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Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron 2024; 112:2091-2111. [PMID: 38754415 DOI: 10.1016/j.neuron.2024.04.021] [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: 12/15/2023] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Since the beautiful images of Santiago Ramón y Cajal provided a first glimpse into the immense diversity and complexity of cell types found in the cerebral cortex, neuroscience has been challenged and inspired to understand how these diverse cells are generated and how they interact with each other to orchestrate the development of this remarkable tissue. Some fundamental questions drive the field's quest to understand cortical development: what are the mechanistic principles that govern the emergence of neuronal diversity? How do extrinsic and intrinsic signals integrate with physical forces and activity to shape cell identity? How do the diverse populations of neurons and glia influence each other during development to guarantee proper integration and function? The advent of powerful new technologies to profile and perturb cortical development at unprecedented resolution and across a variety of modalities has offered a new opportunity to integrate past knowledge with brand new data. Here, we review some of this progress using cortical excitatory projection neurons as a system to draw out general principles of cell diversification and the role of cell-cell interactions during cortical development.
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Affiliation(s)
- Daniela J Di Bella
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Nuria Domínguez-Iturza
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Juliana R Brown
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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2
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Ooi E, Xiang R, Chamberlain AJ, Goddard ME. Archetypal clustering reveals physiological mechanisms linking milk yield and fertility in dairy cattle. J Dairy Sci 2024; 107:4726-4742. [PMID: 38369117 DOI: 10.3168/jds.2023-23699] [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: 05/05/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Fertility in dairy cattle has declined as an unintended consequence of single-trait selection for high milk yield. The unfavorable genetic correlation between milk yield and fertility is now well documented; however, the underlying physiological mechanisms are still uncertain. To understand the relationship between these traits, we developed a method that clusters variants with similar patterns of effects and, after the integration of gene expression data, identifies the genes through which they are likely to act. Biological processes that are enriched in the genes of each cluster were then identified. We identified several clusters with unique patterns of effects. One of the clusters included variants associated with increased milk yield and decreased fertility, where the "archetypal" variant (i.e., the one with the largest effect) was associated with the GC gene, whereas others were associated with TRIM32, LRRK2, and U6-associated snRNA. These genes have been linked to transcription and alternative splicing, suggesting that these processes are likely contributors to the unfavorable relationship between the 2 traits. Another cluster, with archetypal variant near DGAT1 and including variants associated with CDH2, BTRC, SFRP2, ZFHX3, and SLITRK5, appeared to affect milk yield but have little effect on fertility. These genes have been linked to insulin, adipose tissue, and energy metabolism. A third cluster with archetypal variant near ZNF613 and including variants associated with ROBO1, EFNA5, PALLD, GPC6, and PTPRT were associated with fertility but not milk yield. These genes have been linked to GnRH neuronal migration, embryonic development, or ovarian function. The use of archetypal clustering to group variants with similar patterns of effects may assist in identifying the biological processes underlying correlated traits. The method is hypothesis generating and requires experimental confirmation. However, we have uncovered several novel mechanisms potentially affecting milk production and fertility such as GnRH neuronal migration. We anticipate our method to be a starting point for experimental research into novel pathways, which have been previously unexplored within the context of dairy production.
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Affiliation(s)
- E Ooi
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia.
| | - R Xiang
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
| | - A J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
| | - M E Goddard
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia; Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
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O'Connor AM, Hagenauer MH, Thew Forrester LC, Maras PM, Arakawa K, Hebda-Bauer EK, Khalil H, Richardson ER, Rob FI, Sannah Y, Watson SJ, Akil H. Adolescent environmental enrichment induces social resilience and alters neural gene expression in a selectively bred rodent model with anxious phenotype. Neurobiol Stress 2024; 31:100651. [PMID: 38933284 PMCID: PMC11201356 DOI: 10.1016/j.ynstr.2024.100651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 04/10/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Stress is a major influence on mental health status; the ways that individuals respond to or copes with stressors determine whether they are negatively affected in the future. Stress responses are established by an interplay between genetics, environment, and life experiences. Psychosocial stress is particularly impactful during adolescence, a critical period for the development of mood disorders. In this study we compared two established, selectively-bred Sprague Dawley rat lines, the "internalizing" bred Low Responder (bLR) line versus the "externalizing" bred High Responder (bHR) line, to investigate how genetic temperament and adolescent environment impact future responses to social interactions and psychosocial stress, and how these determinants of stress response interact. Male bLR and bHR rats were exposed to social and environmental enrichment in adolescence prior to experiencing social defeat and were then assessed for social interaction and anxiety-like behavior. Adolescent enrichment caused rats to display more social interaction, as well as nominally less social avoidance, less submission during defeat, and resilience to the effects of social stress on corticosterone, in a manner that seemed more notable in bLRs. For bHRs, enrichment also caused greater aggression during a neutral social encounter and nominally during defeat, and decreased anxiety-like behavior. To explore the neurobiology underlying the development of social resilience in the anxious phenotype bLRs, RNA-seq was conducted on the hippocampus and nucleus accumbens, two brain regions that mediate stress regulation and social behavior. Gene sets previously associated with stress, social behavior, aggression and exploratory activity were enriched with differential expression in both regions, with a particularly large effect on gene sets that regulate social behaviors. Our findings provide further evidence that adolescent enrichment can serve as an inoculating experience against future stressors. The ability to induce social resilience in a usually anxious line of animals by manipulating their environment has translational implications, as it underscores the feasibility of intervention strategies targeted at genetically vulnerable adolescent populations.
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Affiliation(s)
| | - Megan Hastings Hagenauer
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Liam Cannon Thew Forrester
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Pamela M. Maras
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Keiko Arakawa
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Elaine K. Hebda-Bauer
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Huzefa Khalil
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Evelyn R. Richardson
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Farizah I. Rob
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Yusra Sannah
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Stanley J. Watson
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
| | - Huda Akil
- Michigan Neuroscience Institute, 205 Zina Pitcher Place, University of Michigan, Ann Arbor, MI, USA, 48109
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房 锦, 刘 立, 林 俊, 陈 逢. [Overexpression of CDHR2 inhibits proliferation of breast cancer cells by inhibiting the PI3K/Akt pathway]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2024; 44:1117-1125. [PMID: 38977341 PMCID: PMC11237307 DOI: 10.12122/j.issn.1673-4254.2024.06.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Indexed: 07/10/2024]
Abstract
OBJECTIVE To investigate the mechanism by which CDHR2 overexpression inhibits breast cancer cell growth and cell cycle pragression via the PI3K/Akt signaling pathway. METHODS Bioinformatic analysis was performed to investigate CDHR2 expression in breast cancer and its correlation with survival outcomes of the patients. Immunohistochemistry was used to examine CDHR2 expressions in surgical specimens of tumor and adjacent tissues from 10 patients with breast cancer. CDHR2 expression levels were also detected in 5 breast cancer cell lines and a normal human mammary epithelial cell line using qRT-PCR and Western blotting. Breast cancer cell lines MDA-MB-231 and MCF7 with low CDHR2 expression were transfected with a CDHR2-overexpressing plasmid, and the changes in cell proliferation and cell cycle were evaluated using CCK-8 assay, EdU assay, and cell cycle assay; the changes in expressions of PI3K/Akt signaling pathway and cell cycle pathway proteins were detected with Western blotting. RESULTS Bioinformatic analysis showed low CDHR2 expression level in both breast cancer and adjacent tissues without significant difference between them (P > 0.05), but breast cancer patients with a high expression of CDHR2 had a more favorable prognosis. Immunohistochemistry, qRT-PCR and Western blotting showed that the expression of CDHR2 was significantly down-regulated in breast cancer tissues and breast cancer cells (P < 0.01), and its overexpression strongly inhibited cell proliferation, caused cell cycle arrest, and significantly inhibited PI3K and Akt phosphorylation and the expression of cyclin D1. CONCLUSION Overexpression of CDHR2 inhibits proliferation and causes cell cycle arrest in breast cancer cells possibly by inhibiting the PI3K/Akt signaling pathway.
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Aerts T, Boonen A, Geenen L, Stulens A, Masin L, Pancho A, Francis A, Pepermans E, Baggerman G, Van Roy F, Wöhr M, Seuntjens E. Altered socio-affective communication and amygdala development in mice with protocadherin10-deficient interneurons. Open Biol 2024; 14:240113. [PMID: 38889770 DOI: 10.1098/rsob.240113] [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: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Autism spectrum disorder (ASD) is a group of neurodevelopmental conditions associated with deficits in social interaction and communication, together with repetitive behaviours. The cell adhesion molecule protocadherin10 (PCDH10) is linked to ASD in humans. Pcdh10 is expressed in the nervous system during embryonic and early postnatal development and is important for neural circuit formation. In mice, strong expression of Pcdh10 in the ganglionic eminences and in the basolateral complex (BLC) of the amygdala was observed at mid and late embryonic stages, respectively. Both inhibitory and excitatory neurons expressed Pcdh10 in the BLC at perinatal stages and vocalization-related genes were enriched in Pcdh10-expressing neurons in adult mice. An epitope-tagged Pcdh10-HAV5 mouse line revealed endogenous interactions of PCDH10 with synaptic proteins in the young postnatal telencephalon. Nuanced socio-affective communication changes in call emission rates, acoustic features and call subtype clustering were primarily observed in heterozygous pups of a conditional knockout (cKO) with selective deletion of Pcdh10 in Gsh2-lineage interneurons. These changes were less prominent in heterozygous ubiquitous Pcdh10 KO pups, suggesting that altered anxiety levels associated with Gsh2-lineage interneuron functioning might drive the behavioural effects. Together, loss of Pcdh10 specifically in interneurons contributes to behavioural alterations in socio-affective communication with relevance to ASD.
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Affiliation(s)
- Tania Aerts
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Anneleen Boonen
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Lieve Geenen
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Anne Stulens
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Luca Masin
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Neural Circuit Development and Regeneration, KU Leuven , Leuven 3000, Belgium
| | - Anna Pancho
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
- Developmental Genetics, Department of Biomedicine, University of Basel , Basel 4058, Switzerland
| | - Annick Francis
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Elise Pepermans
- Centre for Proteomics, University of Antwerp , Antwerp, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp , Antwerp, Belgium
- Department of Computer Science, University of Antwerp , Antwerp, Belgium
| | - Frans Van Roy
- Faculty of Science, Department of Biomedical Molecular Biology; Inflammation Research Center, VIB, Ghent University , Cancer Research Institute Ghent (CRIG) 9000, Belgium
| | - Markus Wöhr
- Faculty of Psychology and Educational Sciences, Research Unit Brain and Cognition, Laboratory of Biological Psychology, Social and Affective Neuroscience Research Group, KU Leuven , Leuven 3000, Belgium
- KU Leuven, Leuven Brain Institute , Leuven 3000, Belgium
- Faculty of Psychology, Experimental and Biological Psychology, Behavioral Neuroscience, Philipps-University of Marburg , Marburg 35032, Germany
- Center for Mind, Brain and Behavior, Philipps-University of Marburg , Marburg 35032, Germany
| | - Eve Seuntjens
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
- KU Leuven, Leuven Brain Institute , Leuven 3000, Belgium
- KU Leuven, Leuven Institute for Single Cell Omics , Leuven 3000, Belgium
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Piergiorge RM, Vasconcelos ATRD, Santos-Rebouças CB. Understanding the (epi)genetic dysregulation in Parkinson's disease through an integrative brain competitive endogenous RNA network. Mech Ageing Dev 2024; 219:111942. [PMID: 38762037 DOI: 10.1016/j.mad.2024.111942] [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: 04/03/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Parkinson's disease (PD) is a rapidly growing neurodegenerative disorder characterized by dopaminergic neuron loss in the substantia nigra pars compacta (SN) and aggregation of α-synuclein. Its aetiology involves a multifaceted interplay among genetic, environmental, and epigenetic factors. We integrated brain gene expression data from PD patients to construct a comprehensive regulatory network encompassing messenger RNAs (mRNAs), microRNAs (miRNAs), circular RNAs (circRNAs) and, for the first time, RNA binding proteins (RBPs). Expression data from the SN of PD patients and controls were systematically selected from public databases to identify combined differentially expressed genes (DEGs). Brain co-expression analysis revealed modules comprising significant DEGs that function cooperatively. The relationships among co-expressed DEGs, miRNAs, circRNAs, and RBPs revealed an intricate competitive endogenous RNA (ceRNA) network responsible for post-transcriptional dysregulation in PD. Many genes in the ceRNA network, including the TOMM20 and HMGCR genes, overlap with the most relevant genes in our previous Alzheimer's disease-associated ceRNA network, suggesting common underlying mechanisms between both conditions. Moreover, in the ceRNA subnetwork, the RBP Aly/REF export factor (ALYREF), which acts as an RNA 5-methylcytosine(m5C)-binding protein, stood out. Our data sheds new light on the potential role of brain ceRNA networks in PD pathogenesis.
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Affiliation(s)
- Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | | | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil.
