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Wang C, Wang X, Wang W, Chen Y, Chen H, Wang W, Ye T, Dong J, Sun C, Li X, Li C, Li J, Wang Y, Feng X, Ding H, Xu D, Shi J. Single‑cell RNA sequencing analysis of human embryos from the late Carnegie to fetal development. Cell Biosci 2024; 14:118. [PMID: 39267141 PMCID: PMC11395182 DOI: 10.1186/s13578-024-01302-9] [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: 04/27/2024] [Accepted: 09/03/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND The cell development atlas of transition stage from late Carnegie to fetal development (7-9 weeks) remain unclear. It can be seen that the early period of human embryos (7-9 weeks) is a critical research gap. Therefore, we employed single‑cell RNA sequencing to identify cell types and elucidate differentiation relationships. RESULTS The single‑cell RNA sequencing analysis determines eighteen cell clusters in human embryos during the 7-9 weeks period. We uncover two distinct pathways of cellular development and differentiation. Initially, mesenchymal progenitor cells differentiated into osteoblast progenitor cells and neural stem cells, respectively. Neural stem cells further differentiated into neurons. Alternatively, multipotential stem cells differentiated into adipocyte, hematopoietic stem cells and neutrophil, respectively. Additionally, COL1A2-(ITGA1 + ITGB1) mediated the cell communication between mesenchymal progenitor cells and osteoblast progenitor cells. NCAM1-FGFR1 facilitated the cell communication between mesenchymal progenitor cells and neural stem cells. Notably, NCAM1-NCAM1 as a major contributor mediated the cell communication between neural stem cells and neurons. Moreover, CGA-FSHR simultaneously mediated the communication between multipotential stem cells, adipocyte, hematopoietic stem cells and neutrophil. Distinct cell clusters activated specific transcription factors such as HIC1, LMX1B, TWIST1, and et al., which were responsible for their specific functions. These coregulators, such as HOXB13, VSX2, PAX5, and et al., may mediate cell development and differentiation in human embryos. CONCLUSIONS We provide the cell development atlas for human embryos (7-9 weeks). Two distinct cell development and differentiation pathways are revealed.
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Affiliation(s)
- Chengniu Wang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226001, Jiangsu, China
| | - Xiaorong Wang
- Center for Reproductive Medicine, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, 226018, Jiangsu, China
- Nantong Institute of Genetics and Reproductive Medicine, Affiliated Maternity and Child Healthcare Hospital of Nantong University, Nantong, 226018, Jiangsu, China
- Nantong Key Laboratory of Genetics and Reproductive Medicine, Nantong, 226018, Jiangsu, China
| | - Wenran Wang
- Blood Purification Centre, Third People's Hospital of Rugao, Nantong, 226531, Jiangsu, China
| | - Yufei Chen
- Basic Medical Research Centre, Medical School, Nantong University, Nantong, 226001, Jiangsu, China
| | - Hanqing Chen
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226001, Jiangsu, China
| | - Weizhen Wang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226001, Jiangsu, China
| | - Taowen Ye
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226001, Jiangsu, China
| | - Jin Dong
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226001, Jiangsu, China
| | - Chenliang Sun
- Department of Critical Care Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China
| | - Xiaoran Li
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226001, Jiangsu, China
| | - Chunhong Li
- Blood Purification Centre, Third People's Hospital of Rugao, Nantong, 226531, Jiangsu, China
| | - Jiaying Li
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, 226001, Jiangsu, China
| | - Yong Wang
- Department of Neurosurgery, Affiliated Hospital 2 of Nantong University, Nantong, 226006, Jiangsu, China
| | - Xingmei Feng
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China.
| | - Hongping Ding
- Blood Purification Centre, Third People's Hospital of Rugao, Nantong, 226531, Jiangsu, China.
| | - Dawei Xu
- Department of Orthopedics, Affiliated Hospital 2 of Nantong University, Nantong, 226000, Jiangsu, China.
| | - Jianwu Shi
- Basic Medical Research Centre, Medical School, Nantong University, Nantong, 226001, Jiangsu, China.
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Desideri F, Grazzi A, Lisi M, Setti A, Santini T, Colantoni A, Proietti G, Carvelli A, Tartaglia GG, Ballarino M, Bozzoni I. CyCoNP lncRNA establishes cis and trans RNA-RNA interactions to supervise neuron physiology. Nucleic Acids Res 2024; 52:9936-9952. [PMID: 38989616 PMCID: PMC11381359 DOI: 10.1093/nar/gkae590] [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: 11/06/2023] [Revised: 05/30/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
The combination of morphogenetic and transcription factors together with the synergic aid of noncoding RNAs and their cognate RNA binding proteins contribute to shape motor neurons (MN) identity. Here, we extend the noncoding perspective of human MN, by detailing the molecular and biological activity of CyCoNP (as Cytoplasmic Coordinator of Neural Progenitors) a highly expressed and MN-enriched human lncRNA. Through in silico prediction, in vivo RNA purification and loss of function experiments followed by RNA-sequencing, we found that CyCoNP sustains a specific neuron differentiation program, required for the physiology of both neuroblastoma cells and hiPSC-derived MN, which mainly involves miR-4492 and NCAM1 mRNA. We propose a novel lncRNA-mediated 'dual mode' of action, in which CyCoNP acts in trans as a classical RNA sponge by sequestering miR-4492 from its pro-neuronal targets, including NCAM1 mRNA, and at the same time it plays an additional role in cis by interacting with NCAM1 mRNA and regulating the availability and localization of the miR-4492 in its proximity. These data highlight novel insights into the noncoding RNA-mediated control of human neuron physiology and point out the importance of lncRNA-mediated interactions for the spatial distribution of regulatory molecules.
