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Yamaguchi H, Barrell WB, Faisal M, Liu KJ, Komatsu Y. Ciliary and non-ciliary functions of Rab34 during craniofacial bone development. Biochem Biophys Res Commun 2024; 724:150174. [PMID: 38852507 DOI: 10.1016/j.bbrc.2024.150174] [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: 05/22/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
The primary cilium is a hair-like projection that controls cell development and tissue homeostasis. Although accumulated studies identify the molecular link between cilia and cilia-related diseases, the underlying etiology of ciliopathies has not been fully understood. In this paper, we determine the function of Rab34, a small GTPase, as a key regulator for controlling ciliogenesis and type I collagen trafficking in craniofacial development. Mechanistically, Rab34 is required to form cilia that control osteogenic proliferation, survival, and differentiation via cilia-mediated Hedgehog signaling. In addition, Rab34 is indispensable for regulating type I collagen trafficking from the ER to the Golgi. These results demonstrate that Rab34 has both ciliary and non-ciliary functions to regulate osteogenesis. Our study highlights the critical function of Rab34, which may contribute to understanding the novel etiology of ciliopathies that are associated with the dysfunction of RAB34 in humans.
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Affiliation(s)
- Hiroyuki Yamaguchi
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - William B Barrell
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Maryam Faisal
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA; Department of Bioengineering, Rice University George R. Brown School of Engineering, Houston, TX, 77005, USA
| | - Karen J Liu
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Yoshihiro Komatsu
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA; Graduate Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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2
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Chen L, Xing X, Zhang P, Chen L, Pei H. Homeostatic regulation of NAD(H) and NADP(H) in cells. Genes Dis 2024; 11:101146. [PMID: 38988322 PMCID: PMC11233901 DOI: 10.1016/j.gendis.2023.101146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/31/2023] [Accepted: 09/11/2023] [Indexed: 07/12/2024] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+)/reduced NAD+ (NADH) and nicotinamide adenine dinucleotide phosphate (NADP+)/reduced NADP+ (NADPH) are essential metabolites involved in multiple metabolic pathways and cellular processes. NAD+ and NADH redox couple plays a vital role in catabolic redox reactions, while NADPH is crucial for cellular anabolism and antioxidant responses. Maintaining NAD(H) and NADP(H) homeostasis is crucial for normal physiological activity and is tightly regulated through various mechanisms, such as biosynthesis, consumption, recycling, and conversion between NAD(H) and NADP(H). The conversions between NAD(H) and NADP(H) are controlled by NAD kinases (NADKs) and NADP(H) phosphatases [specifically, metazoan SpoT homolog-1 (MESH1) and nocturnin (NOCT)]. NADKs facilitate the synthesis of NADP+ from NAD+, while MESH1 and NOCT convert NADP(H) into NAD(H). In this review, we summarize the physiological roles of NAD(H) and NADP(H) and discuss the regulatory mechanisms governing NAD(H) and NADP(H) homeostasis in three key aspects: the transcriptional and posttranslational regulation of NADKs, the role of MESH1 and NOCT in maintaining NAD(H) and NADP(H) homeostasis, and the influence of the circadian clock on NAD(H) and NADP(H) homeostasis. In conclusion, NADKs, MESH1, and NOCT are integral to various cellular processes, regulating NAD(H) and NADP(H) homeostasis. Dysregulation of these enzymes results in various human diseases, such as cancers and metabolic disorders. Hence, strategies aiming to restore NAD(H) and NADP(H) homeostasis hold promise as novel therapeutic approaches for these diseases.
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Affiliation(s)
- Luojun Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
| | - Xiaoke Xing
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Pingfeng Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
| | - Lulu Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Huadong Pei
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
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Laugwitz L, Cheng F, Collins SC, Hustinx A, Navarro N, Welsch S, Cox H, Hsieh TC, Vijayananth A, Buchert R, Bender B, Efthymiou S, Murphy D, Zafar F, Rana N, Grasshoff U, Falb RJ, Grimmel M, Seibt A, Zheng W, Ghaedi H, Thirion M, Couette S, Azizimalamiri R, Sadeghian S, Galehdari H, Zamani M, Zeighami J, Sedaghat A, Ramshe SM, Zare A, Alipoor B, Klee D, Sturm M, Ossowski S, Houlden H, Riess O, Wieczorek D, Gavin R, Maroofian R, Krawitz P, Yalcin B, Distelmaier F, Haack TB. ZSCAN10 deficiency causes a neurodevelopmental disorder with characteristic oto-facial malformations. Brain 2024; 147:2471-2482. [PMID: 38386308 PMCID: PMC11224597 DOI: 10.1093/brain/awae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 12/21/2023] [Accepted: 01/21/2024] [Indexed: 02/23/2024] Open
Abstract
Neurodevelopmental disorders are major indications for genetic referral and have been linked to more than 1500 loci including genes encoding transcriptional regulators. The dysfunction of transcription factors often results in characteristic syndromic presentations; however, at least half of these patients lack a genetic diagnosis. The implementation of machine learning approaches has the potential to aid in the identification of new disease genes and delineate associated phenotypes. Next generation sequencing was performed in seven affected individuals with neurodevelopmental delay and dysmorphic features. Clinical characterization included reanalysis of available neuroimaging datasets and 2D portrait image analysis with GestaltMatcher. The functional consequences of ZSCAN10 loss were modelled in mouse embryonic stem cells (mESCs), including a knockout and a representative ZSCAN10 protein truncating variant. These models were characterized by gene expression and western blot analyses, chromatin immunoprecipitation and quantitative PCR (ChIP-qPCR) and immunofluorescence staining. Zscan10 knockout mouse embryos were generated and phenotyped. We prioritized bi-allelic ZSCAN10 loss-of-function variants in seven affected individuals from five unrelated families as the underlying molecular cause. RNA-sequencing analyses in Zscan10-/- mESCs indicated dysregulation of genes related to stem cell pluripotency. In addition, we established in mESCs the loss-of-function mechanism for a representative human ZSCAN10 protein truncating variant by showing alteration of its expression levels and subcellular localization, interfering with its binding to DNA enhancer targets. Deep phenotyping revealed global developmental delay, facial asymmetry and malformations of the outer ear as consistent clinical features. Cerebral MRI showed dysplasia of the semicircular canals as an anatomical correlate of sensorineural hearing loss. Facial asymmetry was confirmed as a clinical feature by GestaltMatcher and was recapitulated in the Zscan10 mouse model along with inner and outer ear malformations. Our findings provide evidence of a novel syndromic neurodevelopmental disorder caused by bi-allelic loss-of-function variants in ZSCAN10.
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Affiliation(s)
- Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, Tübingen 72076, Germany
| | - Fubo Cheng
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | | | - Alexander Hustinx
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Nicolas Navarro
- Biogeosciences, UMR 6282 CNRS, EPHE, Université de Bourgogne, Dijon 2100, France
- EPHE, PSL University, Paris 75014, France
| | - Simon Welsch
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s Hospitals NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Aswinkumar Vijayananth
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Benjamin Bender
- Diagnostic and Interventional Neuroradiology, Radiologic Clinics, University of Tübingen, Tübingen 72076, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Faisal Zafar
- Pediatric Neurology, Children’s Hospital, Multan 60000, Pakistan
| | - Nuzhat Rana
- Pediatric Neurology, Children’s Hospital, Multan 60000, Pakistan
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Center for Rare Disease, University of Tübingen, Tübingen 72072, Germany
| | - Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Annette Seibt
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Wenxu Zheng
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Marie Thirion
- Inserm UMR1231, Université de Bourgogne, Dijon Cedex 21070, France
| | - Sébastien Couette
- Biogeosciences, UMR 6282 CNRS, EPHE, Université de Bourgogne, Dijon 2100, France
- EPHE, PSL University, Paris 75014, France
| | - Reza Azizimalamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 6155689467, Iran
| | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 6155689467, Iran
| | - Alireza Sedaghat
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 6155689467, Iran
- Diabetes Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Samira Molaei Ramshe
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Ali Zare
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Behnam Alipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj 7591741417, Iran
| | - Dirk Klee
- Department of Pediatric Radiology, Medical Faculty, Institute of Radiology, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Genomics England, Queen Mary University of London, London EC1M 6BQ, UK
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen 72076, Germany
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Center for Rare Disease, University of Tübingen, Tübingen 72072, Germany
| | - Dagmar Wieczorek
- Medical Faculty and University Hospital Düsseldorf, Institute of Human Genetics, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Ryan Gavin
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham B15 2TG, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Binnaz Yalcin
- Inserm UMR1231, Université de Bourgogne, Dijon Cedex 21070, France
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Center for Rare Disease, University of Tübingen, Tübingen 72072, Germany
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Jacinto JGP, Letko A, Häfliger IM, Drögemüller C, Agerholm JS. Congenital syndromic Chiari-like malformation (CSCM) in Holstein cattle: towards unravelling of possible genetic causes. Acta Vet Scand 2024; 66:29. [PMID: 38965607 PMCID: PMC11229497 DOI: 10.1186/s13028-024-00752-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Chiari malformation type II (CMII) was originally reported in humans as a rare disorder characterized by the downward herniation of the hindbrain and towering cerebellum. The congenital brain malformation is usually accompanied by spina bifida, a congenital spinal anomaly resulting from incomplete closure of the dorsal aspect of the spinal neural tube, and occasionally by other lesions. A similar disorder has been reported in several animal species, including cattle, particularly as a congenital syndrome. A cause of congenital syndromic Chiari-like malformation (CSCM) in cattle has not been reported to date. We collected a series of 14 CSCM-affected Holstein calves (13 purebred, one Red Danish Dairy F1 cross) and performed whole-genome sequencing (WGS). WGS was performed on 33 cattle, including eight cases with parents (trio-based; group 1), three cases with one parent (group 2), and three single cases (solo-based; group 3). RESULTS Sequencing-based genome-wide association study of the 13 Holstein calves with CSCM and 166 controls revealed no significantly associated genome region. Assuming a single Holstein breed-specific recessive allele, no region of shared homozygosity was detected suggesting heterogeneity. Subsequent filtering for protein-changing variants that were only homozygous in the genomes of the individual cases allowed the identification of two missense variants affecting different genes, SHC4 in case 4 in group 1 and WDR45B in case 13 in group 3. Furthermore, these two variants were only observed in Holstein cattle when querying WGS data of > 5,100 animals. Alternatively, potential de novo mutational events were assessed in each case. Filtering for heterozygous private protein-changing variants identified one DYNC1H1 frameshift variant as a candidate causal dominant acting allele in case 12 in group 3. Finally, the presence of larger structural DNA variants and chromosomal abnormalities was investigated in all cases. Depth of coverage analysis revealed two different partial monosomies of chromosome 2 segments in cases 1 and 7 in group 1 and a trisomy of chromosome 12 in the WDR45B homozygous case 13 in group 3. CONCLUSIONS This study presents for the first time a detailed genomic evaluation of CSCM in Holstein cattle and suggests an unexpected genetic and allelic heterogeneity considering the mode of inheritance, as well as the type of variant. For the first time, we propose candidate causal variants that may explain bovine CSCM in a certain proportion of affected calves. We present cattle as a large animal model for human CMII and propose new genes and genomic variants as possible causes for related diseases in both animals and humans.