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Yang SL, Ma BJ, Lu YS, Chen J, Yu J, Qiu J, Qian YZ, Xu YY. Multi-omics reveals the molecular mechanism of the combined toxic effects of PFOA and 4-HBP exposure in MCF-7 cells and the key player: mTORC1. ENVIRONMENT INTERNATIONAL 2024; 188:108778. [PMID: 38815467 DOI: 10.1016/j.envint.2024.108778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/06/2024] [Accepted: 05/25/2024] [Indexed: 06/01/2024]
Abstract
With the discovery of evidence that many endocrine-disrupting chemicals (EDCs) in the environment influence human health, their toxic effects and mechanisms have become a hot topic of research. However, investigations into their endocrine-disrupting toxicity under combined binary exposure, especially the molecular mechanism of combined effects, have rarely been documented. In this study, two typical EDCs, perfluorooctanoic acid (PFOA) and 4-hydroxybenzophenone (4-HBP), were selected to examine their combined effects and molecular mechanism on MCF-7 cell proliferation at environmentally relevant exposure concentrations. We have successfully established a model to evaluate the binary combined toxic effects of endocrine disruptors, presenting combined effects in a simple and direct way. Results indicated that the combined effect changed from additive to synergistic from 1.25 × 10-8 M to 4 × 10-7 M. Metabolomics analyses suggested that exposure to PFOA and 4-HBP caused significant alterations in purine metabolism, arginine, and proline metabolism and had superimposed influences on metabolism. Enhanced combined effects were observed in glycine, serine, and threonine metabolic pathways compared to exposure to PFOS and 4-HBP alone. Additionally, the differentially expressed genes (DEGs) are primarily involved in Biological Processes, especially protein targeting the endoplasmic reticulum, and significantly impact the oxidative phosphorylation and thermogenesis-related KEGG pathway. By integrating metabolome and transcriptome analyses, PFOA and 4-HBP regulate purine metabolism, the TCA cycle, and endoplasmic reticulum protein synthesis in MCF-7 cells via mTORC1, which provides genetic material, protein, and energy for cell proliferation. Furthermore, molecular docking confirmed the ability of PFOA and 4-HBP to stably bind the estrogen receptor, indicating that they have different binding pockets. Collectively, these findings will offer new insights into understanding the mechanisms by which EDCs produce combined toxicity.
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Affiliation(s)
- Shang-Lin Yang
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing-Jie Ma
- Faculty of Printing and Packaging and Digital Media, Xi' an University of Technology, Xi'an 710048, China
| | - Yu-Shun Lu
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ju Chen
- Faculty of Printing and Packaging and Digital Media, Xi' an University of Technology, Xi'an 710048, China
| | - Jiang Yu
- Faculty of Printing and Packaging and Digital Media, Xi' an University of Technology, Xi'an 710048, China
| | - Jing Qiu
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong-Zhong Qian
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan-Yang Xu
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Pottmeier P, Nikolantonaki D, Lanner F, Peuckert C, Jazin E. Sex-biased gene expression during neural differentiation of human embryonic stem cells. Front Cell Dev Biol 2024; 12:1341373. [PMID: 38764741 PMCID: PMC11101176 DOI: 10.3389/fcell.2024.1341373] [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: 11/20/2023] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Sex differences in the developing human brain are primarily attributed to hormonal influence. Recently however, genetic differences and their impact on the developing nervous system have attracted increased attention. To understand genetically driven sexual dimorphisms in neurodevelopment, we investigated genome-wide gene expression in an in vitro differentiation model of male and female human embryonic stem cell lines (hESC), independent of the effects of human sex hormones. Four male and four female-derived hESC lines were differentiated into a population of mixed neurons over 37 days. Differential gene expression and gene set enrichment analyses were conducted on bulk RNA sequencing data. While similar differentiation tendencies in all cell lines demonstrated the robustness and reproducibility of our differentiation protocol, we found sex-biased gene expression already in undifferentiated ESCs at day 0, but most profoundly after 37 days of differentiation. Male and female cell lines exhibited sex-biased expression of genes involved in neurodevelopment, suggesting that sex influences the differentiation trajectory. Interestingly, the highest contribution to sex differences was found to arise from the male transcriptome, involving both Y chromosome and autosomal genes. We propose 13 sex-biased candidate genes (10 upregulated in male cell lines and 3 in female lines) that are likely to affect neuronal development. Additionally, we confirmed gene dosage compensation of X/Y homologs escaping X chromosome inactivation through their Y homologs and identified a significant overexpression of the Y-linked demethylase UTY and KDM5D in male hESC during neuron development, confirming previous results in neural stem cells. Our results suggest that genetic sex differences affect neuronal differentiation trajectories, which could ultimately contribute to sex biases during human brain development.
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Affiliation(s)
- Philipp Pottmeier
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Danai Nikolantonaki
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fredrik Lanner
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Christiane Peuckert
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Elena Jazin
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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9
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Song QH, Zhao KX, Huang S, Chen T, He L. Escape from X-chromosome inactivation and sex differences in Alzheimer's disease. Rev Neurosci 2024; 35:341-354. [PMID: 38157427 DOI: 10.1515/revneuro-2023-0108] [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: 09/06/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
Sex differences exist in the onset and progression of Alzheimer's disease. Globally, women have a higher prevalence, while men with Alzheimer's disease experience earlier mortality and more pronounced cognitive decline than women. The cause of sex differences in Alzheimer's disease remains unclear. Accumulating evidence suggests the potential role of X-linked genetic factors in the sex difference of Alzheimer's disease (AD). During embryogenesis, a remarkable process known as X-chromosome inactivation (XCI) occurs in females, leading to one of the X chromosomes undergoing transcriptional inactivation, which balances the effects of two X chromosomes in females. Nevertheless, certain genes exceptionally escape from XCI, which provides a basis for dual expression dosage of specific genes in females. Based on recent research findings, we explore key escape genes and their potential therapeutic use associated with Alzheimer's disease. Also, we discuss their possible role in driving the sex differences in Alzheimer's disease. This will provide new perspectives for precision medicine and gender-specific treatment of AD.
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Affiliation(s)
- Qing-Hua Song
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Ke-Xuan Zhao
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Shuai Huang
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Tong Chen
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Ling He
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
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10
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O'Connor AM, Hagenauer MH, Forrester LCT, Maras PM, Arakawa K, Hebda-Bauer EK, Khalil H, Richardson ER, Rob FI, Sannah Y, Watson SJ, Akil H. Adolescent environmental enrichment induces social resilience and alters neural gene expression in a selectively bred rodent model with anxious phenotype. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.03.560702. [PMID: 38645129 PMCID: PMC11030238 DOI: 10.1101/2023.10.03.560702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Stress is a major influence on mental health status; the ways that individuals respond to or copes with stressors determine whether they are negatively affected in the future. Stress responses are established by an interplay between genetics, environment, and life experiences. Psychosocial stress is particularly impactful during adolescence, a critical period for the development of mood disorders. In this study we compared two established, selectively-bred Sprague Dawley rat lines, the "internalizing" bred Low Responder (bLR) line versus the "externalizing" bred High Responder (bHR) line, to investigate how genetic temperament and adolescent environment impact future responses to social interactions and psychosocial stress, and how these determinants of stress response interact. Male bLR and bHR rats were exposed to social and environmental enrichment in adolescence prior to experiencing social defeat and were then assessed for social interaction and anxiety-like behavior. Adolescent enrichment caused rats to display more social interaction, as well as nominally less social avoidance, less submission during defeat, and resilience to the effects of social stress on corticosterone, in a manner that seemed more notable in bLRs. For bHRs, enrichment also caused greater aggression during a neutral social encounter and nominally during defeat, and decreased anxiety-like behavior. To explore the neurobiology underlying the development of social resilience in the anxious phenotype bLRs, RNA-seq was conducted on the hippocampus and nucleus accumbens, two brain regions that mediate stress regulation and social behavior. Gene sets previously associated with stress, social behavior, aggression and exploratory activity were enriched with differential expression in both regions, with a particularly large effect on gene sets that regulate social behaviors. Our findings provide further evidence that adolescent enrichment can serve as an inoculating experience against future stressors. The ability to induce social resilience in a usually anxious line of animals by manipulating their environment has translational implications, as it underscores the feasibility of intervention strategies targeted at genetically vulnerable adolescent populations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Huda Akil
- Univ. of Michigan, Ann Arbor, MI, USA
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11
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Godavarthi SK, Hiramoto M, Ignatyev Y, Levin JB, Li HQ, Pratelli M, Borchardt J, Czajkowski C, Borodinsky LN, Sweeney L, Cline HT, Spitzer NC. Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges. Proc Natl Acad Sci U S A 2024; 121:e2318041121. [PMID: 38568976 PMCID: PMC11009644 DOI: 10.1073/pnas.2318041121] [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: 10/17/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
Stable matching of neurotransmitters with their receptors is fundamental to synapse function and reliable communication in neural circuits. Presynaptic neurotransmitters regulate the stabilization of postsynaptic transmitter receptors. Whether postsynaptic receptors regulate stabilization of presynaptic transmitters has received less attention. Here, we show that blockade of endogenous postsynaptic acetylcholine receptors (AChR) at the neuromuscular junction destabilizes the cholinergic phenotype in motor neurons and stabilizes an earlier, developmentally transient glutamatergic phenotype. Further, expression of exogenous postsynaptic gamma-aminobutyric acid type A receptors (GABAA receptors) in muscle cells stabilizes an earlier, developmentally transient GABAergic motor neuron phenotype. Both AChR and GABAA receptors are linked to presynaptic neurons through transsynaptic bridges. Knockdown of specific components of these transsynaptic bridges prevents stabilization of the cholinergic or GABAergic phenotypes. Bidirectional communication can enforce a match between transmitter and receptor and ensure the fidelity of synaptic transmission. Our findings suggest a potential role of dysfunctional transmitter receptors in neurological disorders that involve the loss of the presynaptic transmitter.
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Affiliation(s)
- Swetha K. Godavarthi
- Neurobiology Department, University of California San Diego, La Jolla, CA92093
- Kavli Institute for Brain & Mind, University of California San Diego, La Jolla, CA92093
| | - Masaki Hiramoto
- Neuroscience Department, The Scripps Research Institute, La Jolla, CA92037
| | - Yuri Ignatyev
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
| | - Jacqueline B. Levin
- Department of Physiology & Membrane Biology Shriners Hospital for Children Northern California, University of California Davis School of Medicine, Sacramento, CA95817
| | - Hui-quan Li
- Neurobiology Department, University of California San Diego, La Jolla, CA92093
- Kavli Institute for Brain & Mind, University of California San Diego, La Jolla, CA92093
| | - Marta Pratelli
- Neurobiology Department, University of California San Diego, La Jolla, CA92093
- Kavli Institute for Brain & Mind, University of California San Diego, La Jolla, CA92093
| | - Jennifer Borchardt
- Neuroscience Department, University of Wisconsin Madison, Madison, WI53705
| | - Cynthia Czajkowski
- Neuroscience Department, University of Wisconsin Madison, Madison, WI53705
| | - Laura N. Borodinsky
- Department of Physiology & Membrane Biology Shriners Hospital for Children Northern California, University of California Davis School of Medicine, Sacramento, CA95817
| | - Lora Sweeney
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
| | - Hollis T. Cline
- Neuroscience Department, The Scripps Research Institute, La Jolla, CA92037
| | - Nicholas C. Spitzer
- Neurobiology Department, University of California San Diego, La Jolla, CA92093
- Kavli Institute for Brain & Mind, University of California San Diego, La Jolla, CA92093
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12
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Mincheva-Tasheva S, Pfitzner C, Kumar R, Kurtsdotter I, Scherer M, Ritchie T, Muhr J, Gecz J, Thomas PQ. Mapping combinatorial expression of non-clustered protocadherins in the developing brain identifies novel PCDH19-mediated cell adhesion properties. Open Biol 2024; 14:230383. [PMID: 38629124 PMCID: PMC11037505 DOI: 10.1098/rsob.230383] [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: 10/19/2023] [Revised: 01/25/2024] [Accepted: 02/29/2024] [Indexed: 04/19/2024] Open
Abstract
Non-clustered protocadherins (ncPcdhs) are adhesive molecules with spatio-temporally regulated overlapping expression in the developing nervous system. Although their unique role in neurogenesis has been widely studied, their combinatorial role in brain physiology and pathology is poorly understood. Using probabilistic cell typing by in situ sequencing, we demonstrate combinatorial inter- and intra-familial expression of ncPcdhs in the developing mouse cortex and hippocampus, at single-cell resolution. We discovered the combinatorial expression of Protocadherin-19 (Pcdh19), a protein involved in PCDH19-clustering epilepsy, with Pcdh1, Pcdh9 or Cadherin 13 (Cdh13) in excitatory neurons. Using aggregation assays, we demonstrate a code-specific adhesion function of PCDH19; mosaic PCDH19 absence in PCDH19+9 and PCDH19 + CDH13, but not in PCDH19+1 codes, alters cell-cell interaction. Interestingly, we found that PCDH19 as a dominant protein in two heterophilic adhesion codes could promote trans-interaction between them. In addition, we discovered increased CDH13-mediated cell adhesion in the presence of PCDH19, suggesting a potential role of PCDH19 as an adhesion mediator of CDH13. Finally, we demonstrated novel cis-interactions between PCDH19 and PCDH1, PCDH9 and CDH13. These observations suggest that there is a unique combinatorial code with a cell- and region-specific characteristic where a single molecule defines the heterophilic cell-cell adhesion properties of each code.