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Affiliation(s)
- Fabio Desideri
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Alessandro Grazzi
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Michela Lisi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Alessio Colantoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Gabriele Proietti
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Andrea Carvelli
- Department of Neuroscience, The Scripps Research institute, La Jolla, CA 92037, USA
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
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Feng Y, Sun L, Dang X, Liu D, Liao Z, Yao J, Zhang Y, Deng Z, Li J, Zhao M, Liu F. Aberrant glycosylation in schizophrenia: insights into pathophysiological mechanisms and therapeutic potentials. Front Pharmacol 2024; 15:1457811. [PMID: 39286629 PMCID: PMC11402814 DOI: 10.3389/fphar.2024.1457811] [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: 07/01/2024] [Accepted: 08/22/2024] [Indexed: 09/19/2024] Open
Abstract
Schizophrenia (SCZ) is a severe neuropsychiatric disorder characterized by cognitive, affective, and social dysfunction, resulting in hallucinations, delusions, emotional blunting, and disordered thinking. In recent years, proteomics has been increasingly influential in SCZ research. Glycosylation, a key post-translational modification, can alter neuronal stability and normal signaling in the nervous system by affecting protein folding, stability, and cellular signaling. Recent research evidence suggests that abnormal glycosylation patterns exist in different brain regions in autopsy samples from SCZ patients, and that there are significant differences in various glycosylation modification types and glycosylation modifying enzymes. Therefore, this review explores the mechanisms of aberrant modifications of N-glycosylation, O-glycosylation, glycosyltransferases, and polysialic acid in the brains of SCZ patients, emphasizing their roles in neurotransmitter receptor function, synaptic plasticity, and neural adhesion. Additionally, the effects of antipsychotic drugs on glycosylation processes and the potential for glycosylation-targeted therapies are discussed. By integrating these findings, this review aims to provide a comprehensive perspective to further understand the role of aberrant glycosylation modifications in the pathophysiology of SCZ.
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Affiliation(s)
- Yanchen Feng
- The First Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
- Traditional Chinese Medicine (Zhong Jing) School, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lu Sun
- The First Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xue Dang
- Traditional Chinese Medicine (Zhong Jing) School, Henan University of Chinese Medicine, Zhengzhou, China
| | - Diyan Liu
- Traditional Chinese Medicine (Zhong Jing) School, Henan University of Chinese Medicine, Zhengzhou, China
| | - Ziyun Liao
- College of Acupuncture, Moxibustion and Tuina, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jianping Yao
- Traditional Chinese Medicine (Zhong Jing) School, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yunke Zhang
- School of Rehabilitation Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Ziqi Deng
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jinyao Li
- Traditional Chinese Medicine (Zhong Jing) School, Henan University of Chinese Medicine, Zhengzhou, China
| | - Min Zhao
- The First Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
- Hospital of Encephalopathy, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Feixiang Liu
- The First Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
- Hospital of Encephalopathy, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
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Roma L, Ercan C, Conticelli F, Akyürek N, Savic Prince S, Mertz KD, Diebold J, Lardinois D, Piscuoglio S, Ng CK, Bubendorf L. Tracing Tumor Heterogeneity of Pleomorphic Carcinoma of the Lung. J Thorac Oncol 2024; 19:1284-1296. [PMID: 38723776 DOI: 10.1016/j.jtho.2024.04.019] [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: 02/21/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024]
Abstract
INTRODUCTION Pulmonary pleomorphic carcinoma (PPC) is an aggressive and highly heterogeneous NSCLC whose underlying biology is still poorly understood. METHODS A total of 42 tumor areas from 20 patients with PPC were microdissected, including 39 primary tumors and three metastases, and the histologically distinct components were subjected to whole exome sequencing separately. We further performed in silico analysis of microdissected bulk RNA sequencing and methylation data of 28 samples from 14 patients with PPC. We validated our findings using immunohistochemistry. RESULTS The epithelial and the sarcomatoid components of PPCs shared a large number of genomic alterations. Most mutations in cancer driver genes were clonal and truncal between the two components of PPCs suggesting a common ancestor. The high number of alterations in the RTK-RAS pathway suggests that it plays an important role in the evolution of PPC. The metastases morphologically and genetically resembled the epithelial or the sarcomatoid components of the tumor. The transcriptomic and epigenetic profiles of the sarcomatoid components of PPCs with matched squamous-like or adenocarcinoma-like components differed from each other, and they shared more similarities to their matched epithelial components. NCAM1/CD56 was preferentially expressed in the sarcomatoid component of squamous-like PPCs, whereas CDH1/E-Cadherin expression was down-regulated in the sarcomatoid component of most PPCs. CONCLUSION Lung adenocarcinoma-like PPCs are mainly driven by RTK-RAS signaling, whereas epithelial-mesenchymal transition programs as highlighted by increased NCAM1 and decreased CDH1 expression govern the epithelial-sarcomatoid transition between the clonally related tumor components. Several alterations in PPCs pinpoint therapeutic opportunities.
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Affiliation(s)
- Luca Roma
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Caner Ercan
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Floriana Conticelli
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland; Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Nalan Akyürek
- Department of Pathology, Faculty of Medicine, Gazi University, Ankara, Turkey
| | - Spasenija Savic Prince
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Kirsten D Mertz
- Institute for Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Joachim Diebold
- Institute of Pathology, Cantonal Hospital Lucerne, Lucerne, Switzerland
| | - Didier Lardinois
- Division of Thoracic Surgery, University Hospital Basel, Basel, Switzerland
| | - Salvatore Piscuoglio
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland; IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Charlotte Ky Ng
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lukas Bubendorf
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
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Zhu J, Dai H, Chen L. Revealing cell-cell communication pathways with their spatially coupled gene programs. Brief Bioinform 2024; 25:bbae202. [PMID: 38706319 PMCID: PMC11070651 DOI: 10.1093/bib/bbae202] [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: 01/24/2024] [Revised: 03/14/2024] [Accepted: 04/05/2024] [Indexed: 05/07/2024] Open
Abstract
Inference of cell-cell communication (CCC) provides valuable information in understanding the mechanisms of many important life processes. With the rise of spatial transcriptomics in recent years, many methods have emerged to predict CCCs using spatial information of cells. However, most existing methods only describe CCCs based on ligand-receptor interactions, but lack the exploration of their upstream/downstream pathways. In this paper, we proposed a new method to infer CCCs, called Intercellular Gene Association Network (IGAN). Specifically, it is for the first time that we can estimate the gene associations/network between two specific single spatially adjacent cells. By using the IGAN method, we can not only infer CCCs in an accurate manner, but also explore the upstream/downstream pathways of ligands/receptors from the network perspective, which are actually exhibited as a new panoramic cell-interaction-pathway graph, and thus provide extensive information for the regulatory mechanisms behind CCCs. In addition, IGAN can measure the CCC activity at single cell/spot resolution, and help to discover the CCC spatial heterogeneity. Interestingly, we found that CCC patterns from IGAN are highly consistent with the spatial microenvironment patterns for each cell type, which further indicated the accuracy of our method. Analyses on several public datasets validated the advantages of IGAN.