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Affiliation(s)
- Joana Goncalves Pontes Jacinto
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3012, Switzerland
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3012, Switzerland
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3012, Switzerland
| | - Irene Monika Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3012, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern, 3012, Switzerland.
| | - Jørgen Steen Agerholm
- Department of Veterinary Clinical Sciences, University of Copenhagen, Højbakkegaard Allé 5A, Taastrup, 2630, Denmark
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Roston RA, Whikehart SM, Rolfe SM, Maga M. Morphological simulation tests the limits on phenotype discovery in 3D image analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.30.601430. [PMID: 39005442 PMCID: PMC11244899 DOI: 10.1101/2024.06.30.601430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In the past few decades, advances in 3D imaging have created new opportunities for reverse genetic screens. Rapidly growing datasets of 3D images of genetic knockouts require high-throughput, automated computational approaches for identifying and characterizing new phenotypes. However, exploratory, discovery-oriented image analysis pipelines used to discover these phenotypes can be difficult to validate because, by their nature, the expected outcome is not known a priori . Introducing known morphological variation through simulation can help distinguish between real phenotypic differences and random variation; elucidate the effects of sample size; and test the sensitivity and reproducibility of morphometric analyses. Here we present a novel approach for 3D morphological simulation that uses open-source, open-access tools available in 3D Slicer, SlicerMorph, and Advanced Normalization Tools in R (ANTsR). While we focus on diffusible-iodine contrast-enhanced micro-CT (diceCT) images, this approach can be used on any volumetric image. We then use our simulated datasets to test whether tensor-based morphometry (TBM) can recover our introduced differences; to test how effect size and sample size affect detectability; and to determine the reproducibility of our results. In our approach to morphological simulation, we first generate a simulated deformation based on a reference image and then propagate this deformation to subjects using inverse transforms obtained from the registration of subjects to the reference. This produces a new dataset with a shifted population mean while retaining individual variability because each sample deforms more or less based on how different or similar it is from the reference. TBM is a widely-used technique that statistically compares local volume differences associated with local deformations. Our results showed that TBM recovered our introduced morphological differences, but that detectability was dependent on the effect size, the sample size, and the region of interest (ROI) included in the analysis. Detectability of subtle phenotypes can be improved both by increasing the sample size and by limiting analyses to specific body regions. However, it is not always feasible to increase sample sizes in screens of essential genes. Therefore, methodical use of ROIs is a promising way to increase the power of TBM to detect subtle phenotypes. Generating known morphological variation through simulation has broad applicability in developmental, evolutionary, and biomedical morphometrics and is a useful way to distinguish between a failure to detect morphological difference and a true lack of morphological difference. Morphological simulation can also be applied to AI-based supervised learning to augment datasets and overcome dataset limitations.
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6
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Cacheiro P, Lawson S, Van den Veyver IB, Marengo G, Zocche D, Murray SA, Duyzend M, Robinson PN, Smedley D. Lethal phenotypes in Mendelian disorders. Genet Med 2024; 26:101141. [PMID: 38629401 PMCID: PMC11232373 DOI: 10.1016/j.gim.2024.101141] [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: 02/05/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
PURPOSE Existing resources that characterize the essentiality status of genes are based on either proliferation assessment in human cell lines, viability evaluation in mouse knockouts, or constraint metrics derived from human population sequencing studies. Several repositories document phenotypic annotations for rare disorders; however, there is a lack of comprehensive reporting on lethal phenotypes. METHODS We queried Online Mendelian Inheritance in Man for terms related to lethality and classified all Mendelian genes according to the earliest age of death recorded for the associated disorders, from prenatal death to no reports of premature death. We characterized the genes across these lethality categories, examined the evidence on viability from mouse models and explored how this information could be used for novel gene discovery. RESULTS We developed the Lethal Phenotypes Portal to showcase this curated catalog of human essential genes. Differences in the mode of inheritance, physiological systems affected, and disease class were found for genes in different lethality categories, as well as discrepancies between the lethal phenotypes observed in mouse and human. CONCLUSION We anticipate that this resource will aid clinicians in the diagnosis of early lethal conditions and assist researchers in investigating the properties that make these genes essential for human development.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Samantha Lawson
- ITS Research, Queen Mary University of London, London, United Kingdom
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | - Gabriel Marengo
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park and St Mark's Hospitals, London, United Kingdom
| | | | - Michael Duyzend
- Massachusetts General Hospital, Boston, MA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Peter N Robinson
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom.
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7
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He XD, Phillips S, Hioki K, Majhi PD, Babbitt C, Tremblay KD, Pobezinsky LA, Mager J. TATA-binding associated factors have distinct roles during early mammalian development. Dev Biol 2024; 511:53-62. [PMID: 38593904 PMCID: PMC11143476 DOI: 10.1016/j.ydbio.2024.04.002] [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: 12/21/2023] [Revised: 03/06/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
Early embryonic development is a finely orchestrated process that requires precise regulation of gene expression coordinated with morphogenetic events. TATA-box binding protein-associated factors (TAFs), integral components of transcription initiation coactivators like TFIID and SAGA, play a crucial role in this intricate process. Here we show that disruptions in TAF5, TAF12 and TAF13 individually lead to embryonic lethality in the mouse, resulting in overlapping yet distinct phenotypes. Taf5 and Taf12 mutant embryos exhibited a failure to implant post-blastocyst formation, and Taf5 mutants have aberrant lineage specification within the inner cell mass. In contrast, Taf13 mutant embryos successfully implant and form egg-cylinder stages but fail to initiate gastrulation. Strikingly, we observed a depletion of pluripotency factors in TAF13-deficient embryos, including OCT4, NANOG and SOX2, highlighting an indispensable role of TAF13 in maintaining pluripotency. Transcriptomic analysis revealed distinct gene targets affected by the loss of TAF5, TAF12 and TAF13. Thus, we propose that TAF5, TAF12 and TAF13 convey locus specificity to the TFIID complex throughout the mouse genome.
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Affiliation(s)
- Xinjian Doris He
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Shelby Phillips
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Kaito Hioki
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Prabin Dhangada Majhi
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Courtney Babbitt
- Department of Biology, University of Massachusetts, Amherst, MA, USA
| | - Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Leonid A Pobezinsky
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA.
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8
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Abe K, Masuya H, Shiroishi T. The 36th International Mammalian Genome Conference: A scientific gathering under the cherry blossoms in Tsukuba. Genes Cells 2024; 29:525-531. [PMID: 38845473 DOI: 10.1111/gtc.13131] [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: 10/04/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024]
Abstract
The 36th International Mammalian Genome Conference (IMGC) was held in a hybrid format at the Tsukuba International Congress Center in Tsukuba, Ibaraki, Japan, for 4 days from March 28 to 31, 2023. This international conference on functional genomics of mouse, human, and other mammalian species attracted 246 participants in total, of which 129 were from outside Japan, including Europe, the United States and Asia, and 117 participants were from Japan. The conference included three technical workshops, keynote lectures by domestic researchers, commemorative lectures for the conference awards, 57 oral presentations, and 97 poster presentations. The event was a great success. Topics included the establishment and analysis of disease models using genetically engineered or spontaneous mutant mice, systems genetic analysis using mouse strains such as wild-derived mice and recombinant inbred mouse strains, infectious diseases, immunology, and epigenetics. In addition, as a joint program, a two-day RIKEN Symposium was held, and active discussions continued over the four-day period. Also, there was a trainee symposium, in which young researchers were encouraged to participate, and excellent papers were selected as oral presentations in the main session.
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Affiliation(s)
- Kuniya Abe
- RIKEN BioResource Research Center, Ibaraki, Japan
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9
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Khadka P, Young CKJ, Sachidanandam R, Brard L, Young MJ. Our current understanding of the biological impact of endometrial cancer mtDNA genome mutations and their potential use as a biomarker. Front Oncol 2024; 14:1394699. [PMID: 38993645 PMCID: PMC11236604 DOI: 10.3389/fonc.2024.1394699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/10/2024] [Indexed: 07/13/2024] Open
Abstract
Endometrial cancer (EC) is a devastating and common disease affecting women's health. The NCI Surveillance, Epidemiology, and End Results Program predicted that there would be >66,000 new cases in the United States and >13,000 deaths from EC in 2023, and EC is the sixth most common cancer among women worldwide. Regulation of mitochondrial metabolism plays a role in tumorigenesis. In proliferating cancer cells, mitochondria provide the necessary building blocks for biosynthesis of amino acids, lipids, nucleotides, and glucose. One mechanism causing altered mitochondrial activity is mitochondrial DNA (mtDNA) mutation. The polyploid human mtDNA genome is a circular double-stranded molecule essential to vertebrate life that harbors genes critical for oxidative phosphorylation plus mitochondrial-derived peptide genes. Cancer cells display aerobic glycolysis, known as the Warburg effect, which arises from the needs of fast-dividing cells and is characterized by increased glucose uptake and conversion of glucose to lactate. Solid tumors often contain at least one mtDNA substitution. Furthermore, it is common for cancer cells to harbor mixtures of wild-type and mutant mtDNA genotypes, known as heteroplasmy. Considering the increase in cancer cell energy demand, the presence of functionally relevant carcinogenesis-inducing or environment-adapting mtDNA mutations in cancer seems plausible. We review 279 EC tumor-specific mtDNA single nucleotide variants from 111 individuals from different studies. Many transition mutations indicative of error-prone DNA polymerase γ replication and C to U deamination events were present. We examine the spectrum of mutations and their heteroplasmy and discuss the potential biological impact of recurrent, non-synonymous, insertion, and deletion mutations. Lastly, we explore current EC treatments, exploiting cancer cell mitochondria for therapy and the prospect of using mtDNA variants as an EC biomarker.
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Affiliation(s)
- Pabitra Khadka
- Department of Biomedical Sciences, Division of Biochemistry & Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States
| | - Carolyn K J Young
- Department of Biomedical Sciences, Division of Biochemistry & Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States
| | | | - Laurent Brard
- Obstetrics & Gynecology, Southern Illinois University School of Medicine, Springfield, IL, United States
- Simmons Cancer Institute, Springfield, IL, United States
| | - Matthew J Young
- Department of Biomedical Sciences, Division of Biochemistry & Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States
- Simmons Cancer Institute, Springfield, IL, United States
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10
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Han Z, Yang C, He H, Huang T, Yin Q, Tian G, Wu Y, Hu W, Lu L, Bajpai AK, Mi J, Xu F. Systems Genetics Analyses Reveals Key Genes Related to Behavioral Traits in the Striatum of CFW Mice. J Neurosci 2024; 44:e0252242024. [PMID: 38777602 PMCID: PMC11211725 DOI: 10.1523/jneurosci.0252-24.2024] [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: 02/06/2024] [Revised: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
The striatum plays a central role in directing many complex behaviors ranging from motor control to action choice and reward learning. In our study, we used 55 male CFW mice with rapid decay linkage disequilibrium to systematically mine the striatum-related behavioral functional genes by analyzing their striatal transcriptomes and 79 measured behavioral phenotypic data. By constructing a gene coexpression network, we clustered the genes into 13 modules, with most of them being positively correlated with motor traits. Based on functional annotations as well as Fisher's exact and hypergeometric distribution tests, brown and magenta modules were identified as core modules. They were significantly enriched for striatal-related functional genes. Subsequent Mendelian randomization analysis verified the causal relationship between the core modules and dyskinesia. Through the intramodular gene connectivity analysis, Adcy5 and Kcnma1 were identified as brown and magenta module hub genes, respectively. Knock outs of both Adcy5 and Kcnma1 lead to motor dysfunction in mice, and KCNMA1 acts as a risk gene for schizophrenia and smoking addiction in humans. We also evaluated the cellular composition of each module and identified oligodendrocytes in the striatum to have a positive role in motor regulation.
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Affiliation(s)
- Zhe Han
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Chunhua Yang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Hongjie He
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Tingting Huang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Quanting Yin
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Geng Tian
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Yuyong Wu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
| | - Wei Hu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Akhilesh Kumar Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Jia Mi
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
| | - Fuyi Xu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, Shandong Province, China
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Yantai 264003, Shandong Province, China
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11
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Foley K, McKee C, Mayer A, Ganguly A, Barnett D, Ward N, Zhang Y, Nairn A, Xia H. PP1β opposes classic PP1 function, inhibiting spine maturation and promoting LTP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.26.525737. [PMID: 36747779 PMCID: PMC9901188 DOI: 10.1101/2023.01.26.525737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Protein phosphatase 1 (PP1) regulates synaptic plasticity and has been described as a molecular constraint on learning and memory. There are three neuronal isoforms, PP1α, PP1β, and PP1γ, but little is known about their individual functions. PP1α and PP1γ are assumed to mediate the effects of PP1 on learning and memory based on their enrichment at dendritic spines and their preferential binding to neurabin and spinophilin, major PP1 synaptic scaffolding proteins. However, it was recently discovered that human de novo PP1β mutations cause intellectual disability, suggesting an important but ill-defined role for PP1β. In this study, we investigated the functions of each PP1 isoform in hippocampal synaptic physiology using conditional CA1-specific knockout mice. In stark contrast to classic PP1 function, we found that PP1β promotes synaptic plasticity as well as spatial memory. These changes in synaptic plasticity and memory are accompanied by changes in GluA1 phosphorylation, GluN2A levels, and dendritic spine density and morphology, including silent synapse number. These functions of PP1β reveal a previously unidentified signaling pathway regulating spine maturation and plasticity, broadening our understanding of the complex role of PP1 in synaptic physiology.
