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Singh D, Qiu Z, Jonathan SM, Fa P, Thomas H, Prasad CB, Cai S, Wang JJ, Yan C, Zhang X, Venere M, Li Z, Sizemore ST, Wang QE, Zhang J. PP2A B55α inhibits epithelial-mesenchymal transition via regulation of Slug expression in non-small cell lung cancer. Cancer Lett 2024; 598:217110. [PMID: 38986733 DOI: 10.1016/j.canlet.2024.217110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
Abstract
PP2A B55α, encoded by PPP2R2A, acts as a regulatory subunit of the serine/threonine phosphatase PP2A. Despite a frequent loss of heterozygosity of PPP2R2A in cases of non-small cell lung cancer (NSCLC), research on PP2A B55α's functions remains limited and controversial. To investigate the biological roles of PP2A B55α, we conducted bulk RNA-sequencing to assess the impact of PPP2R2A knockdown using two shRNAs in a NSCLC cell line. Gene set enrichment analysis (GSEA) of the RNA-sequencing data revealed significant enrichment of the epithelial-mesenchymal transition (EMT) pathway, with SNAI2 (the gene encoding Slug) emerging as one of the top candidates. Our findings demonstrate that PP2A B55α suppresses EMT, as PPP2R2A deficiency through knockdown or homozygous or hemizygous depletion promotes EMT and metastatic behavior in NSCLC cells, as evidenced by changes in EMT biomarkers, invasion and migration abilities, as well as metastasis in a tail vein assay. Mechanistically, PP2A B55α inhibits EMT by downregulating SNAI2 expression via the GSK3β-β-catenin pathway. Importantly, PPP2R2A deficiency also slows cell proliferation by disrupting DNA replication, particularly in PPP2R2A-/- cells. Furthermore, PPP2R2A deficiency, especially PPP2R2A-/- cells, leads to an increase in the cancer stem cell population, which correlates with enhanced resistance to chemotherapy. Overall, the decrease in PP2A B55α levels due to hemizygous/homozygous depletion heightens EMT and the metastatic or stemness/drug resistance potential of NSCLC cells despite their proliferation disadvantage. Our study highlights the significance of PP2A B55α in EMT and metastasis and suggests that targeting EMT/stemness could be a potential therapeutic strategy for treating PPP2R2A-deficient NSCLC.
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Affiliation(s)
- Deepika Singh
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States
| | - Zhaojun Qiu
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States
| | - Spehar M Jonathan
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States
| | - Pengyan Fa
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States
| | - Hannah Thomas
- The Ohio State University, Columbus, OH, United States
| | - Chandra Bhushan Prasad
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States
| | - Shurui Cai
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States
| | - Jing J Wang
- The Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA, United States
| | - Xiaoli Zhang
- Center for Biostatistics, The Ohio State University, United States; Department of Biomedical Informatics, College of Medicine, The Ohio State University, United States
| | - Monica Venere
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States; The James Comprehensive Cancer Center, Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, United States
| | - Zaibo Li
- Department of Pathology, The Ohio State University Wexner Medical Center, College of Medicine, Columbus, OH, 43210, United States
| | - Steven T Sizemore
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States
| | - Qi-En Wang
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States
| | - Junran Zhang
- The Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center and College of Medicine, Columbus, OH, United States; The James Comprehensive Cancer Center, Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, United States; The James Comprehensive Cancer Center, Center for Metabolism, United States.
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2
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He Q, Li R, Zhong N, Ma J, Nie F, Zhang R. The role and molecular mechanisms of the early growth response 3 gene in schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32969. [PMID: 38327141 DOI: 10.1002/ajmg.b.32969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024]
Abstract
Schizophrenia is a chronic, debilitating mental illness caused by both genetic and environmental factors. Genetic factors play a major role in schizophrenia development. Early growth response 3 (EGR3) is a member of the EGR family, which is associated with schizophrenia. Accumulating studies have investigated the relationship between EGR3 and schizophrenia. However, the role of EGR3 in schizophrenia pathogenesis remains unclear. In the present review, we focus on the progress of research related to the role of EGR3 in schizophrenia, including association studies between EGR3 and schizophrenia, abnormal gene expressional analysis of EGR3 in schizophrenia, biological function studies of EGR3 in schizophrenia, the molecular regulatory mechanism of EGR3 and schizophrenia susceptibility candidate genes, and possible role of EGR3 in the immune system function in schizophrenia. In summary, EGR3 is a schizophrenia risk candidate factor and has comprehensive regulatory roles in schizophrenia pathogenesis. Further studies investigating the molecular mechanisms of EGR3 in schizophrenia are warranted for understanding the pathophysiology of this disorder as well as the development of new therapeutic strategies for the treatment and control of this disorder.
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Affiliation(s)
- Qi He
- School of Basic Medicine, Shaanxi Key Laboratory of Acupuncture and Medicine, Shannxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Ruochun Li
- Department of Medical Technology, Guiyang Healthcare Vocational University, Guiyang, Guizhou, China
| | - Nannan Zhong
- Department of Medical Technology, Guiyang Healthcare Vocational University, Guiyang, Guizhou, China
| | - Jie Ma
- Department of Electron Microscope, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Fayi Nie
- School of Basic Medicine, Shaanxi Key Laboratory of Acupuncture and Medicine, Shannxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Rui Zhang
- Department of Medical Technology, Guiyang Healthcare Vocational University, Guiyang, Guizhou, China
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Zhao X, Wang Y, Mouilleau V, Solak AC, Garcia J, Chen X, Wilkinson CJ, Royer L, Dong Z, Guo S. PCM1 conveys centrosome asymmetry to polarized endosome dynamics in regulating daughter cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599416. [PMID: 38948739 PMCID: PMC11212863 DOI: 10.1101/2024.06.17.599416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Vertebrate radial glia progenitors (RGPs), the principal neural stem cells, balance self-renewal and differentiation through asymmetric cell division (ACD), during which unequal inheritance of centrosomes is observed. Mechanistically, how centrosome asymmetry leads to distinct daughter cell fate remains largely unknown. Here we find that the centrosome protein Pericentriolar Material 1 (Pcm1), asymmetrically distributed at the centrosomes, regulates polarized endosome dynamics and RGP fate. In vivo time-lapse imaging and nanoscale-resolution expansion microscopy of zebrafish embryonic RGPs detect Pcm1 on Notch ligand-containing endosomes, in a complex with the polarity regulator Par-3 and dynein motor. Loss of pcm1 disrupts endosome dynamics, with clonal analysis uncovering increased neuronal production at the expense of progenitors. Pcm1 facilitates an exchange of Rab5b (early) for Rab11a (recycling) endosome markers and promotes the formation of Par-3 and dynein macromolecular complexes on recycling endosomes. Finally, in human-induced pluripotent stem cell-derived brain organoids, PCM1 shows asymmetry and co-localization with PARD3 and RAB11A in mitotic neural progenitors. Our data reveal a new mechanism by which centrosome asymmetry is conveyed by Pcm1 to polarize endosome dynamics and Notch signaling in regulating ACD and progenitor fate.
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Zhang J, Li H, Niswander LA. m 5C methylated lncRncr3-MeCP2 interaction restricts miR124a-initiated neurogenesis. Nat Commun 2024; 15:5136. [PMID: 38879605 PMCID: PMC11180186 DOI: 10.1038/s41467-024-49368-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 06/03/2024] [Indexed: 06/19/2024] Open
Abstract
Coordination of neuronal differentiation with expansion of the neuroepithelial/neural progenitor cell (NEPC/NPC) pool is essential in early brain development. Our in vitro and in vivo studies identify independent and opposing roles for two neural-specific and differentially expressed non-coding RNAs derived from the same locus: the evolutionarily conserved lncRNA Rncr3 and the embedded microRNA miR124a-1. Rncr3 regulates NEPC/NPC proliferation and controls the biogenesis of miR124a, which determines neuronal differentiation. Rncr3 conserved exons 2/3 are cytosine methylated and bound by methyl-CpG binding protein MeCP2, which restricts expression of miR124a embedded in exon 4 to prevent premature neuronal differentiation, and to orchestrate proper brain growth. MeCP2 directly binds cytosine-methylated Rncr3 through previously unrecognized lysine residues and suppresses miR124a processing by recruiting PTBP1 to block access of DROSHA-DGCR8. Thus, miRNA processing is controlled by lncRNA m5C methylation along with the defined m5C epitranscriptomic RNA reader protein MeCP2 to coordinate brain development.
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Affiliation(s)
- Jing Zhang
- Department of Molecular, Cellular, and Developmental Biology. University of Colorado Boulder, Boulder, CO, 80309, USA.
| | - Huili Li
- Department of Molecular, Cellular, and Developmental Biology. University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Lee A Niswander
- Department of Molecular, Cellular, and Developmental Biology. University of Colorado Boulder, Boulder, CO, 80309, USA.
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Begar E, Seyrek E, Firat-Karalar EN. Navigating centriolar satellites: the role of PCM1 in cellular and organismal processes. FEBS J 2024. [PMID: 38825736 DOI: 10.1111/febs.17194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/20/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024]
Abstract
Centriolar satellites are ubiquitous membrane-less organelles that play critical roles in numerous cellular and organismal processes. They were initially discovered through electron microscopy as cytoplasmic granules surrounding centrosomes in vertebrate cells. These structures remained enigmatic until the identification of pericentriolar material 1 protein (PCM1) as their molecular marker, which has enabled their in-depth characterization. Recently, centriolar satellites have come into the spotlight due to their links to developmental and neurodegenerative disorders. This review presents a comprehensive summary of the major advances in centriolar satellite biology, with a focus on studies that investigated their biology associated with the essential scaffolding protein PCM1. We begin by exploring the molecular, cellular, and biochemical properties of centriolar satellites, laying the groundwork for a deeper understanding of their functions and mechanisms at both cellular and organismal levels. We then examine the implications of their dysregulation in various diseases, particularly highlighting their emerging roles in neurodegenerative and developmental disorders, as revealed by organismal models of PCM1. We conclude by discussing the current state of knowledge and posing questions about the adaptable nature of these organelles, thereby setting the stage for future research.
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Affiliation(s)
- Efe Begar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Ece Seyrek
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
- School of Medicine, Koç University, Istanbul, Turkey
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Rubio JM, Kane JM, Tanskanen A, Tiihonen J, Taipale H. Long-term persistence of the risk of agranulocytosis with clozapine compared with other antipsychotics: a nationwide cohort and case-control study in Finland. Lancet Psychiatry 2024; 11:443-450. [PMID: 38697177 DOI: 10.1016/s2215-0366(24)00097-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 05/04/2024]
Abstract
BACKGROUND Agranulocytosis is a life-threatening side-effect of clozapine, the only approved drug for treatment-resistant schizophrenia. The long-term profile of this complication has not yet been well established. Here we aim to describe the risk of clozapine-induced agranulocytosis over the long term. METHODS We used the entire population of Finland to identify people diagnosed with schizophrenia or schizoaffective disorder between 1972 and 2014 and developed a Kaplan-Meier model of time to diagnosis of agranulocytosis during clozapine versus non-clozapine treatment over a 22-year observation period (1996 to 2017). Next, we developed a nested case-control model for agranulocytosis matching by sex, age, time since diagnosis, and being in the incident cohort on a 1 to 5 ratio. Various durations of use for clozapine and non-clozapine antipsychotic treatment were compared to the modal antipsychotic use duration, deriving adjusted odds ratios (aORs) in a multivariable regression model. Recurrence and lethality rates for clozapine-induced agranulocytosis were described. These data reflect on all individuals with lived experience of schizophrenia in Finland during the study time, although individuals with lived experience were not included in the design of the study. FINDINGS We identified 61 769 people with schizophrenia or schizoaffective disorder (14 037 individuals treated with clozapine and 47 732 individuals treated with non-clozapine antipsychotics), with a mean age of 46·67 years (IQR 34·44-57·61), of whom 30 721 (49·7%) were female and 31 048 (50·3%) were male (data on ethnicity not available). Among those, 398 individuals were diagnosed with agranulocytosis (231 individuals treated with clozapine and 167 individuals treated with non-clozapine antipsychotics), representing a cumulative incidence of agranulocytosis for 1·37% (95% CI 0·58-3·16) on clozapine and 0·13% (0·04-0·23) on non-clozapine antipsychotics. In the case (n=398) versus control (n=1987) model, the risk of clozapine-induced agranulocytosis decreased steeply over time from an aOR of 36·01 (95% CI 16·79-77·22) for less than 6 months on clozapine to 4·38 (1·86-10·34) for clozapine use of 54 months or more. Only one of 3559 individuals starting clozapine died because of clozapine-induced agranulocytosis. INTERPRETATION The risk of clozapine-induced agranulocytosis decreases steeply over time but might be persistently greater than that of non-clozapine antipsychotics. This long-term risk excess seems small in absolute terms compared with the known magnitude of the advantages of clozapine in relevant outcomes, including life expectancy. Given the widespread underuse of clozapine, relaxing the long-term neutrophil monitoring could favour the advantages of long-term clozapine use, including greater life expectancy, without incurring the intolerable risk of clozapine-induced agranulocytosis. FUNDING Northwell Health and Sigrid Jusèlius Foundation.