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Affiliation(s)
- Junchao Zhu
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Cell building, No. 320 Yueyang Road, Xuhui District, Shanghai 200031, China
| | - Hao Dai
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Cell building, No. 320 Yueyang Road, Xuhui District, Shanghai 200031, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Cell building, No. 320 Yueyang Road, Xuhui District, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, No. 1, Xiangshan Zhinong, Xihu District, Hangzhou 310024, China
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Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P, Rhie A, Formenti G, Phillippy AM, Harris RS, Wood JMD, Howe K, Kirilenko BM, Munegowda C, Hiller M, Jain A, Kihara D, Johnston JS, Ionkov A, Raja K, Toh H, Lang A, Wolf M, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Mol Biol Evol 2024; 41:msae036. [PMID: 38376487 PMCID: PMC10919930 DOI: 10.1093/molbev/msae036] [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: 03/08/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.
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Affiliation(s)
- Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Li-Fang Chu
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | | | | | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Maylie Gonzales
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Cara Argus
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jennifer Bolin
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Mark E Berres
- University of Wisconsin Biotechnology Center, Bioinformatics Resource Center, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
| | - John Steill
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Scott A Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Peng Jiang
- Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH, USA
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Giulio Formenti
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Bogdan M Kirilenko
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Chetan Munegowda
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Aashish Jain
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Alexander Ionkov
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Kalpana Raja
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Huishi Toh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Aimee Lang
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Magnus Wolf
- Institute for Evolution and Biodiversity (IEB), University of Muenster, 48149, Muenster, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
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Roberts JA, Basu-Roy S, Shin J, Varma VR, Williamson A, Blackshear C, Griswold ME, Candia J, Elango P, Karikkineth AC, Tanaka T, Ferrucci L, Thambisetty M. Serum Proteomic Signatures of Common Health Outcomes among Older Adults. Gerontology 2024; 70:269-278. [PMID: 38219723 DOI: 10.1159/000534753] [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: 04/30/2023] [Accepted: 10/09/2023] [Indexed: 01/16/2024] Open
Abstract
INTRODUCTION In aging populations, the coexistence of multiple health comorbidities represents a significant challenge for clinicians and researchers. Leveraging advances in omics techniques to characterize these health conditions may provide insight into disease pathogenesis as well as reveal biomarkers for monitoring, prognostication, and diagnosis. Researchers have previously established the utility of big data approaches with respect to comprehensive health outcome measurements in younger populations, identifying protein markers that may provide significant health information with a single blood sample. METHODS Here, we employed a similar approach in two cohorts of older adults, the Baltimore Longitudinal Study of Aging (mean age = 76.12 years) and InCHIANTI Study (mean age = 66.05 years), examining the relationship between levels of serum proteins and 5 key health outcomes: kidney function, fasting glucose, physical activity, lean body mass, and percent body fat. RESULTS Correlations between proteins and health outcomes were primarily shared across both older adult cohorts. We further identified that most proteins associated with health outcomes in the older adult cohorts were not associated with the same outcomes in a prior study of a younger population. A subset of proteins, adiponectin, MIC-1, and NCAM-120, were associated with at least three health outcomes in both older adult cohorts but not in the previously published younger cohort, suggesting that they may represent plausible markers of general health in older adult populations. CONCLUSION Taken together, these findings suggest that comprehensive protein health markers have utility in aging populations and are distinct from those identified in younger adults, indicating unique mechanisms of disease with aging.
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Affiliation(s)
- Jackson A Roberts
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA,
- Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA,
| | - Sayantani Basu-Roy
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Jong Shin
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Vijay R Varma
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Andrew Williamson
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Chad Blackshear
- University of Mississippi Medical Center, Jackson, Mississippi, USA
| | | | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Palchamy Elango
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Ajoy C Karikkineth
- Clinical Research Core, National Institute on Aging, National Institutes of Health Intramural Research Program, Baltimore, Maryland, USA
| | - Toshiko Tanaka
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
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Tawfeeq C, Song J, Khaniya U, Madej T, Wang J, Youkharibache P, Abrol R. Towards a structural and functional analysis of the immunoglobulin-fold proteome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 138:135-178. [PMID: 38220423 DOI: 10.1016/bs.apcsb.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The immunoglobulin fold (Ig fold) domain is a super-secondary structural motif consisting of a sandwich with two layers of β-sheets that is present in many proteins with very diverse biological functions covering a wide range of physiological processes. This domain presents a modular architecture built with β strands connected by variable length loops that has a highly conserved structural core of four β-strands and quite variable β-sheet extensions in the two sandwich layers that enable both divergent and convergent evolutionary mechanisms in the known Ig fold proteome. The central role of this Ig fold's structural plasticity in the evolutionary success of antibodies in our immune system is well established. Nature has also utilized this Ig fold in all domains of life in many different physiological contexts that go way beyond the immune system. Here we will present a structural and functional overview of the utilization of the Ig fold in different biological processes and in different cellular contexts to highlight some of the innumerable ways that this structural motif can interact in multidomain proteins to enable their diversity of functions. This includes shareable specific protein structure visualizations behind those functions that serve as starting points for further explorations of the biomolecular interactions spanning the Ig fold proteome. This overview also highlights how this Ig fold is being utilized through natural adaptation, engineering, and even building from scratch for a range of biotechnological applications.
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Affiliation(s)
- Caesar Tawfeeq
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States
| | - James Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Umesh Khaniya
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Thomas Madej
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States.
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States.
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9
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Merritt VC, Maihofer AX, Gasperi M, Chanfreau-Coffinier C, Stein MB, Panizzon MS, Hauger RL, Logue MW, Delano-Wood L, Nievergelt CM. Genome-wide association study of traumatic brain injury in U.S. military veterans enrolled in the VA million veteran program. Mol Psychiatry 2024; 29:97-111. [PMID: 37875548 DOI: 10.1038/s41380-023-02304-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023]
Abstract
Large-scale genetic studies of traumatic brain injury (TBI) are lacking; thus, our understanding of the influence of genetic factors on TBI risk and recovery is incomplete. This study aimed to conduct a genome-wide association study (GWAS) of TBI in VA Million Veteran Program (MVP) enrollees. Participants included a multi-ancestry cohort (European, African, and Hispanic ancestries; N = 304,485; 111,494 TBI cases, 192,991 controls). TBI was assessed using MVP survey data and International Classification of Diseases (ICD) codes from the Veterans Health Administration's electronic health record. GWAS was performed using logistic regression in PLINK, and meta-analyzed in METAL. FUMA was used for post-GWAS analysis. Genomic structural equation modeling (gSEM) was conducted to investigate underlying genetic associations with TBI, and bivariate MiXeR was used to estimate phenotype specific and shared polygenicity. SNP-based heritability was 0.060 (SE = 0.004, p = 7.83×10-66). GWAS analysis identified 15 genome-wide significant (GWS) loci at p < 5×10-8. Gene-based analyses revealed 14 gene-wide significant genes; top genes included NCAM1, APOE, FTO, and FOXP2. Gene tissue expression analysis identified the brain as significantly enriched, particularly in the frontal cortex, anterior cingulate cortex, and nucleus accumbens. Genetic correlations with TBI were significant for risk-taking behaviors and psychiatric disorders, but generally not significant for the neurocognitive variables investigated. gSEM analysis revealed stronger associations with risk-taking traits than with psychiatric traits. Finally, the genetic architecture of TBI was similar to polygenic psychiatric disorders. Neurodegenerative disorders including Alzheimer's and Parkinson's disease showed much less polygenicity, however, the proportion of shared variance with TBI was high. This first well-powered GWAS of TBI identified 15 loci including genes relevant to TBI biology, and showed that TBI is a heritable trait with comparable genetic architecture and high genetic correlation with psychiatric traits. Our findings set the stage for future TBI GWASs that focus on injury severity and diversity and chronicity of symptom sequelae.