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12
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Kuula J, Czamara D, Hauta-Alus H, Lahti J, Hovi P, Miettinen ME, Ronkainen J, Eriksson JG, Andersson S, Järvelin MR, Sebert S, Räikkönen K, Binder EB, Kajantie E. Epigenetic signature of very low birth weight in young adult life. Pediatr Res 2024:10.1038/s41390-024-03354-6. [PMID: 38898107 DOI: 10.1038/s41390-024-03354-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 05/01/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Globally, one in ten babies is born preterm (<37 weeks), and 1-2% preterm at very low birth weight (VLBW, <1500 g). As adults, they are at increased risk for a plethora of health conditions, e.g., cardiometabolic disease, which may partly be mediated by epigenetic regulation. We compared blood DNA methylation between young adults born at VLBW and controls. METHODS 157 subjects born at VLBW and 161 controls born at term, from the Helsinki Study of Very Low Birth Weight Adults, were assessed for peripheral venous blood DNA methylation levels at mean age of 22 years. Significant CpG-sites (5'-C-phosphate-G-3') were meta-analyzed against continuous birth weight in four independent cohorts (pooled n = 2235) with cohort mean ages varying from 0 to 31 years. RESULTS In the discovery cohort, 66 CpG-sites were differentially methylated between VLBW adults and controls. Top hits were located in HIF3A, EBF4, and an intergenic region nearest to GLI2 (distance 57,533 bp). Five CpG-sites, all in proximity to GLI2, were hypermethylated in VLBW and associated with lower birth weight in the meta-analysis. CONCLUSION We identified differentially methylated CpG-sites suggesting an epigenetic signature of preterm birth at VLBW present in adult life. IMPACT Being born preterm at very low birth weight has major implications for later health and chronic disease risk factors. The mechanism linking preterm birth to later outcomes remains unknown. Our cohort study of 157 very low birth weight adults and 161 controls found 66 differentially methylated sites at mean age of 22 years. Our findings suggest an epigenetic mark of preterm birth present in adulthood, which opens up opportunities for mechanistic studies.
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Affiliation(s)
- Juho Kuula
- Population Health Research, Finnish Institute for Health and Welfare, Helsinki, Finland.
- HUS Medical Imaging Center, Department of Radiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Helena Hauta-Alus
- Population Health Research, Finnish Institute for Health and Welfare, Helsinki, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Petteri Hovi
- Population Health Research, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Maija E Miettinen
- Population Health Research, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Justiina Ronkainen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Johan G Eriksson
- Folkhälsan Research Centre, Topeliusgatan 20, 00250, Helsinki, Finland
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Obstetrics & Gynaecology and Human Potential Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sture Andersson
- Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | | | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Eero Kajantie
- Population Health Research, Finnish Institute for Health and Welfare, Helsinki, Finland
- Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Clinical Medicine Research Unit, University of Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
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13
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López-González I, Oseguera-López I, Castillo R, Darszon A. Influence of extracellular ATP on mammalian sperm physiology. Reprod Fertil Dev 2024; 36:RD23227. [PMID: 38870344 DOI: 10.1071/rd23227] [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: 12/14/2023] [Accepted: 05/23/2024] [Indexed: 06/15/2024] Open
Abstract
In addition to its central role in cellular metabolism, adenosine 5'-triphosphate (ATP) is an important extracellular signalling molecule involved in various physiological processes. In reproduction, extracellular ATP participates in both autocrine and paracrine paths regulating gametogenesis, gamete maturation and fertilisation. This review focusses on how extracellular ATP modulates sperm physiology with emphasis on the mammalian acrosome reaction. The presence of extracellular ATP in the reproductive tract is primarily determined by the ion channels and transporters that influence its movement within the cells comprising the tract. The main targets of extracellular ATP in spermatozoa are its own transporters, particularly species-specific sperm purinergic receptors. We also discuss notable phenotypes from knock-out mouse models and human Mendelian inheritance related to ATP release mechanisms, along with immunological, proteomic, and functional observations regarding sperm purinergic receptors and their involvement in sperm signalling.
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Affiliation(s)
- I López-González
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad # 2001, Col. Chamilpa, Cuernavaca, Morelos CP 62210, México
| | - I Oseguera-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad # 2001, Col. Chamilpa, Cuernavaca, Morelos CP 62210, México
| | - R Castillo
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad # 2001, Col. Chamilpa, Cuernavaca, Morelos CP 62210, México
| | - A Darszon
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad # 2001, Col. Chamilpa, Cuernavaca, Morelos CP 62210, México
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14
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Cacheiro P, Pava D, Parkinson H, VanZanten M, Wilson R, Gunes O, The International Mouse Phenotyping Consortium, Smedley D. Computational identification of disease models through cross-species phenotype comparison. Dis Model Mech 2024; 17:dmm050604. [PMID: 38881316 PMCID: PMC11247498 DOI: 10.1242/dmm.050604] [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: 11/13/2023] [Accepted: 06/11/2024] [Indexed: 06/18/2024] Open
Abstract
The use of standardised phenotyping screens to identify abnormal phenotypes in mouse knockouts, together with the use of ontologies to describe such phenotypic features, allows the implementation of an automated and unbiased pipeline to identify new models of disease by performing phenotype comparisons across species. Using data from the International Mouse Phenotyping Consortium (IMPC), approximately half of mouse mutants are able to mimic, at least partially, the human ortholog disease phenotypes as computed by the PhenoDigm algorithm. We found the number of phenotypic abnormalities in the mouse and the corresponding Mendelian disorder, the pleiotropy and severity of the disease, and the viability and zygosity status of the mouse knockout to be associated with the ability of mouse models to recapitulate the human disorder. An analysis of the IMPC impact on disease gene discovery through a publication-tracking system revealed that the resource has been implicated in at least 109 validated rare disease-gene associations over the last decade.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Diego Pava
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maya VanZanten
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert Wilson
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Osman Gunes
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
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15
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Yamaguchi J, Kokuryo T, Yokoyama Y, Oishi S, Sunagawa M, Mizuno T, Onoe S, Watanabe N, Ogura A, Ebata T. Trefoil factor 1 suppresses stemness and enhances chemosensitivity of pancreatic cancer. Cancer Med 2024; 13:e7395. [PMID: 38872370 PMCID: PMC11176577 DOI: 10.1002/cam4.7395] [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: 11/12/2023] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND AND AIMS Pancreatic cancer is one of the most lethal malignancies, partly due to resistance to conventional chemotherapy. The chemoresistance of malignant tumors is associated with epithelial-mesenchymal transition (EMT) and the stemness of cancer cells. The aim of this study is to investigate the availability and functional mechanisms of trefoil factor family 1 (TFF1), a tumor-suppressive protein in pancreatic carcinogenesis, to treat pancreatic cancer. METHODS To investigate the role of endogenous TFF1 in human and mice, specimens of human pancreatic cancer and genetically engineered mouse model of pancreatic cancer (KPC/TFF1KO; Pdx1-Cre/LSL-KRASG12D/LSL-p53R172H/TFF1-/-) were analyzed by immunohistochemistry (IHC). To explore the efficacy of extracellular administration of TFF1, recombinant and chemically synthesized TFF1 were administered to pancreatic cancer cell lines, a xenograft mouse model and a transgenic mouse model. RESULTS The deficiency of TFF1 was associated with increased EMT of cancer cells in mouse models of pancreatic cancer, KPC. The expression of TFF1 in cancer cells was associated with better survival rate of the patients who underwent chemotherapy, and loss of TFF1 deteriorated the benefit of gemcitabine in KPC mice. Extracellular administration of TFF1 inhibited gemcitabine-induced EMT, Wnt pathway activation and cancer stemness, eventually increased apoptosis of pancreatic cancer cells in vitro. In vivo, combined treatment of gemcitabine and subcutaneous administration of TFF1 arrested tumor growth in xenograft mouse model and resulted in the better survival of KPC mice by inhibiting EMT and cancer stemness. CONCLUSION These results indicate that TFF1 can contribute to establishing a novel strategy to treat pancreatic cancer patients by enhancing chemosensitivity.
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Affiliation(s)
- Junpei Yamaguchi
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshio Kokuryo
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukihiro Yokoyama
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Masaki Sunagawa
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Mizuno
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shunsuke Onoe
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuyuki Watanabe
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsushi Ogura
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoki Ebata
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Kasprzyk-Pawelec A, Tan M, Rahhal R, McIntosh A, Fernandez H, Mosaoa R, Jiang L, Pearson GW, Glasgow E, Vockley J, Albanese C, Avantaggiati ML. Loss of the mitochondrial carrier, SLC25A1, during embryogenesis induces a unique senescence program controlled by p53. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.18.549409. [PMID: 37503155 PMCID: PMC10370133 DOI: 10.1101/2023.07.18.549409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Germline inactivating mutations of the SLC25A1 gene contribute to various human developmental disorders, including combined D/L-2-hydroxyglutaric aciduria (D/L-2HGA), a severe systemic syndrome characterized by the accumulation of both enantiomers of 2-hydroxyglutaric acid (2HG). The mechanisms by which SLC25A1 deficiency leads to this disease and the role of 2HG are unclear and no therapies exist. We now show that mice lacking both Slc25a1 alleles display a spectrum of alterations that resemble human D/L-2HGA. Mechanistically, SLC25A1 loss results in a proliferation defect and activates two distinct senescence pathways, oncogene-induced senescence (OIS) and mitochondrial dysfunction-induced senescence (MiDAS), both involving the p53 tumor suppressor and driven by two discernible signals: the accumulation of 2HG, inducing OIS, and mitochondrial dysfunction, triggering MiDAS. Inhibiting these senescence programs or blocking p53 activity reverses the growth defect caused by SLC25A1 dysfunction and restores proliferation. These findings reveal novel pathogenic roles of senescence in human disorders and suggest potential strategies to correct the molecular alterations caused by SLC25A1 loss.
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17
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Zhao Y, Ansarullah, Kumar P, Mahoney JM, He H, Baker C, George J, Li S. Causal network perturbation analysis identifies known and novel type-2 diabetes driver genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595431. [PMID: 38826370 PMCID: PMC11142180 DOI: 10.1101/2024.05.22.595431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The molecular pathogenesis of diabetes is multifactorial, involving genetic predisposition and environmental factors that are not yet fully understood. However, pancreatic β-cell failure remains among the primary reasons underlying the progression of type-2 diabetes (T2D) making targeting β-cell dysfunction an attractive pathway for diabetes treatment. To identify genetic contributors to β-cell dysfunction, we investigated single-cell gene expression changes in β-cells from healthy (C57BL/6J) and diabetic (NZO/HlLtJ) mice fed with normal or high-fat, high-sugar diet (HFHS). Our study presents an innovative integration of the causal network perturbation assessment (ssNPA) framework with meta-cell transcriptome analysis to explore the genetic underpinnings of type-2 diabetes (T2D). By generating a reference causal network and in silico perturbation, we identified novel genes implicated in T2D and validated our candidates using the Knockout Mouse Phenotyping (KOMP) Project database.
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Affiliation(s)
- Yue Zhao
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ansarullah
- Center for Biometric Analysis, The Jackson Laboratory, Bar Harbor, ME, USA
| | - Parveen Kumar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Hao He
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Candice Baker
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
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18
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Dorans E, Jagadeesh K, Dey K, Price AL. Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307813. [PMID: 38826240 PMCID: PMC11142273 DOI: 10.1101/2024.05.24.24307813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown great promise in linking regulatory elements to genes. However, existing methods differ in their modeling assumptions and approaches to account for biological and technical noise-leading to low concordance in their linking scores-and do not capture the effects of genomic distance. We propose pgBoost, an integrative modeling framework that trains a non-linear combination of existing linking strategies (including genomic distance) on fine-mapped eQTL data to assign a probabilistic score to each candidate SNP-gene link. We applied pgBoost to single-cell multiome data from 85k cells representing 6 major immune/blood cell types. pgBoost attained higher enrichment for fine-mapped eSNP-eGene pairs (e.g. 21x at distance >10kb) than existing methods (1.2-10x; p-value for difference = 5e-13 vs. distance-based method and < 4e-35 for each other method), with larger improvements at larger distances (e.g. 35x vs. 0.89-6.6x at distance >100kb; p-value for difference < 0.002 vs. each other method). pgBoost also outperformed existing methods in enrichment for CRISPR-validated links (e.g. 4.8x vs. 1.6-4.1x at distance >10kb; p-value for difference = 0.25 vs. distance-based method and < 2e-5 for each other method), with larger improvements at larger distances (e.g. 15x vs. 1.6-2.5x at distance >100kb; p-value for difference < 0.009 for each other method). Similar improvements in enrichment were observed for links derived from Activity-By-Contact (ABC) scores and GWAS data. We further determined that restricting pgBoost to features from a focal cell type improved the identification of SNP-gene links relevant to that cell type. We highlight several examples where pgBoost linked fine-mapped GWAS variants to experimentally validated or biologically plausible target genes that were not implicated by other methods. In conclusion, a non-linear combination of linking strategies, including genomic distance, improves power to identify target genes underlying GWAS associations.