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Affiliation(s)
- Jose M Rubio
- Northwell Health, New Hyde Park, NY, USA; Department of Psychiatry, Zucker Hillside Hospital, Glen Oaks, NY, USA; Institute of Behavioral Science, Feinstein Institutes of Medical Research, Manhasset, NY, USA.
| | - John M Kane
- Northwell Health, New Hyde Park, NY, USA; Department of Psychiatry, Zucker Hillside Hospital, Glen Oaks, NY, USA; Institute of Behavioral Science, Feinstein Institutes of Medical Research, Manhasset, NY, USA
| | - Antti Tanskanen
- Department of Forensic Psychiatry, Niuvanniemi Hospital, University of Eastern Finland, Kuopio, Finland
| | - Jari Tiihonen
- Department of Forensic Psychiatry, Niuvanniemi Hospital, University of Eastern Finland, Kuopio, Finland; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; Center for Psychiatry Research, Stockholm City Council, Stockholm, Sweden
| | - Heidi Taipale
- Department of Forensic Psychiatry, Niuvanniemi Hospital, University of Eastern Finland, Kuopio, Finland; School of Pharmacy, University of Eastern Finland, Kuopio, Finland; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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7
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Li Y, Liu P, Wang W, Jia H, Bai Y, Yuan Z, Yang Z. A novel genotype-phenotype between persistent-cloaca-related VACTERL and mutations of 8p23 and 12q23.1. Pediatr Res 2024; 95:1246-1253. [PMID: 38135728 DOI: 10.1038/s41390-023-02928-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023]
Abstract
The mechanism underlying anorectal malformations (ARMs)-related VACTERL (vertebral defects, anal atresia, cardiac defects, tracheo-esophageal fistula, and renal and limb abnormalities) remains unclear. Copy number variation (CNV) contributed to VACTERL pathogenicity. Here, we report a novel CNV in 8p23 and 12q23.1 identified in a case of ARMs-related VACTERL association. This 12-year-old girl presented a cloaca (urethra, vagina, and rectum opening together and sharing a single tube length), an isolated kidney, and a perpetuation of the left superior vena cava at birth. Her intelligence, growth, and development were slightly lower than those of normal children of the same age. Array comparative genomic hybridization revealed a 9.6-Mb deletion in 8p23.1-23.3 and a 0.52-Mb duplication in 12q23.1 in her genome. Furthermore, we reviewed the cases involving CNVs in patients with VACTERL, 8p23 deletion, and 12q23.1 duplication, and our case was the first displaying ARMs-related VACTERL association with CNV in 8p23 and 12q23.1. These findings enriched our understanding between VACTERL association and the mutations of 8p23 deletion and 12q23.1 duplication. IMPACT: This is a novel case of a Chinese girl with anorectal malformations (ARMs)-related VACTERL with an 8p23.1-23.3 deletion and 12q23.1 duplication. Cloaca malformation is presented with novel copy number variation in 8p23.1-23.3 deletion and 12q23.1 duplication.
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Affiliation(s)
- Yue Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peiqi Liu
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Weilin Wang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Huimin Jia
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuzuo Bai
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhonghua Yang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
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8
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Liu Z, Deng C, Zhou Z, Xiao Y, Jiang S, Zhu B, Naler LB, Jia X, Yao DD, Lu C. Epigenomic tomography for probing spatially defined chromatin state in the brain. CELL REPORTS METHODS 2024; 4:100738. [PMID: 38508188 PMCID: PMC10985265 DOI: 10.1016/j.crmeth.2024.100738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/24/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Spatially resolved epigenomic profiling is critical for understanding biology in the mammalian brain. Single-cell spatial epigenomic assays were developed recently for this purpose, but they remain costly and labor intensive for examining brain tissues across substantial dimensions and surveying a collection of brain samples. Here, we demonstrate an approach, epigenomic tomography, that maps spatial epigenomes of mouse brain at the scale of centimeters. We individually profiled neuronal and glial fractions of mouse neocortex slices with 0.5 mm thickness. Tri-methylation of histone 3 at lysine 27 (H3K27me3) or acetylation of histone 3 at lysine 27 (H3K27ac) features across these slices were grouped into clusters based on their spatial variation patterns to form epigenomic brain maps. As a proof of principle, our approach reveals striking dynamics in the frontal cortex due to kainic-acid-induced seizure, linked with transmembrane ion transporters, exocytosis of synaptic vesicles, and secretion of neurotransmitters. Epigenomic tomography provides a powerful and cost-effective tool for characterizing brain disorders based on the spatial epigenome.
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Affiliation(s)
- Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, USA
| | - Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ya Xiao
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Shan Jiang
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Xiaoting Jia
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA
| | | | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA.
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Gonzales S, Zhao JZ, Choi NY, Acharya P, Jeong S, Lee MY. SOX7: Novel Autistic Gene Identified by Analysis of Multi-Omics Data. RESEARCH SQUARE 2023:rs.3.rs-3346245. [PMID: 37790478 PMCID: PMC10543249 DOI: 10.21203/rs.3.rs-3346245/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background Despite thousands of variants identified by genome-wide association studies (GWAS) to be associated with autism spectrum disorder (ASD), it is unclear which mutations are causal because most are noncoding. Consequently, reliable diagnostic biomarkers are lacking. RNA-seq analysis captures biomolecular complexity that GWAS cannot by considering transcriptomic patterns. Therefore, integrating DNA and RNA testing may reveal causal genes and useful biomarkers for ASD. Methods We performed gene-based association studies using an adaptive test method with GWAS summary statistics from two large Psychiatric Genomics Consortium (PGC) datasets (ASD2019: 18,382 cases and 27,969 controls; ASD2017: 6,197 cases and 7,377 controls). We also investigated differential expression for genes identified with the adaptive test using an RNA-seq dataset (GSE30573: 3 cases and 3 controls) and DESeq2. Results We identified 5 genes significantly associated with ASD in ASD2019 (KIZ-AS1, p = 8.67×10- 10; KIZ, p = 1.16×10- 9; XRN2, p = 7.73×10- 9; SOX7, p = 2.22×10- 7; LOC101929229 (also known as PINX1-DT), p = 2.14×10- 6). Two of the five genes were replicated in ASD2017: SOX7 (p = 0.00087) and LOC101929229 (p = 0.009), and KIZ was close to the replication boundary of replication (p = 0.06). We identified significant expression differences for SOX7 (p = 0.0017, adjusted p = 0.0085), LOC101929229 (p = 5.83×10- 7, adjusted p = 1.18×10- 5), and KIZ (p = 0.00099, adjusted p = 0.0055). SOX7 encodes a transcription factor that regulates developmental pathways, alterations in which may contribute to ASD. Limitations The limitation of the gene-based analysis is the reliance on a reference population for estimating linkage disequilibrium between variants. The similarity of this reference population to the population of study is crucial to the accuracy of many gene-based analyses, including those performed in this study. As a result, the extent of our findings is limited to European populations, as this was our reference of choice. Future work includes a tighter integration of DNA and RNA information as well as extensions to non-European populations that have been under-researched. Conclusions These findings suggest that SOX7 and its related SOX family genes encode transcription factors that are critical to the downregulation of the canonical Wnt/β-catenin signaling pathway, an important developmental signaling pathway, providing credence to the biologic plausibility of the association between gene SOX7 and autism spectrum disorder.
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Affiliation(s)
| | - Jane Zizhen Zhao
- Miami Dade College Kendall Campus and School for Advanced Studies
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Grycel K, Larsen NY, Feng Y, Qvortrup K, Jensen PH, Fayyaz M, Madsen MG, Midtgaard J, Xu Z, Hasselholt S, Nyengaard JR. CRMP2 conditional knockout changes axonal function and ultrastructure of axons in mice corpus callosum. Mol Cell Neurosci 2023; 126:103882. [PMID: 37479154 DOI: 10.1016/j.mcn.2023.103882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Collapsin response mediator protein 2 (CRMP2) is a member of a protein family, which is highly involved in neurodevelopment, but most of its members become heavily downregulated in adulthood. CRMP2 is an important factor in neuronal polarization, axonal formation and growth cone collapse. The protein remains expressed in adulthood, but is more region specific. CRMP2 is present in adult corpus callosum (CC) and in plastic areas like prefrontal cortex and hippocampus. CRMP2 has been implicated as one of the risk-genes for Schizophrenia (SZ). Here, a CRMP2 conditional knockout (CRMP2-cKO) mouse was used as a model of SZ to investigate how it could affect the white matter and therefore brain connectivity. Multielectrode electrophysiology (MEA) was used to study the function of corpus callosum showing an increase in conduction velocity (CV) measured as Compound Action Potentials (CAPs) in acute brain slices. Light- and electron-microscopy, specifically Serial Block-face Scanning Electron Microscopy (SBF-SEM), methods were used to study the structure of CC in CRMP2-cKO mice. A decrease in CC volume of CRMP2-cKO mice as compared to controls was observed. No differences were found in numbers nor in the size of CC oligodendrocytes (OLs). Similarly, no differences were found in myelin thickness or in node of Ranvier (NR) structure. In contrast, abnormally smaller axons were measured in the CRMP2-cKO mice. Using these state-of-the-art methods it was possible to shed light on specific parts of the dysconnectivity aspect of deletion of CRMP2 related to SZ and add details to previous findings helping further understanding the disease. This paper substantiates the white matter changes in the absence of CRMP2 and ties it to the role it plays in this complex disorder.
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Affiliation(s)
- Katarzyna Grycel
- Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark; Sino-Danish College (SDC), University of Chinese Academy of Sciences, China.
| | - Nick Y Larsen
- Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark.
| | - Yinghang Feng
- Sino-Danish College (SDC), University of Chinese Academy of Sciences, China; State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Klaus Qvortrup
- Core Facility for Integrated Microscopy, Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Poul Henning Jensen
- DANDRITE, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.
| | - Mishal Fayyaz
- Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark; Sino-Danish College (SDC), University of Chinese Academy of Sciences, China
| | - Malene G Madsen
- Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark.
| | - Jens Midtgaard
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Stine Hasselholt
- Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark; Center of Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark.
| | - Jens R Nyengaard
- Center for Molecular Morphology, Section for Stereology and Microscopy, Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark; Sino-Danish College (SDC), University of Chinese Academy of Sciences, China; Department of Pathology, Aarhus University Hospital, 8200 Aarhus N, Denmark.
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11
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Chen C, Zhu B, Tang X, Chen B, Liu M, Gao N, Li S, Gu J. Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide. Genes (Basel) 2023; 14:1211. [PMID: 37372391 DOI: 10.3390/genes14061211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had varying degrees of impact on various horse breeds. However, recent inbreeding events were uncommon, particularly among indigenous horse breeds. Consequently, the ROH-based genomic inbreeding coefficient could aid in monitoring the level of inbreeding. Using the Thoroughbred population as a case study, we discovered 24 ROH islands containing 72 candidate genes associated with artificial selection traits. We found that the candidate genes in Thoroughbreds were involved in neurotransmission (CHRNA6, PRKN, and GRM1), muscle development (ADAMTS15 and QKI), positive regulation of heart rate and heart contraction (HEY2 and TRDN), regulation of insulin secretion (CACNA1S, KCNMB2, and KCNMB3), and spermatogenesis (JAM3, PACRG, and SPATA6L). Our findings provide insight into horse breed characteristics and future breeding strategies.
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Affiliation(s)
- Chujie Chen
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bo Zhu
- Novogene Bioinformatics Institute, Beijing 100015, China
| | - Xiangwei Tang
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bin Chen
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Mei Liu
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Ning Gao
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Sheng Li
- Maxun Biotechnology Institute, Changsha 410024, China
| | - Jingjing Gu
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
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12
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Jansson AK, Söderling J, Reutfors J, Thor A, Sköld C, Cohn-Cedermark G, Ståhl O, Smedby KE, Pettersson A, Glimelius I. Risk and mortality of testicular cancer in patients with neurodevelopmental or other psychiatric disorders. Br J Cancer 2023; 128:2261-2269. [PMID: 37088800 PMCID: PMC10241835 DOI: 10.1038/s41416-023-02260-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Both testicular germ cell tumours (TGCT) and neurodevelopmental disorders are associated with urogenital malformations. Few studies have investigated the association between psychiatric disorders and TGCT. We investigated whether history of any psychiatric or neurodevelopmental disorder is associated with increased risk or mortality of TGCT. METHOD This is a nested case-control study including 6166 TGCT patients diagnosed during 1992-2014, individually matched for age and calendar period to 61,660 controls. We calculated odds ratios (ORs) for the association between type of psychiatric diagnoses and TGCT risk. Among the cases, we used a cohort design and calculated hazard ratios (HRs) of the association between psychiatric diagnose and all-cause and TGCT-specific death. RESULTS History of a neurodevelopmental disorder (attention deficit hyperactivity disorder, autism spectrum disorder and intellectual disabilities) was associated with an increased risk of seminoma (OR: 1.54; 1.09-2.19). Seminoma patients with neurodevelopmental disorders were younger (34 versus 38 years, p = 0.004) and had more stage IV disease (5.4% versus 1.2%) than those without. Psychiatric history overall was not associated with TGCT. Patient history of any psychiatric disorder was associated with an increased all-cause and TGCT-specific death. CONCLUSIONS We report an association between neurodevelopmental disorders and testicular seminoma, and an increased TGCT-specific mortality for TGCT patients with psychiatric disorders.
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Affiliation(s)
- Anna K Jansson
- Department of Immunology, Genetics & Pathology, Uppsala University, Uppsala, Sweden
| | - Jonas Söderling
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Johan Reutfors
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Anna Thor
- Division of Urology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Sköld
- Department of Immunology, Genetics & Pathology, Uppsala University, Uppsala, Sweden
| | - Gabriella Cohn-Cedermark
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Genitourinary Oncology Unit, Department of Pelvic Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Olof Ståhl
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Karin E Smedby
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Pettersson
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Glimelius
- Department of Immunology, Genetics & Pathology, Uppsala University, Uppsala, Sweden.
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.