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Affiliation(s)
- Victoria C Merritt
- VA San Diego Healthcare System (VASDHS), San Diego, CA, USA.
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Center of Excellence for Stress and Mental Health, VASDHS, San Diego, CA, USA.
| | - Adam X Maihofer
- VA San Diego Healthcare System (VASDHS), San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Marianna Gasperi
- VA San Diego Healthcare System (VASDHS), San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, VASDHS, San Diego, CA, USA
| | | | - Murray B Stein
- VA San Diego Healthcare System (VASDHS), San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- School of Public Health, University of California San Diego, La Jolla, CA, USA
| | - Matthew S Panizzon
- VA San Diego Healthcare System (VASDHS), San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - Richard L Hauger
- VA San Diego Healthcare System (VASDHS), San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, VASDHS, San Diego, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - Mark W Logue
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA, USA
- Boston University Chobanian & Avedisian School of Medicine, Department of Psychiatry, Boston, MA, USA
- Boston University Chobanian & Avedisian School of Medicine, Biomedical Genetics, Boston, MA, USA
- Boston University School of Public Health, Department of Biostatistics, Boston, MA, USA
| | - Lisa Delano-Wood
- VA San Diego Healthcare System (VASDHS), San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, VASDHS, San Diego, CA, USA
| | - Caroline M Nievergelt
- VA San Diego Healthcare System (VASDHS), San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, VASDHS, San Diego, CA, USA
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10
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Brandel-Ankrapp KL, Arey RN. Uncovering novel regulators of memory using C. elegans genetic and genomic analysis. Biochem Soc Trans 2023; 51:161-171. [PMID: 36744642 PMCID: PMC10518207 DOI: 10.1042/bst20220455] [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: 10/14/2022] [Revised: 12/20/2022] [Accepted: 01/19/2023] [Indexed: 02/07/2023]
Abstract
How organisms learn and encode memory is an outstanding question in neuroscience research. Specifically, how memories are acquired and consolidated at the level of molecular and gene pathways remains unclear. In addition, memory is disrupted in a wide variety of neurological disorders; therefore, discovering molecular regulators of memory may reveal therapeutic targets for these disorders. C. elegans are an excellent model to uncover molecular and genetic regulators of memory. Indeed, the nematode's invariant neuronal lineage, fully mapped genome, and conserved associative behaviors have allowed the development of a breadth of genetic and genomic tools to examine learning and memory. In this mini-review, we discuss novel and exciting genetic and genomic techniques used to examine molecular and genetic underpinnings of memory from the level of the whole-worm to tissue-specific and cell-type specific approaches with high spatiotemporal resolution.
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Affiliation(s)
- Katie L. Brandel-Ankrapp
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, U.S.A
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, U.S.A
| | - Rachel N. Arey
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, U.S.A
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, U.S.A
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11
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Wilker S, Vukojevic V, Schneider A, Pfeiffer A, Inerle S, Pauly M, Elbert T, Papassotiropoulos A, de Quervain D, Kolassa IT. Epigenetics of traumatic stress: The association of NR3C1 methylation and posttraumatic stress disorder symptom changes in response to narrative exposure therapy. Transl Psychiatry 2023; 13:14. [PMID: 36658116 PMCID: PMC9852425 DOI: 10.1038/s41398-023-02316-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
Epigenetic processes allow plasticity in gene regulation in response to significant environmental events. Accumulating evidence suggests that effective psychotherapy is accompanied by epigenetic changes, rendering DNA methylation a potential biomarker of therapy success. Due to the central role of glucocorticoid dynamics in stress regulation and the alteration of aversive memories, glucocorticoid receptors are likely involved in the molecular processes that are required to successfully treat Posttraumatic Stress Disorder (PTSD). This study aimed to investigate the relationship between methylation at the glucocorticoid receptor gene (NR3C1) and PTSD treatment success of evidence-based psychotherapy. A sample of N = 153 conflict survivors from Northern Uganda (98 females and 55 males) with PTSD were treated with Narrative Exposure Therapy (NET). Diagnostic interviews and saliva sampling took place at pretreatment and 4 and 10 months after treatment completion. We investigated potential associations between PTSD symptom development and methylation changes at 38 CpG sites spanning NR3C1 over the three times of measurement using the repeated measures correlation. After accounting for multiple comparisons, DNA methylation at CpG site cg25535999 remained negatively associated with PTSD symptoms. These results were followed up by mixed models as well as structural equation modelling. These analyses revealed that treatment responders had a significant cg25535999 methylation increase after treatment with NET. Furthermore, lower methylation at cg25535999 pretreatment predicted a higher symptom improvement. Our results suggest different epigenetic profile dynamics at NR3C1 cg25535999 in therapy responders compared to non-responders and underscore the central role of glucocorticoid signaling in trauma-focused therapy.