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Li G, Liu Y, Feng X, Diao S, Zhong Z, Li B, Teng J, Zhang W, Zeng H, Cai X, Gao Y, Liu X, Yuan X, Li J, Zhang Z. Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations. Int J Mol Sci 2024; 25:5689. [PMID: 38891877 PMCID: PMC11171535 DOI: 10.3390/ijms25115689] [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: 04/17/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
The domestic pig (Sus scrofa) and its subfamilies have experienced long-term and extensive gene flow, particularly in Southeast Asia. Here, we analyzed 236 pigs, focusing on Yunnan indigenous, European commercial, East Asian, and Southeast Asian breeds, using the Pig Genomics Reference Panel (PGRP v1) of Pig Genotype-Tissue Expression (PigGTEx) to investigate gene flow and associated complex traits by integrating multiple database resources. In this study, we discovered evidence of admixtures from European pigs into the genome of Yunnan indigenous pigs. Additionally, we hypothesized that a potential conceptual gene flow route that may have contributed to the genetic composition of the Diannan small-ear pig is a gene exchange from the Vietnamese pig. Based on the most stringent gene introgression scan using the fd statistic, we identified three specific loci on chromosome 8, ranging from 51.65 to 52.45 Mb, which exhibited strong signatures of selection and harbored the NAF1, NPY1R, and NPY5R genes. These genes are associated with complex traits, such as fat mass, immunity, and litter weight, in pigs, as supported by multiple bio-functionalization databases. We utilized multiple databases to explore the potential dynamics of genetic exchange in Southeast Asian pig populations and elucidated specific gene functionalities.
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Affiliation(s)
- Guangzhen Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Yuqiang Liu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xueyan Feng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Shuqi Diao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Zhanming Zhong
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Bolang Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Jinyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Wenjing Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Haonan Zeng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xiaodian Cai
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Yahui Gao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Xiaolong Yuan
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
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20
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Ohanele C, Peoples JN, Karlstaedt A, Geiger JT, Gayle AD, Ghazal N, Sohani F, Brown ME, Davis ME, Porter GA, Faundez V, Kwong JQ. Mitochondrial citrate carrier SLC25A1 is a dosage-dependent regulator of metabolic reprogramming and morphogenesis in the developing heart. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.22.541833. [PMID: 37292906 PMCID: PMC10245819 DOI: 10.1101/2023.05.22.541833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The developing mammalian heart undergoes an important metabolic shift from glycolysis toward mitochondrial oxidation, such that oxidative phosphorylation defects may present with cardiac abnormalities. Here, we describe a new mechanistic link between mitochondria and cardiac morphogenesis, uncovered by studying mice with systemic loss of the mitochondrial citrate carrier SLC25A1. Slc25a1 null embryos displayed impaired growth, cardiac malformations, and aberrant mitochondrial function. Importantly, Slc25a1 heterozygous embryos, which are overtly indistinguishable from wild type, exhibited an increased frequency of these defects, suggesting Slc25a1 haploinsuffiency and dose-dependent effects. Supporting clinical relevance, we found a near-significant association between ultrarare human pathogenic SLC25A1 variants and pediatric congenital heart disease. Mechanistically, SLC25A1 may link mitochondria to transcriptional regulation of metabolism through epigenetic control of gene expression to promote metabolic remodeling in the developing heart. Collectively, this work positions SLC25A1 as a novel mitochondrial regulator of ventricular morphogenesis and cardiac metabolic maturation and suggests a role in congenital heart disease.
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21
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Hamilton M, Russell S, Swanson GM, Krawetz SA, Menezes K, Moskovtsev SI, Librach C. A comprehensive analysis of spermatozoal RNA elements in idiopathic infertile males undergoing fertility treatment. Sci Rep 2024; 14:10316. [PMID: 38705876 PMCID: PMC11070429 DOI: 10.1038/s41598-024-60586-6] [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: 12/05/2023] [Accepted: 04/24/2024] [Indexed: 05/07/2024] Open
Abstract
Current approaches to diagnosing male infertility inadequately assess the complexity of the male gamete. Beyond the paternal haploid genome, spermatozoa also deliver coding and non-coding RNAs to the oocyte. While sperm-borne RNAs have demonstrated potential involvement in embryo development, the underlying mechanisms remain unclear. In this study, 47 sperm samples from normozoospermic males undergoing fertility treatment using donor oocytes were sequenced and analyzed to evaluate associations between sperm RNA elements (exon-sized sequences) and blastocyst progression. A total of 366 RNA elements (REs) were significantly associated with blastocyst rate (padj < 0.05), some of which were linked to genes related to critical developmental processes, including mitotic spindle formation and both ectoderm and mesoderm specification. Of note, 27 RE-associated RNAs are predicted targets of our previously reported list of developmentally significant miRNAs. Inverse RE-miRNA expression patterns were consistent with miRNA-mediated down-regulation. This study provides a comprehensive set of REs which differ by the patient's ability to produce blastocysts. This knowledge can be leveraged to improve clinical screening of male infertility and ultimately reduce time to pregnancy.
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Affiliation(s)
| | | | - Grace M Swanson
- Department of Obstetrics and Gynecology, Center for Molecular Medicine & Genetics, C.S. Mott Center, Wayne State University School of Medicine, Detroit, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Center for Molecular Medicine & Genetics, C.S. Mott Center, Wayne State University School of Medicine, Detroit, USA
| | | | - Sergey I Moskovtsev
- CReATe Fertility Centre, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Clifford Librach
- CReATe Fertility Centre, Toronto, ON, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
- Department of Physiology and Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Sunnybrook Research Institute, Toronto, ON, Canada
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22
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Vidović D, Waller A, Holmes J, Sklar LA, Schürer SC. Best practices for managing and disseminating resources and outreach and evaluating the impact of the IDG Consortium. Drug Discov Today 2024; 29:103953. [PMID: 38508231 DOI: 10.1016/j.drudis.2024.103953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
The Illuminating the Druggable Genome (IDG) consortium generated reagents, biological model systems, data, informatic databases, and computational tools. The Resource Dissemination and Outreach Center (RDOC) played a central administrative role, organized internal meetings, fostered collaboration, and coordinated consortium-wide efforts. The RDOC developed and deployed a Resource Management System (RMS) to enable efficient workflows for collecting, accessing, validating, registering, and publishing resource metadata. IDG policies for repositories and standardized representations of resources were established, adopting the FAIR (findable, accessible, interoperable, reusable) principles. The RDOC also developed metrics of IDG impact. Outreach initiatives included digital content, the Protein Illumination Timeline (representing milestones in generating data and reagents), the Target Watch publication series, the e-IDG Symposium series, and leveraging social media platforms.
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Affiliation(s)
- Dušica Vidović
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Anna Waller
- Department of Pathology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Jayme Holmes
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Larry A Sklar
- Department of Pathology, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA; Autophagy, Inflammation, & Metabolism (AIM) Center, University of New Mexico, Albuquerque, NM, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA; Frost Institute for Data Science & Computing, University of Miami, Miami, FL, USA.
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23
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Chander A, Mager J. Loss of KANSL3 leads to defective inner cell mass and early embryonic lethality. Mol Reprod Dev 2024; 91:e23760. [PMID: 38769918 PMCID: PMC11244731 DOI: 10.1002/mrd.23760] [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: 11/07/2023] [Revised: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024]
Abstract
e-Lysine acetylation is a prominent histone mark found at transcriptionally active loci. Among many lysine acetyl transferases, nonspecific lethal complex (NSL) members are known to mediate the modification of histone H4. In addition to histone modifications, the KAT8 regulatory complex subunit 3 gene (Kansl3), a core member of NSL complex, has been shown to be involved in several other cellular processes such as mitosis and mitochondrial activity. Although functional studies have been performed on NSL complex members, none of the four core proteins, including Kansl3, have been studied during early mouse development. Here we show that homozygous knockout Kansl3 embryos are lethal at peri-implantation stages, failing to hatch out of the zona pellucida. When the zona pellucida is removed in vitro, Kansl3 null embryos form an abnormal outgrowth with significantly disrupted inner cell mass (ICM) morphology. We document lineage-specific defects at the blastocyst stage with significantly reduced ICM cell number but no difference in trophectoderm cell numbers. Both epiblast and primitive endoderm lineages are altered with reduced cell numbers in null mutants. These results show that Kansl3 is indispensable during early mouse embryonic development and with defects in both ICM and trophectoderm lineages.
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Affiliation(s)
- Ashmita Chander
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Veterinary and Animal Sciences, University of Massachusetts-Amherst, 661 North Pleasant Street, Amherst, Massachusetts, USA
| | - Jesse Mager
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Veterinary and Animal Sciences, University of Massachusetts-Amherst, 661 North Pleasant Street, Amherst, Massachusetts, USA
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24
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Chong ACN, Vandana JJ, Jeng G, Li G, Meng Z, Duan X, Zhang T, Qiu Y, Duran-Struuck R, Coker K, Wang W, Li Y, Min Z, Zuo X, de Silva N, Chen Z, Naji A, Hao M, Liu C, Chen S. Checkpoint kinase 2 controls insulin secretion and glucose homeostasis. Nat Chem Biol 2024; 20:566-576. [PMID: 37945898 PMCID: PMC11062908 DOI: 10.1038/s41589-023-01466-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 10/03/2023] [Indexed: 11/12/2023]
Abstract
After the discovery of insulin, a century ago, extensive work has been done to unravel the molecular network regulating insulin secretion. Here we performed a chemical screen and identified AZD7762, a compound that potentiates glucose-stimulated insulin secretion (GSIS) of a human β cell line, healthy and type 2 diabetic (T2D) human islets and primary cynomolgus macaque islets. In vivo studies in diabetic mouse models and cynomolgus macaques demonstrated that AZD7762 enhances GSIS and improves glucose tolerance. Furthermore, genetic manipulation confirmed that ablation of CHEK2 in human β cells results in increased insulin secretion. Consistently, high-fat-diet-fed Chk2-/- mice show elevated insulin secretion and improved glucose clearance. Finally, untargeted metabolic profiling demonstrated the key role of the CHEK2-PP2A-PLK1-G6PD-PPP pathway in insulin secretion. This study successfully identifies a previously unknown insulin secretion regulating pathway that is conserved across rodents, cynomolgus macaques and human β cells in both healthy and T2D conditions.
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Affiliation(s)
- Angie Chi Nok Chong
- Department of Surgery, Weill Cornell Medicine, New York City, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York City, NY, USA
| | - J Jeya Vandana
- Department of Surgery, Weill Cornell Medicine, New York City, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York City, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York City, NY, USA
| | - Ginnie Jeng
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ge Li
- Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- Department of Biological Sciences, Bronx Community College, City University of New York, Bronx, NY, USA
| | - Zihe Meng
- Department of Surgery, Weill Cornell Medicine, New York City, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York City, NY, USA
| | - Xiaohua Duan
- Department of Surgery, Weill Cornell Medicine, New York City, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York City, NY, USA
| | - Tuo Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York City, NY, USA
| | - Yunping Qiu
- Department of Medicine, Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Raimon Duran-Struuck
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Kimberly Coker
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Wei Wang
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Yanjing Li
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Zaw Min
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Xi Zuo
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Neranjan de Silva
- Department of Surgery, Weill Cornell Medicine, New York City, NY, USA
| | - Zhengming Chen
- Department of Population Health Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Ali Naji
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Mingming Hao
- Department of Biochemistry, Weill Cornell Medicine, New York City, NY, USA
| | - Chengyang Liu
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York City, NY, USA.
- Center for Genomic Health, Weill Cornell Medicine, New York City, NY, USA.
