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Yan B, Gong B, Zheng Y, Sun L, Wu X. Embryonic Lethal Phenotyping to Identify Candidate Genes Related with Birth Defects. Int J Mol Sci 2024; 25:8788. [PMID: 39201474 PMCID: PMC11354474 DOI: 10.3390/ijms25168788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/04/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Congenital birth defects contribute significantly to preterm birth, stillbirth, perinatal death, infant mortality, and adult disability. As a first step to exploring the mechanisms underlying this major clinical challenge, we analyzed the embryonic phenotypes of lethal strains generated by random mutagenesis. In this study, we report the gross embryonic and perinatal phenotypes of 55 lethal strains randomly picked from a collection of mutants that carry piggyBac (PB) transposon inserts. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested most of the analyzed mutations hit genes involved in heart and nervous development, or in Notch and Wnt signaling. Among them, 12 loci are known to be associated with human diseases. We confirmed 53 strains as embryonic or perinatal lethal, while others were subviable. Gross morphological phenotypes such as body size abnormality (29/55, 52.73%), growth or developmental delay (35/55, 63.64%), brain defects (9/55, 16.36%), vascular/heart development (31/55, 56.36%), and other structural defects (9/55, 16.36%) could be easily observed in the mutants, while three strains showed phenotypes similar to those of human patients. Furthermore, we detected body weight or body composition alterations in the heterozygotes of eight strains. One of them was the TGF-β signaling gene Smad2. The heterozygotes showed increased energy expenditure and a lower fat-to-body weight ratio compared to wild-type mice. This study provided new insights into mammalian embryonic development and will help understand the pathology of congenital birth defects in humans. In addition, it expanded our understanding of the etiology of obesity.
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Affiliation(s)
| | | | | | - Lei Sun
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200441, China; (B.Y.); (B.G.); (Y.Z.)
| | - Xiaohui Wu
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200441, China; (B.Y.); (B.G.); (Y.Z.)
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2
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Imamura I, Kiyama R. Potential involvement of KANK1 haploinsufficiency in centrosome aberrations. Biochim Biophys Acta Gen Subj 2024; 1868:130648. [PMID: 38830559 DOI: 10.1016/j.bbagen.2024.130648] [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: 12/21/2023] [Revised: 05/04/2024] [Accepted: 05/24/2024] [Indexed: 06/05/2024]
Abstract
KANK1 was found as a tumor suppressor gene based on frequent deletions in renal cell carcinoma and the inhibitory activity of tumor cell proliferation. Previously, we reported that knockdown of KANK1 induced centrosomal amplification, leading to abnormal cell division, through the hyperactivation of RhoA small GTPase. Here, we investigated the loss of KANK1 function by performing CRISPR/Cas9-based genome editing to knockout the gene. After several rounds of genome editing, however, there were no cell lines with complete loss of KANK1, and the less the wild-type KANK1 dosage, the greater the number of cells with abnormal numbers of centrosomes and rates of cell-doubling and apoptosis, suggesting the involvement of KANK1 haploinsufficiency in centrosome aberrations. The rescue of KANK1-knockdown cells with a KANK1-expressing plasmid restored the rates of cells exhibiting centrosomal amplification to the control level. RNA-sequencing analysis of the cells with reduced dosages of functional KANK1 revealed potential involvement of other cell proliferation-related genes, such as EGR1, MDGA2, and BMP3, which have been reported to show haploinsufficiency when they function. When EGR1 protein expression was reduced by siRNA technology, the number of cells exhibiting centrosomal amplification increased, along with the reduction of KANK1 protein expression, suggesting their functional relationship. Thus, KANK1 haploinsufficiency may contribute to centrosome aberrations through the network of haploinsufficiency-related genes.
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Affiliation(s)
- Ikumi Imamura
- Faculty of Life Science, Kyushu Sangyo University, Japan
| | - Ryoiti Kiyama
- Faculty of Life Science, Kyushu Sangyo University, Japan.
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3
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Han Y, Han J, Li Z, Chen S, Liu J, Zhou R, Zhao S, Li D, Liu Z, Zhao Y, Hao J, Chai G. Identification and characterization of a novel intronic splicing mutation in CSF1R-related leukoencephalopathy. CNS Neurosci Ther 2024; 30:e14815. [PMID: 38922778 PMCID: PMC11194178 DOI: 10.1111/cns.14815] [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: 10/25/2023] [Revised: 04/16/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024] Open
Abstract
AIMS Colony stimulating factor 1 receptor (CSF1R)-related leukoencephalopathy is a rapidly progressing neurodegenerative disease caused by CSF1R gene mutations. This study aimed to identify and investigate the effect of a novel intronic mutation (c.1754-3C>G) of CSF1R on splicing. METHODS A novel intronic mutation was identified using whole-exome sequencing. To investigate the impact of this mutation, we employed various bioinformatics tools to analyze the transcription of the CSF1R gene and the three-dimensional structure of its encoded protein. Furthermore, reverse transcription polymerase chain reaction (RT-PCR) was performed to validate the findings. RESULTS A novel mutation (c.1754-3C>G) in CSF1R was identified, which results in exon 13 skipping due to the disruption of the 3' splice site consensus sequence NYAG/G. This exon skipping event was further validated in the peripheral blood of the mutation carrier through RT-PCR and Sanger sequencing. Protein structure prediction indicated a disruption in the tyrosine kinase domain, with the truncated protein showing significant structural alterations. CONCLUSIONS Our findings underscore the importance of intronic mis-splicing mutations in the diagnosis and management of CSF1R-related leukoencephalopathy.
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Affiliation(s)
- Yilai Han
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Jinming Han
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Zhen Li
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Siqi Chen
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Ju Liu
- Department of NeurologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Ruxing Zhou
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Shufang Zhao
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Dawei Li
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Zheng Liu
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Yinan Zhao
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Junwei Hao
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
- Beijing Municipal Geriatric Medical Research CenterBeijingChina
- Key Laboratory for Neurodegenerative Diseases of Ministry of EducationBeijingChina
| | - Guoliang Chai
- Department of NeurologyXuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
- Beijing Municipal Geriatric Medical Research CenterBeijingChina
- Chinese Institutes for Medical ResearchBeijingChina
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4
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Shen S, Sobczyk MK, Paternoster L, Brown SJ. From GWASs toward Mechanistic Understanding with Case Studies in Dermatogenetics. J Invest Dermatol 2024; 144:1189-1199.e8. [PMID: 38782533 DOI: 10.1016/j.jid.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/13/2024] [Accepted: 03/06/2024] [Indexed: 05/25/2024]
Abstract
Many human skin diseases result from the complex interplay of genetic and environmental mechanisms that are largely unknown. GWASs have yielded insight into the genetic aspect of complex disease by highlighting regions of the genome or specific genetic variants associated with disease. Leveraging this information to identify causal genes and cell types will provide insight into fundamental biology, inform diagnostics, and aid drug discovery. However, the etiological mechanisms from genetic variant to disease are still unestablished in most cases. There now exists an unprecedented wealth of data and computational methods for variant interpretation in a functional context. It can be challenging to decide where to start owing to a lack of consensus on the best way to identify causal genetic mechanisms. This article highlights 3 key aspects of genetic variant interpretation: prioritizing causal genes, cell types, and pathways. We provide a practical overview of the main methods and datasets, giving examples from recent atopic dermatitis studies to provide a blueprint for variant interpretation. A collection of resources, including brief description and links to the packages and web tools, is provided for researchers looking to start in silico follow-up genetic analysis of associated genetic variants.