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Affiliation(s)
- Sarah Wilker
- Clinical Psychology and Psychotherapy, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany. .,vivo international e.V., P.O. box 5108, 78430, Konstanz, Germany. .,Clinical and Biological Psychology, Ulm University, Albert-Einstein-Allee 47, 89081, Ulm, Germany.
| | - Vanja Vukojevic
- grid.6612.30000 0004 1937 0642Research Platform Molecular and Cognitive Neurosciences (MCN) , Department of Biomedicine, University of Basel, Birmannsgasse 8, 4055 Basel, Switzerland ,grid.6612.30000 0004 1937 0642Psychiatric University Clinics, University of Basel, CH-4055 Basel, Switzerland
| | - Anna Schneider
- vivo international e.V., P.O. box 5108, 78430 Konstanz, Germany ,grid.6582.90000 0004 1936 9748Clinical and Biological Psychology, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany
| | - Anett Pfeiffer
- vivo international e.V., P.O. box 5108, 78430 Konstanz, Germany
| | - Stefan Inerle
- grid.5675.10000 0001 0416 9637Department of Statistics, TU Dortmund University, Joseph-von-Fraunhofer-Straße 2-4, 44227 Dortmund, Germany
| | - Markus Pauly
- grid.5675.10000 0001 0416 9637Department of Statistics, TU Dortmund University, Joseph-von-Fraunhofer-Straße 2-4, 44227 Dortmund, Germany , Research Center Trustworthy Data Science and Security, UA Ruhr, Joseph-von-Fraunhofer-Straße 25, 44227 Dortmund, Germany
| | - Thomas Elbert
- vivo international e.V., P.O. box 5108, 78430 Konstanz, Germany ,grid.9811.10000 0001 0658 7699Clinical Psychology and Neuropsychology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Andreas Papassotiropoulos
- grid.6612.30000 0004 1937 0642Research Platform Molecular and Cognitive Neurosciences (MCN) , Department of Biomedicine, University of Basel, Birmannsgasse 8, 4055 Basel, Switzerland ,grid.6612.30000 0004 1937 0642Psychiatric University Clinics, University of Basel, CH-4055 Basel, Switzerland
| | - Dominique de Quervain
- grid.6612.30000 0004 1937 0642Research Platform Molecular and Cognitive Neurosciences (MCN) , Department of Biomedicine, University of Basel, Birmannsgasse 8, 4055 Basel, Switzerland ,grid.6612.30000 0004 1937 0642Psychiatric University Clinics, University of Basel, CH-4055 Basel, Switzerland
| | - Iris-Tatjana Kolassa
- vivo international e.V., P.O. box 5108, 78430 Konstanz, Germany ,grid.6582.90000 0004 1936 9748Clinical and Biological Psychology, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany
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12
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Keshri N, Nandeesha H. Dysregulation of Synaptic Plasticity Markers in Schizophrenia. Indian J Clin Biochem 2023; 38:4-12. [PMID: 36684500 PMCID: PMC9852406 DOI: 10.1007/s12291-022-01068-2] [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: 03/30/2022] [Accepted: 07/05/2022] [Indexed: 01/25/2023]
Abstract
Schizophrenia is a mental disorder characterized by cognitive impairment resulting in compromised quality of life. Since the regulation of synaptic plasticity has functional implications in various aspects of cognition such as learning, memory, and neural circuit maturation, the dysregulation of synaptic plasticity is considered as a pathobiological feature of schizophrenia. The findings from our recently concluded studies indicate that there is an alteration in levels of synaptic plasticity markers such as neural cell adhesion molecule-1 (NCAM-1), Neurotropin-3 (NT-3) and Matrix-mettaloproteinase-9 (MMP-9) in schizophrenia patients. The objective of the present article is to review the role of markers of synaptic plasticity in schizophrenia. PubMed database (http;//www.ncbi.nlm.nih.gov/pubmed) was used to perform an extensive literature search using the keywords schizophrenia and synaptic plasticity. We conclude that markers of synaptic plasticity are altered in schizophrenia and may lead to complications of schizophrenia including cognitive dysfunction.
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Affiliation(s)
- Neha Keshri
- Department of Biochemistry, JIPMER, Puducherry, 605006 India
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13
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Stoyanova II, Lutz D. Functional Diversity of Neuronal Cell Adhesion and Recognition Molecule L1CAM through Proteolytic Cleavage. Cells 2022; 11:cells11193085. [PMID: 36231047 PMCID: PMC9562852 DOI: 10.3390/cells11193085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
The neuronal cell adhesion and recognition molecule L1 does not only 'keep cells together' by way of homophilic and heterophilic interactions, but can also promote cell motility when cleaved into fragments by several proteases. It has largely been thought that such fragments are signs of degradation. Now, it is clear that proteolysis contributes to the pronounced functional diversity of L1, which we have reviewed in this work. L1 fragments generated at the plasma membrane are released into the extracellular space, whereas other membrane-bound fragments are internalised and enter the nucleus, thus conveying extracellular signals to the cell interior. Post-translational modifications on L1 determine the sequence of cleavage by proteases and the subcellular localisation of the generated fragments. Inside the neuronal cells, L1 fragments interact with various binding partners to facilitate morphogenic events, as well as regenerative processes. The stimulation of L1 proteolysis via injection of L1 peptides or proteases active on L1 or L1 mimetics is a promising tool for therapy of injured nervous systems. The collective findings gathered over the years not only shed light on the great functional diversity of L1 and its fragments, but also provide novel mechanistic insights into the adhesion molecule proteolysis that is active in the developing and diseased nervous system.
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Affiliation(s)
- Irina I. Stoyanova
- Department of Anatomy and Cell Biology, Faculty of Medicine, Medical University, 9002 Varna, Bulgaria
- Department of Brain Ischemia Mechanisms, Research Institute, Medical University, 9002 Varna, Bulgaria
- Correspondence: (I.I.S.); (D.L.)
| | - David Lutz
- Department of Neuroanatomy and Molecular Brain Research, Ruhr University Bochum,
44801 Bochum, Germany
- Correspondence: (I.I.S.); (D.L.)
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14
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Suo Z, Yang J, Zhou B, Qu Y, Xu W, Li M, Xiao T, Zheng H, Ni C. Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period. CNS Neurosci Ther 2022; 28:1576-1595. [PMID: 35899365 PMCID: PMC9437242 DOI: 10.1111/cns.13901] [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: 01/28/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 11/28/2022] Open
Abstract
AIM Perioperative neurocognitive disorders (PND) occur frequently after surgery and anesthesia, especially in aged patients. Previous studies have shown multiple PND related mechanisms in the hippocampus; however, their relationships remain unclear. Meanwhile, the perioperative neuropathological processes are sophisticated and changeable, single period study could not reveal the accurate mechanisms. Thus, multiperiod whole-transcriptome study is necessary to elucidate the gene expression patterns during perioperative period. METHODS Aged C57BL/6 mice were subjected to exploratory laparotomy under sevoflurane anesthesia. Whole-transcriptome sequencing (RNA-seq analysis) was performed on the hippocampi from control condition (Con), 30 min (Day0), 2 days (Day2), and 7 days (Day7) after surgery. Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analyses, quantitative real-time PCR, immunofluorescence, and fear conditioning test were also performed to elucidate the pathological processes and modulation networks during the period. RESULTS Through RNA-seq analysis, 328, 3597, and 4179 differentially expressed genes (DEGs) were screened out in intraoperative period (Day0 vs. Con), early postoperative period (Day2 vs. Day0), and late postoperative period (Day7 vs. Day2). The involved GO biological processes were divided into 9 categories, and positive-regulated processes were more than negative-regulated ones. Seventy-four transcription factors were highlighted. The potential synaptic and neuroinflammatory pathways were constructed for Neurotransmitter, Synapse and Neuronal alteration categories with 9 genes (Htr1a, Rims1, and Ezh2, etc.). The metabolic and mitochondrial pathways were constructed for metabolism, oxidative stress, and biological rhythm categories with 9 genes (Gpld1, Sirt1, and Cry2, etc.). The blood-brain barrier and neurotoxicity related pathways were constructed for blood-brain barrier, neurotoxicity, and cognitive function categories with 10 genes (Mmp2, Itpr1, and Nrf1, etc.). CONCLUSION The results revealed gene expression patterns and modulation networks in the aged hippocampus during perioperative period, which provide insights into overall mechanisms and potential therapeutic targets for prevention and treatment of perioperative central nervous system diseases, such as PND, from the genetic level.