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25
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Stenton SL, O'Leary MC, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O'Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson MW, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JOB, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O'Donnell-Luria A. Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project. Hum Genomics 2024; 18:44. [PMID: 38685113 PMCID: PMC11057178 DOI: 10.1186/s40246-024-00604-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and prioritization of the vast number of variants detected, computational methods are proliferating. Knowing which tools are most effective remains unclear. To evaluate the performance of computational methods, and to encourage innovation in method development, we designed a Critical Assessment of Genome Interpretation (CAGI) community challenge to place variant prioritization models head-to-head in a real-life clinical diagnostic setting. METHODS We utilized genome sequencing (GS) data from families sequenced in the Rare Genomes Project (RGP), a direct-to-participant research study on the utility of GS for rare disease diagnosis and gene discovery. Challenge predictors were provided with a dataset of variant calls and phenotype terms from 175 RGP individuals (65 families), including 35 solved training set families with causal variants specified, and 30 unlabeled test set families (14 solved, 16 unsolved). We tasked teams to identify causal variants in as many families as possible. Predictors submitted variant predictions with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on the rank position of causal variants, and the maximum F-measure, based on precision and recall of causal variants across all EPCR values. RESULTS Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performers recalled causal variants in up to 13 of 14 solved families within the top 5 ranked variants. Newly discovered diagnostic variants were returned to two previously unsolved families following confirmatory RNA sequencing, and two novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant in an unsolved proband with phenotypes consistent with asparagine synthetase deficiency. CONCLUSIONS Model methodology and performance was highly variable. Models weighing call quality, allele frequency, predicted deleteriousness, segregation, and phenotype were effective in identifying causal variants, and models open to phenotype expansion and non-coding variants were able to capture more difficult diagnoses and discover new diagnoses. Overall, computational models can significantly aid variant prioritization. For use in diagnostics, detailed review and conservative assessment of prioritized variants against established criteria is needed.
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Affiliation(s)
- Sarah L Stenton
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Melanie C O'Leary
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace E VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie DiTroia
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay S Ganesh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily O'Heir
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brian Mangilog
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lynn S Pais
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jillian Serrano
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael W Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marwa Abdelhakim
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Azza Althagafi
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computer Science Department, College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Giulia Babbi
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Riccardo Bellazzi
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Maria Giulia Carta
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Manavalan Gajapathy
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Thomas Joseph
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Yulan Lu
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Tarun Karthik Kumar Mamidi
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Mulargia
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giovanna Nicora
- enGenome Srl, Pavia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | | | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yisu Peng
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Maurizio S Podda
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy
- University of Siena, Siena, Italy
- CTGLab, Institute of Informatics and Telematics (IIT), CNR, ViaMoruzzi 1, 56124, Pisa, Italy
| | - Aditya Rao
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | | | - Vangala G Saipradeep
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Peter Schols
- Invitae, San Francisco, CA, USA
- Codon One, Louvain, EU, Belgium
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA
| | - Naveen Sivadasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | | | - Rajgopal Srinivasan
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Uma Sunderam
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Naina Tiwari
- TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India
| | - Xiao Wang
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elizabeth A Worthey
- Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rujie Yin
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Yuning You
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - Daniel Zeiberg
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Constantina Bakolitsa
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
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26
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Son R, Yamazawa K, Oguchi A, Suga M, Tamura M, Yanagita M, Murakawa Y, Kume S. Morphomics via next-generation electron microscopy. J Mol Cell Biol 2024; 15:mjad081. [PMID: 38148118 PMCID: PMC11167312 DOI: 10.1093/jmcb/mjad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/02/2022] [Accepted: 12/23/2023] [Indexed: 12/28/2023] Open
Abstract
The living body is composed of innumerable fine and complex structures. Although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable. However, conventional EM settings are limited to a narrow tissue area, which can bias observations. Recently, new trends in EM research have emerged, enabling coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Moreover, cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological bioimages. Taken together, these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology, which now arises as a new omics science termed 'morphomics'.
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Affiliation(s)
- Raku Son
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kenji Yamazawa
- Advanced Manufacturing Support Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan
| | - Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Mitsuo Suga
- Multimodal Microstructure Analysis Unit, RIKEN–JEOL Collaboration Center, Kobe 650-0047, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
- IFOM—The FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Satoshi Kume
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
- Center for Health Science Innovation, Osaka City University, Osaka 530-0011, Japan
- Osaka Electro-Communication University, Neyagawa 572-8530, Japan
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27
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Lara MK, Brabec JL, Hernan AE, Scott RC, Tyler AL, Mahoney JM. Network-based analysis predicts interacting genetic modifiers from a meta-mapping study of spike-wave discharge in mice. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12879. [PMID: 38444174 PMCID: PMC10915378 DOI: 10.1111/gbb.12879] [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: 05/22/2023] [Revised: 11/29/2023] [Accepted: 12/19/2023] [Indexed: 03/07/2024]
Abstract
Absence seizures are characterized by brief lapses in awareness accompanied by a hallmark spike-and-wave discharge (SWD) electroencephalographic pattern and are common to genetic generalized epilepsies (GGEs). While numerous genes have been associated with increased risk, including some Mendelian forms with a single causal allele, most cases of GGE are idiopathic and there are many unknown genetic modifiers of GGE influencing risk and severity. In a previous meta-mapping study, crosses between transgenic C57BL/6 and C3HeB/FeJ strains, each carrying one of three SWD-causing mutations (Gabrg2tm1Spet(R43Q) , Scn8a8j or Gria4spkw1 ), demonstrated an antagonistic epistatic interaction between loci on mouse chromosomes 2 and 7 influencing SWD. These results implicate universal modifiers in the B6 background that mitigate SWD severity through a common pathway, independent of the causal mutation. In this study, we prioritized candidate modifiers in these interacting loci. Our approach integrated human genome-wide association results with gene interaction networks and mouse brain gene expression to prioritize candidate genes and pathways driving variation in SWD outcomes. We considered candidate genes that are functionally associated with human GGE risk genes and genes with evidence for coding or non-coding allele effects between the B6 and C3H backgrounds. Our analyses output a summary ranking of gene pairs, one gene from each locus, as candidates for explaining the epistatic interaction. Our top-ranking gene pairs implicate microtubule function, cytoskeletal stability and cell cycle regulation as novel hypotheses about the source of SWD variation across strain backgrounds, which could clarify underlying mechanisms driving differences in GGE severity in humans.
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Affiliation(s)
- Montana Kay Lara
- Department of Neurological SciencesUniversity of VermontBurlingtonVermontUSA
| | - Jeffrey L. Brabec
- Department of Neurological SciencesUniversity of VermontBurlingtonVermontUSA
| | - Amanda E. Hernan
- Department of Neurological SciencesUniversity of VermontBurlingtonVermontUSA
- Division of NeuroscienceNemours Children's HealthWilmingtonDelawareUSA
- Department of Psychological and Brain SciencesUniversity of DelawareNewarkDelawareUSA
| | - Rod C. Scott
- Division of NeuroscienceNemours Children's HealthWilmingtonDelawareUSA
- Department of Psychological and Brain SciencesUniversity of DelawareNewarkDelawareUSA
| | | | - J. Matthew Mahoney
- Department of Neurological SciencesUniversity of VermontBurlingtonVermontUSA
- The Jackson LaboratoryBar HarborMaineUSA
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28
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Li ZA, Bajpai AK, Wang R, Liu Y, Webby RJ, Wilk E, Gu W, Schughart K, Li K, Lu L. Systems genetics of influenza A virus-infected mice identifies TRIM21 as a critical regulator of pulmonary innate immune response. Virus Res 2024; 342:199335. [PMID: 38331257 PMCID: PMC10882161 DOI: 10.1016/j.virusres.2024.199335] [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: 12/24/2023] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Tripartite motif 21 (TRIM21) is a cytosolic Fc receptor that targets antibody-bound, internalized pathogens for destruction. Apart from this intrinsic defense role, TRIM21 is implicated in autoimmune diseases, inflammation, and autophagy. Whether TRIM21 participates in host interactions with influenza A virus (IAV), however, is unknown. By computational modeling of body weight and lung transcriptome data from the BXD parents (C57BL/6 J (B6) and DBA/2 J (D2)) and 41 BXD mouse strains challenged by IAV, we reveal that a Trim21-associated gene network modulates the early host responses to IAV infection. Trim21 transcripts were significantly upregulated in infected mice of both B6 and D2 backgrounds. Its expression was significantly higher in infected D2 than in infected B6 early after infection and significantly correlated with body weight loss. We identified significant trans-eQTL on chromosome 14 that regulates Trim21 expression. Nr1d2 and Il3ra were among the strongest candidate genes. Pathway analysis found Trim21 to be involved in inflammation and immunity related pathways, such as inflammation signaling pathways (TNF, IL-17, and NF-κB), viral detection signaling pathways (NOD-like and RIG-I-like), influenza, and other respiratory viral infections. Knockdown of TRIM21 in human lung epithelial A549 cells significantly augmented IAV-induced expression of IFNB1, IFNL1, CCL5, CXCL10, and IFN-stimulated genes including DDX58 and IFIH1, among others. Our data suggest that a TRIM21-associated gene network is involved in several aspects of inflammation and viral detection mechanisms during IAV infection. We identify and validate TRIM21 as a critical regulator of innate immune responses to IAV in human lung epithelial cells.
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Affiliation(s)
- Zhuoyuan Alex Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Akhilesh Kumar Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ruixue Wang
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yaxin Liu
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Esther Wilk
- Rochus Mummert Healthcare Consulting GmbH, Hannover, Germany
| | - Weikuan Gu
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Klaus Schughart
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA; Institute of Virology Münster, University of Münster, Münster, Germany
| | - Kui Li
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
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Peeples ES, Mirnics K, Korade Z. Chemical Inhibition of Sterol Biosynthesis. Biomolecules 2024; 14:410. [PMID: 38672427 PMCID: PMC11048061 DOI: 10.3390/biom14040410] [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: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Cholesterol is an essential molecule of life, and its synthesis can be inhibited by both genetic and nongenetic mechanisms. Hundreds of chemicals that we are exposed to in our daily lives can alter sterol biosynthesis. These also encompass various classes of FDA-approved medications, including (but not limited to) commonly used antipsychotic, antidepressant, antifungal, and cardiovascular medications. These medications can interfere with various enzymes of the post-lanosterol biosynthetic pathway, giving rise to complex biochemical changes throughout the body. The consequences of these short- and long-term homeostatic disruptions are mostly unknown. We performed a comprehensive review of the literature and built a catalogue of chemical agents capable of inhibiting post-lanosterol biosynthesis. This process identified significant gaps in existing knowledge, which fall into two main areas: mechanisms by which sterol biosynthesis is altered and consequences that arise from the inhibitions of the different steps in the sterol biosynthesis pathway. The outcome of our review also reinforced that sterol inhibition is an often-overlooked mechanism that can result in adverse consequences and that there is a need to develop new safety guidelines for the use of (novel and already approved) medications with sterol biosynthesis inhibiting side effects, especially during pregnancy.
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Affiliation(s)
- Eric S. Peeples
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Child Health Research Institute, Omaha, NE 68198, USA;
- Division of Neonatology, Children’s Nebraska, Omaha, NE 68114, USA
| | - Karoly Mirnics
- Child Health Research Institute, Omaha, NE 68198, USA;
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Zeljka Korade
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Child Health Research Institute, Omaha, NE 68198, USA;
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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30
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Armbrust F, Bickenbach K, Altmeppen H, Foggetti A, Winkelmann A, Wulff P, Glatzel M, Pietrzik CU, Becker-Pauly C. A novel mouse model for N-terminal truncated Aβ2-x generation through meprin β overexpression in astrocytes. Cell Mol Life Sci 2024; 81:139. [PMID: 38480559 PMCID: PMC10937767 DOI: 10.1007/s00018-024-05139-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 03/17/2024]
Abstract
Neurotoxic amyloid-β (Aβ) peptides cause neurodegeneration in Alzheimer's disease (AD) patients' brains. They are released upon proteolytic processing of the amyloid precursor protein (APP) extracellularly at the β-secretase site and intramembranously at the γ-secretase site. Several AD mouse models were developed to conduct respective research in vivo. Most of these classical models overexpress human APP with mutations driving AD-associated pathogenic APP processing. However, the resulting pattern of Aβ species in the mouse brains differs from those observed in AD patients' brains. Particularly mutations proximal to the β-secretase cleavage site (e.g., the so-called Swedish APP (APPswe) fostering Aβ1-x formation) lead to artificial Aβ production, as N-terminally truncated Aβ peptides are hardly present in these mouse brains. Meprin β is an alternative β-secretase upregulated in brains of AD patients and capable of generating N-terminally truncated Aβ2-x peptides. Therefore, we aimed to generate a mouse model for the production of so far underestimated Aβ2-x peptides by conditionally overexpressing meprin β in astrocytes. We chose astrocytes as meprin β was detected in this cell type in close proximity to Aβ plaques in AD patients' brains. The meprin β-overexpressing mice showed elevated amyloidogenic APP processing detected with a newly generated neo-epitope-specific antibody. Furthermore, we observed elevated Aβ production from endogenous APP as well as AD-related behavior changes (hyperlocomotion and deficits in spatial memory). The novel mouse model as well as the established tools and methods will be helpful to further characterize APP cleavage and the impact of different Aβ species in future studies.
