1
|
Cathomas F, Lin HY, Chan KL, Li L, Parise LF, Alvarez J, Durand-de Cuttoli R, Aubry AV, Muhareb S, Desland F, Shimo Y, Ramakrishnan A, Estill M, Ferrer-Pérez C, Parise EM, Wilk CM, Kaster MP, Wang J, Sowa A, Janssen WG, Costi S, Rahman A, Fernandez N, Campbell M, Swirski FK, Nestler EJ, Shen L, Merad M, Murrough JW, Russo SJ. Circulating myeloid-derived MMP8 in stress susceptibility and depression. Nature 2024; 626:1108-1115. [PMID: 38326622 PMCID: PMC10901735 DOI: 10.1038/s41586-023-07015-2] [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: 05/11/2022] [Accepted: 12/29/2023] [Indexed: 02/09/2024]
Abstract
Psychosocial stress has profound effects on the body, including the immune system and the brain1,2. Although a large number of pre-clinical and clinical studies have linked peripheral immune system alterations to stress-related disorders such as major depressive disorder (MDD)3, the underlying mechanisms are not well understood. Here we show that expression of a circulating myeloid cell-specific proteinase, matrix metalloproteinase 8 (MMP8), is increased in the serum of humans with MDD as well as in stress-susceptible mice following chronic social defeat stress (CSDS). In mice, we show that this increase leads to alterations in extracellular space and neurophysiological changes in the nucleus accumbens (NAc), as well as altered social behaviour. Using a combination of mass cytometry and single-cell RNA sequencing, we performed high-dimensional phenotyping of immune cells in circulation and in the brain and demonstrate that peripheral monocytes are strongly affected by stress. In stress-susceptible mice, both circulating monocytes and monocytes that traffic to the brain showed increased Mmp8 expression following chronic social defeat stress. We further demonstrate that circulating MMP8 directly infiltrates the NAc parenchyma and controls the ultrastructure of the extracellular space. Depleting MMP8 prevented stress-induced social avoidance behaviour and alterations in NAc neurophysiology and extracellular space. Collectively, these data establish a mechanism by which peripheral immune factors can affect central nervous system function and behaviour in the context of stress. Targeting specific peripheral immune cell-derived matrix metalloproteinases could constitute novel therapeutic targets for stress-related neuropsychiatric disorders.
Collapse
Affiliation(s)
- Flurin Cathomas
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Hsiao-Yun Lin
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kenny L Chan
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Long Li
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lyonna F Parise
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johana Alvarez
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romain Durand-de Cuttoli
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Antonio V Aubry
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samer Muhareb
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fiona Desland
- Department of Oncological Sciences, Marc and Jennifer Lipschultz Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yusuke Shimo
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Ferrer-Pérez
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric M Parise
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - C Matthias Wilk
- Department of Oncological Sciences, Marc and Jennifer Lipschultz Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manuella P Kaster
- Department of Biochemistry, Federal University of Santa Catarina, Santa Catarina, Brazil
| | - Jun Wang
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Allison Sowa
- Microscopy CoRE and Advanced Bioimaging Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - William G Janssen
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Microscopy CoRE and Advanced Bioimaging Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sara Costi
- Depression and Anxiety Center for Discovery and Treatment, Department of Psychiatry, Icahn School of Medicine of Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Department of Oncological Sciences, Marc and Jennifer Lipschultz Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolas Fernandez
- Department of Oncological Sciences, Marc and Jennifer Lipschultz Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Campbell
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Filip K Swirski
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Department of Oncological Sciences, Marc and Jennifer Lipschultz Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James W Murrough
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Depression and Anxiety Center for Discovery and Treatment, Department of Psychiatry, Icahn School of Medicine of Mount Sinai, New York, NY, USA
| | - Scott J Russo
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Brain and Body Research Center of the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
2
|
Meloto CB. Genetics of Postsurgical Pain: Where Do We Go from Here? Anesthesiology 2023; 139:726-729. [PMID: 37934109 DOI: 10.1097/aln.0000000000004780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Affiliation(s)
- Carolina B Meloto
- Faculty of Dental Medicine and Oral Health Sciences and the Alan Edwards Centre for Research on Pain, McGill University, Montréal, Québec, Canada
| |
Collapse
|
3
|
Shi S, Zhang M, Xie W, Ju P, Chen N, Wang F, Lyu D, Wang M, Hong W. Sleep deprivation alleviates depression-like behaviors in mice via inhibiting immune and inflammatory pathways and improving neuroplasticity. J Affect Disord 2023; 340:100-112. [PMID: 37543111 DOI: 10.1016/j.jad.2023.07.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/07/2023]
Abstract
BACKGROUND Sleep deprivation (SD) has been suggested to have a rapid antidepressant effect. There is substantial evidence that neuroinflammation and neuroplasticity play critical roles in the pathophysiology and treatment of depression. Here, we investigated the mechanisms of SD to alleviate depression-like behaviors of mice, and the role of neuroinflammation and neuroplasticity in it. METHODS Adult male C57BL/6 J mice were subjected to chronic restraint stress (CRS) for 6 weeks, and 6 h of SD were administrated. Behavioral tests were performed to measure depression-like behaviors. RNA-sequencing and bioinformatic analysis were performed in the anterior cingulate cortex (ACC). The differentially expressed genes were confirmed by quantitative real-time polymerase chain reaction (RT-qPCR). Neuroinflammation and neuroplasticity were measured by western blotting and immunofluorescence staining. RESULTS Behavioral tests demonstrated that SD swiftly attenuated the depression-like behaviors induced by CRS. RNA-sequencing identified the upregulated immune and inflammatory pathways after CRS exposure were downregulated by SD. Furthermore, SD reversed the levels of immune and inflammation-related mRNA, pro-inflammatory factors and microglia activation in ACC. Additionally, the impaired neuroplasticity elicited by CRS in the prefrontal cortex (PFC) and ACC were improved by SD. LIMITATIONS More in-depth studies are required to determine the role of different SD protocols in depressive symptoms and their underlying mechanisms. CONCLUSIONS Our study revealed the rapid antidepressant effect of SD on CRS mice through the reduction of the neuroinflammatory response in ACC and the improvement of neuroplasticity in PFC and ACC, providing a theoretical basis for the clinical application of SD as a rapid antidepressant treatment.