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Affiliation(s)
- Silvia Shen
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, United Kingdom; Institute for Evolution and Ecology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
| | - Maria K Sobczyk
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Sara J Brown
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, United Kingdom; Department of Dermatology, NHS Lothian, Edinburgh, United Kingdom
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5
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Ali MZ, Guharajan S, Parisutham V, Brewster RC. Regulatory properties of transcription factors with diverse mechanistic function. PLoS Comput Biol 2024; 20:e1012194. [PMID: 38857275 PMCID: PMC11192337 DOI: 10.1371/journal.pcbi.1012194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/21/2024] [Accepted: 05/24/2024] [Indexed: 06/12/2024] Open
Abstract
Transcription factors (TFs) regulate the process of transcription through the modulation of different kinetic steps. Although models can often describe the observed transcriptional output of a measured gene, predicting a TFs role on a given promoter requires an understanding of how the TF alters each step of the transcription process. In this work, we use a simple model of transcription to assess the role of promoter identity, and the degree to which TFs alter binding of RNAP (stabilization) and initiation of transcription (acceleration) on three primary characteristics: the range of steady-state regulation, cell-to-cell variability in expression, and the dynamic response time of a regulated gene. We find that steady state regulation and the response time of a gene behave uniquely for TFs that regulate incoherently, i.e that speed up one step but slow the other. We also find that incoherent TFs have dynamic implications, with one type of incoherent mode configuring the promoter to respond more slowly at intermediate TF concentrations. We also demonstrate that the noise of gene expression for these TFs is sensitive to promoter strength, with a distinct non-monotonic profile that is apparent under stronger promoters. Taken together, our work uncovers the coupling between promoters and TF regulatory modes with implications for understanding natural promoters and engineering synthetic gene circuits with desired expression properties.
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Affiliation(s)
- Md Zulfikar Ali
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Geology, Physics and Environmental Science, University of Southern Indiana, Evansville, Indiana, United States of America
| | - Sunil Guharajan
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Vinuselvi Parisutham
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robert C. Brewster
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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6
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Hull JJ, Heu CC, Gross RJ, LeRoy DM, Schutze IX, Langhorst D, Fabrick JA, Brent CS. Doublesex is essential for masculinization but not feminization in Lygus hesperus. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 166:104085. [PMID: 38307215 DOI: 10.1016/j.ibmb.2024.104085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 02/04/2024]
Abstract
In most holometabolous insects, sex differentiation occurs via a hierarchical cascade of transcription factors, with doublesex (dsx) regulating genes that control sex-specific traits. Although less is known in hemimetabolous insects, early evidence suggests that substantial differences exist from more evolutionarily advanced insects. Here, we identified and characterized dsx in Lygus hesperus (western tarnished plant bug), a hemipteran pest of many agricultural crops in western North America. The full-length transcript for L. hesperus dsx (Lhdsx) and several variants encode proteins with conserved DNA binding and oligomerization domains. Transcript profiling revealed that Lhdsx is ubiquitously expressed, likely undergoes alternative pre-mRNA splicing, and, unlike several model insects, is sex-biased rather than sex-specific. Embryonic RNA interference (RNAi) of Lhdsx only impacted sex development in adult males, which lacked both internal reproductive organs and external genitalia. No discernible impacts on adult female development or reproductivity were observed. RNAi knockdown of Lhdsx in nymphs likewise only affected adult males, which lacked the characteristic dimorphic coloration but had dramatically elevated vitellogenin transcripts. Gene knockout of Lhdsx by CRISPR/Cas9 editing yielded only females in G0 and strongly biased heterozygous G1 offspring to females with the few surviving males showing severely impaired genital development. These results indicate that L. hesperus male development requires Lhdsx, whereas female development proceeds via a basal pathway that functions independently of dsx. A fundamental understanding of sex differentiation in L. hesperus could be important for future gene-based management strategies of this important agricultural pest.
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Affiliation(s)
- J Joe Hull
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA.
| | - Chan C Heu
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Roni J Gross
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Dannialle M LeRoy
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Inana X Schutze
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Daniel Langhorst
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Jeffrey A Fabrick
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Colin S Brent
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA
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7
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Yang L, Lyu J, Li X, Guo G, Zhou X, Chen T, Lin Y, Li T. Phase separation as a possible mechanism for dosage sensitivity. Genome Biol 2024; 25:17. [PMID: 38225666 PMCID: PMC10789095 DOI: 10.1186/s13059-023-03128-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/27/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Deletion of haploinsufficient genes or duplication of triplosensitive ones results in phenotypic effects in a concentration-dependent manner, and the mechanisms underlying these dosage-sensitive effects remain elusive. Phase separation drives functional compartmentalization of biomolecules in a concentration-dependent manner as well, which suggests a potential link between these two processes, and warrants further systematic investigation. RESULTS Here we provide bioinformatic and experimental evidence to show a close link between phase separation and dosage sensitivity. We first demonstrate that haploinsufficient or triplosensitive gene products exhibit a higher tendency to undergo phase separation. Assessing the well-established dosage-sensitive genes HNRNPK, PAX6, and PQBP1 with experiments, we show that these proteins undergo phase separation. Critically, pathogenic variations in dosage-sensitive genes disturb the phase separation process either through reduced protein levels, or loss of phase-separation-prone regions. Analysis of multi-omics data further demonstrates that loss-of-function genetic perturbations on phase-separating genes cause similar dysfunction phenotypes as dosage-sensitive gene perturbations. In addition, dosage-sensitive scores derived from population genetics data predict phase-separating proteins with much better performance than available sequence-based predictors, further illustrating close ties between these two parameters. CONCLUSIONS Together, our study shows that phase separation is functionally linked to dosage sensitivity and provides novel insights for phase-separating protein prediction from the perspective of population genetics data.
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Affiliation(s)
- Liang Yang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jiali Lyu
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xi Li
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Gaigai Guo
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xueya Zhou
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Taoyu Chen
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yi Lin
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Tingting Li
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191, China.
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8
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Navarro-Quiles C, Lup SD, Muñoz-Nortes T, Candela H, Micol JL. The genetic and molecular basis of haploinsufficiency in flowering plants. TRENDS IN PLANT SCIENCE 2024; 29:72-85. [PMID: 37633803 DOI: 10.1016/j.tplants.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 08/28/2023]
Abstract
In diploid organisms, haploinsufficiency can be defined as the requirement for more than one fully functional copy of a gene. In contrast to most genes, whose loss-of-function alleles are recessive, loss-of-function alleles of haploinsufficient genes are dominant. However, forward and reverse genetic screens are biased toward obtaining recessive, loss-of-function mutations, and therefore, dominant mutations of all types are underrepresented in mutant collections. Despite this underrepresentation, haploinsufficient loci have intriguing implications for studies of genome evolution, gene dosage, stability of protein complexes, genetic redundancy, and gene expression. Here we review examples of haploinsufficiency in flowering plants and describe the underlying molecular mechanisms and evolutionary forces driving haploinsufficiency. Finally, we discuss the masking of haploinsufficiency by genetic redundancy, a widespread phenomenon among angiosperms.
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Affiliation(s)
- Carla Navarro-Quiles
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Samuel Daniel Lup
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Tamara Muñoz-Nortes
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain.
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9
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Sun Y, Wiese M, Hmadi R, Karayol R, Seyfferth J, Martinez Greene JA, Erdogdu NU, Deboutte W, Arrigoni L, Holz H, Renschler G, Hirsch N, Foertsch A, Basilicata MF, Stehle T, Shvedunova M, Bella C, Pessoa Rodrigues C, Schwalb B, Cramer P, Manke T, Akhtar A. MSL2 ensures biallelic gene expression in mammals. Nature 2023; 624:173-181. [PMID: 38030723 PMCID: PMC10700137 DOI: 10.1038/s41586-023-06781-3] [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: 05/29/2022] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
In diploid organisms, biallelic gene expression enables the production of adequate levels of mRNA1,2. This is essential for haploinsufficient genes, which require biallelic expression for optimal function to prevent the onset of developmental disorders1,3. Whether and how a biallelic or monoallelic state is determined in a cell-type-specific manner at individual loci remains unclear. MSL2 is known for dosage compensation of the male X chromosome in flies. Here we identify a role of MSL2 in regulating allelic expression in mammals. Allele-specific bulk and single-cell analyses in mouse neural progenitor cells revealed that, in addition to the targets showing biallelic downregulation, a class of genes transitions from biallelic to monoallelic expression after MSL2 loss. Many of these genes are haploinsufficient. In the absence of MSL2, one allele remains active, retaining active histone modifications and transcription factor binding, whereas the other allele is silenced, exhibiting loss of promoter-enhancer contacts and the acquisition of DNA methylation. Msl2-knockout mice show perinatal lethality and heterogeneous phenotypes during embryonic development, supporting a role for MSL2 in regulating gene dosage. The role of MSL2 in preserving biallelic expression of specific dosage-sensitive genes sets the stage for further investigation of other factors that are involved in allelic dosage compensation in mammalian cells, with considerable implications for human disease.