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Affiliation(s)
- Zizheng Suo
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Yang
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Bowen Zhou
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yinyin Qu
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Wenjie Xu
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Min Li
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Zheng
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng Ni
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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15
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Sandau US, McFarland TJ, Smith SJ, Galasko DR, Quinn JF, Saugstad JA. Differential Effects of APOE Genotype on MicroRNA Cargo of Cerebrospinal Fluid Extracellular Vesicles in Females With Alzheimer's Disease Compared to Males. Front Cell Dev Biol 2022; 10:864022. [PMID: 35573689 PMCID: PMC9092217 DOI: 10.3389/fcell.2022.864022] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/25/2022] [Indexed: 12/19/2022] Open
Abstract
Multiple biological factors, including age, sex, and genetics, influence Alzheimer's disease (AD) risk. Of the 6.2 million Americans living with Alzheimer's dementia in 2021, 3.8 million are women and 2.4 million are men. The strongest genetic risk factor for sporadic AD is apolipoprotein E-e4 (APOE-e4). Female APOE-e4 carriers develop AD more frequently than age-matched males and have more brain atrophy and memory loss. Consequently, biomarkers that are sensitive to biological risk factors may improve AD diagnostics and may provide insight into underlying mechanistic changes that could drive disease progression. Here, we have assessed the effects of sex and APOE-e4 on the miRNA cargo of cerebrospinal fluid (CSF) extracellular vesicles (EVs) in AD. We used ultrafiltration (UF) combined with size exclusion chromatography (SEC) to enrich CSF EVs (e.g., Flotillin+). CSF EVs were isolated from female and male AD or controls (CTLs) that were either APOE-e3,4 or -e3,3 positive (n = 7/group, 56 total). MiRNA expression levels were quantified using a custom TaqMan™ array that assayed 190 miRNAs previously found in CSF, including 25 miRNAs that we previously validated as candidate AD biomarkers. We identified changes in the EV miRNA cargo that were affected by both AD and sex. In total, four miRNAs (miR-16-5p, -331-3p, -409-3p, and -454-3p) were significantly increased in AD vs. CTL, independent of sex and APOE-e4 status. Pathway analysis of the predicted gene targets of these four miRNAs with identified pathways was highly relevant to neurodegeneration (e.g., senescence and autophagy). There were also three miRNAs (miR-146b-5p, -150-5p, and -342-3p) that were significantly increased in females vs. males, independent of disease state and APOE-e4 status. We then performed a statistical analysis to assess the effect of APOE genotype in AD within each sex and found that APOE-e4 status affects different subsets of CSF EV miRNAs in females vs. males. Together, this study demonstrates the complexity of the biological factors associated with AD risk and the impact on EV miRNAs, which may contribute to AD pathophysiology.
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Affiliation(s)
- Ursula S. Sandau
- Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Trevor J. McFarland
- Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Sierra J. Smith
- Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Douglas R. Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Joseph F. Quinn
- Department of Neurology, Oregon Health and Science University, Portland, OR, United States
- Parkinson Center and Movement Disorders Program, Oregon Health and Science University, Portland, OR, United States
- Portland VAMC Parkinson’s Disease Research, Education, and Clinical Center, Portland, OR, United States
| | - Julie A. Saugstad
- Department of Anesthesiology and Perioperative Medicine, Oregon Health and Science University, Portland, OR, United States
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16
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Komarasamy TV, Adnan NAA, James W, Balasubramaniam VRMT. Zika Virus Neuropathogenesis: The Different Brain Cells, Host Factors and Mechanisms Involved. Front Immunol 2022; 13:773191. [PMID: 35371036 PMCID: PMC8966389 DOI: 10.3389/fimmu.2022.773191] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/21/2022] [Indexed: 12/16/2022] Open
Abstract
Zika virus (ZIKV), despite being discovered six decades earlier, became a major health concern only after an epidemic in French Polynesia and an increase in the number of microcephaly cases in Brazil. Substantial evidence has been found to support the link between ZIKV and neurological complications in infants. The virus targets various cells in the brain, including radial glial cells, neural progenitor cells (NPCs), astrocytes, microglial and glioblastoma stem cells. It affects the brain cells by exploiting different mechanisms, mainly through apoptosis and cell cycle dysregulation. The modulation of host immune response and the inflammatory process has also been demonstrated to play a critical role in ZIKV induced neurological complications. In addition to that, different ZIKV strains have exhibited specific neurotropism and unique molecular mechanisms. This review provides a comprehensive and up-to-date overview of ZIKV-induced neuroimmunopathogenesis by dissecting its main target cells in the brain, and the underlying cellular and molecular mechanisms. We highlighted the roles of the different ZIKV host factors and how they exploit specific host factors through various mechanisms. Overall, it covers key components for understanding the crosstalk between ZIKV and the brain.