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13
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Gonzales S, Zhao JZ, Choi NY, Acharya P, Jeong S, Lee MY. SOX7: Novel Autistic Gene Identified by Analysis of Multi-Omics Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542456. [PMID: 37292933 PMCID: PMC10245991 DOI: 10.1101/2023.05.26.542456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background Genome-wide association studies and next generation sequencing data analyses based on DNA information have identified thousands of mutations associated with autism spectrum disorder (ASD). However, more than 99% of identified mutations are non-coding. Thus, it is unclear which of these mutations might be functional and thus potentially causal variants. Transcriptomic profiling using total RNA-sequencing has been one of the most utilized approaches to link protein levels to genetic information at the molecular level. The transcriptome captures molecular genomic complexity that the DNA sequence solely does not. Some mutations alter a gene's DNA sequence but do not necessarily change expression and/or protein function. To date, few common variants reliably associated with the diagnosis status of ASD despite consistently high estimates of heritability. In addition, reliable biomarkers used to diagnose ASD or molecular mechanisms to define the severity of ASD do not exist. Objectives It is necessary to integrate DNA and RNA testing together to identify true causal genes and propose useful biomarkers for ASD. Methods We performed gene-based association studies with adaptive test using genome-wide association studies (GWAS) summary statistics with two large GWAS datasets (ASD 2019 data: 18,382 ASD cases and 27,969 controls [discovery data]; ASD 2017 data: 6,197 ASD cases and 7,377 controls [replication data]) which were obtained from the Psychiatric Genomics Consortium (PGC). In addition, we investigated differential expression for genes identified in gene-based GWAS with a RNA-seq dataset (GSE30573: 3 cases and 3 controls) using the DESeq2 package. Results We identified 5 genes significantly associated with ASD in ASD 2019 data (KIZ-AS1, p=8.67×10-10; KIZ, p=1.16×10-9; XRN2, p=7.73×10-9; SOX7, p=2.22×10-7; PINX1-DT, p=2.14×10-6). Among these 5 genes, gene SOX7 (p=0.00087), LOC101929229 (p=0.009), and KIZ-AS1 (p=0.059) were replicated in ASD 2017 data. KIZ (p=0.06) was close to the boundary of replication in ASD 2017 data. Genes SOX7 (p=0.0017, adjusted p=0.0085), LOC101929229 (also known as PINX1-DT, p=5.83×10-7, adjusted p=1.18×10-5), and KIZ (p=0.00099, adjusted p=0.0055) indicated significant expression differences between cases and controls in the RNA-seq data. SOX7 encodes a member of the SOX (SRY-related HMG-box) family of transcription factors pivotally contributing to determining of the cell fate and identity in many lineages. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins leading to autism. Conclusion Gene SOX7 in the transcription factor family could be associated with ASD. This finding may provide new diagnostic and therapeutic strategies for ASD.
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Affiliation(s)
- Samantha Gonzales
- Department of Biostatistics, Florida International University, Miami, FL 33199
| | - Jane Zizhen Zhao
- Miami Dade College Kendall Campus and School for Advanced Studies, Miami, FL 33176
| | - Na Young Choi
- Department of Biomedical Engineering, University of North Texas, Denton, TX 76207
| | - Prabha Acharya
- Department of Biomedical Engineering, University of North Texas, Denton, TX 76207
| | - Sehoon Jeong
- Department of Healthcare Information Technology Inje University, Gimhae, South Korea, 50834
| | - Moo-Yeal Lee
- Department of Biomedical Engineering, University of North Texas, Denton, TX 76207
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14
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Brown JS. Comparison of Oncogenes, Tumor Suppressors, and MicroRNAs Between Schizophrenia and Glioma: The Balance of Power. Neurosci Biobehav Rev 2023; 151:105206. [PMID: 37178944 DOI: 10.1016/j.neubiorev.2023.105206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023]
Abstract
The risk of cancer in schizophrenia has been controversial. Confounders of the issue are cigarette smoking in schizophrenia, and antiproliferative effects of antipsychotic medications. The author has previously suggested comparison of a specific cancer like glioma to schizophrenia might help determine a more accurate relationship between cancer and schizophrenia. To accomplish this goal, the author performed three comparisons of data; the first a comparison of conventional tumor suppressors and oncogenes between schizophrenia and cancer including glioma. This comparison determined schizophrenia has both tumor-suppressive and tumor-promoting characteristics. A second, larger comparison between brain-expressed microRNAs in schizophrenia with their expression in glioma was then performed. This identified a core carcinogenic group of miRNAs in schizophrenia offset by a larger group of tumor-suppressive miRNAs. This proposed "balance of power" between oncogenes and tumor suppressors could cause neuroinflammation. This was assessed by a third comparison between schizophrenia, glioma and inflammation in asbestos-related lung cancer and mesothelioma (ALRCM). This revealed that schizophrenia shares more oncogenic similarity to ALRCM than glioma.
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15
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Nudel R, Christensen RV, Kalnak N, Schwinn M, Banasik K, Dinh KM, Erikstrup C, Pedersen OB, Burgdorf KS, Ullum H, Ostrowski SR, Hansen TF, Werge T. Developmental language disorder - a comprehensive study of more than 46,000 individuals. Psychiatry Res 2023; 323:115171. [PMID: 36963307 DOI: 10.1016/j.psychres.2023.115171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/16/2023] [Accepted: 03/14/2023] [Indexed: 03/26/2023]
Abstract
Developmental language disorder (DLD) is characterized by enduring low language abilities with a significant functional impact, in the absence of biomedical conditions in which language impairment is part of a complex of impairments. There is a lack of awareness of DLD even among healthcare professionals. Here we estimated the prevalence of DLD and its links to reading and learning difficulties and physical and mental health in the Danish Blood Donor Study (N = 46,547), where DLD-related information is based on questionnaires (self-report). We compared the questionnaire-derived DLD status with the relevant language-related diagnoses from hospital registers. We also investigated the genetic architecture of DLD in a subset of the cohort (N = 18,380). DLD was significantly associated with reading and learning difficulties and poorer mental and physical health. DLD prevalence was 3.36%-3.70% based on questionnaires, compared with 0.04% in hospital registers. Our genetic analyses identified one genome-wide significant locus, but not a significant heritability estimate. Our study shows that DLD has health-related implications that may last into adulthood, and that DLD may be undiagnosed in general healthcare. Furthermore, DLD is likely more genetically heterogeneous than narrower developmental language phenotypes. Our results emphasize the need to raise awareness of DLD and consider criteria for molecular studies of DLD to reduce case heterogeneity.
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Affiliation(s)
- Ron Nudel
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark.
| | - Rikke Vang Christensen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Emil Holms Kanal 2, Copenhagen 2300, Denmark.
| | - Nelli Kalnak
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden; Department of Speech-Language Pathology, Helsingborg Hospital, Helsingborg, Sweden.
| | - Michael Schwinn
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Karina Banasik
- Novo Nordisk foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Khoa Manh Dinh
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ole Birger Pedersen
- Department of Immunology, Næstved Hospital, Næstved, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Sølvsten Burgdorf
- Department of Immunology, Rigshospitalet, Copenhagen, Denmark; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Danish Headache Center, Rigshospitalet Glostrup, Glostrup, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Institute of Biological Psychiatry, Roskilde, Denmark
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16
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Elevated Hippocampal CRMP5 Mediates Chronic Stress-Induced Cognitive Deficits by Disrupting Synaptic Plasticity, Hindering AMPAR Trafficking, and Triggering Cytokine Release. Int J Mol Sci 2023; 24:ijms24054898. [PMID: 36902337 PMCID: PMC10003309 DOI: 10.3390/ijms24054898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Chronic stress is a critical risk factor for developing depression, which can impair cognitive function. However, the underlying mechanisms involved in chronic stress-induced cognitive deficits remain unclear. Emerging evidence suggests that collapsin response mediator proteins (CRMPs) are implicated in the pathogenesis of psychiatric-related disorders. Thus, the study aims to examine whether CRMPs modulate chronic stress-induced cognitive impairment. We used the chronic unpredictable stress (CUS) paradigm to mimic stressful life situations in C57BL/6 mice. In this study, we found that CUS-treated mice exhibited cognitive decline and increased hippocampal CRMP2 and CRMP5 expression. In contrast to CRMP2, CRMP5 levels strongly correlated with the severity of cognitive impairment. Decreasing hippocampal CRMP5 levels through shRNA injection rescued CUS-induced cognitive impairment, whereas increasing CRMP5 levels in control mice exacerbated memory decline after subthreshold stress treatment. Mechanistically, hippocampal CRMP5 suppression by regulating glucocorticoid receptor phosphorylation alleviates chronic stress-induced synaptic atrophy, disruption of AMPA receptor trafficking, and cytokine storms. Our findings show that hippocampal CRMP5 accumulation through GR activation disrupts synaptic plasticity, impedes AMPAR trafficking, and triggers cytokine release, thus playing a critical role in chronic stress-induced cognitive deficits.
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17
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Zhang T, Rao Q, Lin K, He Y, Cai J, Yang M, Xu Y, Hou L, Lin Y, Liu H. CYP2C19-rs4986893 confers risk to major depressive disorder and bipolar disorder in the Han Chinese population whereas ABCB1-rs1045642 acts as a protective factor. BMC Psychiatry 2023; 23:69. [PMID: 36698099 PMCID: PMC9875448 DOI: 10.1186/s12888-022-04514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/30/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Genetic risks may predispose individuals to major mood disorders differently. This study investigated the gene polymorphisms of previously reported candidate genes for major depressive disorder (MDD) and bipolar disorder (BPD) in the Han Chinese population. METHODS Twenty loci of 13 candidate genes were detected by MALDI-TOF mass spectrometry in 439 patients with MDD, 600 patients with BPD, and 464 healthy controls. The distribution of genotypes in alleles, Hardy-Weinberg equilibrium, and genetic association were analyzed using the PLINK software. The linkage of disequilibrium and haplotype analyses were performed using the Haploview software. RESULTS Out of the 20 loci analyzed, CYP2C19-rs4986893, ABCB1-rs1045642, and SCN2A-rs17183814 passed Bonferroni correction; their statistical powers were > 55%. The minor allele frequencies (MAF) of CYP2C19-rs4986893 in the MDD group (0.0547) and BPD group (0.0533) were higher than that of the control group (0.0259, P < 0.05), leading to the odds ratios (ORs) of MDD (2.178) and BPD (2.122), respectively. In contrast, the lower MAFs of ABCB1-rs1045642 were observed in both MDD (0.3599, OR = 0.726) and BPD (0.3700, OR = 0.758) groups than controls (0.4364, P < 0.05). The MDD group had a higher MAF of SCN2A-rs17183814 than controls (0.1743 vs. 0.1207, OR = 1.538, P < 0.05). Moreover, a G-A haplotype composed by CYP2C19-rs4986893 and -rs4244285 was associated with BPD (OR = 1.361, P < 0.01), and the A-G haplotype increased the risks to both MDD (OR = 2.306, P < 0.01) and BPD (OR = 2.332, P < 0.001). The CYP2C19 intermediate metabolizer and poor metabolizer (IM&PM) status was related to the raised risk of both MDD (OR = 1.547, P < 0.01) and BPD (OR = 1.808, P < 0.001). CONCLUSION Our data indicate that the impaired CYP2C19 metabolism caused by the haplotypes integrated by CYP2C19 alleles might confer the risk to MDD and BPD, whereas the ABCB1-rs1045642 T allele serves as a protective factor.
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Affiliation(s)
- Ting Zhang
- grid.410737.60000 0000 8653 1072Clinical Laboratory, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qingmin Rao
- grid.410737.60000 0000 8653 1072Clinical Laboratory, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kangguang Lin
- grid.410737.60000 0000 8653 1072Affective Disorder Department, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yongyin He
- grid.410737.60000 0000 8653 1072Clinical Laboratory, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jintai Cai
- grid.410737.60000 0000 8653 1072Clinical Laboratory, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mengxin Yang
- grid.410737.60000 0000 8653 1072Clinical Laboratory, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ying Xu
- grid.410737.60000 0000 8653 1072Clinical Laboratory, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Le Hou
- grid.410737.60000 0000 8653 1072Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yulong Lin
- Clinical Laboratory, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Haiying Liu
- Clinical Laboratory, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China.
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18
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Syu GD, Sutandy FXR, Chen K, Cheng Y, Chen CS, Shih JC. Autoantibody profiling of monoamine oxidase A knockout mice, an autism spectrum disorder model. Brain Behav Immun 2023; 107:193-200. [PMID: 36243286 DOI: 10.1016/j.bbi.2022.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/04/2022] [Accepted: 10/09/2022] [Indexed: 12/05/2022] Open
Abstract
Monoamine oxidase A (MAO A) is the critical enzyme to degrade serotonin in the brain and the knockout mouse exhibits hyperserotonemia and abnormalities that are observed in autism spectrum disorder (ASD). Thus, the MAO A knockout mouse is a valuable model for studying neurological and behavioral impairments in ASD. Based on the immune dysfunction hypothesis, dysregulated humoral immunity may cause neurological impairments. To address this hypothesis, we use high-density proteome microarray to profile the serum antibodies in both wild-type and MAO A knockout mice. The distingue autoantibody signatures were observed in the MAO A knockout and wild-type controls and showed 165 up-regulated and 232 down-regulated autoantibodies. The up-regulated autoantibodies were prone to target brain tissues while down-regulated ones were enriched in sex organs. The identified autoantibodies help bridge the gap between ASD mouse models and humoral immunity, not only yielding insights into the pathological mechanisms but also providing potential biomarkers for translational research in ASD.
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Affiliation(s)
- Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan, Taiwan.
| | - F X Reymond Sutandy
- Institute for Biochemistry II, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Kevin Chen
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, USA
| | - Yawei Cheng
- Department of Physical Medicine and Rehabilitation, National Yang-Ming University Hospital, Yilan, Taiwan; Institute of Neuroscience and Brain Research Center, National Yang-Ming University, Taipei, Taiwan; Department of Education and Research, Taipei City Hospital, Taipei, Taiwan
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC.
| | - Jean C Shih
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, USA; USC-Taiwan Center for Translational Research, University of Southern California, Los Angeles, USA; Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, USA.
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19
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Lim M, Carollo A, Neoh MJY, Esposito G. Mapping miRNA Research in Schizophrenia: A Scientometric Review. Int J Mol Sci 2022; 24:ijms24010436. [PMID: 36613876 PMCID: PMC9820708 DOI: 10.3390/ijms24010436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Micro RNA (miRNA) research has great implications in uncovering the aetiology of neuropsychiatric conditions due to the role of miRNA in brain development and function. Schizophrenia, a complex yet devastating neuropsychiatric disorder, is one such condition that had been extensively studied in the realm of miRNA. Although a relatively new field of research, this area of study has progressed sufficiently to warrant dozens of reviews summarising findings from past to present. However, as a majority of reviews cannot encapsulate the full body of research, there is still a need to synthesise the diversity of publications made in this area in a systematic but easy-to-understand manner. Therefore, this study adopted bibliometrics and scientometrics, specifically document co-citation analysis (DCA), to review the literature on miRNAs in the context of schizophrenia over the course of history. From a literature search on Scopus, 992 papers were found and analysed with CiteSpace. DCA analysis generated a network of 13 major clusters with different thematic focuses within the subject area. Finally, these clusters are qualitatively discussed. miRNA research has branched into schizophrenia, among other medical and psychiatric conditions, due to previous findings in other forms of non-coding RNA. With the rise of big data, bioinformatics analyses are increasingly common in this field of research. The future of research is projected to rely more heavily on interdisciplinary collaboration. Additionally, it can be expected that there will be more translational studies focusing on the application of these findings to the development of effective treatments.