Collapse
Affiliation(s)
- Shuxiang Shi
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 201108, China
| | - Mengke Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 201108, China
| | - Weijie Xie
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 201108, China
| | - Peijun Ju
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 201108, China
| | - Ningning Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 201108, China
| | - Fan Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 201108, China
| | - Dongbin Lyu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 201108, China
| | - Meiti Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 201108, China.
| | - Wu Hong
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 201108, China; Mental Health Branch, China Hospital Development Institute, Shanghai Jiao Tong University, Shanghai 200030, China.
| |
Collapse
|
4
|
Carceller H, Gramuntell Y, Klimczak P, Nacher J. Perineuronal Nets: Subtle Structures with Large Implications. Neuroscientist 2023; 29:569-590. [PMID: 35872660 DOI: 10.1177/10738584221106346] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Perineuronal nets (PNNs) are specialized structures of the extracellular matrix that surround the soma and proximal dendrites of certain neurons in the central nervous system, particularly parvalbumin-expressing interneurons. Their appearance overlaps the maturation of neuronal circuits and the closure of critical periods in different regions of the brain, setting their connectivity and abruptly reducing their plasticity. As a consequence, the digestion of PNNs, as well as the removal or manipulation of their components, leads to a boost in this plasticity and can play a key role in the functional recovery from different insults and in the etiopathology of certain neurologic and psychiatric disorders. Here we review the structure, composition, and distribution of PNNs and their variation throughout the evolutive scale. We also discuss methodological approaches to study these structures. The function of PNNs during neurodevelopment and adulthood is discussed, as well as the influence of intrinsic and extrinsic factors on these specialized regions of the extracellular matrix. Finally, we review current data on alterations in PNNs described in diseases of the central nervous system (CNS), focusing on psychiatric disorders. Together, all the data available point to the PNNs as a promising target to understand the physiology and pathologic conditions of the CNS.
Collapse
Affiliation(s)
- Héctor Carceller
- Neurobiology Unit, Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Spain
- CIBERSAM, Spanish National Network for Research in Mental Health, Instituto de Salud Carlos III, Madrid, Spain
- Biomedical Imaging Unit FISABIO-CIPF, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
| | - Yaiza Gramuntell
- Neurobiology Unit, Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Spain
| | - Patrycja Klimczak
- Neurobiology Unit, Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Spain
- CIBERSAM, Spanish National Network for Research in Mental Health, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Nacher
- Neurobiology Unit, Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Spain
- CIBERSAM, Spanish National Network for Research in Mental Health, Instituto de Salud Carlos III, Madrid, Spain
- Fundación Investigación Hospital Clínico de Valencia, INCLIVA, Valencia, Spain
| |
Collapse
|
5
|
Duan Z, Dai Y, Hwang A, Lee C, Xie K, Xiao C, Xu M, Girgenti MJ, Zhang J. iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease. PLoS Comput Biol 2023; 19:e1011444. [PMID: 37695793 PMCID: PMC10513318 DOI: 10.1371/journal.pcbi.1011444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 09/21/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023] Open
Abstract
Different genes form complex networks within cells to carry out critical cellular functions, while network alterations in this process can potentially introduce downstream transcriptome perturbations and phenotypic variations. Therefore, developing efficient and interpretable methods to quantify network changes and pinpoint driver genes across conditions is crucial. We propose a hierarchical graph representation learning method, called iHerd. Given a set of networks, iHerd first hierarchically generates a series of coarsened sub-graphs in a data-driven manner, representing network modules at different resolutions (e.g., the level of signaling pathways). Then, it sequentially learns low-dimensional node representations at all hierarchical levels via efficient graph embedding. Lastly, iHerd projects separate gene embeddings onto the same latent space in its graph alignment module to calculate a rewiring index for driver gene prioritization. To demonstrate its effectiveness, we applied iHerd on a tumor-to-normal GRN rewiring analysis and cell-type-specific GCN analysis using single-cell multiome data of the brain. We showed that iHerd can effectively pinpoint novel and well-known risk genes in different diseases. Distinct from existing models, iHerd's graph coarsening for hierarchical learning allows us to successfully classify network driver genes into early and late divergent genes (EDGs and LDGs), emphasizing genes with extensive network changes across and within signaling pathway levels. This unique approach for driver gene classification can provide us with deeper molecular insights. The code is freely available at https://github.com/aicb-ZhangLabs/iHerd. All other relevant data are within the manuscript and supporting information files.
Collapse
Affiliation(s)
- Ziheng Duan
- Department of Computer Science, University of California, Irvine, California, United States of America
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, California, United States of America
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, California, United States of America
| | - Cheyu Lee
- Department of Computer Science, University of California, Irvine, California, United States of America
| | - Kaichi Xie
- Department of Computer Science, University of California, Davis, California, United States of America
| | - Chutong Xiao
- Department of Computer Science, University of California, Irvine, California, United States of America
| | - Min Xu
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Matthew J. Girgenti
- Department of Psychiatry, School of Medicine, Yale University, New Haven, Connecticut, United States of America
- Clinical Neurosciences Division, National Center for PTSD, U.S. Department of Veterans Affairs, West Haven, Connecticut, United States of America
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, California, United States of America
| |
Collapse
|
6
|
Yang H, Gou X, Feng C, Zhang Y, Chai F, Hong N, Ye Y, Wang Y, Gao B, Cheng J. Computed tomography-detected extramural venous invasion-related gene signature: a potential negative biomarker of immune checkpoint inhibitor treatment in patients with gastric cancer. J Transl Med 2023; 21:4. [PMID: 36604653 PMCID: PMC9814439 DOI: 10.1186/s12967-022-03845-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND To investigate the association between computed tomography (CT)-detected extramural venous invasion (EMVI)-related genes and immunotherapy resistance and immune escape in patients with gastric cancer (GC). METHODS Thirteen patients with pathologically proven locally advanced GC who had undergone preoperative abdominal contrast-enhanced CT and radical resection surgery were included in this study. Transcriptome sequencing was multidetector performed on the cancerous tissue obtained during surgery, and EMVI-related genes (P value for association < 0.001) were selected. A single-sample gene set enrichment analysis algorithm was also used to divide all GC samples (n = 377) in The Cancer Genome Atlas (TCGA) database into high and low EMVI-immune related groups based on immune-related differential genes. Cluster analysis was used to classify EMVI-immune-related genotypes, and survival among patients was validated in TCGA and Gene Expression Omnibus (GEO) cohorts. The EMVI scores were calculated using principal component analysis (PCA), and GC samples were divided into high and low EMVI score groups. Microsatellite instability (MSI) status, tumor mutation burden (TMB), response rate to immune checkpoint inhibitors (ICIs), immune escape were compared between the high and low EMVI score groups. Hub gene of the model in pan-cancer analysis was also performed. RESULTS There were 17 EMVI-immune-related genes used for cluster analysis. PCA identified 8 genes (PCH17, SEMA6B, GJA4, CD34, ACVRL1, SOX17, CXCL12, DYSF) that were used to calculate EMVI scores. High EMVI score groups had lower MSI, TMB and response rate of ICIs, status but higher immune escape status. Among the 8 genes used for EMVI scores, CXCL12 and SOX17 were at the core of the protein-protein interaction (PPI) network and had a higher priority in pan-cancer analysis. Immunohistochemical analysis showed that the expression of CXCL12 and SOX17 was significantly higher in CT-detected EMVI-positive samples than in EMVI-negative samples (P < 0.0001). CONCLUSION A CT-detected EMVI gene signature could be a potential negative biomarker for ICIs treatment, as the signature is negatively correlated with TMB, and MSI, resulting in poorer prognosis.