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Affiliation(s)
- Thamil Vaani Komarasamy
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Nur Amelia Azreen Adnan
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - William James
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Vinod R M T Balasubramaniam
- Infection and Immunity Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
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17
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Motz CT, Kabat V, Saxena T, Bellamkonda RV, Zhu C. Neuromechanobiology: An Expanding Field Driven by the Force of Greater Focus. Adv Healthc Mater 2021; 10:e2100102. [PMID: 34342167 PMCID: PMC8497434 DOI: 10.1002/adhm.202100102] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 07/06/2021] [Indexed: 12/14/2022]
Abstract
The brain processes information by transmitting signals through highly connected and dynamic networks of neurons. Neurons use specific cellular structures, including axons, dendrites and synapses, and specific molecules, including cell adhesion molecules, ion channels and chemical receptors to form, maintain and communicate among cells in the networks. These cellular and molecular processes take place in environments rich of mechanical cues, thus offering ample opportunities for mechanical regulation of neural development and function. Recent studies have suggested the importance of mechanical cues and their potential regulatory roles in the development and maintenance of these neuronal structures. Also suggested are the importance of mechanical cues and their potential regulatory roles in the interaction and function of molecules mediating the interneuronal communications. In this review, the current understanding is integrated and promising future directions of neuromechanobiology are suggested at the cellular and molecular levels. Several neuronal processes where mechanics likely plays a role are examined and how forces affect ligand binding, conformational change, and signal induction of molecules key to these neuronal processes are indicated, especially at the synapse. The disease relevance of neuromechanobiology as well as therapies and engineering solutions to neurological disorders stemmed from this emergent field of study are also discussed.
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Affiliation(s)
- Cara T Motz
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0363, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332-0363, USA
| | - Victoria Kabat
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0363, USA
| | - Tarun Saxena
- Department of Biomedical Engineering, Duke University, Durham, NC, 27709, USA
| | - Ravi V Bellamkonda
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0363, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332-0363, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332-0363, USA
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18
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Rahmani A, Chew YL. Investigating the molecular mechanisms of learning and memory using Caenorhabditis elegans. J Neurochem 2021; 159:417-451. [PMID: 34528252 DOI: 10.1111/jnc.15510] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/15/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022]
Abstract
Learning is an essential biological process for survival since it facilitates behavioural plasticity in response to environmental changes. This process is mediated by a wide variety of genes, mostly expressed in the nervous system. Many studies have extensively explored the molecular and cellular mechanisms underlying learning and memory. This review will focus on the advances gained through the study of the nematode Caenorhabditis elegans. C. elegans provides an excellent system to study learning because of its genetic tractability, in addition to its invariant, compact nervous system (~300 neurons) that is well-characterised at the structural level. Importantly, despite its compact nature, the nematode nervous system possesses a high level of conservation with mammalian systems. These features allow the study of genes within specific sensory-, inter- and motor neurons, facilitating the interrogation of signalling pathways that mediate learning via defined neural circuits. This review will detail how learning and memory can be studied in C. elegans through behavioural paradigms that target distinct sensory modalities. We will also summarise recent studies describing mechanisms through which key molecular and cellular pathways are proposed to affect associative and non-associative forms of learning.
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Affiliation(s)
- Aelon Rahmani
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Yee Lian Chew
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
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19
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Carleial S, Nätt D, Unternährer E, Elbert T, Robjant K, Wilker S, Vukojevic V, Kolassa IT, Zeller AC, Koebach A. DNA methylation changes following narrative exposure therapy in a randomized controlled trial with female former child soldiers. Sci Rep 2021; 11:18493. [PMID: 34531495 PMCID: PMC8445994 DOI: 10.1038/s41598-021-98067-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
The aftermath of traumatization lives on in the neural and epigenetic traces creating a momentum of affliction in the psychological and social realm. Can psychotherapy reorganise these memories through changes in DNA methylation signatures? Using a randomised controlled parallel group design, we examined methylome-wide changes in saliva samples of 84 female former child soldiers from Eastern DR Congo before and six months after Narrative Exposure Therapy. Treatment predicted differentially methylated positions (DMPs) related to ALCAM, RIPOR2, AFAP1 and MOCOS. In addition, treatment associations overlapped at gene level with baseline clinical and social outcomes. Treatment related DMPs are involved in memory formation-the key agent in trauma focused treatments-and enriched for molecular pathways commonly affected by trauma related disorders. Results were partially replicated in an independent sample of 53 female former child soldiers from Northern Uganda. Our results suggest a molecular impact of psychological treatment in women with war-related childhood trauma.Trial registration: Addressing Heightened Levels of Aggression in Traumatized Offenders With Psychotherapeutic Means (ClinicalTrials.gov Identifier: NCT02992561, 14/12/2016).
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Affiliation(s)
- Samuel Carleial
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany
| | - Daniel Nätt
- grid.5640.70000 0001 2162 9922Division of Neurobiology, Department of Biomedical and Clinical Sciences, University of Linköping, Building 463, Room 12.023, Linköping, Sweden
| | - Eva Unternährer
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany ,grid.6612.30000 0004 1937 0642Child- and Adolescent Research Department, Psychiatric University Hospitals Basel (UPK), University of Basel, Basel, Switzerland
| | - Thomas Elbert
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany ,Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany
| | - Katy Robjant
- Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany
| | - Sarah Wilker
- Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany ,grid.7491.b0000 0001 0944 9128Department of Psychology and Sports Science, University of Bielefeld, 33501 Bielefeld, Germany
| | - Vanja Vukojevic
- grid.6612.30000 0004 1937 0642Psychiatric University Clinics, Transfaculty Research Platform, University of Basel, Wilhelm Klein-Strasse 27, CH-4012 Basel, Switzerland
| | - Iris-Tatjana Kolassa
- Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany ,grid.6582.90000 0004 1936 9748Department of Clinical and Biological Psychology, Institute of Psychology & Education, University of Ulm, Ulm University, Ulm, Germany
| | - Anja C. Zeller
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany ,Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany
| | - Anke Koebach
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany ,Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany
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20
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Decreased Serum NCAM Levels Associated with Cognitive Impairment in Vascular Dementia. DISEASE MARKERS 2021; 2021:2792884. [PMID: 34504627 PMCID: PMC8423537 DOI: 10.1155/2021/2792884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022]
Abstract
Objective Neural cell adhesion molecule (NCAM), a glycoprotein widely distributed in the brain, has recently been shown to regulate neuroplasticity. However, the role of NCAM in vascular dementia (VaD) is still unclear. The purpose of this study is to determine whether NCAM is involved in the course of VaD. Methods Continuous recruitment of VaD patients and control population to join this study. Doctors or nurses are responsible for collecting their clinical characteristics including age, gender, formal education, heart rate, supine systolic blood pressure, supine diastolic blood pressure, fasting glucose, high-density lipoprotein, and low-density lipoprotein. Each participant received the Montreal Cognitive Assessment (MoCA) scale after being enrolled in the group. At the same time, their peripheral blood was collected, and their serum NCAM levels were measured by enzyme-linked immunosorbent assay (ELISA). Results 98 VaD patients and 83 age- and sex-matched controls were enrolled. There was no significant statistical difference between the VaD group and the control group in terms of the comparison of clinical characteristics (p > 0.05). The MoCA score of VaD patients was significantly lower than that of the controls (27.9 ± 1.4 vs. 23.0 ± 2.1 points, p < 0.001). In addition, the circulating NCAM level of VaD patients was also significantly lower than that of controls (21.7 ± 3.8 vs. 17.6 ± 4.2 ng/mL, p < 0.001). The circulating NCAM level of VaD patients was significantly positively correlated with MoCA score (r = 0.285, p = 0.026). After adjusting for clinical characteristics, circulating NCAM levels are still an independent pathogenic factor of VaD (regression coefficient = 0.223, p = 0.034). Conclusions VaD patients have low circulating NCAM levels, which can be used as a potential predictor of VaD.