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Affiliation(s)
- Yidan Sun
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Meike Wiese
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Raed Hmadi
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Remzi Karayol
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Juan Alfonso Martinez Greene
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ward Deboutte
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gina Renschler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Naama Hirsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Arion Foertsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Thomas Stehle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Chiara Bella
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Bjoern Schwalb
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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10
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Mudgett M, Shen Z, Dai X, Briggs SP, Zhao Y. Suppression of pinoid mutant phenotypes by mutations in PIN-FORMED 1 and PIN1-GFP fusion. Proc Natl Acad Sci U S A 2023; 120:e2312918120. [PMID: 37983505 PMCID: PMC10691239 DOI: 10.1073/pnas.2312918120] [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: 08/01/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023] Open
Abstract
Disruption of either the auxin transporter PIN-FORMED 1 (PIN1) or the protein kinase PINOID (PID) leads to the development of pin-like inflorescences. Previous studies have shown that phosphoregulation of PIN1 by AGC kinases including PID directs auxin flux to drive organ initiation. Here, we report unexpected findings on the genetic interactions between these two genes. We deleted the first 2/3 of the PIN1 coding sequence using CRISPR/Cas9, and the resulting pin1 mutant (pin1-27) was a strong allele. Surprisingly, heterozygous pin1-27 suppressed two independent pid null mutants, whereas homozygous pin1-27 enhanced the phenotypes of the pid mutants during embryogenesis. Furthermore, we show that deletion of either the hydrophilic loop or the second half of PIN1 also abolished PIN1 function, yet those heterozygous pin1 mutants were also capable of rescuing pid nulls. Moreover, we inserted green fluorescent protein (GFP) into the hydrophilic loop of PIN1 through CRISPR-mediated homology-directed repair (HDR). The GFP signal and pattern in the PIN1-GFPHDR line are similar to those in the previously reported PIN1-GFP transgenic lines. Interestingly, the PIN1-GFPHDR line also rescued various pid null mutant alleles in a semidominant fashion. We conclude that decreasing the number of functional PIN1 copies is sufficient to suppress the pid mutant phenotype, suggesting that PIN1 is likely part of a larger protein complex required for organogenesis.
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Affiliation(s)
- Michael Mudgett
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093-0116
| | - Zhouxin Shen
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093-0116
| | - Xinhua Dai
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093-0116
| | - Steven P. Briggs
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093-0116
| | - Yunde Zhao
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093-0116
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11
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Saha S, Jungas TT, Ohayon D, Audouard C, Ye T, Fawal MA, Davy A. Dihydrofolate reductase activity controls neurogenic transitions in the developing neocortex. Development 2023; 150:dev201696. [PMID: 37665322 DOI: 10.1242/dev.201696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023]
Abstract
One-carbon/folate (1C) metabolism supplies methyl groups required for DNA and histone methylation, and is involved in the maintenance of self-renewal in stem cells. Dihydrofolate reductase (DHFR), a key enzyme in 1C metabolism, is highly expressed in human and mouse neural progenitors at the early stages of neocortical development. Here, we have investigated the role of DHFR in the developing neocortex and report that reducing its activity in human neural organoids and mouse embryonic neocortex accelerates indirect neurogenesis, thereby affecting neuronal composition of the neocortex. Furthermore, we show that decreasing DHFR activity in neural progenitors leads to a reduction in one-carbon/folate metabolites and correlates with modifications of H3K4me3 levels. Our findings reveal an unanticipated role for DHFR in controlling specific steps of neocortex development and indicate that variations in 1C metabolic cues impact cell fate transitions.
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Affiliation(s)
- Sulov Saha
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Thomas T Jungas
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - David Ohayon
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Christophe Audouard
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Mohamad-Ali Fawal
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Alice Davy
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
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12
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Liu Z, Huang YF. Deep multiple-instance learning accurately predicts gene haploinsufficiency and deletion pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555384. [PMID: 37693607 PMCID: PMC10491176 DOI: 10.1101/2023.08.29.555384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Copy number losses (deletions) are a major contributor to the etiology of severe genetic disorders. Although haploinsufficient genes play a critical role in deletion pathogenicity, current methods for deletion pathogenicity prediction fail to integrate multiple lines of evidence for haploinsufficiency at the gene level, limiting their power to pinpoint deleterious deletions associated with genetic disorders. Here we introduce DosaCNV, a deep multiple-instance learning framework that, for the first time, models deletion pathogenicity jointly with gene haploinsufficiency. By integrating over 30 gene-level features potentially predictive of haploinsufficiency, DosaCNV shows unmatched performance in prioritizing pathogenic deletions associated with a broad spectrum of genetic disorders. Furthermore, DosaCNV outperforms existing methods in predicting gene haploinsufficiency even though it is not trained on known haploinsufficient genes. Finally, DosaCNV leverages a state-of-the-art technique to quantify the contributions of individual gene-level features to haploinsufficiency, allowing for human-understandable explanations of model predictions. Altogether, DosaCNV is a powerful computational tool for both fundamental and translational research.
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Affiliation(s)
- Zhihan Liu
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Molecular, Cellular, and Integrative Biosciences Program, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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13
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Borgese N, Guillén-Samander A, Colombo SF, Mancassola G, Di Berardino F, Zanetti D, Carrera P. Combined Presence in Heterozygosis of Two Variant Usher Syndrome Genes in Two Siblings Affected by Isolated Profound Age-Related Hearing Loss. Biomedicines 2023; 11:2657. [PMID: 37893031 PMCID: PMC10604119 DOI: 10.3390/biomedicines11102657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Sensorineural age-related hearing loss affects a large proportion of the elderly population, and has both environmental and genetic causes. Notwithstanding increasing interest in this debilitating condition, the genetic risk factors remain largely unknown. Here, we report the case of two sisters affected by isolated profound sensorineural hearing loss after the age of seventy. Genomic DNA sequencing revealed that the siblings shared two monoallelic variants in two genes linked to Usher Syndrome (USH genes), a recessive disorder of the ear and the retina: a rare pathogenic truncating variant in USH1G and a previously unreported missense variant in ADGRV1. Structure predictions suggest a negative effect on protein stability of the latter variant, allowing its classification as likely pathogenic according to American College of Medical Genetics criteria. Thus, the presence in heterozygosis of two recessive alleles, which each cause syndromic deafness, may underlie digenic inheritance of the age-related non-syndromic hearing loss of the siblings, a hypothesis that is strengthened by the knowledge that the two genes are integrated in the same functional network, which underlies stereocilium development and organization. These results enlarge the spectrum and complexity of the phenotypic consequences of USH gene mutations beyond the simple Mendelian inheritance of classical Usher syndrome.
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Affiliation(s)
- Nica Borgese
- Consiglio Nazionale delle Ricerche Neuroscience Institute, 20854 Vedano al Lambro, Italy;
| | | | - Sara Francesca Colombo
- Consiglio Nazionale delle Ricerche Neuroscience Institute, 20854 Vedano al Lambro, Italy;
- NeuroMi Milan Center for Neuroscience, Milan, Italy
| | - Giulia Mancassola
- Unit of Genomics for Human Disease Diagnosis, IRCCS Ospedale San Raffaele, 20132 Milan, Italy;
- Laboratory of Clinical Molecular Genetics, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Federica Di Berardino
- Audiology Unit, Department of Specialistic Surgical Sciences, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.D.B.); (D.Z.)
- Department of Clinical Sciences and Community Health, University of Milano, 20122 Milan, Italy
| | - Diego Zanetti
- Audiology Unit, Department of Specialistic Surgical Sciences, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.D.B.); (D.Z.)