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Affiliation(s)
- Mengyu Lim
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore 639818, Singapore
| | - Alessandro Carollo
- Department of Psychology and Cognitive Science, University of Trento, 38068 Rovereto, Italy
| | - Michelle Jin Yee Neoh
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore 639818, Singapore
| | - Gianluca Esposito
- Department of Psychology and Cognitive Science, University of Trento, 38068 Rovereto, Italy
- Correspondence:
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Mompeo O, Freidin MB, Gibson R, Hysi PG, Christofidou P, Segal E, Valdes AM, Spector TD, Menni C, Mangino M. Genome-Wide Association Analysis of Over 170,000 Individuals from the UK Biobank Identifies Seven Loci Associated with Dietary Approaches to Stop Hypertension (DASH) Diet. Nutrients 2022; 14:4431. [PMID: 36297114 PMCID: PMC9611599 DOI: 10.3390/nu14204431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 01/24/2023] Open
Abstract
Diet is a modifiable risk factor for common chronic diseases and mental health disorders, and its effects are under partial genetic control. To estimate the impact of diet on individual health, most epidemiological and genetic studies have focused on individual aspects of dietary intake. However, analysing individual food groups in isolation does not capture the complexity of the whole diet pattern. Dietary indices enable a holistic estimation of diet and account for the intercorrelations between food and nutrients. In this study we performed the first ever genome-wide association study (GWA) including 173,701 individuals from the UK Biobank to identify genetic variants associated with the Dietary Approaches to Stop Hypertension (DASH) diet. DASH was calculated using the 24 h-recall questionnaire collected by UK Biobank. The GWA was performed using a linear mixed model implemented in BOLT-LMM. We identified seven independent single-nucleotide polymorphisms (SNPs) associated with DASH. Significant genetic correlations were observed between DASH and several educational traits with a significant enrichment for genes involved in the AMP-dependent protein kinase (AMPK) activation that controls the appetite by regulating the signalling in the hypothalamus. The colocalization analysis implicates genes involved in body mass index (BMI)/obesity and neuroticism (ARPP21, RP11-62H7.2, MFHAS1, RHEBL1). The Mendelian randomisation analysis suggested that increased DASH score, which reflect a healthy diet style, is causal of lower glucose, and insulin levels. These findings further our knowledge of the pathways underlying the relationship between diet and health outcomes. They may have significant implications for global public health and provide future dietary recommendations for the prevention of common chronic diseases.
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Affiliation(s)
- Olatz Mompeo
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Maxim B. Freidin
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Rachel Gibson
- Department of Nutritional Sciences, King’s College London, London SE1 9NH, UK
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Paraskevi Christofidou
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ana M. Valdes
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
- Academic Rheumatology Clinical Sciences Building, Nottingham City Hospital, University of Nottingham, Nottingham NG5 1PB, UK
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’ Foundation Trust, London SE1 9RT, UK
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21
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Zhou S, Zhong Z, Lu Y, Li Y, Yao H, Zhao Y, Guo T, Yang K, Li Y, Chen S, Huang K, Lian G. A LETM2-Regulated PI3K-Akt Signaling Axis Reveals a Prognostic and Therapeutic Target in Pancreatic Cancer. Cancers (Basel) 2022; 14:cancers14194722. [PMID: 36230646 PMCID: PMC9564284 DOI: 10.3390/cancers14194722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary LEMT2 was a newly discovered protein-encoding gene with little cancer research and an unclear mechanism. This study aimed to illustrate LETM2 as the crucial oncogene for tumor progression in pancreatic ductal adenocarcinoma (PDAC). We analyzed the expression level and prognostic value of LETM2 in multiple cancers using pan-cancer analysis and found that the LETM2 expression was the most significantly related to the dismal prognosis of PDAC. Immunohistochemical analyses showed that high LETM2 expression was correlated with poor outcomes of PDAC. In in vitro and in vivo experiments, LETM2 knockdown significantly inhibited tumor proliferation and metastasis, while LETM2 overexpression exerted the opposite effects. Then, we suggested that LETM2 may facilitate tumor progression by activating downstream PI3K-Akt signaling pathway in PDAC. In conclusion, the study enhanced our understanding of the LETM2-regulated PI3K-Akt signaling axis served as a prognostic and therapeutic target of pancreatic cancer. Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the highest mortalities malignant tumors, which is characterized by difficult diagnosis, rapid progression and high recurrence rate. Nevertheless, PDAC responds poorly to conventional therapies, which highlights the urgency to identify novel prognostic and therapeutic targets. LEMT2 was a newly discovered protein-encoding gene with little cancer research and an unclear mechanism. Thus, this study aimed to illustrate LETM2 as the crucial oncogene for tumor progression in PDAC. In this study, we analyzed the expression level and prognostic value of LETM2 in multiple cancers using pan-cancer analysis. The analyses based on the TCGA-GTEx dataset indicated that the LETM2 expression was obviously elevated in several cancers, and it was the most significantly related to the dismal prognosis of PDAC. Subsequently, we demonstrated the functional role and mechanism of LETM2 by clinical sample evaluation, and in in vitro and in vivo experiments. Immunohistochemical analyses showed that high expression of LETM2 was correlated with poor outcomes of PDAC. Moreover, we demonstrated that LETM2 knockdown significantly inhibited tumor proliferation and metastasis, and promoted cell apoptosis, while LETM2 overexpression exerted the opposite effects. Finally, the impairment caused by LETM2-knockdown could be recovered via excitation of the PI3k-Akt pathway in vitro and in vivo animal models, which suggested that LETM2 could activate the downstream PI3K-Akt pathway to participate in PDAC progression. In conclusion, the study enhanced our understanding of LETM2 as an oncogene hallmark of PDAC. LETM2 may facilitate tumor progression by activating the PI3K-Akt signaling pathway, which provides potential targets for the diagnosis, treatment, and prognosis of pancreatic cancer.
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Affiliation(s)
- Shurui Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Ziyi Zhong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Yanzong Lu
- Department of Ophthalmology, No.903 Hospital of PLA Joint Logistic Support Force, Hangzhou 310013, China
| | - Yunlong Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Hanming Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Yue Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Tairan Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Kege Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Yaqing Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Shaojie Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Kaihong Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
- Correspondence: (K.H.); (G.L.)
| | - Guoda Lian
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
- Correspondence: (K.H.); (G.L.)
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22
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Tao S, Zhang Y, Wang Q, Qiao C, Deng W, Liang S, Wei J, Wei W, Yu H, Li X, Li M, Guo W, Ma X, Zhao L, Li T. Identifying transdiagnostic biological subtypes across schizophrenia, bipolar disorder, and major depressive disorder based on lipidomics profiles. Front Cell Dev Biol 2022; 10:969575. [PMID: 36133917 PMCID: PMC9483200 DOI: 10.3389/fcell.2022.969575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Emerging evidence has demonstrated overlapping biological abnormalities underlying schizophrenia (SCZ), bipolar disorder (BP), and major depressive disorder (MDD); these overlapping abnormalities help explain the high heterogeneity and the similarity of patients within and among diagnostic categories. This study aimed to identify transdiagnostic subtypes of these psychiatric disorders based on lipidomics abnormalities. We performed discriminant analysis to identify lipids that classified patients (N = 349, 112 with SCZ, 132 with BP, and 105 with MDD) and healthy controls (N = 198). Ten lipids that mainly regulate energy metabolism, inflammation, oxidative stress, and fatty acylation of proteins were identified. We found two subtypes (named Cluster 1 and Cluster 2 subtypes) across patients with SCZ, BP, and MDD by consensus clustering analysis based on the above 10 lipids. The distribution of clinical diagnosis, functional impairment measured by Global Assessment of Functioning (GAF) scales, and brain white matter abnormalities measured by fractional anisotropy (FA) and radial diffusivity (RD) differed in the two subtypes. Patients within the Cluster 2 subtype were mainly SCZ and BP patients and featured significantly elevated RD along the genu of corpus callosum (GCC) region and lower GAF scores than patients within the Cluster 1 subtype. The SCZ and BP patients within the Cluster 2 subtype shared similar biological patterns; that is, these patients had comparable brain white matter abnormalities and functional impairment, which is consistent with previous studies. Our findings indicate that peripheral lipid abnormalities might help identify homogeneous transdiagnostic subtypes across psychiatric disorders.
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Affiliation(s)
- Shiwan Tao
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yamin Zhang
- Department of Neurobiology, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiang Wang
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Chunxia Qiao
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wei Deng
- Department of Neurobiology, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sugai Liang
- Department of Neurobiology, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jinxue Wei
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wei Wei
- Department of Neurobiology, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hua Yu
- Department of Neurobiology, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaojing Li
- Department of Neurobiology, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mingli Li
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wanjun Guo
- Department of Neurobiology, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaohong Ma
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Liansheng Zhao
- Mental Health Center and Psychiatric Laboratory, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Tao Li
- Department of Neurobiology, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, China
- *Correspondence: Tao Li,
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23
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Liddiard K, Aston-Evans AN, Cleal K, Hendrickson E, Baird D. POLQ suppresses genome instability and alterations in DNA repeat tract lengths. NAR Cancer 2022; 4:zcac020. [PMID: 35774233 PMCID: PMC9241439 DOI: 10.1093/narcan/zcac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022] Open
Abstract
DNA polymerase theta (POLQ) is a principal component of the alternative non-homologous end-joining (ANHEJ) DNA repair pathway that ligates DNA double-strand breaks. Utilizing independent models of POLQ insufficiency during telomere-driven crisis, we found that POLQ - /- cells are resistant to crisis-induced growth deceleration despite sustaining inter-chromosomal telomere fusion frequencies equivalent to wild-type (WT) cells. We recorded longer telomeres in POLQ - / - than WT cells pre- and post-crisis, notwithstanding elevated total telomere erosion and fusion rates. POLQ - /- cells emerging from crisis exhibited reduced incidence of clonal gross chromosomal abnormalities in accordance with increased genetic heterogeneity. High-throughput sequencing of telomere fusion amplicons from POLQ-deficient cells revealed significantly raised frequencies of inter-chromosomal fusions with correspondingly depreciated intra-chromosomal recombinations. Long-range interactions culminating in telomere fusions with centromere alpha-satellite repeats, as well as expansions in HSAT2 and HSAT3 satellite and contractions in ribosomal DNA repeats, were detected in POLQ - / - cells. In conjunction with the expanded telomere lengths of POLQ - /- cells, these results indicate a hitherto unrealized capacity of POLQ for regulation of repeat arrays within the genome. Our findings uncover novel considerations for the efficacy of POLQ inhibitors in clinical cancer interventions, where potential genome destabilizing consequences could drive clonal evolution and resistant disease.
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Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Alys N Aston-Evans
- Dementia Research Institute, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | - Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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24
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Lesmana MHS, Le NQK, Chiu WC, Chung KH, Wang CY, Irham LM, Chung MH. Genomic-Analysis-Oriented Drug Repurposing in the Search for Novel Antidepressants. Biomedicines 2022; 10:biomedicines10081947. [PMID: 36009493 PMCID: PMC9405592 DOI: 10.3390/biomedicines10081947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022] Open
Abstract
From inadequate prior antidepressants that targeted monoamine neurotransmitter systems emerged the discovery of alternative drugs for depression. For instance, drugs targeted interleukin 6 receptor (IL6R) in inflammatory system. Genomic analysis-based drug repurposing using single nucleotide polymorphism (SNP) inclined a promising method for several diseases. However, none of the diseases was depression. Thus, we aimed to identify drug repurposing candidates for depression treatment by adopting a genomic-analysis-based approach. The 5885 SNPs obtained from the machine learning approach were annotated using HaploReg v4.1. Five sets of functional annotations were applied to determine the depression risk genes. The STRING database was used to expand the target genes and identify drug candidates from the DrugBank database. We validated the findings using the ClinicalTrial.gov and PubMed databases. Seven genes were observed to be strongly associated with depression (functional annotation score = 4). Interestingly, IL6R was auspicious as a target gene according to the validation outcome. We identified 20 drugs that were undergoing preclinical studies or clinical trials for depression. In addition, we identified sarilumab and satralizumab as drugs that exhibit strong potential for use in the treatment of depression. Our findings indicate that a genomic-analysis-based approach can facilitate the discovery of drugs that can be repurposed for treating depression.
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Affiliation(s)
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Wei-Che Chiu
- Department of Psychiatry, Cathay General Hospital, Taipei 10630, Taiwan
- School of Medicine, Fu Jen Catholic University, New Taipei City 242062, Taiwan
| | - Kuo-Hsuan Chung
- Department of Psychiatry, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Department of Psychiatry and Psychiatric Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Lalu Muhammad Irham
- Faculty of Pharmacy, University of Ahmad Dahlan, Yogyakarta 55164, Indonesia
- Correspondence: (L.M.I.); (M.-H.C.); Tel.: +62-851-322-55-414 (L.M.I.); +886-02-2736-1661 (M.-H.C.)
| | - Min-Huey Chung
- School of Nursing, College of Nursing, Taipei Medical University, Taipei 11031, Taiwan
- Department of Nursing, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Correspondence: (L.M.I.); (M.-H.C.); Tel.: +62-851-322-55-414 (L.M.I.); +886-02-2736-1661 (M.-H.C.)
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25
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van der Walt K, Campbell M, Stein DJ, Dalvie S. Systematic review of genome-wide association studies of anxiety disorders and neuroticism. World J Biol Psychiatry 2022; 24:280-291. [PMID: 35815422 DOI: 10.1080/15622975.2022.2099970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
OBJECTIVES To summarise SNP associations identified by genome-wide association studies (GWASs) of anxiety disorders and neuroticism; to appraise the quality of individual studies, and to assess the ancestral diversity of study participants. METHODS We searched PubMed, Scopus, PsychInfo and PubPsych for GWASs of anxiety disorders, non-diagnostic traits (such as anxiety sensitivity), and neuroticism, and extracted all SNPs that surpassed genome-wide significance. We graded study quality using Q-genie scores and reviewed the ancestral diversity of included participants. RESULTS 32 studies met our inclusion criteria. A total of 563 independent significant variants were identified, of which 29 were replicated nominally in independent samples, and 3 were replicated significantly. The studies had good global quality, but many smaller studies were underpowered. Phenotypic heterogeneity for anxiety (and less so for neuroticism) seemed to reflect the complexity of capturing this trait. Ancestral diversity was poor, with 70% of studies including only populations of European ancestry. CONCLUSION The functionality of genes identified by GWASs of anxiety and neuroticism deserves further investigation. Future GWASs should have larger sample sizes, more rigorous phenotyping and include more ancestrally diverse population groups.