Collapse
Affiliation(s)
- Hao Yang
- grid.412463.60000 0004 1762 6325Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinyi Gou
- grid.411634.50000 0004 0632 4559Department of Radiology, Peking University People’s Hospital, 11 Xizhimen South St., Beijing, 100044 China
| | - Caizhen Feng
- grid.411634.50000 0004 0632 4559Department of Radiology, Peking University People’s Hospital, 11 Xizhimen South St., Beijing, 100044 China
| | - Yinli Zhang
- grid.411634.50000 0004 0632 4559Department of Pathology, Peking University People’s Hospital, Beijing, China
| | - Fan Chai
- grid.411634.50000 0004 0632 4559Department of Radiology, Peking University People’s Hospital, 11 Xizhimen South St., Beijing, 100044 China
| | - Nan Hong
- grid.411634.50000 0004 0632 4559Department of Radiology, Peking University People’s Hospital, 11 Xizhimen South St., Beijing, 100044 China
| | - Yingjiang Ye
- grid.411634.50000 0004 0632 4559Department of Gastrointestinal Surgery, Peking University People’s Hospital, Beijing, China
| | - Yi Wang
- grid.411634.50000 0004 0632 4559Department of Radiology, Peking University People’s Hospital, 11 Xizhimen South St., Beijing, 100044 China
| | - Bo Gao
- grid.411634.50000 0004 0632 4559Department of General Surgery, Peking University People’s Hospital, Beijing, 100044 China
| | - Jin Cheng
- grid.411634.50000 0004 0632 4559Department of Radiology, Peking University People’s Hospital, 11 Xizhimen South St., Beijing, 100044 China
| |
Collapse
|
7
|
Andonegui-Elguera S, Silva-Román G, Peña-Martínez E, Taniguchi-Ponciano K, Vela-Patiño S, Remba-Shapiro I, Gómez-Apo E, Espinosa-de-los-Monteros AL, Portocarrero-Ortiz LA, Guinto G, Moreno-Jimenez S, Chavez-Macias L, Saucedo R, Basurto-Acevedo L, Lopez-Felix B, Gonzalez-Torres C, Gaytan-Cervantes J, Ayala-Sumuano JT, Burak-Leipuner A, Marrero-Rodríguez D, Mercado M. The Genomic Landscape of Corticotroph Tumors: From Silent Adenomas to ACTH-Secreting Carcinomas. Int J Mol Sci 2022; 23:ijms23094861. [PMID: 35563252 PMCID: PMC9106092 DOI: 10.3390/ijms23094861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/18/2022] [Accepted: 04/23/2022] [Indexed: 12/22/2022] Open
Abstract
Corticotroph cells give rise to aggressive and rare pituitary neoplasms comprising ACTH-producing adenomas resulting in Cushing disease (CD), clinically silent ACTH adenomas (SCA), Crooke cell adenomas (CCA) and ACTH-producing carcinomas (CA). The molecular pathogenesis of these tumors is still poorly understood. To better understand the genomic landscape of all the lesions of the corticotroph lineage, we sequenced the whole exome of three SCA, one CCA, four ACTH-secreting PA causing CD, one corticotrophinoma occurring in a CD patient who developed Nelson syndrome after adrenalectomy and one patient with an ACTH-producing CA. The ACTH-producing CA was the lesion with the highest number of single nucleotide variants (SNV) in genes such as USP8, TP53, AURKA, EGFR, HSD3B1 and CDKN1A. The USP8 variant was found only in the ACTH-CA and in the corticotrophinoma occurring in a patient with Nelson syndrome. In CCA, SNV in TP53, EGFR, HSD3B1 and CDKN1A SNV were present. HSD3B1 and CDKN1A SNVs were present in all three SCA, whereas in two of these tumors SNV in TP53, AURKA and EGFR were found. None of the analyzed tumors showed SNV in USP48, BRAF, BRG1 or CABLES1. The amplification of 17q12 was found in all tumors, except for the ACTH-producing carcinoma. The four clinically functioning ACTH adenomas and the ACTH-CA shared the amplification of 10q11.22 and showed more copy-number variation (CNV) gains and single-nucleotide variations than the nonfunctioning tumors.
Collapse
Affiliation(s)
- Sergio Andonegui-Elguera
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Gloria Silva-Román
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Eduardo Peña-Martínez
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Keiko Taniguchi-Ponciano
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Sandra Vela-Patiño
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Ilan Remba-Shapiro
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Erick Gómez-Apo
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México “Dr. Eduardo Liceaga”, Ciudad de Mexico 06720, Mexico; (E.G.-A.); (L.C.-M.)
| | - Ana-Laura Espinosa-de-los-Monteros
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Lesly A. Portocarrero-Ortiz
- Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suarez”, Ciudad de Mexico 14269, Mexico; (L.A.P.-O.); (S.M.-J.)
| | - Gerardo Guinto
- Centro Neurológico, Centro Medico ABC, Ciudad de Mexico 01120, Mexico;
| | - Sergio Moreno-Jimenez
- Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suarez”, Ciudad de Mexico 14269, Mexico; (L.A.P.-O.); (S.M.-J.)
- Centro Neurológico, Centro Medico ABC, Ciudad de Mexico 01120, Mexico;
| | - Laura Chavez-Macias
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México “Dr. Eduardo Liceaga”, Ciudad de Mexico 06720, Mexico; (E.G.-A.); (L.C.-M.)