- Department of Clinical Sciences and Community Health, University of Milano, 20122 Milan, Italy
| | - Paola Carrera
- Unit of Genomics for Human Disease Diagnosis, IRCCS Ospedale San Raffaele, 20132 Milan, Italy;
- Laboratory of Clinical Molecular Genetics, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
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14
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LaPolice TM, Huang YF. An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data. BMC Bioinformatics 2023; 24:347. [PMID: 37723435 PMCID: PMC10506225 DOI: 10.1186/s12859-023-05481-z] [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: 09/13/2022] [Accepted: 09/13/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND The ability to accurately predict essential genes intolerant to loss-of-function (LOF) mutations can dramatically improve the identification of disease-associated genes. Recently, there have been numerous computational methods developed to predict human essential genes from population genomic data. While the existing methods are highly predictive of essential genes of long length, they have limited power in pinpointing short essential genes due to the sparsity of polymorphisms in the human genome. RESULTS Motivated by the premise that population and functional genomic data may provide complementary evidence for gene essentiality, here we present an evolution-based deep learning model, DeepLOF, to predict essential genes in an unsupervised manner. Unlike previous population genetic methods, DeepLOF utilizes a novel deep learning framework to integrate both population and functional genomic data, allowing us to pinpoint short essential genes that can hardly be predicted from population genomic data alone. Compared with previous methods, DeepLOF shows unmatched performance in predicting ClinGen haploinsufficient genes, mouse essential genes, and essential genes in human cell lines. Notably, at a false positive rate of 5%, DeepLOF detects 50% more ClinGen haploinsufficient genes than previous methods. Furthermore, DeepLOF discovers 109 novel essential genes that are too short to be identified by previous methods. CONCLUSION The predictive power of DeepLOF shows that it is a compelling computational method to aid in the discovery of essential genes.
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Affiliation(s)
- Troy M LaPolice
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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15
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Watson AJ, Shaffer ML, Bouley RA, Petreaca RC. F-box DNA Helicase 1 (FBH1) Contributes to the Destabilization of DNA Damage Repair Machinery in Human Cancers. Cancers (Basel) 2023; 15:4439. [PMID: 37760409 PMCID: PMC10526855 DOI: 10.3390/cancers15184439] [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: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Homologous recombination (HR) is the major mechanism of rescue of stalled replication forks or repair of DNA double-strand breaks (DSBs) during S phase or mitosis. In human cells, HR is facilitated by the BRCA2-BRCA1-PALB2 module, which loads the RAD51 recombinase onto a resected single-stranded DNA end to initiate repair. Although the process is essential for error-free repair, unrestrained HR can cause chromosomal rearrangements and genome instability. F-box DNA Helicase 1 (FBH1) antagonizes the role of BRCA2-BRCA1-PALB2 to restrict hyper-recombination and prevent genome instability. Here, we analyzed reported FBH1 mutations in cancer cells using the Catalogue of Somatic Mutations in Cancers (COSMIC) to understand how they interact with the BRCA2-BRCA1-PALB2. Consistent with previous results from yeast, we find that FBH1 mutations co-occur with BRCA2 mutations and to some degree BRCA1 and PALB2. We also describe some co-occurring mutations with RAD52, the accessory RAD51 loader and facilitator of single-strand annealing, which is independent of RAD51. In silico modeling was used to investigate the role of key FBH1 mutations on protein function, and a Q650K mutation was found to destabilize the protein structure. Taken together, this work highlights how mutations in several DNA damage repair genes contribute to cellular transformation and immortalization.
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Affiliation(s)
- Alizhah J. Watson
- Biology Program, The Ohio State University, Marion, OH 433023, USA; (A.J.W.); (M.L.S.)
| | - Michaela L. Shaffer
- Biology Program, The Ohio State University, Marion, OH 433023, USA; (A.J.W.); (M.L.S.)
| | - Renee A. Bouley
- Department of Chemistry and Biochemistry, The Ohio State University, Marion, OH 43302, USA
| | - Ruben C. Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
- Cancer Biology Program, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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16
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Naqvi S, Kim S, Hoskens H, Matthews HS, Spritz RA, Klein OD, Hallgrímsson B, Swigut T, Claes P, Pritchard JK, Wysocka J. Precise modulation of transcription factor levels identifies features underlying dosage sensitivity. Nat Genet 2023; 55:841-851. [PMID: 37024583 PMCID: PMC10181932 DOI: 10.1038/s41588-023-01366-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Transcriptional regulation exhibits extensive robustness, but human genetics indicates sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, largely lacking so far. TFs play central roles in both normal-range and disease-associated variation in craniofacial morphology; we therefore developed an approach to precisely modulate TF levels in human facial progenitor cells and applied it to SOX9, a TF associated with craniofacial variation and disease (Pierre Robin sequence (PRS)). Most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, but REs directly and primarily regulated by SOX9 show heightened sensitivity to SOX9 dosage; these RE responses partially predict gene expression responses. Sensitive REs and genes preferentially affect functional chondrogenesis and PRS-like craniofacial shape variation. We propose that such REs and genes underlie the sensitivity of specific phenotypes to TF dosage, while buffering of other genes leads to robust, nonlinear dosage-to-phenotype relationships.
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Affiliation(s)
- Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Genetics and Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Harold S Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program and Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ophir D Klein
- Departments of Orofacial Sciences and Pediatrics, Program in Craniofacial Biology, and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | | | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Mendelian inheritance revisited: dominance and recessiveness in medical genetics. Nat Rev Genet 2023:10.1038/s41576-023-00574-0. [PMID: 36806206 DOI: 10.1038/s41576-023-00574-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/22/2023]
Abstract
Understanding the consequences of genotype for phenotype (which ranges from molecule-level effects to whole-organism traits) is at the core of genetic diagnostics in medicine. Many measures of the deleteriousness of individual alleles exist, but these have limitations for predicting the clinical consequences. Various mechanisms can protect the organism from the adverse effects of functional variants, especially when the variant is paired with a wild type allele. Understanding why some alleles are harmful in the heterozygous state - representing dominant inheritance - but others only with the biallelic presence of pathogenic variants - representing recessive inheritance - is particularly important when faced with the deluge of rare genetic alterations identified by high throughput DNA sequencing. Both awareness of the specific quantitative and/or qualitative effects of individual variants and the elucidation of allelic and non-allelic interactions are essential to optimize genetic diagnosis and counselling.
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18
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Zug R, Uller T. Evolution and dysfunction of human cognitive and social traits: A transcriptional regulation perspective. EVOLUTIONARY HUMAN SCIENCES 2022; 4:e43. [PMID: 37588924 PMCID: PMC10426018 DOI: 10.1017/ehs.2022.42] [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: 05/24/2022] [Revised: 08/11/2022] [Accepted: 09/11/2022] [Indexed: 11/07/2022] Open
Abstract
Evolutionary changes in brain and craniofacial development have endowed humans with unique cognitive and social skills, but also predisposed us to debilitating disorders in which these traits are disrupted. What are the developmental genetic underpinnings that connect the adaptive evolution of our cognition and sociality with the persistence of mental disorders with severe negative fitness effects? We argue that loss of function of genes involved in transcriptional regulation represents a crucial link between the evolution and dysfunction of human cognitive and social traits. The argument is based on the haploinsufficiency of many transcriptional regulator genes, which makes them particularly sensitive to loss-of-function mutations. We discuss how human brain and craniofacial traits evolved through partial loss of function (i.e. reduced expression) of these genes, a perspective compatible with the idea of human self-domestication. Moreover, we explain why selection against loss-of-function variants supports the view that mutation-selection-drift, rather than balancing selection, underlies the persistence of psychiatric disorders. Finally, we discuss testable predictions.
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Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, Lund, Sweden
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
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19
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Galano M, Ezzat S, Papadopoulos V. SCP2 variant is associated with alterations in lipid metabolism, brainstem neurodegeneration, and testicular defects. Hum Genomics 2022; 16:32. [PMID: 35996156 PMCID: PMC9396802 DOI: 10.1186/s40246-022-00408-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/11/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The detoxification of very long-chain and branched-chain fatty acids and the metabolism of cholesterol to form bile acids occur largely through a process called peroxisomal β-oxidation. Mutations in several peroxisomal proteins involved in β-oxidation have been reported, resulting in diseases characterized by neurological defects. The final step of the peroxisomal β-oxidation pathway is catalyzed by sterol carrier protein-x (SCPx), which is encoded by the SCP2 gene. Previously, there have been two reports of SCPx deficiency, which resulted from a homozygous or compound heterozygous SCP2 mutation. We report herein the first patient with a heterozygous SCP2 mutation leading to SCPx deficiency. RESULTS Clinical presentations of the patient included progressive brainstem neurodegeneration, cardiac dysrhythmia, muscle wasting, and azoospermia. Plasma fatty acid analysis revealed abnormal values of medium-, long-, and very long-chain fatty acids. Protein expression of SCPx and other enzymes involved in β-oxidation were altered between patient and normal fibroblasts. RNA sequencing and lipidomic analyses identified metabolic pathways that were altered between patient and normal fibroblasts including PPAR signaling, serotonergic signaling, steroid biosynthesis, and fatty acid degradation. Treatment with fenofibrate or 4-hydroxytamoxifen increased SCPx levels, and certain fatty acid levels in patient fibroblasts. CONCLUSIONS These findings suggest that the patient's SCP2 mutation resulted in decreased protein levels of SCPx, which may be associated with many metabolic pathways. Increasing SCPx levels through pharmacological interventions may reverse some effects of SCPx deficiency. Collectively, this work provides insight into many of the clinical consequences of SCPx deficiency and provides evidence for potential treatment strategies.