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Affiliation(s)
- Kristien van der Walt
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Megan Campbell
- MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics. Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER) program, Harvard T.H. Chan School of Public Health and the Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Boston, Massachusetts, USA
| | - Dan J Stein
- SAMRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Shareefa Dalvie
- SAMRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa.,Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa.,Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Cape Town
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26
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Sharbatoghli M, Fattahi F, Aboulkheyr Es H, Akbari A, Akhavan S, Ebrahimi M, Asadi-Lari M, Totonchi M, Madjd Z. Copy Number Variation of Circulating Tumor DNA (ctDNA) Detected Using NIPT in Neoadjuvant Chemotherapy-Treated Ovarian Cancer Patients. Front Genet 2022; 13:938985. [PMID: 35938032 PMCID: PMC9355329 DOI: 10.3389/fgene.2022.938985] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/15/2022] [Indexed: 12/24/2022] Open
Abstract
Analysis of circulating tumor DNA (ctDNA) can be used to characterize and monitor cancers. Recently, non-invasive prenatal testing (NIPT) as a new next-generation sequencing (NGS)-based approach has been applied for detecting ctDNA. This study aimed to investigate the copy number variations (CNVs) utilizing the non-invasive prenatal testing in plasma ctDNA from ovarian cancer (OC) patients who were treated with neoadjuvant chemotherapy (NAC). The plasma samples of six patients, including stages II–IV, were collected during the pre- and post-NAC treatment that were divided into NAC-sensitive and NAC-resistant groups during the follow-up time. CNV analysis was performed using the NIPT via two methods “an open-source algorithm WISECONDORX and NextGENe software.” Results of these methods were compared in pre- and post-NAC of OC patients. Finally, bioinformatics tools were used for data mining from The Cancer Genome Atlas (TCGA) to investigate CNVs in OC patients. WISECONDORX analysis indicated fewer CNV changes on chromosomes before treatment in the NAC-sensitive rather than NAC-resistant patients. NextGENe data indicated that CNVs are not only observed in the coding genes but also in non-coding genes. CNVs in six genes were identified, including HSF1, TMEM249, MROH1, GSTT2B, ABR, and NOMO2, only in NAC-resistant patients. The comparison of these six genes in NAC-resistant patients with The Cancer Genome Atlas data illustrated that the total alteration frequency is amplification, and the highest incidence of the CNVs (≥35% based on TCGA data) is found in MROH1, TMEM249, and HSF1 genes on the chromosome (Chr) 8. Based on TCGA data, survival analysis showed a significant reduction in the overall survival among chemotherapy-resistant patients as well as a high expression level of these three genes compared to that of sensitive samples (all, p < 0.0001). The continued Chr8 study using WISECONDORX revealed CNV modifications in NAC-resistant patients prior to NAC therapy, but no CNV changes were observed in NAC-sensitive individuals. Our findings showed that low coverage whole-genome sequencing analysis used for NIPT could identify CNVs in ctDNA of OC patients before and after chemotherapy. These CNVs are different in NAC-sensitive and -resistant patients highlighting the potential application of this approach in cancer patient management.
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Affiliation(s)
- Mina Sharbatoghli
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Fahimeh Fattahi
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | | | - Arvand Akbari
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Setareh Akhavan
- Department of Gynecologic Oncology, Vali-Asr Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Ebrahimi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mohsen Asadi-Lari
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Totonchi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- *Correspondence: Zahra Madjd, ; Mehdi Totonchi,
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- *Correspondence: Zahra Madjd, ; Mehdi Totonchi,
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Examples of Inverse Comorbidity between Cancer and Neurodegenerative Diseases: A Possible Role for Noncoding RNA. Cells 2022; 11:cells11121930. [PMID: 35741059 PMCID: PMC9221903 DOI: 10.3390/cells11121930] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the most common causes of death; in parallel, the incidence and prevalence of central nervous system diseases are equally high. Among neurodegenerative diseases, Alzheimer’s dementia is the most common, while Parkinson’s disease (PD) is the second most frequent neurodegenerative disease. There is a significant amount of evidence on the complex biological connection between cancer and neurodegeneration. Noncoding RNAs (ncRNAs) are defined as transcribed nucleotides that perform a variety of regulatory functions. The mechanisms by which ncRNAs exert their functions are numerous and involve every aspect of cellular life. The same ncRNA can act in multiple ways, leading to different outcomes; in fact, a single ncRNA can participate in the pathogenesis of more than one disease—even if these seem very different, as cancer and neurodegenerative disorders are. The ncRNA activates specific pathways leading to one or the other clinical phenotype, sometimes with obvious mechanisms of inverse comorbidity. We aimed to collect from the existing literature examples of inverse comorbidity in which ncRNAs seem to play a key role. We also investigated the example of mir-519a-3p, and one of its target genes Poly (ADP-ribose) polymerase 1, for the inverse comorbidity mechanism between some cancers and PD. We believe it is very important to study the inverse comorbidity relationship between cancer and neurodegenerative diseases because it will help us to better assess these two major areas of human disease.
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Astorkia M, Lachman HM, Zheng D. Characterization of cell-cell communication in autistic brains with single-cell transcriptomes. J Neurodev Disord 2022; 14:29. [PMID: 35501678 PMCID: PMC9059394 DOI: 10.1186/s11689-022-09441-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/18/2022] [Indexed: 12/16/2022] Open
Abstract
Background Autism spectrum disorder is a neurodevelopmental disorder, affecting 1–2% of children. Studies have revealed genetic and cellular abnormalities in the brains of affected individuals, leading to both regional and distal cell communication deficits. Methods Recent application of single-cell technologies, especially single-cell transcriptomics, has significantly expanded our understanding of brain cell heterogeneity and further demonstrated that multiple cell types and brain layers or regions are perturbed in autism. The underlying high-dimensional single-cell data provides opportunities for multilevel computational analysis that collectively can better deconvolute the molecular and cellular events altered in autism. Here, we apply advanced computation and pattern recognition approaches on single-cell RNA-seq data to infer and compare inter-cell-type signaling communications in autism brains and controls. Results Our results indicate that at a global level, there are cell-cell communication differences in autism in comparison with controls, largely involving neurons as both signaling senders and receivers, but glia also contribute to the communication disruption. Although the magnitude of changes is moderate, we find that excitatory and inhibitor neurons are involved in multiple intercellular signaling that exhibits increased strengths in autism, such as NRXN and CNTN signaling. Not all genes in the intercellular signaling pathways show differential expression, but genes in the affected pathways are enriched for axon guidance, synapse organization, neuron migration, and other critical cellular functions. Furthermore, those genes are highly connected to and enriched for genes previously associated with autism risks. Conclusions Overall, our proof-of-principle computational study using single-cell data uncovers key intercellular signaling pathways that are potentially disrupted in the autism brains, suggesting that more studies examining cross-cell type effects can be valuable for understanding autism pathogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s11689-022-09441-1.
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Whole-Transcriptome Analysis of Serum L1CAM-Captured Extracellular Vesicles Reveals Neural and Glycosylation Changes in Autism Spectrum Disorder. J Mol Neurosci 2022; 72:1274-1292. [PMID: 35412111 DOI: 10.1007/s12031-022-01994-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
The pathophysiology of autistic spectrum disorder (ASD) is not fully understood and there are no diagnostic or predictive biomarkers. Extracellular vesicles (EVs) are cell-derived nano-sized vesicles, carrying nucleic acids, proteins, lipids, and other bioactive substances. As reported, serum neural cell adhesion molecule L1 (L1CAM)-captured EVs (LCEVs) can provide reliable biomarkers for neurological diseases; however, little is known about the LCEVs in children with ASD. The study enrolled 100 children with ASD (2.5-6 years of age; 90 males) and 60 age-matched TD children (54 males) as control. The serum sample was collected and pooled into five ASD subgroups and three TD subgroups (n = 20). LCEVs were isolated and characterized meticulously. Whole-transcriptome of LCEVs was analyzed by lncRNA microarray and RNA-sequencing. All raw data was submitted on GEO Profiles, and GEO accession numbers is GSE186493. RNAs expressed differently in LCEVs from ASD sera vs. TD sera were screened, analyzed, and further validated. A total of 1418 mRNAs, 1745 lncRNAs, and 11 miRNAs were differentially expressed, and most of them were downregulated in ASD. Most RNAs were involved in neuron- and glycan-related networks implicated in ASD. The levels of EDNRA, SLC17A6, HTR3A, OSTC, TMEM165, PC-5p-139289_26, and hsa-miR-193a-5p were validated in at least 15 ASD and 15 TD individual serum samples, which were consistent with the results of transcriptome analysis. In conclusion, whole-transcriptome analysis of serum LCEVs reveals neural and glycosylation changes in ASD, which may help detect predictive biomarkers and molecular mechanisms of ASD, and provide reference for diagnoses and therapeutic management of the disease.
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Truong TTT, Bortolasci CC, Spolding B, Panizzutti B, Liu ZSJ, Kidnapillai S, Richardson M, Gray L, Smith CM, Dean OM, Kim JH, Berk M, Walder K. Co-Expression Networks Unveiled Long Non-Coding RNAs as Molecular Targets of Drugs Used to Treat Bipolar Disorder. Front Pharmacol 2022; 13:873271. [PMID: 35462908 PMCID: PMC9024411 DOI: 10.3389/fphar.2022.873271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) may play a role in psychiatric diseases including bipolar disorder (BD). We investigated mRNA-lncRNA co-expression patterns in neuronal-like cells treated with widely prescribed BD medications. The aim was to unveil insights into the complex mechanisms of BD medications and highlight potential targets for new drug development. Human neuronal-like (NT2-N) cells were treated with either lamotrigine, lithium, quetiapine, valproate or vehicle for 24 h. Genome-wide mRNA expression was quantified for weighted gene co-expression network analysis (WGCNA) to correlate the expression levels of mRNAs with lncRNAs. Functional enrichment analysis and hub lncRNA identification was conducted on key co-expressed modules associated with the drug response. We constructed lncRNA-mRNA co-expression networks and identified key modules underlying these treatments, as well as their enriched biological functions. Processes enriched in key modules included synaptic vesicle cycle, endoplasmic reticulum-related functions and neurodevelopment. Several lncRNAs such as GAS6-AS1 and MIR100HG were highlighted as driver genes of key modules. Our study demonstrates the key role of lncRNAs in the mechanism(s) of action of BD drugs. Several lncRNAs have been suggested as major regulators of medication effects and are worthy of further investigation as novel drug targets to treat BD.
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Affiliation(s)
- Trang TT. Truong
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- *Correspondence: Trang TT. Truong,
| | - Chiara C. Bortolasci
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Briana Spolding
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Bruna Panizzutti
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Zoe SJ. Liu
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Srisaiyini Kidnapillai
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Mark Richardson
- Genomics Centre, School of Life and Environmental Sciences, Deakin University, Burwood, VIC, Australia
| | - Laura Gray
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Craig M. Smith
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Olivia M. Dean
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Jee Hyun Kim
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Michael Berk
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
- Orygen, The National Centre of Excellence in Youth Mental Health, Centre for Youth Mental Health, Florey Institute for Neuroscience and Mental Health and the Department of Psychiatry, The University of Melbourne, Melbourne, VIC, Australia
| | - Ken Walder
- School of Medicine, IMPACT, Institute for Innovation in Physical and Mental health and Clinical Translation, Deakin University, Geelong, VIC, Australia
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Moderate Folic Acid Supplementation in Pregnant Mice Results in Altered Sex-Specific Gene Expression in Brain of Young Mice and Embryos. Nutrients 2022; 14:nu14051051. [PMID: 35268026 PMCID: PMC8912750 DOI: 10.3390/nu14051051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 02/07/2023] Open
Abstract
Food fortification and increased vitamin intake have led to higher folic acid (FA) consumption by many pregnant women. We showed that FA-supplemented diet in pregnant mice (fivefold higher FA than the recommended level (5xFASD)) led to hyperactivity-like behavior and memory impairment in pups. Disturbed choline/methyl metabolism and altered placental gene expression were identified. The aim of this study was to examine the impact of 5xFASD on the brain at two developmental stages, postnatal day (P) 30 and embryonic day (E) 17.5. Female C57BL/6 mice were fed a control diet or 5xFASD for 1 month before mating. Diets were maintained throughout the pregnancy and lactation until P30 or during pregnancy until E17.5. The 5xFASD led to sex-specific transcription changes in P30 cerebral cortex and E17.5 cerebrum, with microarrays showing a total of 1003 and 623 changes, respectively. Enhanced mRNA degradation was observed in E17.5 cerebrum. Expression changes of genes involved in neurotransmission, neuronal growth and development, and angiogenesis were verified by qRT-PCR; 12 and 15 genes were verified at P30 and E17.5, respectively. Hippocampal collagen staining suggested decreased vessel density in FASD male embryos. This study provides insight into the mechanisms of neurobehavioral alterations and highlights potential deleterious consequences of moderate folate oversupplementation during pregnancy.
