt LM, Griffiths LR. Investigation of Mitochondrial Related Variants in a Cerebral Small Vessel Disease Cohort. Mol Neurobiol 2022; 59:5366-5378. [PMID: 35699875 PMCID: PMC9395495 DOI: 10.1007/s12035-022-02914-3] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/03/2022] [Indexed: 11/25/2022]
Abstract
Monogenic forms of cerebral small vessel disease (CSVD) can be caused by both variants in nuclear DNA and mitochondrial DNA (mtDNA). Mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is known to have a phenotype similar to Cerebral Autosomal Dominant Arteriopathy with Sub-cortical Infarcts and Leukoencephalopathy (CADASIL), and can be caused by variants in the mitochondrial genome and in several nuclear-encoded mitochondrial protein (NEMP) genes. The aim of this study was to screen for variants in the mitochondrial genome and NEMP genes in a NOTCH3-negative CADASIL cohort, to identify a potential link between mitochondrial dysfunction and CSVD pathology. Whole exome sequencing was performed for 50 patients with CADASIL-like symptomology on the Ion Torrent system. Mitochondrial sequencing was performed using an in-house designed protocol with sequencing run on the Ion GeneStudio S5 Plus (S5 +). NEMP genes and mitochondrial sequencing data were examined for rare (MAF < 0.001), non-synonymous variants that were predicted to have a deleterious effect on the protein. We identified 29 candidate NEMP variants that had links to either MELAS-, encephalopathy-, or Alzheimer’s disease–related phenotypes. Based on these changes, variants affecting POLG, MTO1, LONP1, NDUFAF6, NDUFB3, and TCIRG1 were thought to play a potential role in CSVD pathology in this cohort. Overall, the exploration of the mitochondrial genome identified a potential role for mitochondrial related proteins and mtDNA variants contributing to CSVD pathologies.
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Affiliation(s)
- P J Dunn
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
- Health Sciences and Medicine Faculty, Bond University, 14 University Drive, Robina, Queensland, Australia
| | - N R Harvey
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
- Health Sciences and Medicine Faculty, Bond University, 14 University Drive, Robina, Queensland, Australia
- Department of Medical and Molecular Genetics, Guy's Hospital, Kings College London, London, SE1 9RT, England
| | - N Maksemous
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
| | - R A Smith
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
| | - H G Sutherland
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
| | - L M Haupt
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia
| | - L R Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia.
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Castro-Oropeza R, Piña-Sánchez P. Epigenetic and Transcriptomic Regulation Landscape in HPV+ Cancers: Biological and Clinical Implications. Front Genet 2022; 13:886613. [PMID: 35774512 PMCID: PMC9237502 DOI: 10.3389/fgene.2022.886613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Human Papillomavirus (HPV) is an oncogenic virus that causes the highest number of viral-associated cancer cases and deaths worldwide, with more than 690,000 new cases per year and 342,000 deaths only for cervical cancer (CC). Although the incidence and mortality rates for CC are declining in countries where screening and vaccination programs have been implemented, other types of cancer in which HPV is involved, such as oropharyngeal cancer, are increasing, particularly in men. Mutational and transcriptional profiles of various HPV-associated neoplasms have been described, and accumulated evidence has shown the oncogenic capacity of E6, E7, and E5 genes of high-risk HPV. Interestingly, transcriptomic analysis has revealed that although a vast majority of the human genome is transcribed into RNAs, only 2% of transcripts are translated into proteins. The remaining transcripts lacking protein-coding potential are called non-coding RNAs. In addition to the transfer and ribosomal RNAs, there are regulatory non-coding RNAs classified according to size and structure in long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and small RNAs; such as microRNAs (miRNAs), piwi-associated RNAs (piRNAs), small nucleolar RNAs (snoRNAs) and endogenous short-interfering RNAs. Recent evidence has shown that lncRNAs, miRNAs, and circRNAs are aberrantly expressed under pathological conditions such as cancer. In addition, those transcripts are dysregulated in HPV-related neoplasms, and their expression correlates with tumor progression, metastasis, poor prognosis, and recurrence. Nuclear lncRNAs are epigenetic regulators involved in controlling gene expression at the transcriptional level through chromatin modification and remodeling. Moreover, disruption of the expression profiles of those lncRNAs affects multiple biological processes such as cell proliferation, apoptosis, and migration. This review highlights the epigenetic alterations induced by HPV, from infection to neoplastic transformation. We condense the epigenetic role of non-coding RNA alterations and their potential as biomarkers in transformation’s early stages and clinical applications. We also summarize the molecular mechanisms of action of nuclear lncRNAs to understand better their role in the epigenetic control of gene expression and how they can drive the malignant phenotype of HPV-related neoplasia. Finally, we review several chemical and epigenetic therapy options to prevent and treat HPV-associated neoplasms.
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Liang F, Zhang Y, Wang X, Yang S, Fang T, Zheng S, Zeng L. Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan ( Dimocarpus longan Lour.). Front Plant Sci 2022; 13:923183. [PMID: 35774802 PMCID: PMC9237614 DOI: 10.3389/fpls.2022.923183] [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] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/11/2022] [Indexed: 05/27/2023]
Abstract
Longan (Dimocarpus longan Lour.) is a tropical/subtropical fruit tree of significant economic importance. Floral induction is an essential process for longan flowering and plays decisive effects on the longan yield. Due to the instability of flowering, it is necessary to understand the molecular mechanisms of floral induction in longan. In this study, mRNA and long noncoding RNA (lncRNA) transcriptome sequencing were performed using the apical buds of fruiting branches as materials. A total of 7,221 differential expressions of mRNAs (DEmRNAs) and 3,238 differential expressions of lncRNAs (DElncRNAs) were identified, respectively. KEGG enrichment analysis of DEmRNAs highlighted the importance of starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways during floral induction. Combining the analysis of weighted gene co-expression network (WGCNA) and expression pattern of DEmRNAs in the three pathways, specific transcriptional characteristics at each stage during floral induction and regulatory network involving co-expressed genes were investigated. The results showed that sucrose metabolism and auxin signal transduction may be crucial for the growth and maturity of autumn shoots in September and October (B1-B2 stage); starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways participated in the regulation of floral bud physiological differentiation together in November and December (B3-B4 stage) and the crosstalk among three pathways was also found. Hub genes in the co-expression network and key DEmRNAs in three pathways were identified. The circadian rhythm genes FKF1 and GI were found to activate SOC1gene through the photoperiod core factor COL genes, and they were co-expressed with auxin, gibberellin, abscisic acid, ethylene signaling genes, and sucrose biosynthesis genes at B4 stage. A total of 12 hub-DElncRNAs had potential for positively affecting their distant target genes in three putative key pathways, predominantly in a co-transcriptional manner. A hypothetical model of regulatory pathways and key genes and lncRNAs during floral bud induction in longan was proposed finally. Our studies will provide valuable clues and information to help elucidate the potential molecular mechanisms of floral initiation in longan and woody fruit trees.
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Affiliation(s)
- Fan Liang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yiyong Zhang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaodan Wang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuo Yang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Fang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaoquan Zheng
- Fujian Breeding Engineering Technology Research Center for Longan & Loquat, Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzho, China
| | - Lihui Zeng
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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