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Affiliation(s)
- Melanie Galano
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Ave, Los Angeles, CA, 90089, USA
| | - Shereen Ezzat
- Department of Medicine, University of Toronto and Princess Margaret Cancer Center, Toronto, ON, M5G 2C1, Canada
| | - Vassilios Papadopoulos
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Ave, Los Angeles, CA, 90089, USA.
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20
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Bing H, Li YL, Li D, Zhang C, Chang B. Case Report: A Rare Heterozygous ATP8B1 Mutation in a BRIC1 Patient: Haploinsufficiency? Front Med (Lausanne) 2022; 9:897108. [PMID: 35783636 PMCID: PMC9243653 DOI: 10.3389/fmed.2022.897108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022] Open
Abstract
Benign recurrent intrahepatic cholestasis (BRIC) is an autosomal recessive disorder characterized by recurrent cholestasis. ATPase class I, type 8B, member 1 (ATP8B1) encodes familial intrahepatic cholestasis 1 (FIC1), which acts as a phosphatidylserine reversing enzyme in the tubule membrane of hepatocytes to mediate the inward translocation of phosphatidylserine (PS). At present, dozens of ATP8B1 pathogenic mutations have been identified that mainly cause BRIC1 and progressive familial intrahepatic cholestasis 1 (PFIC1). The diagnosis of BRIC1 is based on symptoms, laboratory tests, imaging, liver histology, and genetic testing. BRIC1 treatment seeks to prevent recurrence and reduce disease severity. At present, the main treatment methods include ursodeoxycholic acid (UDCA), rifampin, cholestyramine and haemofiltration, and endoscopic nasobiliary drainage (ENBD). Here, we report a 17-year-old patient with cholestasis who has a rare heterozygous ATP8B1 gene mutation (p.T888K). The patient was treated with UDCA, glucocorticoids and haemofiltration, after which bilirubin levels gradually returned to normal. This case was thought to be caused by an ATP8B1 heterozygous mutation, which may be related to haploinsufficiency (HI).
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Affiliation(s)
- Hao Bing
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, Shenyang, China
- Department of Gastroenterology, Shengjing Hospital Affiliated by China Medical University, Shenyang, China
| | - Yi-Ling Li
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Dan Li
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Chen Zhang
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Bing Chang
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Bing Chang,
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21
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Kotov AA, Bazylev SS, Adashev VE, Shatskikh AS, Olenina LV. Drosophila as a Model System for Studying of the Evolution and Functional Specialization of the Y Chromosome. Int J Mol Sci 2022; 23:4184. [PMID: 35457001 PMCID: PMC9031259 DOI: 10.3390/ijms23084184] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023] Open
Abstract
The Y chromosome is one of the sex chromosomes found in males of animals of different taxa, including insects and mammals. Among all chromosomes, the Y chromosome is characterized by a unique chromatin landscape undergoing dynamic evolutionary change. Being entirely heterochromatic, the Y chromosome as a rule preserves few functional genes, but is enriched in tandem repeats and transposons. Due to difficulties in the assembly of the highly repetitive Y chromosome sequence, deep analyses of Y chromosome evolution, structure, and functions are limited to a few species, one of them being Drosophila melanogaster. Despite Y chromosomes exhibiting high structural divergence between even closely related species, Y-linked genes have evolved convergently and are mainly associated with spermatogenesis-related activities. This indicates that male-specific selection is a dominant force shaping evolution of Y chromosomes across species. This review presents our analysis of current knowledge concerning Y chromosome functions, focusing on recent findings in Drosophila. Here we dissect the experimental and bioinformatics data about the Y chromosome accumulated to date in Drosophila species, providing comparative analysis with mammals, and discussing the relevance of our analysis to a wide range of eukaryotic organisms, including humans.
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Affiliation(s)
| | | | | | | | - Ludmila V. Olenina
- Institute of Molecular Genetics of National Research Center «Kurchatov Institute», 123182 Moscow, Russia; (A.A.K.); (S.S.B.); (V.E.A.); (A.S.S.)
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22
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Prochownik EV, Wang H. Normal and Neoplastic Growth Suppression by the Extended Myc Network. Cells 2022; 11:747. [PMID: 35203395 PMCID: PMC8870482 DOI: 10.3390/cells11040747] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
Among the first discovered and most prominent cellular oncogenes is MYC, which encodes a bHLH-ZIP transcription factor (Myc) that both activates and suppresses numerous genes involved in proliferation, energy production, metabolism and translation. Myc belongs to a small group of bHLH-ZIP transcriptional regulators (the Myc Network) that includes its obligate heterodimerization partner Max and six "Mxd proteins" (Mxd1-4, Mnt and Mga), each of which heterodimerizes with Max and largely opposes Myc's functions. More recently, a second group of bHLH-ZIP proteins (the Mlx Network) has emerged that bears many parallels with the Myc Network. It is comprised of the Myc-like factors ChREBP and MondoA, which, in association with the Max-like member Mlx, regulate smaller and more functionally restricted repertoires of target genes, some of which are shared with Myc. Opposing ChREBP and MondoA are heterodimers comprised of Mlx and Mxd1, Mxd4 and Mnt, which also structurally and operationally link the two Networks. We discuss here the functions of these "Extended Myc Network" members, with particular emphasis on their roles in suppressing normal and neoplastic growth. These roles are complex due to the temporal- and tissue-restricted expression of Extended Myc Network proteins in normal cells, their regulation of both common and unique target genes and, in some cases, their functional redundancy.
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Affiliation(s)
- Edward V. Prochownik
- Division of Hematology/Oncology, The Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA;
- The Department of Microbiology and Molecular Genetics, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
- The Hillman Cancer Center of UPMC, Pittsburgh, PA 15224, USA
- The Pittsburgh Liver Research Center, Pittsburgh, PA 15224, USA
| | - Huabo Wang
- Division of Hematology/Oncology, The Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA;
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Zug R. Developmental disorders caused by haploinsufficiency of transcriptional regulators: a perspective based on cell fate determination. Biol Open 2022; 11:bio058896. [PMID: 35089335 PMCID: PMC8801891 DOI: 10.1242/bio.058896] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many human birth defects and neurodevelopmental disorders are caused by loss-of-function mutations in a single copy of transcription factor (TF) and chromatin regulator genes. Although this dosage sensitivity has long been known, how and why haploinsufficiency (HI) of transcriptional regulators leads to developmental disorders (DDs) is unclear. Here I propose the hypothesis that such DDs result from defects in cell fate determination that are based on disrupted bistability in the underlying gene regulatory network (GRN). Bistability, a crucial systems biology concept to model binary choices such as cell fate decisions, requires both positive feedback and ultrasensitivity, the latter often achieved through TF cooperativity. The hypothesis explains why dosage sensitivity of transcriptional regulators is an inherent property of fate decisions, and why disruption of either positive feedback or cooperativity in the underlying GRN is sufficient to cause disease. I present empirical and theoretical evidence in support of this hypothesis and discuss several issues for which it increases our understanding of disease, such as incomplete penetrance. The proposed framework provides a mechanistic, systems-level explanation of HI of transcriptional regulators, thus unifying existing theories, and offers new insights into outstanding issues of human disease. This article has an associated Future Leader to Watch interview with the author of the paper.