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Sun S, Mao W, Wan L, Pan K, Deng L, Zhang L, Zhang G, Chen M. Metastatic Immune-Related Genes for Affecting Prognosis and Immune Response in Renal Clear Cell Carcinoma. Front Mol Biosci 2022; 8:794326. [PMID: 35155566 PMCID: PMC8832145 DOI: 10.3389/fmolb.2021.794326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/28/2021] [Indexed: 01/31/2023] Open
Abstract
Background: In renal clear cell carcinoma, a common cancer of the urinary system, 25–30% patients are metastatic at initial diagnosis and 20–30% patients have a tendency of recurrence and metastasis after local surgery. With the rapid development of tumor immunology, immune agents have brought new directions to tumor therapy. However, no relevant studies have explored the role of immune-related genes in kidney cancer metastasis. Methods: Co-expressed metastatic immune-related differentially expressed genes (mIR-DEGs) were screened by GSE12606, GSE47352, and immunorelated genes. Then, differential expression analysis, prognostic analysis, and univariate and multivariate Cox regression analysis in KIRC were performed to determine independent prognostic factors associated, and the risk prognostic model was established. The correlation of hub mIR-DEGs with clinicopathological factors, immune invasion, and immune checkpoints was analyzed, and the expression of hub mIR-DEGs and their effect on tumor were re-evaluated by OCLR scores in KIRC. Results: By comprehensive bioassay, we found that FGF17, PRKCG, SSTR1, and SCTR were mIR-DEGs with independent prognostic values, which were significantly associated with clinicopathological factors and immune checkpoint–related genes. The risk prognostics model built on this basis had good predictive potential. In addition, targeted small molecule drugs, including calmidazolium and sulfasalazine, were predicted for mIR-DEGs. Further experimental results were consistent with the bioinformatics analysis. Conclusion: This study preliminarily confirmed that FGF17, PRKCG, SSTR1, and SCTR were targeted genes affecting renal cancer metastasis and related immune responses and can be used as potential therapeutic targets and prognostic biomarkers for renal cancer. Preliminary validation found that PRKCG and SSTR1 were consistent with predictions.
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Affiliation(s)
- Si Sun
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
- Medical School, Southeast University, Nanjing, China
| | - Weipu Mao
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
| | - Lilin Wan
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
- Medical School, Southeast University, Nanjing, China
| | - Kehao Pan
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
- Medical School, Southeast University, Nanjing, China
| | - Liting Deng
- Medical School, Southeast University, Nanjing, China
| | - Lei Zhang
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
- *Correspondence: Ming Chen, ; Guangyuan Zhang, ; Lei Zhang,
| | - Guangyuan Zhang
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
- *Correspondence: Ming Chen, ; Guangyuan Zhang, ; Lei Zhang,
| | - Ming Chen
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
- *Correspondence: Ming Chen, ; Guangyuan Zhang, ; Lei Zhang,
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Ito K, Takizawa T. Nuclear Architecture in the Nervous System. Results Probl Cell Differ 2022; 70:419-442. [PMID: 36348117 DOI: 10.1007/978-3-031-06573-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Neurons and glial cells in the nervous system exhibit different gene expression programs for neural development and function. These programs are controlled by the epigenetic regulatory layers in the nucleus. The nucleus is a well-organized subcellular organelle that includes chromatin, the nuclear lamina, and nuclear bodies. These subnuclear components operate together as epigenetic regulators of neural development and function and are collectively called the nuclear architecture. In the nervous system, dynamic rearrangement of the nuclear architecture has been observed in each cell type, especially in neurons, allowing for their specialized functions, including learning and memory formation. Although the importance of nuclear architecture has been debated for decades, the paradigm has been changing rapidly, owing to the development of new technologies. Here, we reviewed the latest studies on nuclear geometry, nuclear bodies, and heterochromatin compartments, as well as summarized recent novel insights regarding radial positioning, chromatin condensation, and chromatin interaction between genes and cis-regulatory elements.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, Pennsylvania, USA
| | - Takumi Takizawa
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan.
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Known and Unexplored Post-Translational Modification Pathways in Schizophrenia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1400:75-87. [DOI: 10.1007/978-3-030-97182-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Noguchi A, Ito K, Uosaki Y, Ideta-Otsuka M, Igarashi K, Nakashima H, Kakizaki T, Kaneda R, Uosaki H, Yanagawa Y, Nakashima K, Arakawa H, Takizawa T. Decreased Lamin B1 Levels Affect Gene Positioning and Expression in Postmitotic Neurons. Neurosci Res 2021; 173:22-33. [PMID: 34058264 DOI: 10.1016/j.neures.2021.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 01/01/2023]
Abstract
Gene expression programs and concomitant chromatin regulation change dramatically during the maturation of postmitotic neurons. Subnuclear positioning of gene loci is relevant to transcriptional regulation. However, little is known about subnuclear genome positioning in neuronal maturation. Using cultured murine hippocampal neurons, we found genomic locus 14qD2 to be enriched with genes that are upregulated during neuronal maturation. Reportedly, the locus is homologous to human 8p21.3, which has been extensively studied in neuropsychiatry and neurodegenerative diseases. Mapping of the 14qD2 locus in the nucleus revealed that it was relocated from the nuclear periphery to the interior. Moreover, we found a concomitant decrease in lamin B1 expression. Overexpression of lamin B1 in neurons using a lentiviral vector prevented the relocation of the 14qD2 locus and repressed the transcription of the Egr3 gene on this locus. Taken together, our results suggest that reduced lamin B1 expression during the maturation of neurons is important for appropriate subnuclear positioning of the genome and transcriptional programs.
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Affiliation(s)
- Azumi Noguchi
- Gunma University Graduate School of Medicine, Department of Pediatrics, Maebashi, 371-8511, Japan
| | - Kenji Ito
- Gunma University Graduate School of Medicine, Department of Pediatrics, Maebashi, 371-8511, Japan; University of Pennsylvania, Perelman School of Medicine, Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Philadelphia, PA, 19104-5157, USA
| | - Yuichi Uosaki
- Gunma University Graduate School of Medicine, Department of Pediatrics, Maebashi, 371-8511, Japan
| | - Maky Ideta-Otsuka
- Hoshi University School of Pharmacy Pharmaceutical Science, Life Science Tokyo Advanced Research Center (L-StaR), Tokyo, 142 8501, Japan
| | - Katsuhide Igarashi
- Hoshi University School of Pharmacy Pharmaceutical Science, Life Science Tokyo Advanced Research Center (L-StaR), Tokyo, 142 8501, Japan
| | - Hideyuki Nakashima
- Kyushu University, Department of Stem Cell Biology and Medicine Graduate School of Medical Sciences, Fukuoka, 812 8582, Japan
| | - Toshikazu Kakizaki
- Gunma University Graduate School of Medicine, Department of Genetic and Behavioral Neuroscience, Maebashi, 371 8511, Japan
| | - Ruri Kaneda
- Jichi Medical University, Support Center for Clinical Investigation, Shimotsuke, 329 0498, Japan
| | - Hideki Uosaki
- Jichi Medical University, Division of Regenerative Medicine, Center for Molecular Medicine, Shimotsuke, 329 0498, Japan; Jichi Medical University, Center for Development of Advanced Medical Technology, Shimotsuke, 329 0498, Japan
| | - Yuchio Yanagawa
- Gunma University Graduate School of Medicine, Department of Genetic and Behavioral Neuroscience, Maebashi, 371 8511, Japan
| | - Kinichi Nakashima
- Kyushu University, Department of Stem Cell Biology and Medicine Graduate School of Medical Sciences, Fukuoka, 812 8582, Japan
| | - Hirokazu Arakawa
- Gunma University Graduate School of Medicine, Department of Pediatrics, Maebashi, 371-8511, Japan
| | - Takumi Takizawa
- Gunma University Graduate School of Medicine, Department of Pediatrics, Maebashi, 371-8511, Japan.
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Zhang Y, Yao L, Li X, Meng M, Shang Z, Wang Q, Xiao J, Gu X, Xu Z, Zhang X. Schizophrenia risk-gene Crmp2 deficiency causes precocious critical period plasticity and deteriorated binocular vision. Sci Bull (Beijing) 2021; 66:2225-2237. [PMID: 36654114 DOI: 10.1016/j.scib.2021.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/15/2020] [Accepted: 01/29/2021] [Indexed: 02/03/2023]
Abstract
Brain-specific loss of a microtubule-binding protein collapsin response mediator protein-2 (CRMP2) in the mouse recapitulates many schizophrenia-like behaviors of human patients, possibly resulting from associated developmental deficits in neuronal differentiation, path-finding, and synapse formation. However, it is still unclear how the Crmp2 loss affects neuronal circuit function and plasticity. By conducting in vivo and ex vivo electrophysiological recording in the mouse primary visual cortex (V1), we reveal that CRMP2 exerts a key regulation on the timing of postnatal critical period (CP) for experience-dependent circuit plasticity of sensory cortex. In the developing V1, the Crmp2 deficiency induces not only a delayed maturation of visual tuning functions but also a precocious CP for visual input-induced ocular dominance plasticity and its induction activity - coincident binocular inputs right after eye-opening. Mechanistically, the Crmp2 deficiency accelerates the maturation process of cortical inhibitory transmission and subsequently promotes an early emergence of balanced excitatory-inhibitory cortical circuits during the postnatal development. Moreover, the precocious CP plasticity results in deteriorated binocular depth perception in adulthood. Thus, these findings suggest that the Crmp2 deficiency dysregulates the timing of CP for experience-dependent refinement of circuit connections and further leads to impaired sensory perception in later life.
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Affiliation(s)
- Yuan Zhang
- State Key Laboratory of Cognitive Neuroscience & Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Li Yao
- State Key Laboratory of Cognitive Neuroscience & Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Xiang Li
- State Key Laboratory of Cognitive Neuroscience & Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Meizhen Meng
- State Key Laboratory of Cognitive Neuroscience & Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Ziwei Shang
- State Key Laboratory of Cognitive Neuroscience & Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Qin Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaying Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiang Gu
- State Key Laboratory of Cognitive Neuroscience & Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaohui Zhang
- State Key Laboratory of Cognitive Neuroscience & Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China.
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Hu Y, Tan H, Li C, Zhang H. Identifying genetic risk variants associated with brain volumetric phenotypes via K-sample Ball Divergence method. Genet Epidemiol 2021; 45:710-720. [PMID: 34184773 PMCID: PMC8434958 DOI: 10.1002/gepi.22423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 06/07/2021] [Accepted: 06/17/2021] [Indexed: 02/05/2023]
Abstract
Regional human brain volumes including total area, average thickness, and total volume are heritable and associated with neurological disorders. However, the genetic architecture of brain structure and function is still largely unknown and worthy of exploring. The Pediatric Imaging, Neurocognition, and Genetics (PING) data set provides an excellent resource with genome-wide genetic data and related neuroimaging data. In this study, we perform genome-wide association studies (GWAS) of 315 brain volumetric phenotypes from the PING data set including 1036 samples with 539,865 single-nucleotide polymorphisms (SNPs). We introduce a nonparametric test based on K-sample Ball Divergence (KBD) to identify genetic risk variants that influence regional brain volumes. We carry out simulations to demonstrate that KBD is a powerful test for identifying significant SNPs associated with multivariate phenotypes although controlling the type I error rate. We successfully identify nine SNPs below a significance level of 5 × 10-5 for the PING data. Among the nine identified genetic variants, two SNPs rs486179 and rs562110 are located in the ADRA1A gene that is a well-known risk factor of mental illness, such as schizophrenia and attention deficit hyperactivity disorder. Our study suggests that the nonparametric test KBD is an effective method for identifying genetic variants associated with complex diseases in large-scale GWAS of multiple phenotypes.
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Affiliation(s)
- Yue Hu
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, 06511
| | - Haizhu Tan
- Department of Preventive Medicine, Shantou University Medical College, Xinling Road 22, Shantou, Guangdong, P. R. China
| | - Cai Li
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, 06511
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, 06511
- Correspondence Author: Heping Zhang, 300 George Street, Ste 523, New Haven, CT, 06511. . Phone: 203-785-5185
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Li M, Sun X, Yao H, Chen W, Zhang F, Gao S, Zou X, Chen J, Qiu S, Wei H, Hu Z, Chen W. Genomic methylation variations predict the susceptibility of six chemotherapy related adverse effects and cancer development for Chinese colorectal cancer patients. Toxicol Appl Pharmacol 2021; 427:115657. [PMID: 34332992 DOI: 10.1016/j.taap.2021.115657] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/08/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) remains a major concern with high morbidity and mortality worldwide. Despite the positive influence of chemotherapy on the decline in CRC mortality, the negative influence of chemotherapy-related adverse effects (CRAEs) caused by capecitabine (Cap) remains a challenging problem. DNA methylation alteration plays a pivotal role in gene expression regulation. Here, we aimed to screen reliable and novel biomarkers for CRC diagnosis and CRAE prediction using the advanced Illumina Infinium MethylationEPIC (850 K) BeadChip. Paired tumor and normal tissues from 21 Chinese CRC patients who received Cap-based adjuvant chemotherapy were analyzed. CRC-related methylation was characterized by hypermethylated promoter islands and hypomethylated intragenic openseas; CRAE-related methylation was characterized by hyper- (or hypo-) methylated intragenic (or intergenic) regions. Based on three types of methylation profiles (differentially methylated probes, differentially methylated regions, and gene-function-differentially methylated regions), pathway enrichment analyses revealed that CRC-related genes were significantly enriched in the neuronal system, metabolism of RNA, and extracellular matrix organization; CRAE-related genes were abundantly enriched in pathways controlling regeneration functions and immune response. Finally, based on genes within the mostly related pathways and LASSO logistic regression selection, the integrated-methylation-marker systems developed here demonstrated high discriminative accuracy in both CRC diagnosis (AUROC = 1) and CRAE prediction (AUROC = 0.817-1). In conclusion, we conducted a comprehensive DNA methylation analysis of CRC patients with chemotherapy, which provided new insights into the formation of CRC and CRAEs. Most importantly, our findings identified potentially CRAE-related metabolic pathways and markers, providing a valuable reference for personalized medicine promising better safety. Trail registration:ClinicalTrials.gov,NCT03030508, Registered 25 January 2017,https://www.clinicaltrials.gov/ct2/show/NCT03030508?term=NCT03030508&draw=2&rank=1.