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Affiliation(s)
- Stefka Mincheva-Tasheva
- School of Biomedicine and Robinson Research Institute,
University of Adelaide, Adelaide, South Australia5005, Australia
- Genome Editing Program, South Australian Health and Medical
Research Institute, Adelaide, South Australia5000, Australia
| | - Chandran Pfitzner
- School of Biomedicine and Robinson Research Institute,
University of Adelaide, Adelaide, South Australia5005, Australia
- Genome Editing Program, South Australian Health and Medical
Research Institute, Adelaide, South Australia5000, Australia
| | - Raman Kumar
- School of Medicine and Robinson Research Institute, University
of Adelaide, Adelaide, South Australia5005, Australia
| | - Idha Kurtsdotter
- Department of Cell and Molecular Biology, Karolinska
Institute, Stockholm, Sweden
| | - Michaela Scherer
- School of Biomedicine and Robinson Research Institute,
University of Adelaide, Adelaide, South Australia5005, Australia
- Genome Editing Program, South Australian Health and Medical
Research Institute, Adelaide, South Australia5000, Australia
| | - Tarin Ritchie
- School of Medicine and Robinson Research Institute, University
of Adelaide, Adelaide, South Australia5005, Australia
| | - Jonas Muhr
- Department of Cell and Molecular Biology, Karolinska
Institute, Stockholm, Sweden
| | - Jozef Gecz
- School of Medicine and Robinson Research Institute, University
of Adelaide, Adelaide, South Australia5005, Australia
- South Australian Health and Medical Research
Institute, Adelaide, 5000 ,
Australia
| | - Paul Q. Thomas
- School of Biomedicine and Robinson Research Institute,
University of Adelaide, Adelaide, South Australia5005, Australia
- Genome Editing Program, South Australian Health and Medical
Research Institute, Adelaide, South Australia5000, Australia
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13
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Hung M, Lo HF, Beckmann AG, Demircioglu D, Damle G, Hasson D, Radice GL, Krauss RS. Cadherin-dependent adhesion is required for muscle stem cell niche anchorage and maintenance. Development 2024; 151:dev202387. [PMID: 38456551 PMCID: PMC11057819 DOI: 10.1242/dev.202387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/25/2024] [Indexed: 03/09/2024]
Abstract
Adhesion between stem cells and their niche provides stable anchorage and signaling cues to sustain properties such as quiescence. Skeletal muscle stem cells (MuSCs) adhere to an adjacent myofiber via cadherin-catenin complexes. Previous studies on N- and M-cadherin in MuSCs revealed that although N-cadherin is required for quiescence, they are collectively dispensable for MuSC niche localization and regenerative activity. Although additional cadherins are expressed at low levels, these findings raise the possibility that cadherins are unnecessary for MuSC anchorage to the niche. To address this question, we conditionally removed from MuSCs β- and γ-catenin, and, separately, αE- and αT-catenin, factors that are essential for cadherin-dependent adhesion. Catenin-deficient MuSCs break quiescence similarly to N-/M-cadherin-deficient MuSCs, but exit the niche and are depleted. Combined in vivo, ex vivo and single cell RNA-sequencing approaches reveal that MuSC attrition occurs via precocious differentiation, re-entry to the niche and fusion to myofibers. These findings indicate that cadherin-catenin-dependent adhesion is required for anchorage of MuSCs to their niche and for preservation of the stem cell compartment. Furthermore, separable cadherin-regulated functions govern niche localization, quiescence and MuSC maintenance.
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Affiliation(s)
- Margaret Hung
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hsiao-Fan Lo
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aviva G. Beckmann
- Pathos AI, 600 West Chicago Avenue, Suite 510, Chicago, IL 60654, USA
| | - Deniz Demircioglu
- Bioinformatics for Next Generation Sequencing Core, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gargi Damle
- Bioinformatics for Next Generation Sequencing Core, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Hasson
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Bioinformatics for Next Generation Sequencing Core, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Glenn L. Radice
- Cardiovascular Research Center, Department of Medicine, Division of Cardiology, Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Robert S. Krauss
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Bioinformatics for Next Generation Sequencing Core, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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14
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Chao G, Zukin S, Fortuna PRJ, Boettner B, Church GM. Progress and limitations in engineering cellular adhesion for research and therapeutics. Trends Cell Biol 2024; 34:277-287. [PMID: 37580241 DOI: 10.1016/j.tcb.2023.07.007] [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: 05/03/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/16/2023]
Abstract
Intercellular interactions form the cornerstone of multicellular biology. Despite advances in protein engineering, researchers artificially directing physical cell interactions still rely on endogenous cell adhesion molecules (CAMs) alongside off-target interactions and unintended signaling. Recently, methods for directing cellular interactions have been developed utilizing programmable domains such as coiled coils (CCs), nanobody-antigen, and single-stranded DNA (ssDNA). We first discuss desirable molecular- and systems-level properties in engineered CAMs, using the helixCAM platform as a benchmark. Next, we propose applications for engineered CAMs in immunology, developmental biology, tissue engineering, and neuroscience. Biologists in various fields can readily adapt current engineered CAMs to establish control over cell interactions, and their utilization in basic and translational research will incentivize further expansion in engineered CAM capabilities.
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Affiliation(s)
- George Chao
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Stefan Zukin
- Wyss Institute, Harvard Medical School, Boston, MA, USA
| | | | | | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Wyss Institute, Harvard Medical School, Boston, MA, USA.
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15
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Radenkovic S, Budhraja R, Klein-Gunnewiek T, King AT, Bhatia TN, Ligezka AN, Driesen K, Shah R, Ghesquière B, Pandey A, Kasri NN, Sloan SA, Morava E, Kozicz T. Neural and metabolic dysregulation in PMM2-deficient human in vitro neural models. Cell Rep 2024; 43:113883. [PMID: 38430517 DOI: 10.1016/j.celrep.2024.113883] [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: 08/25/2023] [Revised: 01/18/2024] [Accepted: 02/13/2024] [Indexed: 03/04/2024] Open
Abstract
Phosphomannomutase 2-congenital disorder of glycosylation (PMM2-CDG) is a rare inborn error of metabolism caused by deficiency of the PMM2 enzyme, which leads to impaired protein glycosylation. While the disorder presents with primarily neurological symptoms, there is limited knowledge about the specific brain-related changes caused by PMM2 deficiency. Here, we demonstrate aberrant neural activity in 2D neuronal networks from PMM2-CDG individuals. Utilizing multi-omics datasets from 3D human cortical organoids (hCOs) derived from PMM2-CDG individuals, we identify widespread decreases in protein glycosylation, highlighting impaired glycosylation as a key pathological feature of PMM2-CDG, as well as impaired mitochondrial structure and abnormal glucose metabolism in PMM2-deficient hCOs, indicating disturbances in energy metabolism. Correlation between PMM2 enzymatic activity in hCOs and symptom severity suggests that the level of PMM2 enzyme function directly influences neurological manifestations. These findings enhance our understanding of specific brain-related perturbations associated with PMM2-CDG, offering insights into the underlying mechanisms and potential directions for therapeutic interventions.
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Affiliation(s)
- Silvia Radenkovic
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Teun Klein-Gunnewiek
- Department of Human Genetics, Radboud University Medical Centre, 6525 XZ Nijmegen, the Netherlands
| | - Alexia Tyler King
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Tarun N Bhatia
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Anna N Ligezka
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Karen Driesen
- Metabolomics Expertise Center, VIB-KU Leuven, 3000 Leuven, Belgium
| | - Rameen Shah
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Bart Ghesquière
- Metabolomics Expertise Center, VIB-KU Leuven, 3000 Leuven, Belgium; Laboratory of Applied Mass Spectrometry, KU Leuven, 3000 Leuven, Belgium
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboud University Medical Centre, 6525 XZ Nijmegen, the Netherlands
| | - Steven A Sloan
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Biophysics, University of Pécs Medical School, 7624 Pécs, Hungary; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Tamas Kozicz
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; Department of Anatomy, University of Pécs Medical School, 7624 Pécs, Hungary; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA.
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16
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Jerabek T, Weiß L, Fahrion H, Zeh N, Raab N, Lindner B, Fischer S, Otte K. In pursuit of a minimal CHO genome: Establishment of large-scale genome deletions. N Biotechnol 2024; 79:100-110. [PMID: 38154614 DOI: 10.1016/j.nbt.2023.12.007] [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: 10/20/2023] [Revised: 11/27/2023] [Accepted: 12/24/2023] [Indexed: 12/30/2023]
Abstract
Chinese hamster ovary (CHO) cells are the most commonly used mammalian cell line for the production of complex therapeutic glycoproteins. As CHO cells have evolved as part of a multicellular organism, they harbor many cellular functions irrelevant for their application as production hosts in industrial bioprocesses. Consequently, CHO cells have been the target for numerous genetic engineering efforts in the past, but a tailored host cell chassis holistically optimized for its specific task in a bioreactor is still missing. While the concept of genome reduction has already been successfully applied to bacterial production cells, attempts to create higher eukaryotic production hosts exhibiting reduced genomes have not been reported yet. Here, we present the establishment and application of a large-scale genome deletion strategy for targeted excision of large genomic regions in CHO cells. We demonstrate the feasibility of genome reduction in CHO cells using optimized CRISPR/Cas9 based experimental protocols targeting large non-essential genomic regions with high efficiency. Achieved genome deletions of non-essential genetic regions did not introduce negative effects on bioprocess relevant parameters, although we conducted the largest reported genomic excision of 864 kilobase pairs in CHO cells so far. The concept presented serves as a directive to accelerate the development of a significantly genome-reduced CHO host cell chassis paving the way for a next generation of CHO cell factories.
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Affiliation(s)
- Tobias Jerabek
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany.
| | - Linus Weiß
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| | - Hannah Fahrion
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| | - Nikolas Zeh
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany; Boehringer Ingelheim Pharma GmbH & Co KG, Bioprocess Development Biologicals, Cell Line Development, Biberach, Germany
| | - Nadja Raab
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| | - Benjamin Lindner
- Boehringer Ingelheim Pharma GmbH & Co KG, Bioprocess Development Biologicals, Cell Line Development, Biberach, Germany
| | - Simon Fischer
- Boehringer Ingelheim Pharma GmbH & Co KG, Bioprocess Development Biologicals, Cell Line Development, Biberach, Germany
| | - Kerstin Otte
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
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17
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Meserve JH, Navarro MF, Ortiz EA, Granato M. Celsr3 drives development and connectivity of the acoustic startle hindbrain circuit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583806. [PMID: 38496637 PMCID: PMC10942420 DOI: 10.1101/2024.03.07.583806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
In the developing brain, groups of neurons organize into functional circuits that direct diverse behaviors. One such behavior is the evolutionarily conserved acoustic startle response, which in zebrafish is mediated by a well-defined hindbrain circuit. While numerous molecular pathways that guide neurons to their synaptic partners have been identified, it is unclear if and to what extent distinct neuron populations in the startle circuit utilize shared molecular pathways to ensure coordinated development. Here, we show that the planar cell polarity (PCP)-associated atypical cadherins Celsr3 and Celsr2, as well as the Celsr binding partner Frizzled 3a/Fzd3a, are critical for axon guidance of two neuron types that form synapses with each other: the command-like neuron Mauthner cells that drive the acoustic startle escape response, and spiral fiber neurons which provide excitatory input to Mauthner cells. We find that Mauthner axon growth towards synaptic targets is vital for Mauthner survival. We also demonstrate that symmetric spiral fiber input to Mauthner cells is critical for escape direction, which is necessary to respond to directional threats. Moreover, we identify distinct roles for Celsr3 and Celsr2, as Celsr3 is required for startle circuit development while Celsr2 is dispensable, though Celsr2 can partially compensate for loss of Celsr3 in Mauthner cells. This contrasts with facial branchiomotor neuron migration in the hindbrain, which requires Celsr2 while we find that Celsr3 is dispensable. Combined, our data uncover critical and distinct roles for individual PCP components during assembly of the acoustic startle hindbrain circuit.
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Affiliation(s)
- Joy H Meserve
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Maria F Navarro
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Elelbin A Ortiz
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael Granato
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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18
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Lu Q, Wang J, Tao Y, Zhong J, Zhang Z, Feng C, Wang X, Li T, He R, Wang Q, Xie Y. Small Cajal Body-Specific RNA12 Promotes Carcinogenesis through Modulating Extracellular Matrix Signaling in Bladder Cancer. Cancers (Basel) 2024; 16:483. [PMID: 38339238 PMCID: PMC10854576 DOI: 10.3390/cancers16030483] [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: 12/05/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Background: Small Cajal body-specific RNAs (scaRNAs) are a specific subset of small nucleolar RNAs (snoRNAs) that have recently emerged as pivotal contributors in diverse physiological and pathological processes. However, their defined roles in carcinogenesis remain largely elusive. This study aims to explore the potential function and mechanism of SCARNA12 in bladder cancer (BLCA) and to provide a theoretical basis for further investigations into the biological functionalities of scaRNAs. Materials and Methods: TCGA, GEO and GTEx data sets were used to analyze the expression of SCARNA12 and its clinicopathological significance in BLCA. Quantitative real-time PCR (qPCR) and in situ hybridization were applied to validate the expression of SCARNA12 in both BLCA cell lines and tissues. RNA sequencing (RNA-seq) combined with bioinformatics analyses were conducted to reveal the changes in gene expression patterns and functional pathways in BLCA patients with different expressions of SCARNA12 and T24 cell lines upon SCARNA12 knockdown. Single-cell mass cytometry (CyTOF) was then used to evaluate the tumor-related cell cluster affected by SCARNA12. Moreover, SCARNA12 was stably knocked down in T24 and UMUC3 cell lines by lentivirus-mediated CRISPR/Cas9 approach. The biological effects of SCARNA12 on the proliferation, clonogenic, migration, invasion, cell apoptosis, cell cycle, and tumor growth were assessed by in vitro MTT, colony formation, wound healing, transwell, flow cytometry assays, and in vivo nude mice xenograft models, respectively. Finally, a chromatin isolation by RNA purification (ChIRP) experiment was further conducted to delineate the potential mechanisms of SCARNA12 in BLCA. Results: The expression of SCARNA12 was significantly up-regulated in both BLCA tissues and cell lines. RNA-seq data elucidated that SCARAN12 may play a potential role in cell adhesion and extracellular matrix (ECM) related signaling pathways. CyTOF results further showed that an ECM-related cell cluster with vimentin+, CD13+, CD44+, and CD47+ was enriched in BLCA patients with high SCARNA12 expression. Additionally, SCARNA12 knockdown significantly inhibited the proliferation, colony formation, migration, and invasion abilities in T24 and UMUC3 cell lines. SCARNA12 knockdown prompted cell arrest in the G0/G1 and G2/M phase and promoted apoptosis in T24 and UMUC3 cell lines. Furthermore, SCARNA12 knockdown could suppress the in vivo tumor growth in nude mice. A ChIRP experiment further suggested that SCARNA12 may combine transcription factors H2AFZ to modulate the transcription program and then affect BLCA progression. Conclusions: Our study is the first to propose aberrant alteration of SCARNA12 and elucidate its potential oncogenic roles in BLCA via the modulation of ECM signaling. The interaction of SCARNA12 with the transcriptional factor H2AFZ emerges as a key contributor to the carcinogenesis and progression of BLCA. These findings suggest SCARNA12 may serve as a diagnostic biomarker and potential therapeutic target for the treatment of BLCA.