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Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, 22362 Lund, Sweden
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Chromosome Imbalances in Neuroblastoma-Recent Molecular Insight into Chromosome 1p-deletion, 2p-gain, and 11q-deletion Identifies New Friends and Foes for the Future. Cancers (Basel) 2021; 13:cancers13235897. [PMID: 34885007 PMCID: PMC8657310 DOI: 10.3390/cancers13235897] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Neuroblastoma is a pediatric cancer that arises in the sympathetic nervous system. High-risk neuroblastoma is clinically challenging and identification of novel therapies, particularly those that offer a reduction in morbidity for these patients, is a high priority. Combining genetic analyses with investigation of molecular mechanisms, while considering recent advances in our understanding of key developmental events, provides avenues for future treatment. Here we review and highlight several recently published articles that address novel molecular mechanisms arising from chromosome 1p, 2p, and 11q aberrations, which likely contribute to high-risk neuroblastoma, and discusses their potential impact on treatment options. Abstract Neuroblastoma is the most common extracranial solid pediatric tumor, with around 15% childhood cancer-related mortality. High-risk neuroblastomas exhibit a range of genetic, morphological, and clinical heterogeneities, which add complexity to diagnosis and treatment with existing modalities. Identification of novel therapies is a high priority in high-risk neuroblastoma, and the combination of genetic analysis with increased mechanistic understanding—including identification of key signaling and developmental events—provides optimism for the future. This focused review highlights several recent findings concerning chromosomes 1p, 2p, and 11q, which link genetic aberrations with aberrant molecular signaling output. These novel molecular insights contribute important knowledge towards more effective treatment strategies for neuroblastoma.
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Epstein RJ. The secret identities of TMPRSS2: Fertility factor, virus trafficker, inflammation moderator, prostate protector and tumor suppressor. Tumour Biol 2021; 43:159-176. [PMID: 34420994 DOI: 10.3233/tub-211502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The human TMPRSS2 gene is pathogenetically implicated in both coronaviral lung infection and prostate cancer, suggesting its potential as a drug target in both contexts. SARS-COV-2 spike polypeptides are primed by the host transmembrane TMPRSS2 protease, triggering virus fusion with epithelial cell membranes followed by an endocytotic internalisation process that bypasses normal endosomal activation of cathepsin-mediated innate immunity; viral co-opting of TMPRSS2 thus favors microbial survivability by attenuating host inflammatory responses. In contrast, most early hormone-dependent prostate cancers express TMPRSS2:ERG fusion genes arising from deletions that eliminate the TMPRSS2 coding region while juxtaposing its androgen-inducible promoter and the open reading frame of ERG, upregulating pro-inflammatory ERG while functionally disabling TMPRSS2. Moreover, inflammatory oxidative DNA damage selects for TMPRSS2:ERG-fused cancers, whereas patients treated with antiinflammatory drugs develop fewer of these fusion-dependent tumors. These findings imply that TMPRSS2 protects the prostate by enabling endosomal bypass of pathogens which could otherwise trigger inflammation-induced DNA damage that predisposes to TMPRSS2:ERG fusions. Hence, the high oncogenic selectability of TMPRSS2:ERG fusions may reflect a unique pro-inflammatory synergy between androgenic ERG gain-of-function and fusogenic TMPRSS2 loss-of-function, cautioning against the use of TMPRSS2-inhibitory drugs to prevent or treat early prostate cancer.
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Affiliation(s)
- Richard J Epstein
- New Hope Cancer Center, Beijing United Hospital, Jiangtai Xi Rd 9-11, Chaoyang, Beijing, China.,Garvan Institute of Medical Research, and UNSW Medical School, St Vincent's Hospital, Victoria St, Darlinghurst, Sydney, Australia
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26
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Clepet C, Devani RS, Boumlik R, Hao Y, Morin H, Marcel F, Verdenaud M, Mania B, Brisou G, Citerne S, Mouille G, Lepeltier JC, Koussevitzky S, Boualem A, Bendahmane A. The miR166-SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato. MOLECULAR PLANT 2021; 14:1185-1198. [PMID: 33964458 DOI: 10.1016/j.molp.2021.05.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/22/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Fruit set is inhibited by adverse temperatures, with consequences on yield. We isolated a tomato mutant producing fruits under non-permissive hot temperatures and identified the causal gene as SlHB15A, belonging to class III homeodomain leucine-zipper transcription factors. SlHB15A loss-of-function mutants display aberrant ovule development that mimics transcriptional changes occurring in fertilized ovules and leads to parthenocarpic fruit set under optimal and non-permissive temperatures, in field and greenhouse conditions. Under cold growing conditions, SlHB15A is subjected to conditional haploinsufficiency and recessive dosage sensitivity controlled by microRNA 166 (miR166). Knockdown of SlHB15A alleles by miR166 leads to a continuum of aberrant ovules correlating with parthenocarpic fruit set. Consistent with this, plants harboring an Slhb15a-miRNA166-resistant allele developed normal ovules and were unable to set parthenocarpic fruit under cold conditions. DNA affinity purification sequencing and RNA-sequencing analyses revealed that SlHB15A is a bifunctional transcription factor expressed in the ovule integument. SlHB15A binds to the promoters of auxin-related genes to repress auxin signaling and to the promoters of ethylene-related genes to activate their expression. A survey of tomato genetic biodiversity identified pat and pat-1, two historical parthenocarpic mutants, as alleles of SlHB15A. Taken together, our findings demonstrate the role of SlHB15A as a sentinel to prevent fruit set in the absence of fertilization and provide a mean to enhance fruiting under extreme temperatures.
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Affiliation(s)
- Christian Clepet
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Ravi Sureshbhai Devani
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Rachid Boumlik
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Yanwei Hao
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Halima Morin
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Fabien Marcel
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Marion Verdenaud
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Brahim Mania
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Gwilherm Brisou
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | | | | | | | | | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay, INRAE, CNRS, Université Paris-Saclay, Orsay 91405, France.
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27
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Tran TM, Sherwood JK, Doolittle MJ, Sathler MF, Hofmann F, Stone-Roy LM, Kim S. Loss of cGMP-dependent protein kinase II alters ultrasonic vocalizations in mice, a model for speech impairment in human microdeletion 4q21 syndrome. Neurosci Lett 2021; 759:136048. [PMID: 34126178 DOI: 10.1016/j.neulet.2021.136048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Chromosome 4q21 microdeletion leads to a human syndrome that exhibits restricted growth, facial dysmorphisms, mental retardation, and absent or delayed speech. One of the key genes in the affected region of the chromosome is PRKG2, which encodes cGMP-dependent protein kinase II (cGKII). Mice lacking cGKII exhibit restricted growth and deficits in learning and memory, as seen in the human syndrome. However, vocalization impairments in these mice have not been determined. The molecular pathway underlying vocalization impairment in humans is not fully understood. Here, we employed cGKII knockout (KO) mice as a model for the human microdeletion syndrome to test whether vocalizations are affected by loss of the PRKG2 gene. Mice emit ultrasonic vocalizations (USVs) to communicate in social situations, stress, and isolation. We thus recorded ultrasonic vocalizations as a model for human speech. We isolated postnatal day 5-7 pups from the nest to record and analyze USVs and found significant differences in vocalizations of KO mice relative to wild-type and heterozygous mutant mice. KO mice produced fewer calls that were shorter duration and higher frequency. Because neuronal activation in the arcuate nucleus in the hypothalamus is important for the production of animal USVs following isolation from the nest, we assessed neuronal activity in the arcuate nucleus of KO pups following isolation. We found significant reduction of neuronal activation in cGKII KO pups after isolation. Taken together, our studies indicate that cGKII is important for neuronal activation in the arcuate nucleus, which significantly contributes to the production of USVs in neonatal mice. We further suggest cGKII KO mice can be a valuable animal model to investigate pathophysiology of human microdeletion 4q21 syndrome.
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Affiliation(s)
- Tiffany M Tran
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Jessica K Sherwood
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Michael J Doolittle
- Molecular, Cellular and Integrative Neurosciences Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Matheus F Sathler
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Leslie M Stone-Roy
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; Molecular, Cellular and Integrative Neurosciences Program, Colorado State University, Fort Collins, CO 80523, USA.
| | - Seonil Kim
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; Molecular, Cellular and Integrative Neurosciences Program, Colorado State University, Fort Collins, CO 80523, USA.