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Affiliation(s)
- Mingming Li
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xiaomeng Sun
- Research Institute, GloriousMed Clinical Laboratory Co., Ltd., Shanghai 201318, China
| | - Houshan Yao
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Wei Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Feng Zhang
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Shouhong Gao
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Xun Zou
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Jiani Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Shi Qiu
- Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hua Wei
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Department of Pharmacy, 905th Hospital of PLA Navy, Naval Medical University, Shanghai 200052, China.
| | - Zhiqian Hu
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Department of Gastrointestinal Surgery, Tongji Hospital, Medical College of Tongji University, Shanghai 200065, China.
| | - Wansheng Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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Forés-Martos J, Boullosa C, Rodrigo-Domínguez D, Sánchez-Valle J, Suay-García B, Climent J, Falcó A, Valencia A, Puig-Butillé JA, Puig S, Tabarés-Seisdedos R. Transcriptomic and Genetic Associations between Alzheimer's Disease, Parkinson's Disease, and Cancer. Cancers (Basel) 2021; 13:cancers13122990. [PMID: 34203763 PMCID: PMC8232649 DOI: 10.3390/cancers13122990] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Epidemiological studies have identified a link between neurodegenerative disorders and a reduced risk of overall cancer. Increases and decreases in the risk of site-specific cancers have also been reported. However, it is still unknown whether these associations arise due to shared genetic and molecular factors or are explained by other phenomena (e.g., biases in epidemiological studies or the use of medication). In this study, we aimed to investigate the potential molecular, genetic, and pharmacological links between Alzheimer’s and Parkinson’s diseases and a large panel of 22 cancer types. To examine the overlapping involvement of genes and pathways, we obtained differential gene expression profiles through meta-analyses of post-mortem brain tissues from Alzheimer’s and Parkinson’s disease patients, primary tumors, and tissue-matched controls, and compared them. Genetic similarities were assessed through network-based methods and the computation of genetic correlations. Finally, the potential impact of drugs indicated for each disorder in the identified associations was evaluated using transcriptomic methods. Our research extends previous work in the field by identifying new significant patterns of transcriptomic associations (direct and inverse) between Alzheimer’s disease, Parkinson’s disease, and different site-specific cancers. The results reveal significant genetic correlations between Parkinson’s disease, prostate cancer, and melanoma. In addition, to our knowledge, this is the first time that the role of drugs indicated for the treatment of both sets of disorders has been investigated in the context of their comorbid associations using transcriptomic methods. Abstract Alzheimer’s (AD) and Parkinson’s diseases (PD) are the two most prevalent neurodegenerative disorders in human populations. Epidemiological studies have shown that patients suffering from either condition present a reduced overall risk of cancer than controls (i.e., inverse comorbidity), suggesting that neurodegeneration provides a protective effect against cancer. Reduced risks of several site-specific tumors, including colorectal, lung, and prostate cancers, have also been observed in AD and PD. By contrast, an increased risk of melanoma has been described in PD patients (i.e., direct comorbidity). Therefore, a fundamental question to address is whether these associations are due to shared genetic and molecular factors or are explained by other phenomena, such as flaws in epidemiological studies, exposure to shared risk factors, or the effect of medications. To this end, we first evaluated the transcriptomes of AD and PD post-mortem brain tissues derived from the hippocampus and the substantia nigra and analyzed their similarities to those of a large panel of 22 site-specific cancers, which were obtained through differential gene expression meta-analyses of array-based studies available in public repositories. Genes and pathways that were deregulated in both disorders in each analyzed pair were examined. Second, we assessed potential genetic links between AD, PD, and the selected cancers by establishing interactome-based overlaps of genes previously linked to each disorder. Then, their genetic correlations were computed using cross-trait LD score regression and GWAS summary statistics data. Finally, the potential role of medications in the reported comorbidities was assessed by comparing disease-specific differential gene expression profiles to an extensive collection of differential gene expression signatures generated by exposing cell lines to drugs indicated for AD, PD, and cancer treatment (LINCS L1000). We identified significant inverse associations of transcriptomic deregulation between AD hippocampal tissues and breast, lung, liver, and prostate cancers, and between PD substantia nigra tissues and breast, lung, and prostate cancers. Moreover, significant direct (same direction) associations of deregulation were observed between AD and PD and brain and thyroid cancers, as well as between PD and kidney cancer. Several biological processes, including the immune system, oxidative phosphorylation, PI3K/AKT/mTOR signaling, and the cell cycle, were found to be deregulated in both cancer and neurodegenerative disorders. Significant genetic correlations were found between PD and melanoma and prostate cancers. Several drugs indicated for the treatment of neurodegenerative disorders and cancer, such as galantamine, selegiline, exemestane, and estradiol, were identified as potential modulators of the comorbidities observed between neurodegeneration and cancer.
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Affiliation(s)
- Jaume Forés-Martos
- Biomedical Research Networking Center of Mental Health (CIBERSAM), 28029 Madrid, Spain;
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, 46115 Alfara del Patriarca, Spain; (B.S.-G.); (J.C.); (A.F.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, 46115 Alfara del Patriarca, Spain
| | | | - David Rodrigo-Domínguez
- Consorcio Hospital General de Valencia, Servicio de Medicina Interna, 46014 Valencia, Spain;
| | - Jon Sánchez-Valle
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (J.S.-V.); (A.V.)
| | - Beatriz Suay-García
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, 46115 Alfara del Patriarca, Spain; (B.S.-G.); (J.C.); (A.F.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, 46115 Alfara del Patriarca, Spain
| | - Joan Climent
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, 46115 Alfara del Patriarca, Spain; (B.S.-G.); (J.C.); (A.F.)
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, 46115 Alfara del Patriarca, Spain
| | - Antonio Falcó
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, 46115 Alfara del Patriarca, Spain; (B.S.-G.); (J.C.); (A.F.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, 46115 Alfara del Patriarca, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (J.S.-V.); (A.V.)
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Joan Anton Puig-Butillé
- Biochemical and Molecular Genetics Service, Hospital Clínic and August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain;
- Melanoma Unit, Hospital Clínic, Center for Networked Biomedical Research on Rare Diseases (CIBERER), Carlos III Health Institute (ISCIII), 08036 Barcelona, Spain;
| | - Susana Puig
- Melanoma Unit, Hospital Clínic, Center for Networked Biomedical Research on Rare Diseases (CIBERER), Carlos III Health Institute (ISCIII), 08036 Barcelona, Spain;
- Dermatology Department, Hospital Clínic and August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Rafael Tabarés-Seisdedos
- Biomedical Research Networking Center of Mental Health (CIBERSAM), 28029 Madrid, Spain;
- Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Blasco-Ibañez 15, 46010 Valencia, Spain
- INCLIVA Health Research Institute, 46010 Valencia, Spain
- Correspondence: ; Tel.: +44-(0)1865-617-855
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Methylome-wide change associated with response to electroconvulsive therapy in depressed patients. Transl Psychiatry 2021; 11:347. [PMID: 34091594 PMCID: PMC8179923 DOI: 10.1038/s41398-021-01474-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/10/2021] [Accepted: 05/21/2021] [Indexed: 12/31/2022] Open
Abstract
Electroconvulsive therapy (ECT) is a quick-acting and powerful antidepressant treatment considered to be effective in treating severe and pharmacotherapy-resistant forms of depression. Recent studies have suggested that epigenetic mechanisms can mediate treatment response and investigations about the relationship between the effects of ECT and DNA methylation have so far largely taken candidate approaches. In the present study, we examined the effects of ECT on the methylome associated with response in depressed patients (n = 34), testing for differentially methylated CpG sites before the first and after the last ECT treatment. We identified one differentially methylated CpG site associated with the effect of ECT response (defined as >50% decrease in Hamilton Depression Rating Scale score, HDRS), TNKS (q < 0.05; p = 7.15 × 10-8). When defining response continuously (ΔHDRS), the top suggestive differentially methylated CpG site was in FKBP5 (p = 3.94 × 10-7). Regional analyses identified two differentially methylated regions on chromosomes 8 (Šídák's p = 0.0031) and 20 (Šídák's p = 4.2 × 10-5) associated with ΔHDRS. Functional pathway analysis did not identify any significant pathways. A confirmatory look at candidates previously proposed to be involved in ECT mechanisms found CpG sites associated with response only at the nominally significant level (p < 0.05). Despite the limited sample size, the present study was able to identify epigenetic change associated with ECT response suggesting that this approach, especially when involving larger samples, has the potential to inform the study of mechanisms involved in ECT and severe and treatment-resistant depression.
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41
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Škrlj B, Eržen N, Lavrač N, Kunej T, Konc J. CaNDis: a web server for investigation of causal relationships between diseases, drugs and drug targets. Bioinformatics 2021; 37:885-887. [PMID: 32871004 PMCID: PMC8098028 DOI: 10.1093/bioinformatics/btaa762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/24/2020] [Accepted: 08/25/2020] [Indexed: 01/24/2023] Open
Abstract
MOTIVATION Causal biological interaction networks represent cellular regulatory pathways. Their fusion with other biological data enables insights into disease mechanisms and novel opportunities for drug discovery. RESULTS We developed Causal Network of Diseases (CaNDis), a web server for the exploration of a human causal interaction network, which we expanded with data on diseases and FDA-approved drugs, on the basis of which we constructed a disease-disease network in which the links represent the similarity between diseases. We show how CaNDis can be used to identify candidate genes with known and novel roles in disease co-occurrence and drug-drug interactions. AVAILABILITYAND IMPLEMENTATION CaNDis is freely available to academic users at http://candis.ijs.si and http://candis.insilab.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Blaž Škrlj
- Department of Knowledge Technologies, Jožef Stefan Institute, Slovenia.,Jožef Stefan International Postgraduate School, Slovenia
| | - Nika Eržen
- Department of Knowledge Technologies, Jožef Stefan Institute, Slovenia
| | - Nada Lavrač
- Department of Knowledge Technologies, Jožef Stefan Institute, Slovenia.,Jožef Stefan International Postgraduate School, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Slovenia
| | - Janez Konc
- Theory Department, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
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Cai T, Wang X, Li B, Xiong F, Wu H, Yang X. Deciphering the synergistic network regulation of active components from SiNiSan against irritable bowel syndrome via a comprehensive strategy: Combined effects of synephrine, paeoniflorin and naringin. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 86:153527. [PMID: 33845366 DOI: 10.1016/j.phymed.2021.153527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND SiNiSan (SNS) is an ancient Chinese herbal prescription, and the current clinical treatment of irritable bowel syndrome (IBS) is effective. In the previous study of the research team, the multi-functional co-synergism of SNS against IBS was presented. Some potential drug targets and candidate ligands were predicted. PURPOSE This study attempts to explore the crucial ingredient combinations from SNS formula and reveal their synergistic mechanism for IBS therapy. MATERIALS AND METHODS In present study, a comprehensive strategy was performed to reveal IBS related pathways and biological modules, and explore synergistic effects of the ingredients, including ADME (absorption, distribution, metabolism, excretion) screening, Text mining, Venn analysis, Gene ontology (GO) analysis, Pathway cluster analysis, Molecular docking, Network construction and Experimental verification in visceral hypersensitivity (VHS) rats. RESULTS Three compressed IBS signal pathways were derived from ClueGO KEGG analysis of 63 IBS genes, including Neuroactive ligand-receptor interaction, Inflammatory mediator regulation of TRP (transient receptor potential) channels and Serotonergic synapse. A multi-module network, composed of four IBS therapeutic modules (psychological, inflammation, neuroendocrine and cross-talk modules), was revealed by Target-Pathway network. Nine kernel targets were considered closely associated with the IBS pathways, including ADRA2A, HTR2A, F2RL1, F2RL3, TRPV1, PKC, PKA, IL-1Β and NGF. In silico analysis revealed that three crucial ingredients (synephrine, paeoniflorin and naringin) were assumed to coordinate the network of those IBS therapeutic modules by acting on these kernel targets in the important pathways. In vivo experimental results showed that the crucial ingredient combinations synergistically affected the expressions of the kernel biological molecules, and improved the minimum capacity threshold of AWR in VHS rats. CONCLUSION The study proposes the important IBS associated pathways and the network regulation mechanisms of the crucial ingredients. It reveals the multi-target synergistic effect of the crucial ingredient combinations for the novel therapy on IBS.
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Affiliation(s)
- Tingting Cai
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiang Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Bangjie Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Fei Xiong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Hao Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xinghao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Li D, Zhao W, Zhang X, Lv H, Li C, Sun L. NEFM DNA methylation correlates with immune infiltration and survival in breast cancer. Clin Epigenetics 2021; 13:112. [PMID: 34001208 PMCID: PMC8130356 DOI: 10.1186/s13148-021-01096-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 05/02/2021] [Indexed: 11/25/2022] Open
Abstract
Background This study aims to determine whether NEFM (neurofilament medium) DNA methylation correlates with immune infiltration and prognosis in breast cancer (BRCA) and to explore NEFM-connected immune gene signature. Methods NEFM transcriptional expression was analyzed in BRCA and normal breast tissues using Oncomine and Tumor Immune Estimation Resource (TIMER) databases. The relationship between NEFM DNA methylation and NEFM transcriptional expression was investigated in TCGA. Potential influence of NEFM DNA methylation/expression on clinical outcome was evaluated using TCGA BRCA, The Human Protein Atlas and Kaplan–Meier plotter databases. Association of NEFM transcriptional expression/DNA methylation with cancer immune infiltration was investigated using TIMER and TISIDB databases. Results High expression of NEFM correlated with better overall survival (OS) and recurrence-free survival (RFS) in TCGA BRCA and Kaplan–Meier plotter, whereas NEFM DNA methylation with worse OS in TCGA BRCA. NEFM transcriptional expression negatively correlated with DNA methylation. NEFM DNA methylation significantly negatively correlated with infiltrating levels of B, CD8+ T/CD4+ T cells, macrophages, neutrophils and dendritic cells in TIMER and TISIDB. NEFM expression positively correlated with macrophage infiltration in TIMER and TISIDB. After adjusted with tumor purity, NEFM expression weekly negatively correlated with infiltration level of B cells, whereas positively correlated with CD8+ T cell infiltration in TIMER gene modules. NEFM expression/DNA methylation correlated with diverse immune markers in TCGA and TISIDB. Conclusions NEFM low-expression/DNA methylation correlates with poor prognosis. NEFM expression positively correlates with macrophage infiltration. NEFM DNA methylation strongly negatively correlates with immune infiltration in BRCA. Our study highlights novel potential functions of NEFM expression/DNA methylation in regulation of tumor immune microenvironment. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01096-4.