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de Mexico 04360, Mexico
| | - Renata Saucedo
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Lourdes Basurto-Acevedo
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Blas Lopez-Felix
- Servicio de Neurocirugía, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico;
| | - Carolina Gonzalez-Torres
- Laboratorio de Secuenciacion, Division de Desarrollo de la Investigacion, Centro Medico Nacional Siglo XXI, Ciudad de Mexico 06720, Mexico; (C.G.-T.); (J.G.-C.)
| | - Javier Gaytan-Cervantes
- Laboratorio de Secuenciacion, Division de Desarrollo de la Investigacion, Centro Medico Nacional Siglo XXI, Ciudad de Mexico 06720, Mexico; (C.G.-T.); (J.G.-C.)
| | | | - Andres Burak-Leipuner
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
| | - Daniel Marrero-Rodríguez
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
- Correspondence: (D.M.-R.); (M.M.); Tel.: +52-54401021 (D.M.-R.)
| | - Moisés Mercado
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de Mexico 06720, Mexico; (S.A.-E.); (G.S.-R.); (E.P.-M.); (K.T.-P.); (S.V.-P.); (I.R.-S.); (A.-L.E.-d.-l.-M.); (R.S.); (L.B.-A.); (A.B.-L.)
- Correspondence: (D.M.-R.); (M.M.); Tel.: +52-54401021 (D.M.-R.)
| |
Collapse
|
8
|
Almandil NB, AlSulaiman A, Aldakeel SA, Alkuroud DN, Aljofi HE, Alzahrani S, Al-mana A, Alfuraih AA, Alabdali M, Alkhamis FA, AbdulAzeez S, Borgio JF. Integration of Transcriptome and Exome Genotyping Identifies Significant Variants with Autism Spectrum Disorder. Pharmaceuticals (Basel) 2022; 15:ph15020158. [PMID: 35215271 PMCID: PMC8880056 DOI: 10.3390/ph15020158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
Autism is a complex disease with genetic predisposition factors. Real factors for treatment and early diagnosis are yet to be defined. This study integrated transcriptome and exome genotyping for identifying functional variants associated with autism spectrum disorder and their impact on gene expression to find significant variations. More than 1800 patients were screened, and 70 (47 male/23 female) with an average age of 7.56 ± 3.68 years fulfilled the DSM-5 criteria for autism. Analysis revealed 682 SNPs of 589 genes significantly (p < 0.001) associated with autism among the putative functional exonic variants (n = 243,345) studied. Olfactory receptor genes on chromosome 6 were significant after Bonferroni correction (α = 0.05/243345 = 2.05 × 10−7) with a high degree of linkage disequilibrium on 6p22.1 (p = 6.71 × 10−9). The differentially expressed gene analysis of autistic patients compared to controls in whole RNA sequencing identified significantly upregulated (foldchange ≥ 0.8 and p-value ≤ 0.05; n = 125) and downregulated (foldchange ≤ −0.8 and p-value ≤ 0.05; n = 117) genes. The integration of significantly up- and downregulated genes and genes of significant SNPs identified regulatory variants (rs6657480, rs3130780, and rs1940475) associated with the up- (ITGB3BP) and downregulation (DDR1 and MMP8) of genes in autism spectrum disorder in people of Arab ancestries. The significant variants could be a biomarker of interest for identifying early autism among Arabs and helping to characterize the genes involved in the susceptibility mechanisms for autistic subjects.
Collapse
Affiliation(s)
- Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Abdulla AlSulaiman
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (A.A.); (M.A.); (F.A.A.)
| | - Sumayh A. Aldakeel
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - Deem N. Alkuroud
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - Halah Egal Aljofi
- Environmental Health Research Area, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Safah Alzahrani
- Department of Mental Health, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.); (A.A.-m.)
- King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Aishah Al-mana
- Department of Mental Health, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.); (A.A.-m.)
- King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Asma A. Alfuraih
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - Majed Alabdali
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (A.A.); (M.A.); (F.A.A.)
| | - Fahd A. Alkhamis
- Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (A.A.); (M.A.); (F.A.A.)
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (S.A.A.); (D.N.A.); (A.A.A.); (S.A.)
- Correspondence: ; Tel.: +966-13-3330864
| |
Collapse
|
9
|
Gao B, Feng C, Chai F, Wei S, Hong N, Ye Y, Wang Y, Cheng J. CT-detected extramural venous invasion-related gene signature for the overall survival prediction in patients with gastric cancer. Cancer Med 2021; 10:7816-7830. [PMID: 34510798 PMCID: PMC8559479 DOI: 10.1002/cam4.4266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
Background Computed tomography (CT)‐detected extramural venous invasion (EMVI) has been identified as an independent factor that can be used for risk stratification and prediction of prognosis in patients with gastric cancer (GC). Overall survival (OS) is identified as the most important prognostic indicator for GC patients. However, the molecular mechanism of EMVI development and its potential relationship with OS in GC are not fully understood. In this radiogenomics‐based study, we sought to investigate the molecular mechanism underlying CT‐detected EMVI in patients with GC, and aimed to construct a genomic signature based on EMVI‐related genes with the goal of using this signature to predict the OS. Materials and Methods Whole mRNA genome sequencing of frozen tumor samples from 13 locally advanced GC patients was performed to identify EMVI‐related genes. EMVI‐prognostic hub genes were selected based on overlapping EMVI‐related differentially expressed genes and OS‐related genes, using a training cohort of 176 GC patients who were included in The Cancer Genome Atlas database. Another 174 GC patients from this database comprised the external validation cohort. A risk stratification model using a seven‐gene signature was constructed through the use of a least absolute shrinkage and selection operator Cox regression model. Results Patients with high risk score showed significantly reduced OS (training cohort, p = 1.143e‐04; validation cohort, p = 2.429e‐02). Risk score was an independent predictor of OS in multivariate Cox regression analyses (training cohort, HR = 2.758; 95% CI: 1.825–4.169; validation cohort, HR = 2.173; 95% CI: 1.347–3.505; p < 0.001 for both). Gene functions/pathways of the seven‐gene signature mainly included cell proliferation, cell adhesion, regulation of metal ion transport, and epithelial to mesenchymal transition. Conclusions A CT‐detected EMVI‐related gene model could be used to predict the prognosis in GC patients, potentially providing clinicians with additional information regarding appropriate therapeutic strategy and medical decision‐making.