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21
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An association study in the Taiwan Biobank elicits three novel candidates for cognitive aging in old adults: NCAM1, TTC12 and ZBTB20. Aging (Albany NY) 2021; 13:18769-18788. [PMID: 34285142 PMCID: PMC8351692 DOI: 10.18632/aging.203321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/08/2021] [Indexed: 01/11/2023]
Abstract
The dopamine receptor-related loci have been suggested to be associated with cognitive functions and neurodegenerative diseases. It is unknown whether genetic variants such as single nucleotide polymorphisms (SNPs) in the dopamine receptor-related loci could contribute to cognitive aging independently as well as by virtue of complicated interplays in the elder population. To assess whether SNPs in the dopamine receptor-related loci are associated with cognitive aging in the elder population, we evaluated SNPs in the DRD1, NCAM1-TTC12-ANKK1-DRD2, DRD3-LOC107986115-ZNF80-TIGIT-MIR568-ZBTB20, DRD4, and DRD5-SLC2A9 loci from 25,195 older Taiwanese individuals from the Taiwan Biobank. Mini-Mental State Examination (MMSE) was scrutinized for all participants, where MMSE scores were employed to evaluate cognitive functions. From our analysis, we identified three novel genes for cognitive aging that have not previously been reported: ZBTB20 on chromosome 3 and NCAM1 and TTC12 on chromosome 11. NCAM1 and ZBTB20 are strong candidates for having a role in cognitive aging with mutations in ZBTB20 resulting in intellectual disability, and NCAM1 previously found to be associated with associative memory in humans. Additionally, we found the effects of interplays between physical activity and these three novel genes. Our study suggests that genetic variants in the dopamine receptor-related loci may influence cognitive aging individually and by means of gene-physical activity interactions.
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22
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de Leeuw SM, Davaz S, Wanner D, Milleret V, Ehrbar M, Gietl A, Tackenberg C. Increased maturation of iPSC-derived neurons in a hydrogel-based 3D culture. J Neurosci Methods 2021; 360:109254. [PMID: 34126141 DOI: 10.1016/j.jneumeth.2021.109254] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/20/2021] [Accepted: 06/09/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Induced pluripotent stem cells (iPSCs) can be differentiated into virtually every desired cell type, offering significant potential for modeling human diseases in vitro. A disadvantage is that iPSC-derived cells represent an immature, which presents a major limitation for modeling age-related diseases such as Alzheimer's disease. Evidence suggests that culturing iPSC neurons in a 3D environment may increase neuronal maturity. However, current 3D cell culture systems are cumbersome and time-consuming. NEW METHOD We cultured iPSC-derived excitatory neurons in 3D precast hydrogel plates and compared their maturation to 2D monolayer cultures. COMPARISON WITH EXISTING METHODS In contrast to other hydrogel-based 3D culture techniques, which require full encapsulation of cells, our hydrogel allows the seeded iPSCs and iPSC neurons to simply infiltrate the gel. RESULTS IPSC-neurons grew to a depth of 500 µm into the hydrogel. Cell viability was comparable to 2D cultures over the course of three weeks, with even better neuronal survival in 3D cultures at the one-week time point. Levels of neuronal and synaptic maturation markers, namely, neural cell adhesion molecule 1 (NCAM1) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subunit GluR2, were strongly increased in 3D cultures. Furthermore, we identified 4-repeat (4R) tau in 3D cultures, which was not detectable in 2D cultures. CONCLUSIONS We describe a simple, hydrogel-based method for 3D iPSC culture that can serve as a fast and drug-screening-compatible platform to identify new mechanisms and therapeutic targets for brain diseases. We further provided evidence for the increased maturation of iPSC neurons in a 3D microenvironment.
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Affiliation(s)
- Sherida M de Leeuw
- Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland; Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Stephanie Davaz
- Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland
| | - Debora Wanner
- Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland
| | - Vincent Milleret
- Department of Obstetrics, University and University Hospital of Zurich, Zurich, Switzerland
| | - Martin Ehrbar
- Department of Obstetrics, University and University Hospital of Zurich, Zurich, Switzerland
| | - Anton Gietl
- Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland
| | - Christian Tackenberg
- Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland; Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.
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23
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Kraus A, Buckley KM, Salinas I. Sensing the world and its dangers: An evolutionary perspective in neuroimmunology. eLife 2021; 10:66706. [PMID: 33900197 PMCID: PMC8075586 DOI: 10.7554/elife.66706] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
Detecting danger is key to the survival and success of all species. Animal nervous and immune systems cooperate to optimize danger detection. Preceding studies have highlighted the benefits of bringing neurons into the defense game, including regulation of immune responses, wound healing, pathogen control, and survival. Here, we summarize the body of knowledge in neuroimmune communication and assert that neuronal participation in the immune response is deeply beneficial in each step of combating infection, from inception to resolution. Despite the documented tight association between the immune and nervous systems in mammals or invertebrate model organisms, interdependence of these two systems is largely unexplored across metazoans. This review brings a phylogenetic perspective of the nervous and immune systems in the context of danger detection and advocates for the use of non-model organisms to diversify the field of neuroimmunology. We identify key taxa that are ripe for investigation due to the emergence of key evolutionary innovations in their immune and nervous systems. This novel perspective will help define the primordial principles that govern neuroimmune communication across taxa.
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Affiliation(s)
- Aurora Kraus
- Department of Biology, University of New Mexico, Albuquerque, United States
| | | | - Irene Salinas
- Department of Biology, University of New Mexico, Albuquerque, United States
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24
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Warsi NM, Ibrahim GM. Commentary: Tract-Specific Relationships Between Cerebrospinal Fluid Biomarkers and Periventricular White Matter in Posthemorrhagic Hydrocephalus of Prematurity. Neurosurgery 2021; 88:E267-E268. [PMID: 33369653 DOI: 10.1093/neuros/nyaa483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 09/06/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
- Nebras M Warsi
- Division of Neurosurgery, Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Ontario, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - George M Ibrahim
- Division of Neurosurgery, Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Ontario, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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