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Affiliation(s)
- Dandan Li
- Department of Radiotherapy Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wenhao Zhao
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, No.150 Haping Road, Nangang District, Harbin, 150081, China
| | - Xinyu Zhang
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, No.150 Haping Road, Nangang District, Harbin, 150081, China
| | - Hanning Lv
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, No.150 Haping Road, Nangang District, Harbin, 150081, China
| | - Chunhong Li
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, No.150 Haping Road, Nangang District, Harbin, 150081, China.
| | - Lichun Sun
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, No.150 Haping Road, Nangang District, Harbin, 150081, China.
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Catusi I, Garzo M, Capra AP, Briuglia S, Baldo C, Canevini MP, Cantone R, Elia F, Forzano F, Galesi O, Grosso E, Malacarne M, Peron A, Romano C, Saccani M, Larizza L, Recalcati MP. 8p23.2-pter Microdeletions: Seven New Cases Narrowing the Candidate Region and Review of the Literature. Genes (Basel) 2021; 12:genes12050652. [PMID: 33925474 PMCID: PMC8146486 DOI: 10.3390/genes12050652] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/11/2022] Open
Abstract
To date only five patients with 8p23.2-pter microdeletions manifesting a mild-to-moderate cognitive impairment and/or developmental delay, dysmorphisms and neurobehavioral issues were reported. The smallest microdeletion described by Wu in 2010 suggested a critical region (CR) of 2.1 Mb including several genes, out of which FBXO25, DLGAP2, CLN8, ARHGEF10 and MYOM2 are the main candidates. Here we present seven additional patients with 8p23.2-pter microdeletions, ranging from 71.79 kb to 4.55 Mb. The review of five previously reported and nine Decipher patients confirmed the association of the CR with a variable clinical phenotype characterized by intellectual disability/developmental delay, including language and speech delay and/or motor impairment, behavioral anomalies, autism spectrum disorder, dysmorphisms, microcephaly, fingers/toes anomalies and epilepsy. Genotype analysis allowed to narrow down the 8p23.3 candidate region which includes only DLGAP2, CLN8 and ARHGEF10 genes, accounting for the main signs of the broad clinical phenotype associated to 8p23.2-pter microdeletions. This region is more restricted compared to the previously proposed CR. Overall, our data favor the hypothesis that DLGAP2 is the actual strongest candidate for neurodevelopmental/behavioral phenotypes. Additional patients will be necessary to validate the pathogenic role of DLGAP2 and better define how the two contiguous genes, ARHGEF10 and CLN8, might contribute to the clinical phenotype.
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Affiliation(s)
- Ilaria Catusi
- Istituto Auxologico Italiano, IRCCS, Laboratory of Medical Cytogenetics and Molecular Genetics, 20145 Milan, Italy
| | - Maria Garzo
- Istituto Auxologico Italiano, IRCCS, Laboratory of Medical Cytogenetics and Molecular Genetics, 20145 Milan, Italy
| | - Anna Paola Capra
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, 98100 Messina, Italy
| | - Silvana Briuglia
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, 98100 Messina, Italy
| | - Chiara Baldo
- UOC Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Maria Paola Canevini
- Child Neuropsychiatry Unit-Epilepsy Center, Department of Health Sciences, ASST Santi Paolo e Carlo, San Paolo Hospital, Università Degli Studi di Milano, 20142 Milan, Italy
| | - Rachele Cantone
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Flaviana Elia
- Unit of Psychology, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Francesca Forzano
- Clinical Genetics Department, Guy's & St Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Ornella Galesi
- Laboratory of Medical Genetics, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Enrico Grosso
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Michela Malacarne
- UOC Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Angela Peron
- Child Neuropsychiatry Unit-Epilepsy Center, Department of Health Sciences, ASST Santi Paolo e Carlo, San Paolo Hospital, Università Degli Studi di Milano, 20142 Milan, Italy
- Human Pathology and Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, 20142 Milan, Italy
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Corrado Romano
- Unit of Pediatrics and Medical Genetics, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Monica Saccani
- Child Neuropsychiatry Unit-Epilepsy Center, Department of Health Sciences, ASST Santi Paolo e Carlo, San Paolo Hospital, Università Degli Studi di Milano, 20142 Milan, Italy
| | - Lidia Larizza
- Istituto Auxologico Italiano, IRCCS, Laboratory of Medical Cytogenetics and Molecular Genetics, 20145 Milan, Italy
| | - Maria Paola Recalcati
- Istituto Auxologico Italiano, IRCCS, Laboratory of Medical Cytogenetics and Molecular Genetics, 20145 Milan, Italy
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Dehner C, Moon CI, Zhang X, Zhou Z, Miller C, Xu H, Wan X, Yang K, Mashl J, Gosline SJ, Wang Y, Zhang X, Godec A, Jones PA, Dahiya S, Bhatia H, Primeau T, Li S, Pollard K, Rodriguez FJ, Ding L, Pratilas CA, Shern JF, Hirbe AC. Chromosome 8 gain is associated with high-grade transformation in MPNST. JCI Insight 2021; 6:146351. [PMID: 33591953 PMCID: PMC8026192 DOI: 10.1172/jci.insight.146351] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
One of the most common malignancies affecting adults with Neurofibromatosis type 1 (NF1) is the malignant peripheral nerve sheath tumor (MPNST), an aggressive and often fatal sarcoma that commonly arises from benign plexiform neurofibromas. Despite advances in our understanding of MPNST pathobiology, there are few effective therapeutic options, and no investigational agents have proven successful in clinical trials. To further understand the genomic heterogeneity of MPNST, and to generate a preclinical platform that encompasses this heterogeneity, we developed a collection of NF1-MPNST patient-derived xenografts (PDX). These PDX were compared with the primary tumors from which they were derived using copy number analysis, whole exome sequencing, and RNA sequencing. We identified chromosome 8 gain as a recurrent genomic event in MPNST and validated its occurrence by FISH in the PDX and parental tumors, in a validation cohort, and by single-cell sequencing in the PDX. Finally, we show that chromosome 8 gain is associated with inferior overall survival in soft-tissue sarcomas. These data suggest that chromosome 8 gain is a critical event in MPNST pathogenesis and may account for the aggressive nature and poor outcomes in this sarcoma subtype.
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Affiliation(s)
| | - Chang In Moon
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Xiyuan Zhang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Zhaohe Zhou
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Chris Miller
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hua Xu
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,The First Affiliated Hospital, Nanchang University, Nangchang, China
| | - Xiaodan Wan
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,The First Affiliated Hospital, Nanchang University, Nangchang, China
| | - Kuangying Yang
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jay Mashl
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sara Jc Gosline
- Pacific Northwest National Laboratory, Seattle, Washington, USA
| | - Yuxi Wang
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Xiaochun Zhang
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Abigail Godec
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Paul A Jones
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sonika Dahiya
- Department of Pathology and Immunology and.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
| | - Himanshi Bhatia
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Tina Primeau
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shunqiang Li
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
| | - Kai Pollard
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - Fausto J Rodriguez
- Department of Pathology, John Hopkins University, Baltimore, Maryland, USA
| | - Li Ding
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
| | - Christine A Pratilas
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Angela C Hirbe
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
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8p21.3 deletions are rare causes of non-syndromic autism spectrum disorder. Neurogenetics 2021; 22:207-213. [PMID: 33683518 DOI: 10.1007/s10048-021-00635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
A de novo 0.95 Mb 8p21.3 deletion had been identified in an individual with non-syndromic autism spectrum disorder (ASD) through high-resolution copy number variant analysis. Subsequent screening of in-house and publicly available databases resulted in the identification of six additional individuals with 8p21.3 deletions. Through case-based reasoning, we conclude that 8p21.3 deletions are rare causes of non-syndromic neurodevelopmental and neuropsychiatric disorders. Based on literature data, we highlight six genes within the region of minimal overlap as potential ASD genes or genes for neuropsychiatric disorders: DMTN, EGR3, FGF17, LGI3, PHYHIP, and PPP3CC.
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Liddiard K, Grimstead JW, Cleal K, Evans A, Baird DM. Tracking telomere fusions through crisis reveals conflict between DNA transcription and the DNA damage response. NAR Cancer 2021; 3:zcaa044. [PMID: 33447828 PMCID: PMC7787266 DOI: 10.1093/narcan/zcaa044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/02/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022] Open
Abstract
Identifying attributes that distinguish pre-malignant from senescent cells provides opportunities for targeted disease eradication and revival of anti-tumour immunity. We modelled a telomere-driven crisis in four human fibroblast lines, sampling at multiple time points to delineate genomic rearrangements and transcriptome developments that characterize the transition from dynamic proliferation into replicative crisis. Progression through crisis was associated with abundant intra-chromosomal telomere fusions with increasing asymmetry and reduced microhomology usage, suggesting shifts in DNA repair capacity. Eroded telomeres also fused with genomic loci actively engaged in transcription, with particular enrichment in long genes. Both gross copy number alterations and transcriptional responses to crisis likely underpin the elevated frequencies of telomere fusion with chromosomes 9, 16, 17, 19 and most exceptionally, chromosome 12. Juxtaposition of crisis-regulated genes with loci undergoing de novo recombination exposes the collusive contributions of cellular stress responses to the evolving cancer genome.
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Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Julia W Grimstead
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Kez Cleal
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Anna Evans
- Wales Gene Park, Institute of Medical Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Duncan M Baird
- Division of Cancer and Genetics, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
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48
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Lin YF, Chen KC, Yang YK, Hsiao YH. Collapsin response mediator protein 5 (CRMP5) modulates susceptibility to chronic social defeat stress in mice. Mol Neurobiol 2021; 58:3175-3186. [PMID: 33638112 DOI: 10.1007/s12035-021-02336-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/17/2021] [Indexed: 11/25/2022]
Abstract
Collapsin response mediator protein 5 (CRMP5), a member of the CRMP family, is expressed in the brain, particularly in the hippocampus, an area of the brain that can modulate stress responses. Social stress has a well-known detrimental effect on health and can lead to depression, but not all individuals are equally sensitive to stress. To date, researchers have not conclusively determined how social stress increases the susceptibility of the brain to depression. Here, we used the chronic social defeat stress (CSDS) model and observed higher hippocampal CRMP5 expression in stress-susceptible (SS) mice than in control and stress-resilient (RES) mice. A negative correlation was observed between the expression levels of CRMP5 and the social interaction (SI) ratio. Reduced hippocampal CRMP5 expression increased the SI ratio in SS mice, whereas CRMP5 overexpression was sufficient to induce social avoidance behaviors in control mice following exposure to subthreshold social stress induced by lentivirus-based overexpression and inducible tetracycline-on strategies to upregulate CRMP5. Interestingly, increased CRMP5 expression in SS and lenti-CRMP5-treated mice also caused serum corticosterone concentrations to increase. These findings improve our understanding of the potential mechanism by which CRMP5 triggers susceptibility to social stress, and they support the further development of therapeutic agents for the treatment of stress disorders in humans.
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Affiliation(s)
- Yu-Fen Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Kao Chin Chen
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen Kuang Yang
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Hsin Hsiao
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan.
- Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Lou X, Meng Y, Hou Y. A literature review on function and regulation mechanism of DKK4. J Cell Mol Med 2021; 25:2786-2794. [PMID: 33586359 PMCID: PMC7957263 DOI: 10.1111/jcmm.16372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 01/19/2021] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
Dickkopf-related protein 4 (DKK4) is a member of the dickkopf family and an inhibitor of the Wnt/β-catenin signalling pathway. This review surveyed the single nucleotide polymorphisms (SNPs), copy number variations (CNVs), hypermethylation, regulation mechanism, correlation with clinicopathological parameters and chemotherapeutic resistance of DKK4. The signal pathways involved in DKK4 mainly include Wnt/β-catenin pathway and Wnt-JNK pathway independent β-catenin. DKK4 expression was upregulated in Renal Cell Carcinoma (RCC), Colorectal Cancer, Gastric Cancer (GC), Non-small Cell Lung Cancer (NSCLC) and Epithelial Ovarian Cancer (EOC), while downregulated in Hepatocellular Carcinoma (HCC). DKK4 is not only involved in tumour growth, invasion, migration and chemotherapy resistance, but also in osteoblastogenesis and secondary hair or meibomian gland formation. DKK4 has also been linked to schizophrenia.
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Affiliation(s)
- Xiaoli Lou
- Department of Central Laboratory, Songjiang Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuchen Meng
- Department of Central Laboratory, Songjiang Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yanqiang Hou
- Department of Central Laboratory, Songjiang Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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50
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Genome-wide Association Analysis of Parkinson's Disease and Schizophrenia Reveals Shared Genetic Architecture and Identifies Novel Risk Loci. Biol Psychiatry 2021; 89:227-235. [PMID: 32201043 PMCID: PMC7416467 DOI: 10.1016/j.biopsych.2020.01.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 01/14/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Parkinson's disease (PD) and schizophrenia (SCZ) are heritable brain disorders that involve dysregulation of the dopaminergic system. Epidemiological studies have reported potential comorbidity between the disorders, and movement disturbances are common in patients with SCZ before treatment with antipsychotic drugs. Despite this, little is known about shared genetic etiology between the disorders. METHODS We analyzed recent large genome-wide association studies on patients with SCZ (N = 77,096) and PD (N = 417,508) using a conditional/conjunctional false discovery rate (FDR) approach to evaluate overlap in common genetic variants and improve statistical power for genetic discovery. Using a variety of biological resources, we functionally characterized the identified genomic loci. RESULTS We observed genetic enrichment in PD conditional on associations with SCZ and vice versa, indicating polygenic overlap. We then leveraged this cross-trait enrichment using conditional FDR analysis and identified 9 novel PD risk loci and 1 novel SCZ locus at conditional FDR < .01. Furthermore, we identified 9 genomic loci jointly associated with PD and SCZ at conjunctional FDR < .05. There was an even distribution of antagonistic and agonistic effect directions among the shared loci, in line with the insignificant genetic correlation between the disorders. Of 67 genes mapped to the shared loci, 65 are expressed in the human brain and show cell type-specific expression profiles. CONCLUSIONS Altogether, the study increases understanding of the genetic architectures underlying SCZ and PD, indicating that common molecular genetic mechanisms may contribute to overlapping pathophysiological and clinical features between the disorders.
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