Collapse
Affiliation(s)
- Bo Gao
- Department of General Surgery, Peking University People's Hospital, Beijing, China
| | - Caizhen Feng
- Department of Radiology, Peking University People's Hospital, Beijing, China
| | - Fan Chai
- Department of Radiology, Peking University People's Hospital, Beijing, China
| | - Shengcai Wei
- Department of Radiology, Peking University People's Hospital, Beijing, China
| | - Nan Hong
- Department of Radiology, Peking University People's Hospital, Beijing, China
| | - Yingjiang Ye
- Department of Gastrointestinal Surgery, Peking University People's Hospital, Beijing, China
| | - Yi Wang
- Department of Radiology, Peking University People's Hospital, Beijing, China
| | - Jin Cheng
- Department of Radiology, Peking University People's Hospital, Beijing, China
| |
Collapse
|
10
|
Genome-wide gene expression changes in postpartum depression point towards an altered immune landscape. Transl Psychiatry 2021; 11:155. [PMID: 33664235 PMCID: PMC7933180 DOI: 10.1038/s41398-021-01270-5] [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: 08/11/2020] [Revised: 01/19/2021] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
Maternal postpartum depression (PPD) is a significant public health concern due to the severe negative impact on maternal and child health and well-being. In this study, we aimed to identify genes associated with PPD. To do this, we investigated genome-wide gene expression profiles of pregnant women during their third trimester of pregnancy and tested the association of gene expression with perinatal depressive symptoms. A total of 137 women from a cohort from the University of North Carolina, USA were assessed. The main phenotypes analysed were Edinburgh Postnatal Depression Scale (EPDS) scores at 2 months postpartum and PPD (binary yes/no) based on an EPDS cutoff of 10. Illumina NextSeq500/550 transcriptomic sequencing from whole blood was analysed using the edgeR package. We identified 71 genes significantly associated with postpartum depression scores at 2 months, after correction for multiple testing at 5% FDR. These included several interesting candidates including TNFRSF17, previously reported to be significantly upregulated in women with PPD and MMP8, a matrix metalloproteinase gene, associated with depression in a genome-wide association study. Functional annotation of differentially expressed genes revealed an enrichment of immune response-related biological processes. Additional analysis of genes associated with changes in depressive symptoms from recruitment to 2 months postpartum identified 66 genes significant at an FDR of 5%. Of these genes, 33 genes were also associated with depressive symptoms at 2 months postpartum. Comparing the results with previous studies, we observed that 15.4% of genes associated with PPD in this study overlapped with 700 core maternal genes that showed significant gene expression changes across multiple brain regions (P = 7.9e-05) and 29-53% of the genes were also associated with estradiol changes in a pharmacological model of depression (P values range = 1.2e-4-2.1e-14). In conclusion, we identified novel genes and validated genes previously associated with oestrogen sensitivity in PPD. These results point towards the role of an altered immune transcriptomic landscape as a vulnerability factor for PPD.
Collapse
|
11
|
Yuan Y, Chen J, Wang J, Xu M, Zhang Y, Sun P, Liang L. Development and Clinical Validation of a Novel 4-Gene Prognostic Signature Predicting Survival in Colorectal Cancer. Front Oncol 2020; 10:595. [PMID: 32509568 PMCID: PMC7251179 DOI: 10.3389/fonc.2020.00595] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/31/2020] [Indexed: 01/02/2023] Open
Abstract
In this study, we collected genes related to energy metabolism, used gene expression data from public databases to classify molecular subtypes of colon cancer (COAD) based on the genes related to energy metabolism, and further evaluated the relationships between the molecular subtypes and prognosis and clinical characteristics. Differential expression analysis of the molecular subtypes yielded 1948 differentially expressed genes (DEGs), whose functions were closely related to the occurrence and development of cancer. Based on the DEGs, we constructed a 4-gene prognostic risk model and identified the high expression of FOXD4, ENPEP, HOXC6, and ALOX15B as a risk factor associated with a high risk of developing COAD. The 4-gene signature has strong robustness and a stable predictive performance in datasets from different platforms not only in patients with early COAD but also in all patients with colon cancer. The enriched pathways of the 4-gene signature in the high- and low-risk groups obtained by GSEA were significantly related to the occurrence and development of colon cancer. Moreover, the results of qPCR, immunohistochemistry staining and Western blot assay revealed that FOXD4, ENPEP, HOXC6, and ALOX15B are over expressed in CRC tissues and cells. These results suggesting that the signature could potentially be used as a prognostic marker for clinical diagnosis.
Collapse
Affiliation(s)
- Yihang Yuan
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ji Chen
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jue Wang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Xu
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunpeng Zhang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Sun
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leilei Liang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
12
|
Al-Naama N, Mackeh R, Kino T. C 2H 2-Type Zinc Finger Proteins in Brain Development, Neurodevelopmental, and Other Neuropsychiatric Disorders: Systematic Literature-Based Analysis. Front Neurol 2020; 11:32. [PMID: 32117005 PMCID: PMC7034409 DOI: 10.3389/fneur.2020.00032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/10/2020] [Indexed: 12/15/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are multifaceted pathologic conditions manifested with intellectual disability, autistic features, psychiatric problems, motor dysfunction, and/or genetic/chromosomal abnormalities. They are associated with skewed neurogenesis and brain development, in part through dysfunction of the neural stem cells (NSCs) where abnormal transcriptional regulation on key genes play significant roles. Recent accumulated evidence highlights C2H2-type zinc finger proteins (C2H2-ZNFs), the largest transcription factor family in humans, as important targets for the pathologic processes associated with NDDs. In this review, we identified their significant accumulation (74 C2H2-ZNFs: ~10% of all human member proteins) in brain physiology and pathology. Specifically, we discuss their physiologic contribution to brain development, particularly focusing on their actions in NSCs. We then explain their pathologic implications in various forms of NDDs, such as morphological brain abnormalities, intellectual disabilities, and psychiatric disorders. We found an important tendency that poly-ZNFs and KRAB-ZNFs tend to be involved in the diseases that compromise gross brain structure and human-specific higher-order functions, respectively. This may be consistent with their characteristic appearance in the course of species evolution and corresponding contribution to these brain activities.
Collapse
Affiliation(s)
- Njoud Al-Naama
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Rafah Mackeh
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Tomoshige Kino
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| |
Collapse
|
13
|
Shadrina M, Bondarenko EA, Slominsky PA. Genetics Factors in Major Depression Disease. Front Psychiatry 2018; 9:334. [PMID: 30083112 PMCID: PMC6065213 DOI: 10.3389/fpsyt.2018.00334] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/02/2018] [Indexed: 12/22/2022] Open
Abstract
Depressive disorders (DDs) are one of the most widespread forms of psychiatric pathology. According to the World Health Organization, about 350 million people in the world are affected by this condition. Family and twin studies have demonstrated that the contribution of genetic factors to the risk of the onset of DDs is quite large. Various methodological approaches (analysis of candidate genes, genome-wide association analysis, genome-wide sequencing) have been used, and a large number of the associations between genes and different clinical DD variants and DD subphenotypes have been published. However, in most cases, these associations have not been confirmed in replication studies, and only a small number of genes have been proven to be associated with DD development risk. To ascertain the role of genetic factors in DD pathogenesis, further investigations of the relevant conditions are required. Special consideration should be given to the polygenic characteristics noted in whole-genome studies of the heritability of the disorder without a pronounced effect of the major gene. These observations accentuate the relevance of the analysis of gene-interaction roles in DD development and progression. It is important that association studies of the inherited variants of the genome should be supported by analysis of dynamic changes during DD progression. Epigenetic changes that cause modifications of a gene's functional state without changing its coding sequence are of primary interest. However, the opportunities for studying changes in the epigenome, transcriptome, and proteome during DD are limited by the nature of the disease and the need for brain tissue analysis, which is possible only postmortem. Therefore, any association studies between DD pathogenesis and epigenetic factors must be supplemented through the use of different animal models of depression. A threefold approach comprising the combination of gene association studies, assessment of the epigenetic state in DD patients, and analysis of different "omic" changes in animal depression models will make it possible to evaluate the contribution of genetic, epigenetic, and environmental factors to the development of different forms of depression and to help develop ways to decrease the risk of depression and improve the treatment of DD.