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28
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Niborski LL, Paces-Fessy M, Ricci P, Bourgeois A, Magalhães P, Kuzma-Kuzniarska M, Lesaulnier C, Reczko M, Declercq E, Zürbig P, Doucet A, Umbhauer M, Cereghini S. Hnf1b haploinsufficiency differentially affects developmental target genes in a new renal cysts and diabetes mouse model. Dis Model Mech 2021; 14:dmm047498. [PMID: 33737325 PMCID: PMC8126479 DOI: 10.1242/dmm.047498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/09/2021] [Indexed: 12/26/2022] Open
Abstract
Heterozygous mutations in HNF1B cause the complex syndrome renal cysts and diabetes (RCAD), characterized by developmental abnormalities of the kidneys, genital tracts and pancreas, and a variety of renal, pancreas and liver dysfunctions. The pathogenesis underlying this syndrome remains unclear as mice with heterozygous null mutations have no phenotype, while constitutive/conditional Hnf1b ablation leads to more severe phenotypes. We generated a novel mouse model carrying an identified human mutation at the intron-2 splice donor site. Unlike heterozygous mice previously characterized, mice heterozygous for the splicing mutation exhibited decreased HNF1B protein levels and bilateral renal cysts from embryonic day 15, originated from glomeruli, early proximal tubules (PTs) and intermediate nephron segments, concurrently with delayed PT differentiation, hydronephrosis and rare genital tract anomalies. Consistently, mRNA sequencing showed that most downregulated genes in embryonic kidneys were primarily expressed in early PTs and the loop of Henle and involved in ion/drug transport, organic acid and lipid metabolic processes, while the expression of previously identified targets upon Hnf1b ablation, including cystic disease genes, was weakly or not affected. Postnatal analyses revealed renal abnormalities, ranging from glomerular cysts to hydronephrosis and, rarely, multicystic dysplasia. Urinary proteomics uncovered a particular profile predictive of progressive decline in kidney function and fibrosis, and displayed common features with a recently reported urine proteome in an RCAD pediatric cohort. Altogether, our results show that reduced HNF1B levels lead to developmental disease phenotypes associated with the deregulation of a subset of HNF1B targets. They further suggest that this model represents a unique clinical/pathological viable model of the RCAD disease.
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MESH Headings
- Animals
- Animals, Newborn
- Cell Polarity
- Central Nervous System Diseases/genetics
- Central Nervous System Diseases/pathology
- Cilia/pathology
- Dental Enamel/abnormalities
- Dental Enamel/pathology
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/pathology
- Disease Models, Animal
- Embryo, Mammalian/pathology
- Gene Dosage
- Gene Expression Profiling
- Genes, Developmental
- Haploinsufficiency/genetics
- Hepatocyte Nuclear Factor 1-beta/genetics
- Heterozygote
- Humans
- Hydronephrosis/complications
- Kidney Diseases, Cystic/genetics
- Kidney Diseases, Cystic/pathology
- Kidney Glomerulus/pathology
- Kidney Tubules/pathology
- Mice, Inbred C57BL
- Mutation/genetics
- Nephrons/pathology
- RNA Splicing/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Severity of Illness Index
- Mice
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Affiliation(s)
- Leticia L. Niborski
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Mélanie Paces-Fessy
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Pierbruno Ricci
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Adeline Bourgeois
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Pedro Magalhães
- Mosaiques Diagnostics, 30659 Hannover, Germany
- Department of Pediatric Nephrology, Hannover Medical School, 30625 Hannover, Germany
| | - Maria Kuzma-Kuzniarska
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Celine Lesaulnier
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Martin Reczko
- Biomedical Sciences Research Center Alexander Fleming, Institute for Fundamental Biomedical Science, 16672 Athens, Greece
| | - Edwige Declercq
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | | | - Alain Doucet
- Sorbonne Université, Université Paris Descartes, UMRS 1138, CNRS, ERL 8228, Centre de Recherche des Cordeliers, F-75006 Paris, France
| | - Muriel Umbhauer
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
| | - Silvia Cereghini
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement, IBPS, UMR7622, F-75005 Paris, France
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29
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Forkhead Transcription Factors in Health and Disease. Trends Genet 2021; 37:460-475. [DOI: 10.1016/j.tig.2020.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
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30
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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31
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Rapaport F, Boisson B, Gregor A, Béziat V, Boisson-Dupuis S, Bustamante J, Jouanguy E, Puel A, Rosain J, Zhang Q, Zhang SY, Gleeson JG, Quintana-Murci L, Casanova JL, Abel L, Patin E. Negative selection on human genes underlying inborn errors depends on disease outcome and both the mode and mechanism of inheritance. Proc Natl Acad Sci U S A 2021; 118:e2001248118. [PMID: 33408250 PMCID: PMC7826345 DOI: 10.1073/pnas.2001248118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genetic variants underlying life-threatening diseases, being unlikely to be transmitted to the next generation, are gradually and selectively eliminated from the population through negative selection. We study the determinants of this evolutionary process in human genes underlying monogenic diseases by comparing various negative selection scores and an integrative approach, CoNeS, at 366 loci underlying inborn errors of immunity (IEI). We find that genes underlying autosomal dominant (AD) or X-linked IEI have stronger negative selection scores than those underlying autosomal recessive (AR) IEI, whose scores are not different from those of genes not known to be disease causing. Nevertheless, genes underlying AR IEI that are lethal before reproductive maturity with complete penetrance have stronger negative selection scores than other genes underlying AR IEI. We also show that genes underlying AD IEI by loss of function have stronger negative selection scores than genes underlying AD IEI by gain of function, while genes underlying AD IEI by haploinsufficiency are under stronger negative selection than other genes underlying AD IEI. These results are replicated in 1,140 genes underlying inborn errors of neurodevelopment. Finally, we propose a supervised classifier, SCoNeS, which predicts better than state-of-the-art approaches whether a gene is more likely to underlie an AD or AR disease. The clinical outcomes of monogenic inborn errors, together with their mode and mechanisms of inheritance, determine the levels of negative selection at their corresponding loci. Integrating scores of negative selection may facilitate the prioritization of candidate genes and variants in patients suspected to carry an inborn error.
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Affiliation(s)
- Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065;
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Anne Gregor
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
- Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
- Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, La Jolla, CA 92093
- Rady Children's Institute of Genomic Medicine, Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
- Laboratory for Pediatric Brain Disease, The Rockefeller University, New York, NY 10065
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, 75015 Paris, France
- Chair of Human Genomics and Evolution, Collège de France, 75231 Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
- Howard Hughes Medical Institute, New York, NY 10065
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France
- University of Paris, Imagine Institute, 75015 Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, 75015 Paris, France
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32
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Braverman-Gross C, Benvenisty N. Modeling Maturity Onset Diabetes of the Young in Pluripotent Stem Cells: Challenges and Achievements. Front Endocrinol (Lausanne) 2021; 12:622940. [PMID: 33692757 PMCID: PMC7937923 DOI: 10.3389/fendo.2021.622940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Maturity onset diabetes of the young (MODY), is a group of monogenic diabetes disorders. Rodent models for MODY do not fully recapitulate the human phenotypes, calling for models generated in human cells. Human pluripotent stem cells (hPSCs), capable of differentiation towards pancreatic cells, possess a great opportunity to model MODY disorders in vitro. Here, we review the models for MODY diseases in hPSCs to date and the molecular lessons learnt from them. We also discuss the limitations and challenges that these types of models are still facing.
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Borgese N, Navone F, Nukina N, Yamanaka T. Mutant VAPB: Culprit or Innocent Bystander of Amyotrophic Lateral Sclerosis? CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2021; 4:25152564211022515. [PMID: 37366377 PMCID: PMC10243577 DOI: 10.1177/25152564211022515] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/08/2021] [Accepted: 05/12/2021] [Indexed: 06/28/2023]
Abstract
Nearly twenty years ago a mutation in the VAPB gene, resulting in a proline to serine substitution (p.P56S), was identified as the cause of a rare, slowly progressing, familial form of the motor neuron degenerative disease Amyotrophic Lateral Sclerosis (ALS). Since then, progress in unravelling the mechanistic basis of this mutation has proceeded in parallel with research on the VAP proteins and on their role in establishing membrane contact sites between the ER and other organelles. Analysis of the literature on cellular and animal models reviewed here supports the conclusion that P56S-VAPB, which is aggregation-prone, non-functional and unstable, is expressed at levels that are insufficient to support toxic gain-of-function or dominant negative effects within motor neurons. Instead, insufficient levels of the product of the single wild-type allele appear to be required for pathological effects, and may be the main driver of the disease. In light of the multiple interactions of the VAP proteins, we address the consequences of specific VAPB depletion and highlight various affected processes that could contribute to motor neuron degeneration. In the future, distinction of specific roles of each of the two VAP paralogues should help to further elucidate the basis of p.P56S familial ALS, as well as of other more common forms of the disease.