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Affiliation(s)
- Fred Armbrust
- Biochemical Institute, Unit for Degradomics of the Protease Web, University of Kiel, Otto-Hahn-Platz 9, 24118, Kiel, Germany.
| | - Kira Bickenbach
- Biochemical Institute, Unit for Degradomics of the Protease Web, University of Kiel, Otto-Hahn-Platz 9, 24118, Kiel, Germany
| | - Hermann Altmeppen
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Angelica Foggetti
- Institute of Physiology, University of Kiel, Kiel, Germany
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, 314400, China
- College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Anne Winkelmann
- Biochemical Institute, Unit for Degradomics of the Protease Web, University of Kiel, Otto-Hahn-Platz 9, 24118, Kiel, Germany
| | - Peer Wulff
- Institute of Physiology, University of Kiel, Kiel, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claus U Pietrzik
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christoph Becker-Pauly
- Biochemical Institute, Unit for Degradomics of the Protease Web, University of Kiel, Otto-Hahn-Platz 9, 24118, Kiel, Germany.
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31
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Chen YH, Cheng WH. Hexosamine biosynthesis and related pathways, protein N-glycosylation and O-GlcNAcylation: their interconnection and role in plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1349064. [PMID: 38510444 PMCID: PMC10951099 DOI: 10.3389/fpls.2024.1349064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/22/2024]
Abstract
N-Acetylglucosamine (GlcNAc), a fundamental amino sugar moiety, is essential for protein glycosylation, glycolipid, GPI-anchor protein, and cell wall components. Uridine diphosphate-GlcNAc (UDP-GlcNAc), an active form of GlcNAc, is synthesized through the hexosamine biosynthesis pathway (HBP). Although HBP is highly conserved across organisms, the enzymes involved perform subtly distinct functions among microbes, mammals, and plants. A complete block of HBP normally causes lethality in any life form, reflecting the pivotal role of HBP in the normal growth and development of organisms. Although HBP is mainly composed of four biochemical reactions, HBP is exquisitely regulated to maintain the homeostasis of UDP-GlcNAc content. As HBP utilizes substrates including fructose-6-P, glutamine, acetyl-CoA, and UTP, endogenous nutrient/energy metabolites may be integrated to better suit internal growth and development, and external environmental stimuli. Although the genes encoding HBP enzymes are well characterized in microbes and mammals, they were less understood in higher plants in the past. As the HBP-related genes/enzymes have largely been characterized in higher plants in recent years, in this review we update the latest advances in the functions of the HBP-related genes in higher plants. In addition, HBP's salvage pathway and GlcNAc-mediated two major co- or post-translational modifications, N-glycosylation and O-GlcNAcylation, are also included in this review. Further knowledge on the function of HBP and its product conjugates, and the mechanisms underlying their response to deleterious environments might provide an alternative strategy for agricultural biofortification in the future.
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Affiliation(s)
| | - Wan-Hsing Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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32
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Li Y, Mo Y, Chen C, He J, Guo Z. Research advances of polycomb group proteins in regulating mammalian development. Front Cell Dev Biol 2024; 12:1383200. [PMID: 38505258 PMCID: PMC10950033 DOI: 10.3389/fcell.2024.1383200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Polycomb group (PcG) proteins are a subset of epigenetic factors that are highly conserved throughout evolution. In mammals, PcG proteins can be classified into two muti-proteins complexes: Polycomb repressive complex 1 (PRC1) and PRC2. Increasing evidence has demonstrated that PcG complexes play critical roles in the regulation of gene expression, genomic imprinting, chromosome X-inactivation, and chromatin structure. Accordingly, the dysfunction of PcG proteins is tightly orchestrated with abnormal developmental processes. Here, we summarized and discussed the current knowledge of the biochemical and molecular functions of PcG complexes, especially the PRC1 and PRC2 in mammalian development including embryonic development and tissue development, which will shed further light on the deep understanding of the basic knowledge of PcGs and their functions for reproductive health and developmental disorders.
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Affiliation(s)
| | | | | | - Jin He
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhiheng Guo
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, Jilin, China
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33
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Kunisetty B, Martin-Giacalone BA, Zhao X, Luna PN, Brooks BP, Hufnagel RB, Shaw CA, Rosenfeld JA, Agopian AJ, Lupo PJ, Scott DA. High Clinical Exome Sequencing Diagnostic Rates and Novel Phenotypic Expansions for Nonisolated Microphthalmia, Anophthalmia, and Coloboma. Invest Ophthalmol Vis Sci 2024; 65:25. [PMID: 38502138 PMCID: PMC10959191 DOI: 10.1167/iovs.65.3.25] [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: 11/22/2023] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Purpose A molecular diagnosis is only made in a subset of individuals with nonisolated microphthalmia, anophthalmia, and coloboma (MAC). This may be due to underutilization of clinical (whole) exome sequencing (cES) and an incomplete understanding of the genes that cause MAC. The purpose of this study is to determine the efficacy of cES in cases of nonisolated MAC and to identify new MAC phenotypic expansions. Methods We determined the efficacy of cES in 189 individuals with nonisolated MAC. We then used cES data, a validated machine learning algorithm, and previously published expression data, case reports, and animal models to determine which candidate genes were most likely to contribute to the development of MAC. Results We found the efficacy of cES in nonisolated MAC to be between 32.3% (61/189) and 48.1% (91/189). Most genes affected in our cohort were not among genes currently screened in clinically available ophthalmologic gene panels. A subset of the genes implicated in our cohort had not been clearly associated with MAC. Our analyses revealed sufficient evidence to support low-penetrance MAC phenotypic expansions involving nine of these human disease genes. Conclusions We conclude that cES is an effective means of identifying a molecular diagnosis in individuals with nonisolated MAC and may identify putatively damaging variants that would be missed if only a clinically available ophthalmologic gene panel was obtained. Our data also suggest that deleterious variants in BRCA2, BRIP1, KAT6A, KAT6B, NSF, RAC1, SMARCA4, SMC1A, and TUBA1A can contribute to the development of MAC.
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Affiliation(s)
- Bhavana Kunisetty
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Bailey A. Martin-Giacalone
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, United States
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Baylor Genetics, Houston, Texas, United States
| | - Pamela N. Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Brian P. Brooks
- Ophthalmic Genetics & Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, United States
| | - Robert B. Hufnagel
- Ophthalmic Genetics & Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, United States
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - A. J. Agopian
- Department of Epidemiology, Human Genetics & Environmental Sciences, UTHealth School of Public Health, Houston, Texas, United States
| | - Philip J. Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States
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34
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Greene TT, Jo Y, Macal M, Fang Z, Khatri FS, Codrington AL, Kazane KR, Chiale C, Akbulut E, Swaminathan S, Fujita Y, Fitzgerald-Bocarsly P, Cordes T, Metallo C, Scott DA, Zuniga EI. Metabolic Deficiencies Underlie Plasmacytoid Dendritic Cell Exhaustion After Viral Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582551. [PMID: 38464328 PMCID: PMC10925345 DOI: 10.1101/2024.02.28.582551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Type I Interferons (IFN-I) are central to host protection against viral infections 1 . While any cell can produce IFN-I, Plasmacytoid Dendritic Cells (pDCs) make greater quantities and more varieties of these cytokines than any other cell type 2 . However, following an initial burst of IFN- I, pDCs lose their exceptional IFN-I production capacity and become "exhausted", a phenotype that associates with enhanced susceptibility to secondary infections 3-5 . Despite this apparent cost for the host, pDC exhaustion is conserved across multiple species and viral infections, but the underlying mechanisms and the potential evolutionary advantages are not well understood. Here we characterize pDC exhaustion and demonstrate that it is associated with a reduced capacity of pDCs to engage both oxidative and glycolytic metabolism. Mechanistically, we identify lactate dehydrogenase B (LDHB) as a novel positive regulator of pDC IFN-I production in mice and humans, show that LDHB deficiency is associated with suppressed IFN-I production, pDC metabolic capacity, and viral control following a viral infection, and demonstrate that preservation of LDHB expression is sufficient to partially restore exhausted pDC function in vitro and in vivo . Furthermore, restoring LDHB in vivo in exhausted pDCs increased IFNAR dependent infection- associated pathology. Therefore, our work identifies a novel and conserved mechanism for balancing immunity and pathology during viral infections, while also providing insight into the highly preserved but previously unexplained phenomenon of pDC exhaustion.
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Morel M, Long W. FBXL16 promotes cell growth and drug resistance in lung adenocarcinomas with KRAS mutation by stabilizing IRS1 and upregulating IRS1/AKT signaling. Mol Oncol 2024; 18:762-777. [PMID: 37983945 PMCID: PMC10920083 DOI: 10.1002/1878-0261.13554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/17/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Lung adenocarcinomas (LUADs) are a major subtype of non-small-cell lung cancers (NSCLCs). About 25% of LUADs harbor GTPase KRAS mutations associated with poor prognosis and limited treatment options. While encouraging tumor response to novel covalent inhibitors specifically targeting KRASG12C has been shown in the clinic, either intrinsic resistance exists or acquired therapeutic resistance arises upon treatment. There is an unmet need to identify new therapeutic targets for treating LUADs with activating KRAS mutations, particularly those with resistance to KRASG12C inhibitor(s). In this study, we have revealed that F-box/LRR-repeat protein 16 (FBXL16) is selectively upregulated in LUAD with KRAS mutations. It promotes LUAD cell growth and transforms lung epithelial cells. Importantly, FBXL16 depletion greatly enhances sensitivity to the KRASG12C inhibitor (sotorasib) in resistant cells by downregulating phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PKB; also known as AKT) signaling. Mechanistically, FBXL16 upregulates insulin receptor substrate 1 (IRS1) protein stability, leading to an increase of IGF1/AKT signaling, thereby promoting cell growth and migration. Taken together, our study highlights the potential of FBXL16 as a therapeutic target for treating LUAD with KRAS activating mutations.
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Affiliation(s)
- Marion Morel
- Department of Biochemistry and Molecular Biology, Boonshoft School of MedicineWright State UniversityDaytonOHUSA
| | - Weiwen Long
- Department of Biochemistry and Molecular Biology, Boonshoft School of MedicineWright State UniversityDaytonOHUSA
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Adams DJ, Barlas B, McIntyre RE, Salguero I, van der Weyden L, Barros A, Vicente JR, Karimpour N, Haider A, Ranzani M, Turner G, Thompson NA, Harle V, Olvera-León R, Robles-Espinoza CD, Speak AO, Geisler N, Weninger WJ, Geyer SH, Hewinson J, Karp NA, Fu B, Yang F, Kozik Z, Choudhary J, Yu L, van Ruiten MS, Rowland BD, Lelliott CJ, Del Castillo Velasco-Herrera M, Verstraten R, Bruckner L, Henssen AG, Rooimans MA, de Lange J, Mohun TJ, Arends MJ, Kentistou KA, Coelho PA, Zhao Y, Zecchini H, Perry JRB, Jackson SP, Balmus G. Genetic determinants of micronucleus formation in vivo. Nature 2024; 627:130-136. [PMID: 38355793 PMCID: PMC10917660 DOI: 10.1038/s41586-023-07009-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/21/2023] [Indexed: 02/16/2024]
Abstract
Genomic instability arising from defective responses to DNA damage1 or mitotic chromosomal imbalances2 can lead to the sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of ageing and diseases associated with genomic instability, the catalogue of genetic players that regulate the generation of MN remains to be determined. Here we analyse 997 mouse mutant lines, revealing 145 genes whose loss significantly increases (n = 71) or decreases (n = 74) MN formation, including many genes whose orthologues are linked to human disease. We found that mice null for Dscc1, which showed the most significant increase in MN, also displayed a range of phenotypes characteristic of patients with cohesinopathy disorders. After validating the DSCC1-associated MN instability phenotype in human cells, we used genome-wide CRISPR-Cas9 screening to define synthetic lethal and synthetic rescue interactors. We found that the loss of SIRT1 can rescue phenotypes associated with DSCC1 loss in a manner paralleling restoration of protein acetylation of SMC3. Our study reveals factors involved in maintaining genomic stability and shows how this information can be used to identify mechanisms that are relevant to human disease biology1.