Collapse
Affiliation(s)
- Maria Shadrina
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elena A Bondarenko
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Petr A Slominsky
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
14
|
van Dongen J, Bonder MJ, Dekkers KF, Nivard MG, van Iterson M, Willemsen G, Beekman M, van der Spek A, van Meurs JBJ, Franke L, Heijmans BT, van Duijn CM, Slagboom PE, Boomsma DI. DNA methylation signatures of educational attainment. NPJ SCIENCE OF LEARNING 2018; 3:7. [PMID: 30631468 PMCID: PMC6220239 DOI: 10.1038/s41539-018-0020-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/18/2017] [Accepted: 02/09/2018] [Indexed: 05/09/2023]
Abstract
Educational attainment is a key behavioural measure in studies of cognitive and physical health, and socioeconomic status. We measured DNA methylation at 410,746 CpGs (N = 4152) and identified 58 CpGs associated with educational attainment at loci characterized by pleiotropic functions shared with neuronal, immune and developmental processes. Associations overlapped with those for smoking behaviour, but remained after accounting for smoking at many CpGs: Effect sizes were on average 28% smaller and genome-wide significant at 11 CpGs after adjusting for smoking and were 62% smaller in never smokers. We examined sources and biological implications of education-related methylation differences, demonstrating correlations with maternal prenatal folate, smoking and air pollution signatures, and associations with gene expression in cis, dynamic methylation in foetal brain, and correlations between blood and brain. Our findings show that the methylome of lower-educated people resembles that of smokers beyond effects of their own smoking behaviour and shows traces of various other exposures.
Collapse
Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Koen F. Dekkers
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G. Nivard
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marian Beekman
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Ashley van der Spek
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | - P. Eline Slagboom
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | |
Collapse
|
15
|
Genetic Contributions of Inflammation to Depression. Neuropsychopharmacology 2017; 42:81-98. [PMID: 27555379 PMCID: PMC5143493 DOI: 10.1038/npp.2016.169] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/04/2016] [Accepted: 08/08/2016] [Indexed: 01/05/2023]
Abstract
This paper describes the effects of immune genes genetic variants and mRNA expression on depression's risk, severity, and response to antidepressant treatment, through a systematic review on all papers published between 2000 and 2016. Our results, based largely on case-control studies, suggest that common genetic variants and gene-expression pathways are involved in both immune activation and depression. The most replicated and relevant genetic variants include polymorphisms in the genes for interleukin (IL)-1β, IL-6, IL-10, monocyte chemoattractant protein-1, tumor necrosis factor-alpha, C-reactive protein, and phospholipase A2. Moreover, increased blood cytokines mRNA expression (especially of IL-1β) identifies patients that are less likely to respond to conventional antidepressants. However, even for the most replicated findings there are inconsistent results, not only between studies, but also between the immune effects of the genetic variants and the resulting effects on depression. We find evidence that these discrepant findings may be explained, at least in part, by the heterogeneity of the depression immunophenotype, by environmental influences and gene × environment interactions, and by the complex interfacing of genetic variants with gene expression. Indeed, some of the most robust findings have been obtained in patients developing depression in the context of treatment with interferon-alpha, a widely used model to mimic depression in the context of inflammation. Further 'omics' approaches, through GWAS and transcriptomics, will finally shed light on the interaction between immune genes, their expression, and the influence of the environment, in the pathogenesis of depression.
Collapse
|
16
|
Klein M, Schmoeger M, Kasper S, Schosser A. Meta-analysis of the COMT Val158Met polymorphism in major depressive disorder: the role of gender. World J Biol Psychiatry 2016; 17:147-58. [PMID: 26813412 DOI: 10.3109/15622975.2015.1083615] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Many studies have reported an association of the COMT Val158Met polymorphism and major depressive disorder (MDD), although with conflicting results. The role of gender is a possible modulator. To overcome the problem of poor sample size detecting genes of small effect, we perform a meta-analysis of the current literature, investigating the influence of the COMT Val158Met polymorphism on the pathogenesis of MDD, with a major focus on the effect of gender. METHODS Out of 977 retrieved articles, 21 included case-control studies allowed the analysis of 9005 patients with MDD and 12,095 controls. Allelic and genotypic pooled odds ratios (OR) were calculated for the total sample and gender-subgroups. RESULTS In the absence of publication bias, allelic and genotypic analyses showed no significant association in the total sample, as well as in gender-specific subgroups. Sensitivity analysis did not alter the ORs. CONCLUSIONS The results imply a complex nature of the genotype × phenotype interaction. Further studies of the COMT gene or the locus remain to be justified given the important positional and functional relevance and the plethora of gender-specific findings. A possible way to further dissect this topic is shifting the focus to gene-based or genome-wide analyses of intermediate phenotypes.