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Affiliation(s)
- Qinchen Lu
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (Q.L.); (J.W.)
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, China
| | - Jiandong Wang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (Q.L.); (J.W.)
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, China
| | - Yuting Tao
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
| | - Jialing Zhong
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;
| | - Chao Feng
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
| | - Xi Wang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
| | - Tianyu Li
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China;
| | - Rongquan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China;
| | - Qiuyan Wang
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China; (Y.T.); (J.Z.); (C.F.); (X.W.)
| | - Yuanliang Xie
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning 530021, China; (Q.L.); (J.W.)
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19
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Joshi D, Coon BG, Chakraborty R, Deng H, Fernandez-Tussy P, Meredith E, Traylor JG, Orr AW, Fernandez-Hernando C, Schwartz MA. Gamma protocadherins in vascular endothelial cells inhibit Klf2/4 to promote atherosclerosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575958. [PMID: 38293157 PMCID: PMC10827163 DOI: 10.1101/2024.01.16.575958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Atherosclerotic cardiovascular disease (ASCVD) is the leading cause of mortality worldwide1. Laminar shear stress (LSS) from blood flow in straight regions of arteries protects against ASCVD by upregulating the Klf2/4 anti-inflammatory program in endothelial cells (ECs)2-8. Conversely, disturbed shear stress (DSS) at curves or branches predisposes these regions to plaque formation9,10. We previously reported a whole genome CRISPR knockout screen11 that identified novel inducers of Klf2/4. Here we report suppressors of Klf2/4 and characterize one candidate, protocadherin gamma A9 (Pcdhga9), a member of the clustered protocadherin gene family12. Pcdhg deletion increases Klf2/4 levels in vitro and in vivo and suppresses inflammatory activation of ECs. Pcdhg suppresses Klf2/4 by inhibiting the Notch pathway via physical interaction of cleaved Notch1 intracellular domain (NICD Val1744) with nuclear Pcdhg C-terminal constant domain (CCD). Pcdhg inhibition by EC knockout (KO) or blocking antibody protects from atherosclerosis. Pcdhg is elevated in the arteries of human atherosclerosis. This study identifies a novel fundamental mechanism of EC resilience and therapeutic target for treating inflammatory vascular disease.
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Affiliation(s)
- Divyesh Joshi
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06511, USA
| | - Brian G Coon
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06511, USA
| | - Raja Chakraborty
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06511, USA
| | - Hanqiang Deng
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06511, USA
| | - Pablo Fernandez-Tussy
- Vascular Biology and Therapeutics Program, Yale University, New Haven, CT 06520, USA
| | - Emily Meredith
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06511, USA
| | - James G Traylor
- Department of Pathology and Translational Pathobiology, LSU Health Shreveport, LA 71103, USA
| | - Anthony Wayne Orr
- Department of Pathology and Translational Pathobiology, LSU Health Shreveport, LA 71103, USA
| | | | - Martin A Schwartz
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06511, USA
- Department of Cell Biology, Yale University, New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06510, USA
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Mukherjee S, Goswami S, Dash S, Samanta D. Structural basis of molecular recognition among classical cadherins mediating cell adhesion. Biochem Soc Trans 2023; 51:2103-2115. [PMID: 37970977 DOI: 10.1042/bst20230356] [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: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Cadherins are type-I membrane glycoproteins that primarily participate in calcium-dependent cell adhesion and homotypic cell sorting in various stages of embryonic development. Besides their crucial role in cellular and physiological processes, increasing studies highlight their involvement in pathophysiological functions ranging from cancer progression and metastasis to being entry receptors for pathogens. Cadherins mediate these cellular processes through homophilic, as well as heterophilic interactions (within and outside the superfamily) by their membrane distal ectodomains. This review provides an in-depth structural perspective of molecular recognition among type-I and type-II classical cadherins. Furthermore, this review offers structural insights into different dimeric assemblies like the 'strand-swap dimer' and 'X-dimer' as well as mechanisms relating these dimer forms like 'two-step adhesion' and 'encounter complex'. Alongside providing structural details, this review connects structural studies to bond mechanics merging crystallographic and single-molecule force spectroscopic findings. Finally, the review discusses the recent discoveries on dimeric intermediates that uncover prospects of further research beyond two-step adhesion.
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Affiliation(s)
- Sarbartha Mukherjee
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Saumyadeep Goswami
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Sagarika Dash
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Dibyendu Samanta
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
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Chess MM, Douglas W, Saunders J, Ettensohn CA. Genome-wide identification and spatiotemporal expression analysis of cadherin superfamily members in echinoderms. EvoDevo 2023; 14:15. [PMID: 38124068 PMCID: PMC10734073 DOI: 10.1186/s13227-023-00219-7] [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: 10/09/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Cadherins are calcium-dependent transmembrane cell-cell adhesion proteins that are essential for metazoan development. They consist of three subfamilies: classical cadherins, which bind catenin, protocadherins, which contain 6-7 calcium-binding repeat domains, and atypical cadherins. Their functions include forming adherens junctions, establishing planar cell polarity (PCP), and regulating cell shape, proliferation, and migration. Because they are basal deuterostomes, echinoderms provide important insights into bilaterian evolution, but their only well-characterized cadherin is G-cadherin, a classical cadherin that is expressed by many embryonic epithelia. We aimed to better characterize echinoderm cadherins by conducting phylogenetic analyses and examining the spatiotemporal expression patterns of cadherin-encoding genes during Strongylocentrotus purpuratus development. RESULTS Our phylogenetic analyses conducted on two echinoid, three asteroid, and one crinoid species identified ten echinoderm cadherins, including one deuterostome-specific ortholog, cadherin-23, and an echinoderm-specific atypical cadherin that possibly arose in an echinoid-asteroid ancestor. Catenin-binding domains in dachsous-2 orthologs were found to be a deuterostome-specific innovation that was selectively lost in mouse, while those in Fat4 orthologs appeared to be Ambulacraria-specific and were selectively lost in non-crinoid echinoderms. The identified suite of echinoderm cadherins lacks vertebrate-specific innovations but contains two proteins that are present in protostomes and absent from mouse. The spatiotemporal expression patterns of four embryonically expressed cadherins (fat atypical cadherins 1 and 4, dachsous-2, and protocadherin-9) were dynamic and mirrored the expression pattern of Frizzled 5/8, a non-canonical Wnt PCP pathway receptor protein essential for archenteron morphogenesis. CONCLUSIONS The echinoderm cadherin toolkit is more similar to that of an ancient bilaterian predating protostomes and deuterostomes than it is to the suite of cadherins found in extant vertebrates. However, it also appears that deuterostomes underwent several cadherin-related innovations. Based on their similar spatiotemporal expression patterns and orthologous relationships to PCP-related and tumor-suppressing proteins, we hypothesize that sea urchin cadherins may play a role in regulating the shape and growth of embryonic epithelia and organs. Future experiments will examine cadherin expression in non-echinoid echinoderms and explore the functions of cadherins during echinoderm development.
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Affiliation(s)
- Macie M Chess
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - William Douglas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Josiah Saunders
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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22
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Przybylowicz PK, Sokolowska KE, Rola H, Wojdacz TK. DNA Methylation Changes in Blood Cells of Fibromyalgia and Chronic Fatigue Syndrome Patients. J Pain Res 2023; 16:4025-4036. [PMID: 38054109 PMCID: PMC10695140 DOI: 10.2147/jpr.s439412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
Purpose Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) affect 0.4% and 1% of society, respectively, and the prevalence of these pain syndromes is increasing. To date, no strong association between these syndromes and the genetic background of affected individuals has been shown. Therefore, it is plausible that epigenetic changes might play a role in the development of these syndromes. Patients and Methods Three previous studies have attempted to elaborate the involvement of genome-wide methylation changes in blood cells in the development of fibromyalgia and chronic fatigue syndrome. These studies included 22 patients with fibromyalgia and 127 patients with CFS, and the results of the studies were largely discrepant. Contradicting results of those studies may be attributed to differences in the omics data analysis approaches used in each study. We reanalyzed the data collected in these studies using an updated and coherent data-analysis framework. Results Overall, the methylation changes that we observed overlapped with previous results only to some extent. However, the gene set enrichment analyses based on genes annotated to methylation changes identified in each of the analyzed datasets were surprisingly coherent and uniformly associated with the physiological processes that, when affected, may result in symptoms characteristic of fibromyalgia and chronic fatigue syndrome. Conclusion Methylomes of the blood cells of patients with FM and CFS in three independent studies have shown methylation changes that appear to be implicated in the pathogenesis of these syndromes.
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Affiliation(s)
| | | | - Hubert Rola
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Szczecin, Poland
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Martinez AP, Chung AC, Huang S, Bisogni AJ, Lin Y, Cao Y, Williams EO, Kim JY, Yang JY, Lin DM. Pcdh19 mediates olfactory sensory neuron coalescence during postnatal stages and regeneration. iScience 2023; 26:108220. [PMID: 37965156 PMCID: PMC10641745 DOI: 10.1016/j.isci.2023.108220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/12/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
The mouse olfactory system regenerates constantly throughout life. While genes critical for the initial projection of olfactory sensory neurons (OSNs) to the olfactory bulb have been identified, what genes are important for maintaining the olfactory map during regeneration are still unknown. Here we show a mutation in Protocadherin 19 (Pcdh19), a cell adhesion molecule and member of the cadherin superfamily, leads to defects in OSN coalescence during regeneration. Surprisingly, lateral glomeruli were more affected and males in particular showed a more severe phenotype. Single cell analysis unexpectedly showed OSNs expressing the MOR28 odorant receptor could be subdivided into two major clusters. We showed that at least one protocadherin is differentially expressed between OSNs coalescing on the medial and lateral glomeruli. Moreover, females expressed a slightly different complement of genes from males. These features may explain the differential effects of mutating Pcdh19 on medial and lateral glomeruli in males and females.
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Affiliation(s)
- Andrew P. Martinez
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Alexander C. Chung
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Suihong Huang
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Adam J. Bisogni
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Yingxin Lin
- School of Mathematics and Statistics, F07 University of Sydney, NSW 2006, Australia
| | - Yue Cao
- School of Mathematics and Statistics, F07 University of Sydney, NSW 2006, Australia
| | - Eric O. Williams
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Jin Y. Kim
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Jean Y.H. Yang
- School of Mathematics and Statistics, F07 University of Sydney, NSW 2006, Australia
| | - David M. Lin
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
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24
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Hecker M, Fitzner B, Boxberger N, Putscher E, Engelmann R, Bergmann W, Müller M, Ludwig-Portugall I, Schwartz M, Meister S, Dudesek A, Winkelmann A, Koczan D, Zettl UK. Transcriptome alterations in peripheral blood B cells of patients with multiple sclerosis receiving immune reconstitution therapy. J Neuroinflammation 2023; 20:181. [PMID: 37533036 PMCID: PMC10394872 DOI: 10.1186/s12974-023-02859-x] [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: 10/12/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic, inflammatory and neurodegenerative disease that leads to irreversible damage to the brain and spinal cord. The goal of so-called "immune reconstitution therapies" (IRTs) is to achieve long-term disease remission by eliminating a pathogenic immune repertoire through intense short-term immune cell depletion. B cells are major targets for effective immunotherapy in MS. OBJECTIVES The aim of this study was to analyze the gene expression pattern of B cells before and during IRT (i.e., before B-cell depletion and after B-cell repopulation) to better understand the therapeutic effects and to identify biomarker candidates of the clinical response to therapy. METHODS B cells were obtained from blood samples of patients with relapsing-remitting MS (n = 50), patients with primary progressive MS (n = 13) as well as healthy controls (n = 28). The patients with relapsing MS received either monthly infusions of natalizumab (n = 29) or a pulsed IRT with alemtuzumab (n = 15) or cladribine (n = 6). B-cell subpopulation frequencies were determined by flow cytometry, and transcriptome profiling was performed using Clariom D arrays. Differentially expressed genes (DEGs) between the patient groups and controls were examined with regard to their functions and interactions. We also tested for differences in gene expression between patients with and without relapse following alemtuzumab administration. RESULTS Patients treated with alemtuzumab or cladribine showed on average a > 20% lower proportion of memory B cells as compared to before IRT. This was paralleled by profound transcriptome shifts, with > 6000 significant DEGs after adjustment for multiple comparisons. The top DEGs were found to regulate apoptosis, cell adhesion and RNA processing, and the most highly connected nodes in the network of encoded proteins were ESR2, PHB and RC3H1. Higher mRNA levels of BCL2, IL13RA1 and SLC38A11 were seen in patients with relapse despite IRT, though these differences did not pass the false discovery rate correction. CONCLUSIONS We show that B cells circulating in the blood of patients with MS undergoing IRT present a distinct gene expression signature, and we delineated the associated biological processes and gene interactions. Moreover, we identified genes whose expression may be an indicator of relapse risk, but further studies are needed to verify their potential value as biomarkers.