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Affiliation(s)
- D J Adams
- Wellcome Sanger Institute, Cambridge, UK.
| | - B Barlas
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - I Salguero
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - A Barros
- Wellcome Sanger Institute, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J R Vicente
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - N Karimpour
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - A Haider
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - M Ranzani
- Wellcome Sanger Institute, Cambridge, UK
| | - G Turner
- Wellcome Sanger Institute, Cambridge, UK
| | | | - V Harle
- Wellcome Sanger Institute, Cambridge, UK
| | | | - C D Robles-Espinoza
- Wellcome Sanger Institute, Cambridge, UK
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, México
| | - A O Speak
- Wellcome Sanger Institute, Cambridge, UK
| | - N Geisler
- Wellcome Sanger Institute, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Wien, Austria
| | - S H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Wien, Austria
| | - J Hewinson
- Wellcome Sanger Institute, Cambridge, UK
| | - N A Karp
- Wellcome Sanger Institute, Cambridge, UK
| | - B Fu
- Wellcome Sanger Institute, Cambridge, UK
| | - F Yang
- Wellcome Sanger Institute, Cambridge, UK
| | - Z Kozik
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - J Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - L Yu
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - M S van Ruiten
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - B D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - L Bruckner
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - A G Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M A Rooimans
- Department of Human Genetics, Section of Oncogenetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - J de Lange
- Department of Human Genetics, Section of Oncogenetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - T J Mohun
- Division of Developmental Biology, MRC, National Institute for Medical Research, London, UK
| | - M J Arends
- Division of Pathology, Cancer Research UK Scotland Centre, Institute of Genetics & Cancer The University of Edinburgh, Edinburgh, UK
| | - K A Kentistou
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - P A Coelho
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Y Zhao
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - H Zecchini
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - J R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - S P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - G Balmus
- Wellcome Sanger Institute, Cambridge, UK.
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK.
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, Cluj-Napoca, Romania.
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Srinivasan S, He X, Mirza S, Mager J. Exosome complex components 1 and 2 are vital for early mammalian development. Gene Expr Patterns 2024; 51:119346. [PMID: 37940010 PMCID: PMC10939940 DOI: 10.1016/j.gep.2023.119346] [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: 06/07/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
Exosome Complex Components 1 and 2 (EXOSC1 and 2) are two proteins in the RNA Exosome complex whose main function is 5' → 3' RNA degradation and processing. The RNA exosome complex is comprised of nine subunits that form two separate components: the S1/KH cap and the PH-core. EXOSC1 and 2 are both part of the S1/KH cap and are involved in binding nascent RNA. As part of a systemic characterization of early lethal alleles produced by the Knockout Mouse Project, we have examined Exosc1 and Exosc2 homozygous null (mutant) embryos to determine developmental and molecular phenotypes of embryos lacking their functions. Our studies reveal that Exosc1 null embryos implant and form an egg cylinder but are developmentally delayed and fail to initiate gastrulation by embryonic day 7.5. In contrast, Exosc2 null embryos are lethal during peri-implantation stages, and while they do form a morphologically normal blastocyst at E3.5, they cannot be recovered at post-implantation stages. We show the absence of stage-specific developmental and altered lineage-specification in both Exosc1 and Exosc2 mutant embryos and conclude that these genes are essential for the successful progression through early mammalian development.
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Affiliation(s)
- Sanjana Srinivasan
- Department of Veterinary and Animal Sciences, University of Massachusetts- Amherst, Amherst, MA, 01002, USA
| | - Xinjian He
- Department of Veterinary and Animal Sciences, University of Massachusetts- Amherst, Amherst, MA, 01002, USA
| | - Sarah Mirza
- Department of Veterinary and Animal Sciences, University of Massachusetts- Amherst, Amherst, MA, 01002, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts- Amherst, Amherst, MA, 01002, USA.
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38
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Hurabielle C, LaFlam TN, Gearing M, Ye CJ. Functional genomics in inborn errors of immunity. Immunol Rev 2024; 322:53-70. [PMID: 38329267 PMCID: PMC10950534 DOI: 10.1111/imr.13309] [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] [Indexed: 02/09/2024]
Abstract
Inborn errors of immunity (IEI) comprise a diverse spectrum of 485 disorders as recognized by the International Union of Immunological Societies Committee on Inborn Error of Immunity in 2022. While IEI are monogenic by definition, they illuminate various pathways involved in the pathogenesis of polygenic immune dysregulation as in autoimmune or autoinflammatory syndromes, or in more common infectious diseases that may not have a significant genetic basis. Rapid improvement in genomic technologies has been the main driver of the accelerated rate of discovery of IEI and has led to the development of innovative treatment strategies. In this review, we will explore various facets of IEI, delving into the distinctions between PIDD and PIRD. We will examine how Mendelian inheritance patterns contribute to these disorders and discuss advancements in functional genomics that aid in characterizing new IEI. Additionally, we will explore how emerging genomic tools help to characterize new IEI as well as how they are paving the way for innovative treatment approaches for managing and potentially curing these complex immune conditions.
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Affiliation(s)
- Charlotte Hurabielle
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Taylor N LaFlam
- Division of Pediatric Rheumatology, Department of Pediatrics, UCSF, San Francisco, California, USA
| | - Melissa Gearing
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, UCSF, San Francisco, California, USA
- Institute of Computational Health Sciences, UCSF, San Francisco, California, USA
- Gladstone Genomic Immunology Institute, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, UCSF, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, California, USA
- Arc Institute, Palo Alto, California, USA
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39
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Vogt CC, Zipple MN, Sprockett DD, Miller CH, Hardy SX, Arthur MK, Greenstein AM, Colvin MS, Michel LM, Moeller AH, Sheehan MJ. Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures. BMC Biol 2024; 22:35. [PMID: 38355587 PMCID: PMC10865716 DOI: 10.1186/s12915-024-01809-0] [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: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Social behavior and social organization have major influences on individual health and fitness. Yet, biomedical research focuses on studying a few genotypes under impoverished social conditions. Understanding how lab conditions have modified social organizations of model organisms, such as lab mice, relative to natural populations is a missing link between socioecology and biomedical science. RESULTS Using a common garden design, we describe the formation of social structure in the well-studied laboratory mouse strain, C57BL/6J, in replicated mixed-sex populations over 10-day trials compared to control trials with wild-derived outbred house mice in outdoor field enclosures. We focus on three key features of mouse social systems: (i) territory establishment in males, (ii) female social relationships, and (iii) the social networks formed by the populations. Male territorial behaviors were similar but muted in C57 compared to wild-derived mice. Female C57 sharply differed from wild-derived females, showing little social bias toward cage mates and exploring substantially more of the enclosures compared to all other groups. Female behavior consistently generated denser social networks in C57 than in wild-derived mice. CONCLUSIONS C57 and wild-derived mice individually vary in their social and spatial behaviors which scale to shape overall social organization. The repeatable societies formed under field conditions highlights opportunities to experimentally study the interplay between society and individual biology using model organisms.
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Affiliation(s)
- Caleb C Vogt
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
| | - Matthew N Zipple
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Caitlin H Miller
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Summer X Hardy
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew K Arthur
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Adam M Greenstein
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Melanie S Colvin
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Lucie M Michel
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Michael J Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
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40
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Bhattacharjee R, Jolly LA, Corbett MA, Wee IC, Rao SR, Gardner AE, Ritchie T, van Hugte EJH, Ciptasari U, Piltz S, Noll JE, Nazri N, van Eyk CL, White M, Fornarino D, Poulton C, Baynam G, Collins-Praino LE, Snel MF, Nadif Kasri N, Hemsley KM, Thomas PQ, Kumar R, Gecz J. Compromised transcription-mRNA export factor THOC2 causes R-loop accumulation, DNA damage and adverse neurodevelopment. Nat Commun 2024; 15:1210. [PMID: 38331934 PMCID: PMC10853216 DOI: 10.1038/s41467-024-45121-5] [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: 06/16/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
We implicated the X-chromosome THOC2 gene, which encodes the largest subunit of the highly-conserved TREX (Transcription-Export) complex, in a clinically complex neurodevelopmental disorder with intellectual disability as the core phenotype. To study the molecular pathology of this essential eukaryotic gene, we generated a mouse model based on a hypomorphic Thoc2 exon 37-38 deletion variant of a patient with ID, speech delay, hypotonia, and microcephaly. The Thoc2 exon 37-38 deletion male (Thoc2Δ/Y) mice recapitulate the core phenotypes of THOC2 syndrome including smaller size and weight, and significant deficits in spatial learning, working memory and sensorimotor functions. The Thoc2Δ/Y mouse brain development is significantly impacted by compromised THOC2/TREX function resulting in R-loop accumulation, DNA damage and consequent cell death. Overall, we suggest that perturbed R-loop homeostasis, in stem cells and/or differentiated cells in mice and the patient, and DNA damage-associated functional alterations are at the root of THOC2 syndrome.
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Affiliation(s)
- Rudrarup Bhattacharjee
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Lachlan A Jolly
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Mark A Corbett
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ing Chee Wee
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sushma R Rao
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Alison E Gardner
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tarin Ritchie
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Eline J H van Hugte
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Ummi Ciptasari
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Sandra Piltz
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Jacqueline E Noll
- School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide and Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Nazzmer Nazri
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Clare L van Eyk
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Melissa White
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Dani Fornarino
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Rare Care Centre, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Lyndsey E Collins-Praino
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Marten F Snel
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Kim M Hemsley
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Paul Q Thomas
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Raman Kumar
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jozef Gecz
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia.
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia.
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Zhao S, Zhao H, Zhao L, Cheng X, Zheng Z, Wu M, Wen W, Wang S, Zhou Z, Xie H, Ruan D, Li Q, Liu X, Ou C, Li G, Zhao Z, Chen G, Niu Y, Yin X, Hu Y, Zhang X, Liu P, Qiu G, Liu W, Zhao C, Wu Z, Zhang J, Wu N. Unraveling the genetic architecture of congenital vertebral malformation with reference to the developing spine. Nat Commun 2024; 15:1125. [PMID: 38321032 PMCID: PMC10847475 DOI: 10.1038/s41467-024-45442-5] [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: 09/02/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Congenital vertebral malformation, affecting 0.13-0.50 per 1000 live births, has an immense locus heterogeneity and complex genetic architecture. In this study, we analyze exome/genome sequencing data from 873 probands with congenital vertebral malformation and 3794 control individuals. Clinical interpretation identifies Mendelian etiologies in 12.0% of the probands and reveals a muscle-related disease mechanism. Gene-based burden test of ultra-rare variants identifies risk genes with large effect sizes (ITPR2, TBX6, TPO, H6PD, and SEC24B). To further investigate the biological relevance of the genetic association signals, we perform single-nucleus RNAseq on human embryonic spines. The burden test signals are enriched in the notochord at early developmental stages and myoblast/myocytes at late stages, highlighting their critical roles in the developing spine. Our work provides insights into the developmental biology of the human spine and the pathogenesis of spine malformation.
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Affiliation(s)
- Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lina Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xi Cheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhifa Zheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Mengfan Wu
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Wen Wen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zixiang Zhou
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Haibo Xie
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Dengfeng Ruan
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Qing Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xinquan Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Chengzhu Ou
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Guilin Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuchen Niu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangjie Yin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuhong Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaochen Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Chengtian Zhao
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Zhihong Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Banerjee S, Daetwyler S, Bai X, Michaud M, Jouhet J, Madhugiri S, Johnson E, Wang CW, Fiolka R, Toulmay A, Prinz WA. The Vps13-like protein BLTP2 is pro-survival and regulates phosphatidylethanolamine levels in the plasma membrane to maintain its fluidity and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578804. [PMID: 38370643 PMCID: PMC10871178 DOI: 10.1101/2024.02.04.578804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Lipid transport proteins (LTPs) facilitate nonvesicular lipid exchange between cellular compartments and have critical roles in lipid homeostasis1. A new family of bridge-like LTPs (BLTPs) is thought to form lipid-transporting conduits between organelles2. One, BLTP2, is conserved across species but its function is not known. Here, we show that BLTP2 and its homolog directly regulate plasma membrane (PM) fluidity by increasing the phosphatidylethanolamine (PE) level in the PM. BLTP2 localizes to endoplasmic reticulum (ER)-PM contact sites34, 5, suggesting it transports PE from the ER to the PM. We find BLTP2 works in parallel with another pathway that regulates intracellular PE distribution and PM fluidity6, 7. BLTP2 expression correlates with breast cancer aggressiveness8-10. We found BLTP2 facilitates growth of a human cancer cell line and sustains its aggressiveness in an in vivo model of metastasis, suggesting maintenance of PM fluidity by BLTP2 may be critical for tumorigenesis in humans.