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Affiliation(s)
- Nica Borgese
- CNR Institute of
Neuroscience, Vedano al Lambro (MB), Italy
| | | | - Nobuyuki Nukina
- Laboratory of Structural
Neuropathology, Doshisha University Graduate School of Brain Science,
Kyoto, Japan
| | - Tomoyuki Yamanaka
- Laboratory of Structural
Neuropathology, Doshisha University Graduate School of Brain Science,
Kyoto, Japan
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Kim HY, Song JY, Kim WI, Ko HC, Park SE, Jang JH, Kim SH. The First Case of an Infant with Familial A20 Haploinsufficiency in Korea. J Korean Med Sci 2020; 35:e252. [PMID: 32743991 PMCID: PMC7402923 DOI: 10.3346/jkms.2020.35.e252] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
Haploinsufficiency of A20 (HA20) is a newly described autoinflammatory disease caused by loss-of-function mutations in the TNFAIP3 gene. Clinical phenotypes are heterogenous and resemble Behçet's disease, juvenile idiopathic arthritis, inflammatory bowel disease, or periodic fever syndrome, with symptoms developing at an early age. Here, we report the first case of infantile familial HA20 in Korea, which mimics neonatal lupus erythematosus (NLE). A 2-month-old infant exhibited symptoms including recurrent fever, erythematous rashes, and oral ulcers, with elevated liver enzymes, and tested positive for several autoantibodies, similar to systemic lupus erythematosus (SLE); therefore, she was suspected to have NLE. However, six months after birth, symptoms and autoantibodies persisted. Then, we considered the possibility of other diseases that could cause early onset rashes and abnormal autoantibodies, including autoinflammatory syndrome, monogenic SLE, or complement deficiency, all of which are rare. The detailed family history revealed that her father had recurrent symptoms, including oral and genital ulcers, knee arthralgia, abdominal pain, and diarrhea. These Behcet-like symptoms last for many years since he was a teenager, and he takes medications irregularly only when those are severe, but doesn't want the full-scale treatment. Whole-exome sequencing was conducted to identify a possible genetic disorder, which manifested as pathogenic variant nonsense mutation in the TNFAIP3 gene, leading to HA20. In conclusion, HA20 should be considered in the differential diagnosis of an infant with an early-onset dominantly inherited inflammatory disease that presents with recurrent oral and genital ulcerations and fluctuating autoantibodies. Additionally, it also should be considered in an infant with suspected NLE, whose symptoms and abnormal autoantibodies persist.
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Affiliation(s)
- Hye Young Kim
- Department of Pediatrics, Medical Research Institute, Pusan National University School of Medicine, Pusan National University Hospital, Busan, Korea
| | - Ji Yeon Song
- Department of Pediatrics, Pusan National University Children's Hospital, Yangsan, Korea
| | - Woo Il Kim
- Department of Dermatology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Hyun Chang Ko
- Department of Dermatology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Su Eun Park
- Department of Pediatrics, Pusan National University Children's Hospital, Yangsan, Korea
| | - Ja Hyun Jang
- Laboratory Medicine, Green Cross Genome, Yongin, Korea
| | - Seong Heon Kim
- Department of Pediatrics, Pusan National University Children's Hospital, Yangsan, Korea
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea.
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35
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Cody JD. The Consequences of Abnormal Gene Dosage: Lessons from Chromosome 18. Trends Genet 2020; 36:764-776. [PMID: 32660784 DOI: 10.1016/j.tig.2020.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022]
Abstract
Accurate interpretation of genomic copy number variation (CNV) remains a challenge and has important consequences for both congenital and late-onset disease. Hemizygosity dosage characterization of the genes on chromosome 18 reveals a spectrum of outcomes ranging from no clinical effect, to risk factors for disease, to both low- and high-penetrance disease. These data are important for accurate and predictive clinical management. Additionally, the potential mechanisms of reduced penetrance due to dosage compensation are discussed as a key to understanding avenues for potential treatment. This review describes the chromosome 18 findings, and discusses the molecular mechanisms that allow haploinsufficiency, reduced penetrance, and dosage compensation.
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Affiliation(s)
- Jannine DeMars Cody
- Department of Pediatrics, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Chromosome 18 Registry and Research Society, San Antonio, TX 78229, USA.
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Shin SM, Skaar S, Danielson E, Lee SH. Aberrant expression of S-SCAM causes the loss of GABAergic synapses in hippocampal neurons. Sci Rep 2020; 10:83. [PMID: 31919468 PMCID: PMC6952429 DOI: 10.1038/s41598-019-57053-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/19/2019] [Indexed: 02/07/2023] Open
Abstract
The duplication and deletion mutations of the S-SCAM/MAGI-2 gene are associated with schizophrenia and infantile spasms, respectively. S-SCAM is a unique synaptic scaffolding protein that localizes to both excitatory and GABAergic synapses. However, consequences of aberrant S-SCAM expression on GABAergic synapses is little studied. Here we report the effect of S-SCAM knockdown and overexpression on GABAergic synapses. S-SCAM knockdown in cultured hippocampal neurons caused a drastic loss of both pre- and post-synaptic components of GABAergic synapses, indicating its essential role in GABAergic synapse formation and maintenance. Surprisingly, S-SCAM overexpression also attenuated GABAergic synapses, but the effect is mediated by the loss of postsynaptic GABAA receptors, gephyrin, and neuroligin 2 and does not involve presynaptic component vesicular GABA transporters. Overexpression studies using S-SCAM mutants with various domain deletions indicated that GABAergic synapse loss correlates with their ability to increase excitatory synaptic function. Consistently, AMPA receptor antagonist CNQX or calcineurin inhibitor FK506 abolished the S-SCAM overexpression-induced loss of GABAA receptors, supporting that GABAergic synapse loss by S-SCAM overexpression is due to the activity-induced dispersal of synaptic GABAA receptors. These results suggest that abnormal S-SCAM protein levels disrupt excitation/inhibition balance in neurons, which may explain the pathogenic nature of S-SCAM copy number variations.
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Affiliation(s)
- Seung Min Shin
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
| | - Samantha Skaar
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
| | - Eric Danielson
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA
| | - Sang H Lee
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA. .,Neuroscience Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, USA.
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Fowler DA, Larsson HCE. The benefits differential equations bring to limb development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 9:e364. [PMID: 31637866 DOI: 10.1002/wdev.364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/22/2019] [Accepted: 09/07/2019] [Indexed: 11/07/2022]
Abstract
Systems biology is a large field, offering a number of advantages to a variety of biological disciplines. In limb development, differential-equation based models can provide insightful hypotheses about the gene/protein interactions and tissue differentiation events that form the core of limb development research. Differential equations are like any other communicative tool, with misuse and limitations that can come along with their advantages. Every theory should be critically analyzed to best ascertain whether they reflect the reality in biology as well they claim. Differential equation-based models have consistent features which researchers have drawn upon to aid in more realistic descriptions and hypotheses. Nine features are described that highlight these trade-offs. The advantages range from more detailed descriptions of gene interactions and their consequence and the capacity to model robustness to the incorporation of tissue size and shape. The drawbacks come with the added complication that additional genes and signaling pathways that require additional terms within the mathematical model. They also come in the translation between the mathematical terms of the model, values and matrices, to the real world of genes, proteins, and tissues that constitute limb development. A critical analysis is necessary to ensure that these models effectively expand the understanding of the origins of a diversity of limb anatomy, from evolution to teratology. This article is categorized under: Vertebrate Organogenesis > Musculoskeletal and Vascular Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Establishment of Spatial and Temporal Patterns > Repeating Patterns and Lateral Inhibition.
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Affiliation(s)
- Donald A Fowler
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
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