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Affiliation(s)
- Michael Hecker
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany.
| | - Brit Fitzner
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Nina Boxberger
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Elena Putscher
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Robby Engelmann
- Clinic III (Hematology, Oncology and Palliative Medicine), Special Hematology Laboratory, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Wendy Bergmann
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Michael Müller
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | | | - Margit Schwartz
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Stefanie Meister
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Ales Dudesek
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Alexander Winkelmann
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Dirk Koczan
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Uwe Klaus Zettl
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
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25
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Hewitt SC, Gruzdev A, Willson CJ, Wu SP, Lydon JP, Galjart N, DeMayo FJ. Chromatin architectural factor CTCF is essential for progesterone-dependent uterine maturation. FASEB J 2023; 37:e23103. [PMID: 37489832 PMCID: PMC10372848 DOI: 10.1096/fj.202300862r] [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: 05/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023]
Abstract
Receptors for estrogen and progesterone frequently interact, via Cohesin/CTCF loop extrusion, at enhancers distal from regulated genes. Loss-of-function CTCF mutation in >20% of human endometrial tumors indicates its importance in uterine homeostasis. To better understand how CTCF-mediated enhancer-gene interactions impact endometrial development and function, the Ctcf gene was selectively deleted in female reproductive tissues of mice. Prepubertal Ctcfd/d uterine tissue exhibited a marked reduction in the number of uterine glands compared to those without Ctcf deletion (Ctcff/f mice). Post-pubertal Ctcfd/d uteri were hypoplastic with significant reduction in both the amount of the endometrial stroma and number of glands. Transcriptional profiling revealed increased expression of stem cell molecules Lif, EOMES, and Lgr5, and enhanced inflammation pathways following Ctcf deletion. Analysis of the response of the uterus to steroid hormone stimulation showed that CTCF deletion affects a subset of progesterone-responsive genes. This finding indicates (1) Progesterone-mediated signaling remains functional following Ctcf deletion and (2) certain progesterone-regulated genes are sensitive to Ctcf deletion, suggesting they depend on gene-enhancer interactions that require CTCF. The progesterone-responsive genes altered by CTCF ablation included Ihh, Fst, and Errfi1. CTCF-dependent progesterone-responsive uterine genes enhance critical processes including anti-tumorigenesis, which is relevant to the known effectiveness of progesterone in inhibiting progression of early-stage endometrial tumors. Overall, our findings reveal that uterine Ctcf plays a key role in progesterone-dependent expression of uterine genes underlying optimal post-pubertal uterine development.
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Affiliation(s)
| | | | | | - San-Pin Wu
- Pregnancy & Female Reproduction, DIR RDBL, NIEHS RTP, NC
| | | | - Niels Galjart
- Dept. of Cell Biology, Erasmus MC, Rotterdam, Netherlands
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26
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Jovanovic M, Mitra A, Besio R, Contento BM, Wong KW, Derkyi A, To M, Forlino A, Dale RK, Marini JC. Absence of TRIC-B from type XIV Osteogenesis Imperfecta osteoblasts alters cell adhesion and mitochondrial function - A multi-omics study. Matrix Biol 2023; 121:127-148. [PMID: 37348683 PMCID: PMC10634967 DOI: 10.1016/j.matbio.2023.06.004] [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: 03/03/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/24/2023]
Abstract
Osteogenesis Imperfecta (OI) is a heritable collagen-related bone dysplasia characterized by bone fractures, growth deficiency and skeletal deformity. Type XIV OI is a recessive OI form caused by null mutations in TMEM38B, which encodes the ER membrane intracellular cation channel TRIC-B. Previously, we showed that absence of TMEM38B alters calcium flux in the ER of OI patient osteoblasts and fibroblasts, which further disrupts collagen synthesis and secretion. How the absence of TMEM38B affects osteoblast function is still poorly understood. Here we further investigated the role of TMEM38B in human osteoblast differentiation and mineralization. TMEM38B-null osteoblasts showed altered expression of osteoblast marker genes and decreased mineralization. RNA-Seq analysis revealed that cell-cell adhesion was one of the most downregulated pathways in TMEM38B-null osteoblasts, with further validation by real-time PCR and Western blot. Gap and tight junction proteins were also decreased by TRIC-B absence, both in patient osteoblasts and in calvarial osteoblasts of Tmem38b-null mice. Disrupted cell adhesion decreased mutant cell proliferation and cell cycle progression. An important novel finding was that TMEM38B-null osteoblasts had elongated mitochondria with altered fusion and fission markers, MFN2 and DRP1. In addition, TMEM38B-null osteoblasts exhibited a significant increase in superoxide production in mitochondria, further supporting mitochondrial dysfunction. Together these results emphasize the novel role of TMEM38B/TRIC-B in osteoblast differentiation, affecting cell-cell adhesion processes, gap and tight junction, proliferation, cell cycle, and mitochondrial function.
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Affiliation(s)
- Milena Jovanovic
- Section on Heritable Disorders of Bone and Extracellular Matrix, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Apratim Mitra
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Roberta Besio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | | | - Ka Wai Wong
- Department of Orthopaedics and Traumatology, The University of Hong Kong-Shenzhen Hospital (HKU-SZH), Shenzhen, China; Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alberta Derkyi
- Office of the Clinical Director, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Michael To
- Department of Orthopaedics and Traumatology, The University of Hong Kong-Shenzhen Hospital (HKU-SZH), Shenzhen, China; Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Joan C Marini
- Section on Heritable Disorders of Bone and Extracellular Matrix, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States.
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27
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Zhen Y, Pavez M, Li X. The role of Pcdh10 in neurological disease and cancer. J Cancer Res Clin Oncol 2023; 149:8153-8164. [PMID: 37058252 PMCID: PMC10374755 DOI: 10.1007/s00432-023-04743-w] [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: 03/06/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
BACKGROUND Protocadherin 10 (PCDH 10), a member of the superfamily of protocadherins, is a Ca2+-dependent homophilic cell-cell adhesion molecule expressed on the surface of cell membranes. Protocadherin 10 plays a critical role in the central nervous system including in cell adhesion, formation and maintenance of neural circuits and synapses, regulation of actin assembly, cognitive function and tumor suppression. Additionally, Pcdh10 can serve as a non-invasive diagnostic and prognostic indicator for various cancers. METHODS This paper collects and reviews relevant literature in Pubmed. CONCLUSION This review describes the latest research understanding the role of Pcdh10 in neurological disease and human cancer, highlighting the importance of scrutinizing its properties for the development of targeted therapies and identifying a need for further research to explore Pcdh10 functions in other pathways, cell types and human pathologies.
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Affiliation(s)
- Yilan Zhen
- Menzies Institute for Medical Research, University of Tasmania, Liverpool street, Hobart, 7000, Australia
| | - Macarena Pavez
- Department of Anatomy, University of Otago, Dunedin, Otago, New Zealand.
| | - Xinying Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China.
- School of Life Sciences, Anhui Medical University, Hefei, People's Republic of China.
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28
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Huang S, Xie Z, Han J, Wang H, Yang G, Li M, Zhou G, Wang Y, Li L, Li L, Zeng Z, Yu J, Chen M, Zhang S. Protocadherin 20 maintains intestinal barrier function to protect against Crohn's disease by targeting ATF6. Genome Biol 2023; 24:159. [PMID: 37407995 DOI: 10.1186/s13059-023-02991-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Intestinal barrier dysfunction plays a central role in the pathological onset of Crohn's disease. We identify the cadherin superfamily member protocadherin 20 (PCDH20) as a crucial factor in Crohn's disease. Here we describe the function of PCDH20 and its mechanisms in gut homeostasis, barrier integrity, and Crohn's disease development. RESULTS PCDH20 mRNA and protein expression is significantly downregulated in the colonic epithelium of Crohn's disease patients and mice with induced colitis compared with controls. In mice, intestinal-specific Pcdh20 knockout causes defects in enterocyte proliferation and differentiation, while causing morphological abnormalities. Specifically, the deletion disrupts barrier integrity by unzipping adherens junctions via β-catenin regulation and p120-catenin phosphorylation, thus aggravating colitis in DSS- and TNBS-induced colitis mouse models. Furthermore, we identify activating transcription factor 6 (ATF6), a key chaperone of endoplasmic reticulum stress, as a functional downstream effector of PCDH20. By administering a selective ATF6 activator, the impairment of intestinal barrier integrity and dysregulation of CHOP/β-catenin/p-p120-catenin pathway was reversed in Pcdh20-ablated mice with colitis and PCDH20-deficient colonic cell lines. CONCLUSIONS PCDH20 is an essential factor in maintaining intestinal epithelial homeostasis and barrier integrity. Specifically, PCDH20 helps to protect against colitis by tightening adherens junctions through the ATF6/CHOP/β-catenin/p-p120-catenin axis.
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Affiliation(s)
- Shanshan Huang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Zhuo Xie
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Jing Han
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Huiling Wang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, Henan Province, People's Republic of China
- People's Hospital of Henan University, Kaifeng, 475000, Henan Province, People's Republic of China
| | - Guang Yang
- Department of Minimally Invasive & Interventional Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong Province, People's Republic of China
| | - Manying Li
- Department of Medical Ultrasonics, Institute of Diagnostic and Interventional Ultrasound, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Gaoshi Zhou
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Ying Wang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Lixuan Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Li Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, 999077, People's Republic of China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China.
| | - Shenghong Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan II Road, Guangzhou, 510080, Guangdong Province, People's Republic of China.
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Mısır E, Akay GG. Synaptic dysfunction in schizophrenia. Synapse 2023:e22276. [PMID: 37210696 DOI: 10.1002/syn.22276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/25/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Schizophrenia is a chronic disease presented with psychotic symptoms, negative symptoms, impairment in the reward system, and widespread neurocognitive deterioration. Disruption of synaptic connections in neural circuits is responsible for the disease's development and progression. Because deterioration in synaptic connections results in the impaired effective processing of information. Although structural impairments of the synapse, such as a decrease in dendritic spine density, have been shown in previous studies, functional impairments have also been revealed with the development of genetic and molecular analysis methods. In addition to abnormalities in protein complexes regulating exocytosis in the presynaptic region and impaired vesicle release, especially, changes in proteins related to postsynaptic signaling have been reported. In particular, impairments in postsynaptic density elements, glutamate receptors, and ion channels have been shown. At the same time, effects on cellular adhesion molecular structures such as neurexin, neuroligin, and cadherin family proteins were detected. Of course, the confusing effect of antipsychotic use in schizophrenia research should also be considered. Although antipsychotics have positive and negative effects on synapses, studies indicate synaptic deterioration in schizophrenia independent of drug use. In this review, the deterioration in synapse structure and function and the effects of antipsychotics on the synapse in schizophrenia will be discussed.
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Affiliation(s)
- Emre Mısır
- Department of Psychiatry, Baskent University Faculty of Medicine, Ankara, Turkey
- Department of Interdisciplinary Neuroscience, Ankara University, Ankara, Turkey
| | - Güvem Gümüş Akay
- Department of Interdisciplinary Neuroscience, Ankara University, Ankara, Turkey
- Faculty of Medicine, Department of Physiology, Ankara University, Ankara, Turkey
- Brain Research Center (AÜBAUM), Ankara University, Ankara, Turkey
- Department of Cellular Neuroscience and Advanced Microscopic Neuroimaging, Neuroscience and Neurotechnology Center of Excellence (NÖROM), Ankara, Turkey
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Hershkovits AS, Gelley S, Hanna R, Kleifeld O, Shulman A, Fishman A. Shifting the balance: soluble ADAM10 as a potential treatment for Alzheimer's disease. Front Aging Neurosci 2023; 15:1171123. [PMID: 37266401 PMCID: PMC10229884 DOI: 10.3389/fnagi.2023.1171123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/20/2023] [Indexed: 06/03/2023] Open
Abstract
Introduction Accumulation of amyloid β in the brain is regarded as a key initiator of Alzheimer's disease pathology. Processing of the amyloid precursor protein (APP) in the amyloidogenic pathway yields neurotoxic amyloid β species. In the non-amyloidogenic pathway, APP is processed by membrane-bound ADAM10, the main α-secretase in the nervous system. Here we present a new enzymatic approach for the potential treatment of Alzheimer's disease using a soluble form of ADAM10. Methods The ability of the soluble ADAM10 to shed overexpressed and endogenous APP was determined with an ADAM10 knockout cell line and a human neuroblastoma cell line, respectively. We further examined its effect on amyloid β aggregation by thioflavin T fluorescence, HPLC, and confocal microscopy. Using N-terminal and C-terminal enrichment proteomic approaches, we identified soluble ADAM10 substrates. Finally, a truncated soluble ADAM10, based on the catalytic domain, was expressed in Escherichia coli for the first time, and its activity was evaluated. Results The soluble enzyme hydrolyzes APP and releases the neuroprotective soluble APPα when exogenously added to cell cultures. The soluble ADAM10 inhibits the formation and aggregation of characteristic amyloid β extracellular neuronal aggregates. The proteomic investigation identified new and verified known substrates, such as VGF and N-cadherin, respectively. The truncated variant also exhibited α-secretase capacity as shown with a specific ADAM10 fluorescent substrate in addition to shedding overexpressed and endogenous APP. Discussion Our in vitro study demonstrates that exogenous treatment with a soluble variant of ADAM10 would shift the balance toward the non-amyloidogenic pathway, thus utilizing its natural neuroprotective effect and inhibiting the main neurotoxic amyloid β species. The potential of such a treatment for Alzheimer's disease needs to be further evaluated in vivo.
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Affiliation(s)
- Ayelet Sarah Hershkovits
- Department of Biotechnology and Food Engineering Technion-Israel Institute of Technology, Haifa, Israel
- The Interdisciplinary Program for Biotechnology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Sivan Gelley
- Department of Biotechnology and Food Engineering Technion-Israel Institute of Technology, Haifa, Israel
| | - Rawad Hanna
- Department of Biology Technion-Israel Institute of Technology, Haifa, Israel
| | - Oded Kleifeld
- Department of Biology Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Ayelet Fishman
- Department of Biotechnology and Food Engineering Technion-Israel Institute of Technology, Haifa, Israel
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Višnić A, Čanadi Jurešić G, Domitrović R, Klarić M, Šepić TS, Barišić D. Proteins in urine - Possible biomarkers of endometriosis. J Reprod Immunol 2023; 157:103941. [PMID: 36948095 DOI: 10.1016/j.jri.2023.103941] [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: 01/21/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
In the pathogenesis of endometriosis, a number of pathological reactions occur. Proteins secreted in the urine are thought to interact with each other and stimulate the pathological processes in endometriosis. Identifying one or more proteins that are specific enough and could serve as biomarkers for endometriosis is both a challenge and a necessity that would facilitate diagnosis. The urine of patients treated in a tertiary university hospital between July 1, 2020 and June 30, 2021 was analyzed. The studied group consists of patients who were treated surgically for endometriosis and in whom the diagnosis was confirmed by pathohistological analysis. The control group consists of patients who were operated for functional ovarian cysts. Urinary proteins were analyzed by chromatography and mass spectrometry (LC-MS/MS). We identified 17 proteins in urine whose concentrations were statistically significantly different in the group with endometriosis (N = 16) compared with the control groups (N = 16). The detected proteins were classified into groups according to their function in invasion, migration and proliferation, proteolysis, immune system, cell adhesion and vascular system. For all mentioned proteins the difference in concentration is statistically significant p < 0.005. Proteins are secreted in the urine of patients with endometriosis that may be involved in the pathogenesis of the disease and are possible biomarkers for endometriosis.