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Affiliation(s)
- Subhrajit Banerjee
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofei Bai
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Morgane Michaud
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Juliette Jouhet
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Shruthi Madhugiri
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emma Johnson
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao-Wen Wang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alexandre Toulmay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - William A Prinz
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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43
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Aminbeidokhti M, Qu JH, Belur S, Cakmak H, Jaswa E, Lathi RB, Sirota M, Snyder MP, Yatsenko SA, Rajkovic A. Miscarriage risk assessment: a bioinformatic approach to identifying candidate lethal genes and variants. Hum Genet 2024; 143:185-195. [PMID: 38302665 PMCID: PMC10881709 DOI: 10.1007/s00439-023-02637-y] [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: 10/16/2023] [Accepted: 12/25/2023] [Indexed: 02/03/2024]
Abstract
PURPOSE Miscarriage, often resulting from a variety of genetic factors, is a common pregnancy outcome. Preconception genetic carrier screening (PGCS) identifies at-risk partners for newborn genetic disorders; however, PGCS panels currently lack miscarriage-related genes. In this study, we evaluated the potential impact of both known and candidate genes on prenatal lethality and the effectiveness of PGCS in diverse populations. METHODS We analyzed 125,748 human exome sequences and mouse and human gene function databases. Our goals were to identify genes crucial for human fetal survival (lethal genes), to find variants not present in a homozygous state in healthy humans, and to estimate carrier rates of known and candidate lethal genes in various populations and ethnic groups. RESULTS This study identified 138 genes in which heterozygous lethal variants are present in the general population with a frequency of 0.5% or greater. Screening for these 138 genes could identify 4.6% (in the Finnish population) to 39.8% (in the East Asian population) of couples at risk of miscarriage. This explains the cause of pregnancy loss in approximately 1.1-10% of cases affected by biallelic lethal variants. CONCLUSION This study has identified a set of genes and variants potentially associated with lethality across different ethnic backgrounds. The variation of these genes across ethnic groups underscores the need for a comprehensive, pan-ethnic PGCS panel that includes genes related to miscarriage.
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Affiliation(s)
- Mona Aminbeidokhti
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jia-Hua Qu
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Shweta Belur
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Hakan Cakmak
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Eleni Jaswa
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Ruth B Lathi
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, 94305, USA
| | - Marina Sirota
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, 94143, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Svetlana A Yatsenko
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Magee-Women Research Institute, Pittsburgh, PA, 15213, USA
| | - Aleksandar Rajkovic
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143, USA.
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA.
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44
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [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: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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Feng Y, Xie N, Inoue F, Fan S, Saskin J, Zhang C, Zhang F, Hansen MEB, Nyambo T, Mpoloka SW, Mokone GG, Fokunang C, Belay G, Njamnshi AK, Marks MS, Oancea E, Ahituv N, Tishkoff SA. Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Nat Genet 2024; 56:258-272. [PMID: 38200130 PMCID: PMC11005318 DOI: 10.1038/s41588-023-01626-1] [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: 09/15/2022] [Accepted: 11/28/2023] [Indexed: 01/12/2024]
Abstract
Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.
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Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ning Xie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Human Phenome Institute, School of Life Science, Fudan University, Shanghai, China
| | - Joshua Saskin
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Chao Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN); Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Elena Oancea
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, USA.
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Yim YI, Pedrosa A, Wu X, Chinthalapudi K, Cheney RE, Hammer JA. Mechanisms underlying Myosin 10's contribution to the maintenance of mitotic spindle bipolarity. Mol Biol Cell 2024; 35:ar14. [PMID: 38019611 PMCID: PMC10881153 DOI: 10.1091/mbc.e23-07-0282] [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: 07/24/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
Myosin 10 (Myo10) couples microtubules and integrin-based adhesions to movement along actin filaments via its microtubule-binding MyTH4 domain and integrin-binding FERM domain, respectively. Here we show that Myo10-depleted HeLa cells and mouse embryo fibroblasts (MEFs) both exhibit a pronounced increase in the frequency of multipolar spindles. Staining of unsynchronized metaphase cells showed that the primary driver of spindle multipolarity in Myo10-depleted MEFs and in Myo10-depleted HeLa cells lacking supernumerary centrosomes is pericentriolar material (PCM) fragmentation, which creates y-tubulin-positive acentriolar foci that serve as extra spindle poles. For HeLa cells possessing supernumerary centrosomes, Myo10 depletion further accentuates spindle multipolarity by impairing the clustering of the extra spindle poles. Complementation experiments show that Myo10 must interact with both microtubules and integrins to promote PCM/pole integrity. Conversely, Myo10 only needs interact with integrins to promote supernumerary centrosome clustering. Importantly, images of metaphase Halo-Myo10 knockin cells show that the myosin localizes exclusively to the spindle and the tips of adhesive retraction fibers. We conclude that Myo10 promotes PCM/pole integrity in part by interacting with spindle microtubules, and that it promotes supernumerary centrosome clustering by supporting retraction fiber-based cell adhesion, which likely serves to anchor the microtubule-based forces driving pole focusing.
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Affiliation(s)
- Yang-In Yim
- Cell and Developmental Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Antonio Pedrosa
- Cell and Developmental Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Xufeng Wu
- Cell and Developmental Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Krishna Chinthalapudi
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH 43210
| | - Richard E. Cheney
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599
| | - John A. Hammer
- Cell and Developmental Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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47
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Jeon YG, Nahmgoong H, Oh J, Lee D, Kim DW, Kim JE, Kim YY, Ji Y, Han JS, Kim SM, Sohn JH, Lee WT, Kim SW, Park J, Huh JY, Jo K, Cho JY, Park J, Kim JB. Ubiquitin ligase RNF20 coordinates sequential adipose thermogenesis with brown and beige fat-specific substrates. Nat Commun 2024; 15:940. [PMID: 38296968 PMCID: PMC10831072 DOI: 10.1038/s41467-024-45270-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024] Open
Abstract
In mammals, brown adipose tissue (BAT) and inguinal white adipose tissue (iWAT) execute sequential thermogenesis to maintain body temperature during cold stimuli. BAT rapidly generates heat through brown adipocyte activation, and further iWAT gradually stimulates beige fat cell differentiation upon prolonged cold challenges. However, fat depot-specific regulatory mechanisms for thermogenic activation of two fat depots are poorly understood. Here, we demonstrate that E3 ubiquitin ligase RNF20 orchestrates adipose thermogenesis with BAT- and iWAT-specific substrates. Upon cold stimuli, BAT RNF20 is rapidly downregulated, resulting in GABPα protein elevation by controlling protein stability, which stimulates thermogenic gene expression. Accordingly, BAT-specific Rnf20 suppression potentiates BAT thermogenic activity via GABPα upregulation. Moreover, upon prolonged cold stimuli, iWAT RNF20 is gradually upregulated to promote de novo beige adipogenesis. Mechanistically, iWAT RNF20 mediates NCoR1 protein degradation, rather than GABPα, to activate PPARγ. Together, current findings propose fat depot-specific regulatory mechanisms for temporal activation of adipose thermogenesis.
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Affiliation(s)
- Yong Geun Jeon
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hahn Nahmgoong
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jiyoung Oh
- Department of Biological Sciences, College of Information and Bioengineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, South Korea
| | - Dabin Lee
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea
| | - Dong Wook Kim
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea
| | - Jane Eunsoo Kim
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Ye Young Kim
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Yul Ji
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Ji Seul Han
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sung Min Kim
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jee Hyung Sohn
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Won Taek Lee
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sun Won Kim
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jeu Park
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin Young Huh
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
- Department of Life Science, Sogang University, Seoul, 04107, South Korea
| | - Kyuri Jo
- Department of Computer Engineering, Chungbuk National University, Cheongju, 28644, South Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea
| | - Jiyoung Park
- Department of Biological Sciences, College of Information and Bioengineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, South Korea
| | - Jae Bum Kim
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.
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48
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Zhang T, Xue Y, Su S, Altouma V, Ho K, Martindale JL, Lee SK, Shen W, Park A, Zhang Y, De S, Gorospe M, Wang W. RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames. Nucleic Acids Res 2024; 52:885-905. [PMID: 38000373 PMCID: PMC10810208 DOI: 10.1093/nar/gkad1122] [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: 06/20/2023] [Revised: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
RNA-binding proteins (RBPs) with intrinsically disordered regions (IDRs) are linked to multiple human disorders, but their mechanisms of action remain unclear. Here, we report that one such protein, Nocte, is essential for Drosophila eye development by regulating a critical gene expression cascade at translational level. Knockout of nocte in flies leads to lethality, and its eye-specific depletion impairs eye size and morphology. Nocte preferentially enhances translation of mRNAs with long upstream open reading frames (uORFs). One of the key Nocte targets, glass mRNA, encodes a transcription factor critical for differentiation of photoreceptor neurons and accessory cells, and re-expression of Glass largely rescued the eye defects caused by Nocte depletion. Mechanistically, Nocte counteracts long uORF-mediated translational suppression by promoting translation reinitiation downstream of the uORF. Nocte interacts with translation factors eIF3 and Rack1 through its BAT2 domain, and a Nocte mutant lacking this domain fails to promote translation of glass mRNA. Notably, de novo mutations of human orthologs of Nocte have been detected in schizophrenia patients. Our data suggest that Nocte family of proteins can promote translation reinitiation to overcome long uORFs-mediated translational suppression, and disruption of this function can lead to developmental defects and neurological disorders.
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Affiliation(s)
- Tianyi Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Valerie Altouma
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Katherine Ho
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung-Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Aaron Park
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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Sotomayor-Lugo F, Iglesias-Barrameda N, Castillo-Aleman YM, Casado-Hernandez I, Villegas-Valverde CA, Bencomo-Hernandez AA, Ventura-Carmenate Y, Rivero-Jimenez RA. The Dynamics of Histone Modifications during Mammalian Zygotic Genome Activation. Int J Mol Sci 2024; 25:1459. [PMID: 38338738 PMCID: PMC10855761 DOI: 10.3390/ijms25031459] [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: 12/29/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Mammalian fertilization initiates the reprogramming of oocytes and sperm, forming a totipotent zygote. During this intricate process, the zygotic genome undergoes a maternal-to-zygotic transition (MZT) and subsequent zygotic genome activation (ZGA), marking the initiation of transcriptional control and gene expression post-fertilization. Histone modifications are pivotal in shaping cellular identity and gene expression in many mammals. Recent advances in chromatin analysis have enabled detailed explorations of histone modifications during ZGA. This review delves into conserved and unique regulatory strategies, providing essential insights into the dynamic changes in histone modifications and their variants during ZGA in mammals. The objective is to explore recent advancements in leading mechanisms related to histone modifications governing this embryonic development phase in depth. These considerations will be useful for informing future therapeutic approaches that target epigenetic regulation in diverse biological contexts. It will also contribute to the extensive areas of evolutionary and developmental biology and possibly lay the foundation for future research and discussion on this seminal topic.
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Affiliation(s)
| | | | | | | | | | | | | | - Rene Antonio Rivero-Jimenez
- Abu Dhabi Stem Cells Center, Abu Dhabi P.O. Box 4600, United Arab Emirates; (F.S.-L.); (N.I.-B.); (Y.M.C.-A.); (I.C.-H.); (C.A.V.-V.); (A.A.B.-H.); (Y.V.-C.)
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50
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Gupta P, Dholaniya PS, Princy K, Madhavan AS, Sreelakshmi Y, Sharma R. Augmenting tomato functional genomics with a genome-wide induced genetic variation resource. FRONTIERS IN PLANT SCIENCE 2024; 14:1290937. [PMID: 38328621 PMCID: PMC10848261 DOI: 10.3389/fpls.2023.1290937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/22/2023] [Indexed: 02/09/2024]
Abstract
Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Department of Biological Sciences, SRM University-AP, Amaravati, Andhra Pradesh, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Kunnappady Princy
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Athira Sethu Madhavan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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