Collapse
Affiliation(s)
- Martina Klein
- a Department of Psychiatry and Psychotherapy , Medical University of Vienna , Vienna , Austria
| | - Michaela Schmoeger
- b Department of Neurology , Medical University of Vienna , Vienna , Austria
| | - Siegfried Kasper
- a Department of Psychiatry and Psychotherapy , Medical University of Vienna , Vienna , Austria
| | - Alexandra Schosser
- a Department of Psychiatry and Psychotherapy , Medical University of Vienna , Vienna , Austria.,c Zentrum Für Seelische Gesundheit Leopoldau , Vienna , Austria
| |
Collapse
|
17
|
The expression of glial cell line-derived neurotrophic factor mRNA by antidepressants involves matrix metalloproteinase-9 activation in rat astroglial cells. Biochem Biophys Res Commun 2016; 479:907-912. [DOI: 10.1016/j.bbrc.2016.09.070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/14/2016] [Indexed: 11/23/2022]
|
18
|
He S, Liu X, Jiang K, Peng D, Hong W, Fang Y, Qian Y, Yu S, Li H. Alterations of microRNA-124 expression in peripheral blood mononuclear cells in pre- and post-treatment patients with major depressive disorder. J Psychiatr Res 2016; 78:65-71. [PMID: 27078210 DOI: 10.1016/j.jpsychires.2016.03.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 03/06/2016] [Accepted: 03/30/2016] [Indexed: 11/17/2022]
Abstract
Recently, increasing evidence has indicated that dysfunction of microRNA-124 (miR-124) might be involved in the pathophysiology and treatment of major depressive disorder (MDD) in some animal models of depression. However, the role of miR-124 in MDD patients remains unclear. The objective of this study was to investigate whether the miR-124 expression levels in peripheral blood mononuclear cells (PBMCs) were associated with MDD and to evaluate the effects of antidepressant treatment on miR-124 levels. Quantitative real-time PCR was applied to detect miR-124 expression in 32 pre- and post-treatment MDD patients and 30 healthy controls. Our results showed that expression levels of miR-124 from PBMCs in MDD patients were significantly higher than those in healthy controls (p < 0.001), and that the area under the curve of miR-124 from ROC analysis was 0.762 with a sensitivity of 83.33% and specificity of 66.67% in distinguishing MDD patients from healthy controls. In addition, the expression levels of miR-124 were significantly down-regulated after eight weeks of treatment (p < 0.001). MiRNA target gene prediction and functional annotation analysis indicated that altered miR-124 was involved in affecting some important biological processes and pathways related to MDD. These results provide new information on miR-124 involvement in the biological alterations of MDD and in antidepressant effects.
Collapse
Affiliation(s)
- Shen He
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Xiaohua Liu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.
| | - Kaida Jiang
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Daihui Peng
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Wu Hong
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Yiru Fang
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Yiping Qian
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Shunying Yu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Huafang Li
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Institution of Drug Clinical Trials, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.
| |
Collapse
|
19
|
Smoller JW. The Genetics of Stress-Related Disorders: PTSD, Depression, and Anxiety Disorders. Neuropsychopharmacology 2016; 41:297-319. [PMID: 26321314 PMCID: PMC4677147 DOI: 10.1038/npp.2015.266] [Citation(s) in RCA: 256] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/05/2015] [Accepted: 08/26/2015] [Indexed: 02/06/2023]
Abstract
Research into the causes of psychopathology has largely focused on two broad etiologic factors: genetic vulnerability and environmental stressors. An important role for familial/heritable factors in the etiology of a broad range of psychiatric disorders was established well before the modern era of genomic research. This review focuses on the genetic basis of three disorder categories-posttraumatic stress disorder (PTSD), major depressive disorder (MDD), and the anxiety disorders-for which environmental stressors and stress responses are understood to be central to pathogenesis. Each of these disorders aggregates in families and is moderately heritable. More recently, molecular genetic approaches, including genome-wide studies of genetic variation, have been applied to identify specific risk variants. In this review, I summarize evidence for genetic contributions to PTSD, MDD, and the anxiety disorders including genetic epidemiology, the role of common genetic variation, the role of rare and structural variation, and the role of gene-environment interaction. Available data suggest that stress-related disorders are highly complex and polygenic and, despite substantial progress in other areas of psychiatric genetics, few risk loci have been identified for these disorders. Progress in this area will likely require analysis of much larger sample sizes than have been reported to date. The phenotypic complexity and genetic overlap among these disorders present further challenges. The review concludes with a discussion of prospects for clinical translation of genetic findings and future directions for research.
Collapse
Affiliation(s)
- Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| |
Collapse
|
20
|
Sharma A. Systems Genomics Support for Immune and Inflammation Hypothesis of Depression. Curr Neuropharmacol 2016; 14:749-58. [PMID: 26733279 PMCID: PMC5050401 DOI: 10.2174/1570159x14666160106155331] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 11/02/2015] [Accepted: 11/09/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Immune system plays an important role in brain development and function. With the discovery of increased circulating inflammatory cytokine levels in depression over two decades ago, evidence implicating immune system alterations in the disease has increasingly accumulated. OBJECTIVE To assess the underlying etiology and pathophysiology, a brief overview of the hypothesis free genomic, transcriptomic and proteomic studies in depression is presented here in order to specifically examine if the immune and inflammation hypothesis of depression is supported. RESULTS It is observed that genes identified in genome-wide association studies, and genes showing differential expression in transcriptomic studies in human depression do separately overrepresent processes related to both development as well as functioning of the immune system, and inflammatory response. These processes are also enriched in differentially expressed genes reported in animal models of antidepressant treatment. It is further noted that some of the genes identified in genome sequencing and proteomic analyses in human depression, and transcriptomic studies in chronic social defeat stress, an established animal model of depression, relate to immune and inflammatory pathways. CONCLUSION In conclusion, integrative genomics evidence supports the immune and inflammation hypothesis of depression.
Collapse
Affiliation(s)
- Abhay Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, New Delhi 110025, India
| |
Collapse
|
21
|
Plattner F, Hayashi K, Hernández A, Benavides DR, Tassin TC, Tan C, Day J, Fina MW, Yuen EY, Yan Z, Goldberg MS, Nairn AC, Greengard P, Nestler EJ, Taussig R, Nishi A, Houslay MD, Bibb JA. The role of ventral striatal cAMP signaling in stress-induced behaviors. Nat Neurosci 2015; 18:1094-100. [PMID: 26192746 PMCID: PMC4519694 DOI: 10.1038/nn.4066] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/19/2015] [Indexed: 12/25/2022]
Abstract
The cAMP and cAMP-dependent protein kinase A (PKA) signaling cascade is a ubiquitous pathway acting downstream of multiple neuromodulators. We found that the phosphorylation of phosphodiesterase-4 (PDE4) by cyclin-dependent protein kinase 5 (Cdk5) facilitated cAMP degradation and homeostasis of cAMP/PKA signaling. In mice, loss of Cdk5 throughout the forebrain elevated cAMP levels and increased PKA activity in striatal neurons, and altered behavioral responses to acute or chronic stressors. Ventral striatum- or D1 dopamine receptor-specific conditional knockout of Cdk5, or ventral striatum infusion of a small interfering peptide that selectively targeted the regulation of PDE4 by Cdk5, produced analogous effects on stress-induced behavioral responses. Together, our results demonstrate that altering cAMP signaling in medium spiny neurons of the ventral striatum can effectively modulate stress-induced behavioral states. We propose that targeting the Cdk5 regulation of PDE4 could be a new therapeutic approach for clinical conditions associated with stress, such as depression.