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Affiliation(s)
- Alenka Višnić
- Clinical Hospital Center Rijeka, Clinic for Gynecology and Obstetrics, Rijeka, Croatia
| | - Gordana Čanadi Jurešić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University in Rijeka, Rijeka, Croatia.
| | - Robert Domitrović
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University in Rijeka, Rijeka, Croatia
| | - Marko Klarić
- Clinical Hospital Center Rijeka, Clinic for Gynecology and Obstetrics, Rijeka, Croatia
| | - Tina Sušanj Šepić
- Clinical Hospital Center Rijeka, Clinic for Gynecology and Obstetrics, Rijeka, Croatia
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PCDH19 in Males: Are Hemizygous Variants Linked to Autism? Genes (Basel) 2023; 14:genes14030598. [PMID: 36980870 PMCID: PMC10048232 DOI: 10.3390/genes14030598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/09/2023] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
Background: Autism spectrum disorder (ASD) is a complex developmental disability that impairs the social communication and interaction of affected individuals and leads to restricted or repetitive behaviors or interests. ASD is genetically heterogeneous, with inheritable and de novo genetic variants in more than hundreds of genes contributing to the disease. However, these account for only around 20% of cases, while the molecular basis of the majority of cases remains unelucidated as of yet. Material and methods: Two unrelated Lebanese patients, a 7-year-old boy (patient A) and a 4-year-old boy (patient B), presenting with ASD were included in this study. Whole-exome sequencing (WES) was carried out for these patients to identify the molecular cause of their diseases. Results: WES analysis revealed hemizygous variants in PCDH19 (NM_001184880.1) as being the candidate causative variants: p.Arg787Leu was detected in patient A and p.Asp1024Asn in patient B. PCDH19, located on chromosome X, encodes a membrane glycoprotein belonging to the protocadherin family. Heterozygous PCDH19 variants have been linked to epilepsy in females with mental retardation (EFMR), while mosaic PCDH19 mutations in males are responsible for treatment-resistant epilepsy presenting similarly to EFMR, with some reported cases of comorbid intellectual disability and autism. Interestingly, a hemizygous PCDH19 variant affecting the same amino acid that is altered in patient A was previously reported in a male patient with ASD. Conclusion: Here, we report hemizygous PCDH19 variants in two males with autism without epilepsy. Reporting further PCDH19 variants in male patients with ASD is important to assess the possible involvement of this gene in autism.
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Du J, Wu K. PCDHA1 High Expression is Associated With Poor Prognosis and Correlated With Immune Cell Infiltration in Breast Cancer. Clin Breast Cancer 2023; 23:397-407. [PMID: 36858841 DOI: 10.1016/j.clbc.2023.02.001] [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: 07/11/2022] [Revised: 01/28/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023]
Abstract
INTRODUCTION Breast cancer (BC) remains one of the biggest threats to women's health. Protocadherin gene Protocadherin Alpha 1 (PCDHA1) is abnormally highly expressed in breast cancer tissues. However, the biological role of PCDHA1 in breast cancer has not been fully elucidated and the relationship with the immune microenvironment needs to be further studied. MATERIALS AND METHODS TCGA-BRCA gene expression profiles were used to characterize PCDHA1. Kaplan-Meier method was used to estimate PCDHA1 prognosis potential. Gene set enrichment analysis (GSEA) analysis was performed to determine the signaling pathways altered by PCDHA1 aberrant expression. The correlations between PCDHA1 and immune cell infiltration levels were analyzed by CIBERSORT. Wilcoxon's rank-sum test was used to identify chemokine and chemokine receptors significantly associated with PCDHA1. The CCK8 assay and the transwell invasion assay were occupied to evaluate the effect of PCDHA1 overexpression on BC cells. RESULTS Survival analysis revealed PCDHA1 overexpression was associated with poor prognosis in BC. Enrichment analysis uncovered several metabolism pathways were activated by PCDHA1 overexpression. Moreover, PCDHA1 was positively correlated with activated NK cells but negatively correlated with resting NK cells infiltration. In addition, chemokines CCL28, CXCL17, and receptor CCR9 expression were associated with PCDHA1 overexpression. The CCK8 assay and the transwell invasion assay proved that PCDHA1 overexpression enhanced MCF-7 and MDA-MB-231 cell proliferation and invasion. CONCLUSION This study demonstrated that PCDHA1 effectively predicted BC prognosis. Upregulated PCDHA1 activated metabolism pathways, and promoted NK cells and chemokines. PCDHA1 overexpression enhanced BC cell proliferation and invasion. Therefore, an understanding of PCDHA1's function in BC may yield insights into the mechanisms of BC development.
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Affiliation(s)
- Jiawei Du
- Ultrasonography Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Kaidi Wu
- Ultrasonography Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China.
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34
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Liu H, Liu Y, Jin SG, Johnson J, Xuan H, Lu D, Li J, Zhai L, Li X, Zhao Y, Liu M, Craig SEL, Floramo JS, Molchanov V, Li J, Li JD, Krawczyk C, Shi X, Pfeifer GP, Yang T. TRIM28 secures skeletal stem cell fate during skeletogenesis by silencing neural gene expression and repressing GREM1/AKT/mTOR signaling axis. Cell Rep 2023; 42:112012. [PMID: 36680774 DOI: 10.1016/j.celrep.2023.112012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/16/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Long bones are generated by mesoderm-derived skeletal progenitor/stem cells (SSCs) through endochondral ossification, a process of sequential chondrogenic and osteogenic differentiation tightly controlled by the synergy between intrinsic and microenvironment cues. Here, we report that loss of TRIM28, a transcriptional corepressor, in mesoderm-derived cells expands the SSC pool, weakens SSC osteochondrogenic potential, and endows SSCs with properties of ectoderm-derived neural crest cells (NCCs), leading to severe defects of skeletogenesis. TRIM28 preferentially enhances H3K9 trimethylation and DNA methylation on chromatin regions more accessible in NCCs; loss of this silencing upregulates neural gene expression and enhances neurogenic potential. Moreover, TRIM28 loss causes hyperexpression of GREM1, which is an extracellular signaling factor promoting SSC self-renewal and SSC neurogenic potential by activating AKT/mTORC1 signaling. Our results suggest that TRIM28-mediated chromatin silencing establishes a barrier for maintaining the SSC lineage trajectory and preventing a transition to ectodermal fate by regulating both intrinsic and microenvironment cues.
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Affiliation(s)
- Huadie Liu
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ye Liu
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jennifer Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Hongwen Xuan
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Di Lu
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jianshuang Li
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Lukai Zhai
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Xianfeng Li
- Hunan International Scientific and Technological Cooperation Base of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Yaguang Zhao
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA; Hunan International Scientific and Technological Cooperation Base of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Minmin Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Sonya E L Craig
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Joseph S Floramo
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Vladimir Molchanov
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jie Li
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jia-Da Li
- Hunan International Scientific and Technological Cooperation Base of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Connie Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Xiaobing Shi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Tao Yang
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI 49503, USA.
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Dionisi C, Chazalon M, Rai M, Keime C, Imbault V, Communi D, Puccio H, Schiffmann SN, Pandolfo M. Proprioceptors-enriched neuronal cultures from induced pluripotent stem cells from Friedreich ataxia patients show altered transcriptomic and proteomic profiles, abnormal neurite extension, and impaired electrophysiological properties. Brain Commun 2023; 5:fcad007. [PMID: 36865673 PMCID: PMC9972525 DOI: 10.1093/braincomms/fcad007] [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: 04/13/2022] [Revised: 09/28/2022] [Accepted: 01/14/2023] [Indexed: 01/19/2023] Open
Abstract
Friedreich ataxia is an autosomal recessive multisystem disorder with prominent neurological manifestations and cardiac involvement. The disease is caused by large GAA expansions in the first intron of the FXN gene, encoding the mitochondrial protein frataxin, resulting in downregulation of gene expression and reduced synthesis of frataxin. The selective loss of proprioceptive neurons is a hallmark of Friedreich ataxia, but the cause of the specific vulnerability of these cells is still unknown. We herein perform an in vitro characterization of human induced pluripotent stem cell-derived sensory neuronal cultures highly enriched for primary proprioceptive neurons. We employ neurons differentiated from healthy donors, Friedreich ataxia patients and Friedreich ataxia sibling isogenic control lines. The analysis of the transcriptomic and proteomic profile suggests an impairment of cytoskeleton organization at the growth cone, neurite extension and, at later stages of maturation, synaptic plasticity. Alterations in the spiking profile of tonic neurons are also observed at the electrophysiological analysis of mature neurons. Despite the reversal of the repressive epigenetic state at the FXN locus and the restoration of FXN expression, isogenic control neurons retain many features of Friedreich ataxia neurons. Our study suggests the existence of abnormalities affecting proprioceptors in Friedreich ataxia, particularly their ability to extend towards their targets and transmit proper synaptic signals. It also highlights the need for further investigations to better understand the mechanistic link between FXN silencing and proprioceptive degeneration in Friedreich ataxia.
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Affiliation(s)
| | | | - Myriam Rai
- Laboratory of Experimental Neurology, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Céline Keime
- Institut de Génétique et de Biologie Moléculaire et Cellulaire UMR 7104 CNRS-UdS / INSERM U1258, Université de Strasbourg, 67404 Illkirch Cedex, Strasbourg, France
| | - Virginie Imbault
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - David Communi
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Hélène Puccio
- Institut de Génétique et de Biologie Moléculaire et Cellulaire UMR 7104 CNRS-UdS / INSERM U1258, Université de Strasbourg, 67404 Illkirch Cedex, Strasbourg, France,Institut NeuroMyoGene (INMG) UMR5310—INSERM U1217, Faculté de Médecine, Université Claude Bernard—Lyon I, 69008 Lyon, France
| | - Serge N Schiffmann
- Laboratory of Neurophysiology, ULB-Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Massimo Pandolfo
- Correspondence to: Massimo Pandolfo Department of Neurology and Neurosurgery McGill University, Montreal Neurological Institute 3801 University Street, Montreal, Quebec H3A 2B4, Canada E-mail:
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Mao X, Grigsby KB, Kelty TJ, Kerr NR, Childs TE, Booth FW. Transcriptomic analysis reveals novel molecular signaling networks involved in low voluntary running behavior after AP-1 inhibition. Neuroscience 2023; 509:173-186. [PMID: 36395916 DOI: 10.1016/j.neuroscience.2022.11.008] [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: 05/23/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Understanding the neuro-molecular mechanisms that mediate the quantity of daily physical activity (PA) level is of medical significance, given the tremendous health benefits associated with greater physical activity. Here, we examined the effects of intra-nucleus accumbens (NAc) inhibition of activator protein-1 (AP-1), an important transcriptional factor downstream of cAMP response element binding protein (CREB; a reward-related transcriptional regulator), on voluntary wheel running behavior in wild-type (WT) and low voluntary running (LVR) female rats. Transcriptome analysis of the nucleus accumbens (NAc; a brain region critical for PA reward and motivation) was performed to further determine molecular responses to intra-NAc AP-1 inhibition in these rat lines. Within WT rats, intra-NAc AP-1 inhibition caused a significant decrease in overnight running distance in comparison to control rats (p = 0.009). Transcriptomic and bioinformatic analysis in WT rats identified involvement of gene products that regulate cellular proliferation and development, which were cellular processes regulated by AP-1. In contrast to above decreased WT distances, intra-NAc AP-1 inhibition in LVR rats increased nightly running distance in comparison to LVR control rats (p = 0.0008). Further analysis identified gene products that are associated with regulating intracellular Ca2+ homeostasis, calcium ion binding and neuronal excitability. In short, our study aims to gain a comprehensive understanding of transcriptional profile that was due to AP-1 inhibition in NAc, in which it could not only enhance the knowledge regarding molecular regulatory loops within NAc for modulating voluntary running behavior, but also provide further insights into molecular targets for future investigations.
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Affiliation(s)
- Xuansong Mao
- Department of Biomedical Sciences, University of Missouri, Columbia 65211, MO, USA
| | - Kolter B Grigsby
- Department of Biomedical Sciences, University of Missouri, Columbia 65211, MO, USA
| | - Taylor J Kelty
- Department of Biomedical Sciences, University of Missouri, Columbia 65211, MO, USA
| | - Nathan R Kerr
- Department of Biomedical Sciences, University of Missouri, Columbia 65211, MO, USA
| | - Thomas E Childs
- Department of Biomedical Sciences, University of Missouri, Columbia 65211, MO, USA
| | - Frank W Booth
- Department of Biomedical Sciences, University of Missouri, Columbia 65211, MO, USA; Department of Nutrition and Exercise Physiology, University of Missouri, Columbia 65211, MO, USA; Department of Medical Pharmacology and Physiology, University of Missouri, Columbia 65211, MO, USA; Dalton Cardiovascular Research Center, University of Missouri, Columbia 65211, MO, USA.