Collapse
Affiliation(s)
- Florian Plattner
- Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kanehiro Hayashi
- Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adan Hernández
- Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David R Benavides
- Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tara C Tassin
- Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chunfeng Tan
- Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jonathan Day
- Division of Neuroscience and Molecular Pharmacology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Maggy W Fina
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Eunice Y Yuen
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
| | - Matthew S Goldberg
- 1] Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA. [2] Department of Neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Angus C Nairn
- 1] Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA. [2] Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York, USA
| | - Paul Greengard
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York, USA
| | - Eric J Nestler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ronald Taussig
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Akinori Nishi
- Department of Pharmacology, Kurume University School of Medicine, Fukuoka, Japan
| | - Miles D Houslay
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - James A Bibb
- 1] Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA. [2] Department of Neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA. [3] Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
22
|
Abstract
Predictive factors of for the occurrence of depressive episodes include psychosocial and biological risk factors. These factors reflect the heterogeneity and complexity of the disease. They can identify groups that would benefit from preventive measures and provide indications for suitable preventive strategies. In recent decades considerable scientific effort, for example in the field of psychiatric genetics, has been undertaken to identify predictive factors for individual antidepressant therapy response and as an aid for individual treatment decisions. However, no clinically usable conclusions could yet be drawn from the respective findings. In practice clinical factors, such as symptom cluster of the depressive disorder and specific properties of the antidepressant, individual factors and contextual factors, such as the type of treatment facility, decision support and economic aspects, are factors influencing the choice of a specific antidepressant. Early clinical improvement under antidepressant medication in the first 2 weeks of treatment is one of the best predictors for the long-term treatment outcome in patients with major depressive disorder.
Collapse
|
23
|
Sullivan PF, Posthuma D. Biological pathways and networks implicated in psychiatric disorders. Curr Opin Behav Sci 2015. [DOI: 10.1016/j.cobeha.2014.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
24
|
Garbett KA, Vereczkei A, Kálmán S, Brown JA, Taylor WD, Faludi G, Korade Ž, Shelton RC, Mirnics K. Coordinated messenger RNA/microRNA changes in fibroblasts of patients with major depression. Biol Psychiatry 2015; 77:256-265. [PMID: 25016317 PMCID: PMC4254393 DOI: 10.1016/j.biopsych.2014.05.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/30/2014] [Accepted: 05/22/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Peripheral biomarkers for major psychiatric disorders have been an elusive target for the last half a century. Dermal fibroblasts are a simple, relevant, and much underutilized model for studying molecular processes of patients with affective disorders, as they share considerable similarity of signal transduction with neuronal tissue. METHODS Cultured dermal fibroblast samples from patients with major depressive disorder (MDD) and matched control subjects (n = 16 pairs, 32 samples) were assayed for genome-wide messenger RNA (mRNA) expression using microarrays. In addition, a simultaneous quantitative polymerase chain reaction-based assessment of >1000 microRNA (miRNA) species was performed. Finally, to test the relationship between the mRNA-miRNA expression changes, the two datasets were correlated with each other. RESULTS Our data revealed that MDD fibroblasts, when compared with matched control subjects, showed a strong mRNA gene expression pattern change in multiple molecular pathways, including cell-to-cell communication, innate/adaptive immunity, and cell proliferation. Furthermore, the same patient fibroblasts showed altered expression of a distinct panel of 38 miRNAs, which putatively targeted many of the differentially expressed mRNAs. The miRNA-mRNA expression changes appeared to be functionally connected, as the majority of the miRNA and mRNA changes were in the opposite direction. CONCLUSIONS Our data suggest that combined miRNA-mRNA assessments are informative about the disease process and that analyses of dermal fibroblasts might lead to the discovery of promising peripheral biomarkers of MDD that could be potentially used to aid the diagnosis and allow mechanistic testing of disturbed molecular pathways.
Collapse
Affiliation(s)
| | - Andrea Vereczkei
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee; Institute for Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest
| | - Sára Kálmán
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee; Department of Psychiatry, University of Szeged, Szeged
| | - Jacquelyn A Brown
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee
| | - Warren D Taylor
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee
| | - Gábor Faludi
- Department of Psychiatry, Kútvölgyi Clinical Centre, Semmelweis University, Budapest, Hungary
| | - Željka Korade
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee; Vanderbilt Kennedy Center for Research on Human Development (ZK, KM), Vanderbilt University, Nashville, Tennessee
| | - Richard C Shelton
- Department of Psychiatry, University of Alabama, Birmingham, Alabama
| | - Károly Mirnics
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee; Department of Psychiatry, University of Szeged, Szeged; Vanderbilt Kennedy Center for Research on Human Development (ZK, KM), Vanderbilt University, Nashville, Tennessee..
| |
Collapse
|
25
|
Brodie A, Tovia-Brodie O, Ofran Y. Large scale analysis of phenotype-pathway relationships based on GWAS results. PLoS One 2014; 9:e100887. [PMID: 25007247 PMCID: PMC4090199 DOI: 10.1371/journal.pone.0100887] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 05/28/2014] [Indexed: 12/13/2022] Open
Abstract
The widely used pathway-based approach for interpreting Genome Wide Association Studies (GWAS), assumes that since function is executed through the interactions of multiple genes, different perturbations of the same pathway would result in a similar phenotype. This assumption, however, was not systemically assessed on a large scale. To determine whether SNPs associated with a given complex phenotype affect the same pathways more than expected by chance, we analyzed 368 phenotypes that were studied in >5000 GWAS. We found 216 significant phenotype-pathway associations between 70 of the phenotypes we analyzed and known pathways. We also report 391 strong phenotype-phenotype associations between phenotypes that are affected by the same pathways. While some of these associations confirm previously reported connections, others are new and could shed light on the molecular basis of these diseases. Our findings confirm that phenotype-associated SNPs cluster into pathways much more than expected by chance. However, this is true for <20% (70/368) of the phenotypes. Different types of phenotypes show markedly different tendencies: Virtually all autoimmune phenotypes show strong clustering of SNPs into pathways, while most cancers and metabolic conditions, and all electrophysiological phenotypes, could not be significantly associated with any pathway despite being significantly associated with a large number of SNPs. While this may be due to missing data, it may also suggest that these phenotypes could result only from perturbations of specific genes and not from other perturbations of the same pathway. Further analysis of pathway-associated versus gene-associated phenotypes is, therefore, needed in order to understand disease etiology and in order to promote better drug target selection.
Collapse
Affiliation(s)
- Aharon Brodie
- The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan, Israel
| | - Oholi Tovia-Brodie
- Department of Cardiology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Yanay Ofran
- The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan, Israel
| |
Collapse
|