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37
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Using Single-Cell RNA Sequencing and MicroRNA Targeting Data to Improve Colorectal Cancer Survival Prediction. Cells 2023; 12:cells12020228. [PMID: 36672162 PMCID: PMC9856396 DOI: 10.3390/cells12020228] [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: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Colorectal cancer has proven to be difficult to treat as it is the second leading cause of cancer death for both men and women worldwide. Recent work has shown the importance of microRNA (miRNA) in the progression and metastasis of colorectal cancer. Here, we develop a metric based on miRNA-gene target interactions, previously validated to be associated with colorectal cancer. We use this metric with a regularized Cox model to produce a small set of top-performing genes related to colon cancer. We show that using the miRNA metric and a Cox model led to a meaningful improvement in colon cancer survival prediction and correct patient risk stratification. We show that our approach outperforms existing methods and that the top genes identified by our process are implicated in NOTCH3 signaling and general metabolism pathways, which are essential to colon cancer progression.
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38
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Burek M, Kaupp V, Blecharz-Lang K, Dilling C, Meybohm P. Protocadherin gamma C3: a new player in regulating vascular barrier function. Neural Regen Res 2023. [PMID: 35799511 PMCID: PMC9241426 DOI: 10.4103/1673-5374.343896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Defects in the endothelial cell barrier accompany diverse malfunctions of the central nervous system such as neurodegenerative diseases, stroke, traumatic brain injury, and systemic diseases such as sepsis, viral and bacterial infections, and cancer. Compromised endothelial sealing leads to leaking blood vessels, followed by vasogenic edema. Brain edema as the most common complication caused by stroke and traumatic brain injury is the leading cause of death. Brain microvascular endothelial cells, together with astrocytes, pericytes, microglia, and neurons form a selective barrier, the so-called blood-brain barrier, which regulates the movement of molecules inside and outside of the brain. Mechanisms that regulate blood-brain barrier permeability in health and disease are complex and not fully understood. Several newly discovered molecules that are involved in the regulation of cellular processes in brain microvascular endothelial cells have been described in the literature in recent years. One of these molecules that are highly expressed in brain microvascular endothelial cells is protocadherin gamma C3. In this review, we discuss recent evidence that protocadherin gamma C3 is a newly identified key player involved in the regulation of vascular barrier function.
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39
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Styfhals R, Zolotarov G, Hulselmans G, Spanier KI, Poovathingal S, Elagoz AM, De Winter S, Deryckere A, Rajewsky N, Ponte G, Fiorito G, Aerts S, Seuntjens E. Cell type diversity in a developing octopus brain. Nat Commun 2022; 13:7392. [PMID: 36450803 PMCID: PMC9712504 DOI: 10.1038/s41467-022-35198-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
Octopuses are mollusks that have evolved intricate neural systems comparable with vertebrates in terms of cell number, complexity and size. The brain cell types that control their sophisticated behavioral repertoire are still unknown. Here, we profile the cell diversity of the paralarval Octopus vulgaris brain to build a cell type atlas that comprises mostly neural cells, but also multiple glial subtypes, endothelial cells and fibroblasts. We spatially map cell types to the vertical, subesophageal and optic lobes. Investigation of cell type conservation reveals a shared gene signature between glial cells of mouse, fly and octopus. Genes related to learning and memory are enriched in vertical lobe cells, which show molecular similarities with Kenyon cells in Drosophila. We construct a cell type taxonomy revealing transcriptionally related cell types, which tend to appear in the same brain region. Together, our data sheds light on cell type diversity and evolution in the octopus brain.
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Affiliation(s)
- Ruth Styfhals
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Grygoriy Zolotarov
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115, Berlin, Germany
| | - Gert Hulselmans
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | - Katina I Spanier
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | | | - Ali M Elagoz
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | - Astrid Deryckere
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
- Department of Biological Sciences, Columbia University, New York, US
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Stein Aerts
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
- VIB Center for Brain & Disease Research, KU Leuven, Leuven, 3000, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium.
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Carrier A, Desjobert C, Lobjois V, Rigal L, Busato F, Tost J, Ensenyat-Mendez M, Marzese DM, Pradines A, Favre G, Lamant L, Lanfrancone L, Etievant C, Arimondo PB, Riond J. Epigenetically regulated PCDHB15 impairs aggressiveness of metastatic melanoma cells. Clin Epigenetics 2022; 14:156. [PMID: 36443814 PMCID: PMC9707039 DOI: 10.1186/s13148-022-01364-x] [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: 06/06/2022] [Accepted: 10/25/2022] [Indexed: 11/29/2022] Open
Abstract
The protocadherin proteins are cell adhesion molecules at the crossroad of signaling pathways playing a major role in neuronal development. It is now understood that their role as signaling hubs is not only important for the normal physiology of cells but also for the regulation of hallmarks of cancerogenesis. Importantly, protocadherins form a cluster of genes that are regulated by DNA methylation. We have identified for the first time that PCDHB15 gene is DNA-hypermethylated on its unique exon in the metastatic melanoma-derived cell lines and patients' metastases compared to primary tumors. This DNA hypermethylation silences the gene, and treatment with the DNA demethylating agent 5-aza-2'-deoxycytidine reinduces its expression. We explored the role of PCDHB15 in melanoma aggressiveness and showed that overexpression impairs invasiveness and aggregation of metastatic melanoma cells in vitro and formation of lung metastasis in vivo. These findings highlight important modifications of the methylation of the PCDHβ genes in melanoma and support a functional role of PCDHB15 silencing in melanoma aggressiveness.
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Affiliation(s)
- Arnaud Carrier
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France ,Cancer Epigenetics Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Cécile Desjobert
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France
| | - Valérie Lobjois
- grid.508721.9Institut des Technologies Avancées en Sciences du Vivant – ITAV-USR3505, CNRS, Université de Toulouse, Université Paul Sabatier-UT3, Toulouse, France ,grid.15781.3a0000 0001 0723 035XLaboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, CNRS UMR 5088, Université Paul Sabatier-UT3, Toulouse, France
| | - Lise Rigal
- grid.508721.9Institut des Technologies Avancées en Sciences du Vivant – ITAV-USR3505, CNRS, Université de Toulouse, Université Paul Sabatier-UT3, Toulouse, France
| | - Florence Busato
- grid.460789.40000 0004 4910 6535Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humain, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, France
| | - Jörg Tost
- grid.460789.40000 0004 4910 6535Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humain, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, France
| | - Miquel Ensenyat-Mendez
- grid.507085.fCancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d’Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Diego M. Marzese
- grid.507085.fCancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d’Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Anne Pradines
- grid.15781.3a0000 0001 0723 035XInserm, CNRS, Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Université Toulouse III-Paul Sabatier, Toulouse, France ,grid.417829.10000 0000 9680 0846Laboratoire de Biologie Médicale Oncologique, Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Gilles Favre
- grid.15781.3a0000 0001 0723 035XInserm, CNRS, Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Université Toulouse III-Paul Sabatier, Toulouse, France ,grid.417829.10000 0000 9680 0846Laboratoire de Biologie Médicale Oncologique, Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Laurence Lamant
- grid.488470.7Laboratoire d’Anatomopathologie, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France
| | - Luisa Lanfrancone
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology, Instituto Europeo di Oncologia, Via Adamello 16, 20139 Milan, Italy
| | - Chantal Etievant
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France
| | - Paola B. Arimondo
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France ,grid.428999.70000 0001 2353 6535EpiCBio, Epigenetic Chemical Biology, Department Structural Biology and Chemistry, CNRS UMR N°3523, Institut Pasteur, 28 Rue du Dr Roux, 75015 Paris, France
| | - Joëlle Riond
- Unité de Service et de Recherche USR n°3388 CNRS-Pierre Fabre, Epigenetic Targeting of Cancer (ETaC), Toulouse, France ,grid.15781.3a0000 0001 0723 035XInserm, CNRS, Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Université Toulouse III-Paul Sabatier, Toulouse, France
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Pancho A, Mitsogiannis MD, Aerts T, Dalla Vecchia M, Ebert LK, Geenen L, Noterdaeme L, Vanlaer R, Stulens A, Hulpiau P, Staes K, Van Roy F, Dedecker P, Schermer B, Seuntjens E. Modifying PCDH19 levels affects cortical interneuron migration. Front Neurosci 2022; 16:887478. [PMID: 36389226 PMCID: PMC9642031 DOI: 10.3389/fnins.2022.887478] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2023] Open
Abstract
PCDH19 is a transmembrane protein and member of the protocadherin family. It is encoded by the X-chromosome and more than 200 mutations have been linked to the neurodevelopmental PCDH-clustering epilepsy (PCDH19-CE) syndrome. A disturbed cell-cell contact that arises when random X-inactivation creates mosaic absence of PCDH19 has been proposed to cause the syndrome. Several studies have shown roles for PCDH19 in neuronal proliferation, migration, and synapse function, yet most of them have focused on cortical and hippocampal neurons. As epilepsy can also be caused by impaired interneuron migration, we studied the role of PCDH19 in cortical interneurons during embryogenesis. We show that cortical interneuron migration is affected by altering PCDH19 dosage by means of overexpression in brain slices and medial ganglionic eminence (MGE) explants. We also detect subtle defects when PCDH19 expression was reduced in MGE explants, suggesting that the dosage of PCDH19 is important for proper interneuron migration. We confirm this finding in vivo by showing a mild reduction in interneuron migration in heterozygote, but not in homozygote PCDH19 knockout animals. In addition, we provide evidence that subdomains of PCDH19 have a different impact on cell survival and interneuron migration. Intriguingly, we also observed domain-dependent differences in migration of the non-targeted cell population in explants, demonstrating a non-cell-autonomous effect of PCDH19 dosage changes. Overall, our findings suggest new roles for the extracellular and cytoplasmic domains of PCDH19 and support that cortical interneuron migration is dependent on balanced PCDH19 dosage.
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Affiliation(s)
- Anna Pancho
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuela D. Mitsogiannis
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Tania Aerts
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Marco Dalla Vecchia
- Laboratory for NanoBiology, Department of Chemistry, KU Leuven, Leuven, Belgium
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Lena K. Ebert
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Cologne Cluster of Excellence on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Lieve Geenen
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
- Laboratory of Neuroplasticity and Neuroproteomics, Animal Physiology and Neurobiology Division, Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lut Noterdaeme
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Ria Vanlaer
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Anne Stulens
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Paco Hulpiau
- Department of Biomedical Molecular Biology, Ghent University, Inflammation Research Center, VIB, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- BioInformatics Knowledge Center (BiKC), Howest University of Applied Sciences, Bruges, Belgium
| | - Katrien Staes
- Department of Biomedical Molecular Biology, Ghent University, Inflammation Research Center, VIB, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Frans Van Roy
- Department of Biomedical Molecular Biology, Ghent University, Inflammation Research Center, VIB, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Peter Dedecker
- Laboratory for NanoBiology, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Cologne Cluster of Excellence on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Eve Seuntjens
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
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Abstract
Since the proposal of the differential adhesion hypothesis, scientists have been fascinated by how cell adhesion mediates cellular self-organization to form spatial patterns during development. The search for molecular tool kits with homophilic binding specificity resulted in a diverse repertoire of adhesion molecules. Recent understanding of the dominant role of cortical tension over adhesion binding redirects the focus of differential adhesion studies to the signaling function of adhesion proteins to regulate actomyosin contractility. The broader framework of differential interfacial tension encompasses both adhesion and nonadhesion molecules, sharing the common function of modulating interfacial tension during cell sorting to generate diverse tissue patterns. Robust adhesion-based patterning requires close coordination between morphogen signaling, cell fate decisions, and changes in adhesion. Current advances in bridging theoretical and experimental approaches present exciting opportunities to understand molecular, cellular, and tissue dynamics during adhesion-based tissue patterning across multiple time and length scales.
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Affiliation(s)
- Tony Y-C Tsai
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Rikki M Garner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA;
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA;
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Molecular Classification of Hepatocellular Carcinoma Using Wnt-Hippo Signaling Pathway-Related Genes. Cancers (Basel) 2022; 14:cancers14194580. [PMID: 36230503 PMCID: PMC9559216 DOI: 10.3390/cancers14194580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 12/05/2022] Open
Abstract
Simple Summary The characters of Taiwanese hepatocellular carcinoma (HCC) are different from other parts of the world. We characterized the molecular features of HCC using a newly developed classification system based on the expression of the Wnt–Hippo signaling pathway-related genes. We analyzed the data in terms of prognostic value, transcriptome features, immune infiltration, and clinical characteristics, and compared the resulting subclasses with previously published classifications. A new molecular classification method based on a 272 gene panel of Wnt–Hippo pathways that may provide a new target for the treatment. Abstract In Taiwan, a combination of hepatitis B and C infection, economic boom-related food and alcohol overconsumption, and Chinese medicine prescriptions has led to a high rate of hepatocellular carcinoma (HCC). However, the causative factors and underlying tumor biology for this unique HCC environment have not been identified. Wnt and Hippo signaling pathways play an important regulatory role in HCC development, and their functions are generally considered as positive and negative regulators of cell proliferation, respectively. In this study, we characterized the molecular features of HCC using a newly developed classification system based on the expression of the Wnt–Hippo signaling pathway-related genes. RNA sequencing (RNA-Seq) was performed on liver tumor tissues from 100 patients with liver cancer. RNA-Seq data for 272 previously characterized Wnt–Hippo signaling pathway-related genes were used for hierarchical clustering. We analyzed the data in terms of prognostic value, transcriptome features, immune infiltration, and clinical characteristics, and compared the resulting subclasses with previously published classifications. Four subclasses of HCC (HCCW1–4) were identified. Subclass HCCW1 displayed the highest PCDHB4 expression. Subclass HCCW2 displayed lower Edmondson–Steiner grades (I and II) and CTNNB1 mutation frequencies. Subclass HCCW3 was associated with a good prognosis, the highest PCDHGB7 expression, high CD8+ naïve T cells abundance, and relatively low TP53 mutation rates. Subclass HCCW4 was associated with a poor prognosis, the highest PCDHB2 and PCDHB6 expression, a relatively high abundance of Th1 cells, NKT and class-switched memory B cells, relatively low enrichment of cDC, iDC, and CD4+ memory T cells, and high Edmondson–Steiner grades (III and IV). We also identified Wnt–Hippo signaling pathway-related genes that may influence immune cell infiltration. We developed a panel of 272 Wnt–Hippo signaling pathway-related genes to classify HCC into four groups based on Taiwanese HCC and The Cancer Genome Atlas Liver Hepatocellular Carcinoma datasets. This novel molecular classification system may aid the treatment of HCC.
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Pan-cancer analysis of co-occurring mutations in RAD52 and the BRCA1-BRCA2-PALB2 axis in human cancers. PLoS One 2022; 17:e0273736. [PMID: 36107942 PMCID: PMC9477347 DOI: 10.1371/journal.pone.0273736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
In human cells homologous recombination (HR) is critical for repair of DNA double strand breaks (DSBs) and rescue of stalled or collapsed replication forks. HR is facilitated by RAD51 which is loaded onto DNA by either BRCA2-BRCA1-PALB2 or RAD52. In human culture cells, double-knockdowns of RAD52 and genes in the BRCA1-BRCA2-PALB2 axis are lethal. Mutations in BRCA2, BRCA1 or PALB2 significantly impairs error free HR as RAD51 loading relies on RAD52 which is not as proficient as BRCA2-BRCA1-PALB2. RAD52 also facilitates Single Strand Annealing (SSA) that produces intra-chromosomal deletions. Some RAD52 mutations that affect the SSA function or decrease RAD52 association with DNA can suppress certain BRCA2 associated phenotypes in breast cancers. In this report we did a pan-cancer analysis using data reported on the Catalogue of Somatic Mutations in Cancers (COSMIC) to identify double mutants between RAD52 and BRCA1, BRCA2 or PALB2 that occur in cancer cells. We find that co-occurring mutations are likely in certain cancer tissues but not others. However, all mutations occur in a heterozygous state. Further, using computational and machine learning tools we identified only a handful of pathogenic or driver mutations predicted to significantly affect the function of the proteins. This supports previous findings that co-inactivation of RAD52 with any members of the BRCA2-BRCA1-PALB2 axis is lethal. Molecular modeling also revealed that pathogenic RAD52 mutations co-occurring with mutations in BRCA2-BRCA1-PALB2 axis are either expected to attenuate its SSA function or its interaction with DNA. This study extends previous breast cancer findings to other cancer types and shows that co-occurring mutations likely destabilize HR by similar mechanisms as in breast cancers.
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Luo W, Cruz-Ochoa NA, Seng C, Egger M, Lukacsovich D, Lukacsovich T, Földy C. Pcdh11x controls target specification of mossy fiber sprouting. Front Neurosci 2022; 16:888362. [PMID: 36117624 PMCID: PMC9475199 DOI: 10.3389/fnins.2022.888362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Circuit formation is a defining characteristic of the developing brain. However, multiple lines of evidence suggest that circuit formation can also take place in adults, the mechanisms of which remain poorly understood. Here, we investigated the epilepsy-associated mossy fiber (MF) sprouting in the adult hippocampus and asked which cell surface molecules define its target specificity. Using single-cell RNAseq data, we found lack and expression of Pcdh11x in non-sprouting and sprouting neurons respectively. Subsequently, we used CRISPR/Cas9 genome editing to disrupt the Pcdh11x gene and characterized its consequences on sprouting. Although MF sprouting still developed, its target specificity was altered. New synapses were frequently formed on granule cell somata in addition to dendrites. Our findings shed light onto a key molecular determinant of target specificity in MF sprouting and contribute to understanding the molecular mechanism of adult brain rewiring.
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Liu Y, Zhang Y, Du D, Gu X, Zhou S. PCDH17 is regulated by methylation of DNMT3B and affects the malignant biological behavior of HCC through EMT. Exp Cell Res 2022; 418:113245. [DOI: 10.1016/j.yexcr.2022.113245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/19/2022] [Accepted: 06/04/2022] [Indexed: 11/26/2022]
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Protocadherin 15 suppresses oligodendrocyte progenitor cell proliferation and promotes motility through distinct signalling pathways. Commun Biol 2022; 5:511. [PMID: 35637313 PMCID: PMC9151716 DOI: 10.1038/s42003-022-03470-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/10/2022] [Indexed: 12/15/2022] Open
Abstract
Oligodendrocyte progenitor cells (OPCs) express protocadherin 15 (Pcdh15), a member of the cadherin superfamily of transmembrane proteins. Little is known about the function of Pcdh15 in the central nervous system (CNS), however, Pcdh15 expression can predict glioma aggression and promote the separation of embryonic human OPCs immediately following a cell division. Herein, we show that Pcdh15 knockdown significantly increases extracellular signal-related kinase (ERK) phosphorylation and activation to enhance OPC proliferation in vitro. Furthermore, Pcdh15 knockdown elevates Cdc42-Arp2/3 signalling and impairs actin kinetics, reducing the frequency of lamellipodial extrusion and slowing filopodial withdrawal. Pcdh15 knockdown also reduces the number of processes supported by each OPC and new process generation. Our data indicate that Pcdh15 is a critical regulator of OPC proliferation and process motility, behaviours that characterise the function of these cells in the healthy CNS, and provide mechanistic insight into the role that Pcdh15 might play in glioma progression. Protocadherin 15 promotes lamellipodial and filopodial dynamics in oligodendrocyte progenitor cells by regulating Cdc42-Arp2/3 activity, but also suppresses ERK1/2 phosphorylation to reduce proliferation.
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Notter DR, Heidaritabar M, Burke JM, Shirali M, Murdoch BM, Morgan JLM, Morota G, Sonstegard TS, Becker GM, Spangler GL, MacNeil MD, Miller JE. Single Nucleotide Polymorphism Effects on Lamb Fecal Egg Count Estimated Breeding Values in Progeny-Tested Katahdin Sires. Front Genet 2022; 13:866176. [PMID: 35591856 PMCID: PMC9110833 DOI: 10.3389/fgene.2022.866176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/14/2022] [Indexed: 01/31/2023] Open
Abstract
Estimated breeding values (EBV) for fecal egg counts (FEC) at 42–90 days of age (WFEC) and 91–150 days of age (PFEC) for 84 progeny-tested Katahdin sires were used to identify associations of deregressed EBV with single-nucleotide polymorphisms (SNP) using 388,000 SNP with minor-allele frequencies ≥0.10 on an Illumina high-density ovine array. Associations between markers and FEC EBV were initially quantified by single-SNP linear regression. Effects of linkage disequilibrium (LD) were minimized by assigning SNP to 2,535 consecutive 1-Mb bins and focusing on the effect of the most significant SNP in each bin. Bonferroni correction was used to define bin-based (BB) genome- and chromosome-wide significance. Six bins on chromosome 5 achieved BB genome-wide significance for PFEC EBV, and three of those SNP achieved chromosome-wide significance after Bonferroni correction based on the 14,530 total SNP on chromosome 5. These bins were nested within 12 consecutive bins between 59 and 71 Mb on chromosome 5 that reached BB chromosome-wide significance. The largest SNP effects were at 63, 67, and 70 Mb, with LD among these SNP of r2 ≤ 0.2. Regional heritability mapping (RHM) was then used to evaluate the ability of different genomic regions to account for additive variance in FEC EBV. Chromosome-level RHM indicated that one 500-SNP window between 65.9 and 69.9 Mb accounted for significant variation in PFEC EBV. Five additional 500-SNP windows between 59.3 and 71.6 Mb reached suggestive (p < 0.10) significance for PFEC EBV. Although previous studies rarely identified markers for parasite resistance on chromosome 5, the IL12B gene at 68.5 Mb codes for the p40 subunit of both interleukins 12 and 23. Other immunoregulatory genes are also located in this region of chromosome 5, providing opportunity for additive or associative effects.
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Affiliation(s)
- David R. Notter
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: David R. Notter,
| | - Marzieh Heidaritabar
- Livestock Gentec, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Joan M. Burke
- United States Department of Agriculture, Agricultural Research Service, Dale Bumpers Small Farms Research Center, Booneville, AR, United States
| | - Masoud Shirali
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Brenda M. Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | | | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Gabrielle M. Becker
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Gordon L. Spangler
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Michael D. MacNeil
- Delta G, Miles City, MT, United States
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - James E. Miller
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
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Kleinberger I, Sanders E, Staes K, Van Troys M, Hirano S, Hochepied T, Lemeire K, Martens L, Ampe C, van Roy F. Innovative mouse models for the tumor suppressor activity of Protocadherin-10 isoforms. BMC Cancer 2022; 22:451. [PMID: 35468745 PMCID: PMC9040349 DOI: 10.1186/s12885-022-09381-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/02/2022] [Indexed: 11/12/2022] Open
Abstract
Background Nonclustered mouse protocadherin genes (Pcdh) encode proteins with a typical single ectodomain and a cytoplasmic domain with conserved motifs completely different from those of classic cadherins. Alternative splice isoforms differ in the size of these cytoplasmic domains. In view of the compelling evidence for gene silencing of protocadherins in human tumors, we started investigations on Pcdh functions in mouse cancer models. Methods For Pcdh10, we generated two mouse lines: one with floxed exon 1, leading to complete Pcdh10 ablation upon Cre action, and one with floxed exons 2 and 3, leading to ablation of only the long isoforms of Pcdh10. In a mouse medulloblastoma model, we used GFAP-Cre action to locally ablate Pcdh10 in combination with Trp53 and Rb1 ablation. From auricular tumors, that also arose, we obtained tumor-derived cell lines, which were analyzed for malignancy in vitro and in vivo. By lentiviral transduction, we re-expressed Pcdh10 cDNAs. RNA-Seq analyses were performed on these cell families. Results Surprisingly, not only medulloblastomas were generated in our model but also tumors of tagged auricles (pinnae). For both tumor types, ablation of either all or only long isoforms of Pcdh10 aggravated the disease. We argued that the perichondrial stem cell compartment is at the origin of the pinnal tumors. Immunohistochemical analysis of these tumors revealed different subtypes. We obtained several pinnal-tumor derived (PTD) cell lines and analyzed these for anchorage-independent growth, invasion into collagen matrices, tumorigenicity in athymic mice. Re-expression of either the short or a long isoform of Pcdh10 in two PTD lines counteracted malignancy in all assays. RNA-Seq analyses of these two PTD lines and their respective Pcdh10-rescued cell lines allowed to identify many interesting differentially expressed genes, which were largely different in the two cell families. Conclusions A new mouse model was generated allowing for the first time to examine the remarkable tumor suppression activity of protocadherin-10 in vivo. Despite lacking several conserved motifs, the short isoform of Pcdh10 was fully active as tumor suppressor. Our model contributes to scrutinizing the complex molecular mechanisms of tumor initiation and progression upon PCDH10 silencing in many human cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09381-y.
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Affiliation(s)
- Irene Kleinberger
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Ellen Sanders
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Katrien Staes
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Marleen Van Troys
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052, Ghent, Belgium
| | - Shinji Hirano
- Department of Cell Biology, Kansai Medical University, Hirakata City, Osaka, 573-1010, Japan
| | - Tino Hochepied
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Kelly Lemeire
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Liesbet Martens
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium.,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium
| | - Christophe Ampe
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052, Ghent, Belgium
| | - Frans van Roy
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium. .,VIB-UGent Center for Inflammation Research (IRC), VIB, 9052, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), 9052, Ghent, Belgium.
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50
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Sun H, Xu J, Hu B, Liu Y, Zhai Y, Sun Y, Sun H, Li F, Wang J, Feng A, Tang Y, Zhao J. Association of DNA Methylation Patterns in 7 Novel Genes With Ischemic Stroke in the Northern Chinese Population. Front Genet 2022; 13:844141. [PMID: 35480311 PMCID: PMC9035884 DOI: 10.3389/fgene.2022.844141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Ischemic stroke is a highly complex disorder. This study aims to identify novel methylation changes in ischemic stroke.Methods: We carried out an epigenome-wide study of ischemic stroke using an Infinium HumanMethylation 850K array (cases:controls = 4:4). 10 CpG sites in 8 candidate genes from gene ontology analytics top-ranked pathway were selected to validate 850K BeadChip results (cases:controls = 20:20). We further qualified the methylation level of promoter regions in 8 candidate genes (cases:controls = 188:188). Besides, we performed subgroup analysis, dose-response relationship and diagnostic prediction polygenic model of candidate genes.Results: In the discovery stage, we found 462 functional DNA methylation positions to be associated with ischemic stroke. Gene ontology analysis highlighted the “calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules” item, including 8 candidate genes (CDH2/PCDHB10/PCDHB11/PCDHB14/PCDHB16/PCDHB3/PCDHB6/PCDHB9). In the replication stage, we identified 5 differentially methylated loci in 20 paired samples and 7 differentially methylated genes (CDH2/PCDHB10/PCDHB11/PCDHB14/PCDHB16/PCDHB3/PCDHB9) in 188 paired samples. Subgroup analysis showed that the methylation level of above 7 genes remained significantly different in the male subgroup, large-artery atherosclerosis subgroup and right hemisphere subgroup. The methylation level of each gene was grouped into quartiles, and Q4 groups of the 7 genes were associated with higher risk of ischemic stroke than Q1 groups (p < 0.05). Besides, the polygenic model showed high diagnostic specificity (0.8723), sensitivity (0.883), and accuracy (0.8777).Conclusion: Our results demonstrate that DNA methylation plays a crucial part in ischemic stroke. The methylation of these 7 genes may be potential diagnostic biomarker for ischemic stroke.
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Affiliation(s)
- Hongwei Sun
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jia Xu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Bifeng Hu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yue Liu
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yun Zhai
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanyan Sun
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongwei Sun
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fang Li
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiamin Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Anqi Feng
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Ying Tang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Jingbo Zhao, ; Ying Tang,
| | - Jingbo Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
- *Correspondence: Jingbo Zhao, ; Ying Tang,
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