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Promsut W, Yamada R, Takami S, Miyazaki N, Uemura M, Hiramatsu R, Takahashi N, Kanai Y. External genitalia phenotypes of a Mab21l1-null mouse model for cerebellar, ocular, craniofacial, and genital (COFG) syndrome. Anat Rec (Hoboken) 2024; 307:1943-1959. [PMID: 37750449 DOI: 10.1002/ar.25330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
The cerebellar, ocular, craniofacial, and genital (COFG) syndrome is a human genetic disease that is caused by MAB21L1 mutations. A COFG mouse model with Mab21l1-null mutation causes severe microphthalmia and fontanelle dysosteogenesis, similar to the symptoms in human patients. One of the typical symptoms is scrotal agenesis in male infants, while male Mab21l1-null mice show hypoplastic preputial glands, a rodent-specific derivative of the cranial scrotal fold. However, it is still unclear where and how MAB21Ll acts in the external genitalia in both mice and humans. Here we show that, at the neonatal stage, MAB21L1 expression in the external genitalia was restricted to two mesenchymal cell populations-underneath the scrotal and labial skin and around the preputial and clitoral glands (PG/CG). Morphometric analyses of the Mab21l1-/- pups revealed a significant reduction in the external size of the scrotum, vulva, and CG, as well as PG. In the periglandular region around PG and CG, the periglandular mesenchymal cells showed a drastic reduction in both cell density and immunoreactive signals for several extracellular matrix proteins (e.g., collagen I, fibronectin, and proteoglycans), together with their reduced Ki67-positive cell proliferation index. In the Mab21l1-/- PG/CG, together with reduced vascularization, the glandular epithelia displayed atrophy with discontinuous basal lamina along the basal surface and defective glycogen accumulation in their cytoplasm. Under a 5-day organ culture of the isolated PG, the Mab21l1-/- explants showed poor outgrowth and retention of the glandular structure in vitro. However, the addition of exogenous Matrigel could partially rescue such tissue-autonomous phenotypes, showing glandular morphology similar to that of the wild-type explants. These findings suggest that MAB21L1+ mesenchymal cells play a crucial role in providing nutrient ECM support for glandular outgrowth and morphogenesis in the peripheral external genitalia.
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Affiliation(s)
| | - Ryuichi Yamada
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo, Japan
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
- RNA Company Limited, Tokyo, Japan
| | - Shohei Takami
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo, Japan
| | - Nanae Miyazaki
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo, Japan
| | - Mami Uemura
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo, Japan
| | - Ryuji Hiramatsu
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo, Japan
| | - Naoki Takahashi
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
- RNA Company Limited, Tokyo, Japan
| | - Yoshiakira Kanai
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo, Japan
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Vöcking O, Famulski JK. Single cell transcriptome analyses of the developing zebrafish eye- perspectives and applications. Front Cell Dev Biol 2023; 11:1213382. [PMID: 37457291 PMCID: PMC10346855 DOI: 10.3389/fcell.2023.1213382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
Within a relatively short period of time, single cell transcriptome analyses (SCT) have become increasingly ubiquitous with transcriptomic research, uncovering plentiful details that boost our molecular understanding of various biological processes. Stemming from SCT analyses, the ever-growing number of newly assigned genetic markers increases our understanding of general function and development, while providing opportunities for identifying genes associated with disease. SCT analyses have been carried out using tissue from numerous organisms. However, despite the great potential of zebrafish as a model organism, other models are still preferably used. In this mini review, we focus on eye research as an example of the advantages in using zebrafish, particularly its usefulness for single cell transcriptome analyses of developmental processes. As studies have already shown, the unique opportunities offered by zebrafish, including similarities to the human eye, in combination with the possibility to analyze and extract specific cells at distinct developmental time points makes the model a uniquely powerful one. Particularly the practicality of collecting large numbers of embryos and therefore isolation of sufficient numbers of developing cells is a distinct advantage compared to other model organisms. Lastly, the advent of highly efficient genetic knockouts methods offers opportunities to characterize target gene function in a more cost-efficient way. In conclusion, we argue that the use of zebrafish for SCT approaches has great potential to further deepen our molecular understanding of not only eye development, but also many other organ systems.
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Affiliation(s)
| | - Jakub K. Famulski
- Department of Biology, University of Kentucky, Lexington, KY, United States
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Seese SE, Muheisen S, Gath N, Gross JM, Semina EV. Identification of HSPA8 as an interacting partner of MAB21L2 and an important factor in eye development. Dev Dyn 2023; 252:510-526. [PMID: 36576422 PMCID: PMC10947772 DOI: 10.1002/dvdy.560] [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: 06/19/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Pathogenic variants in human MAB21L2 result in microphthalmia, anophthalmia, and coloboma. The exact molecular function of MAB21L2 is currently unknown. We conducted a series of yeast two-hybrid (Y2H) experiments to determine protein interactomes of normal human and zebrafish MAB21L2/mab21l2 as well as human disease-associated variant MAB21L2-p.(Arg51Gly) using human adult retina and zebrafish embryo libraries. RESULTS These screens identified klhl31, tnpo1, TNPO2/tnpo2, KLC2/klc2, and SPTBN1/sptbn1 as co-factors of MAB21L2/mab21l2. Several factors, including hspa8 and hspa5, were found to interact with MAB21L2-p.Arg51Gly but not wild-type MAB21L2/mab21l2 in Y2H screens. Further analyses via 1-by-1 Y2H assays, co-immunoprecipitation, and mass spectrometry revealed that both normal and variant MAB21L2 interact with HSPA5 and HSPA8. In situ hybridization detected co-expression of hspa5 and hspa8 with mab21l2 during eye development in zebrafish. Examination of zebrafish mutant hspa8hi138Tg identified reduced hspa8 expression associated with severe ocular developmental defects, including small eye, coloboma, and anterior segment dysgenesis. To investigate the effects of hspa8 deficiency on the mab21l2Arg51_Phe52del allele, corresponding zebrafish double mutants were generated and found to be more severely affected than single mutant lines. CONCLUSION This study identifies heat shock proteins as interacting partners of MAB21L2/mab21l2 and suggests a role for this interaction in vertebrate eye development.
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Affiliation(s)
- Sarah E. Seese
- Department of Pediatrics The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sanaa Muheisen
- Department of Pediatrics The Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Natalie Gath
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jeffrey M. Gross
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Elena V. Semina
- Department of Pediatrics The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Children’s of Wisconsin, Milwaukee, WI 53226, USA
- Children’s Research Institute, Medical College of Wisconsin, Children’s of Wisconsin, Milwaukee, WI 53226, USA
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Ge F, Li C, Iqbal S, Muhammad A, Li F, Thafar MA, Yan Z, Worachartcheewan A, Xu X, Song J, Yu DJ. VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Brief Bioinform 2023; 24:6931725. [PMID: 36528806 DOI: 10.1093/bib/bbac535] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 11/08/2022] [Indexed: 12/23/2022] Open
Abstract
Determining the pathogenicity and functional impact (i.e. gain-of-function; GOF or loss-of-function; LOF) of a variant is vital for unraveling the genetic level mechanisms of human diseases. To provide a 'one-stop' framework for the accurate identification of pathogenicity and functional impact of variants, we developed a two-stage deep-learning-based computational solution, termed VPatho, which was trained using a total of 9619 pathogenic GOF/LOF and 138 026 neutral variants curated from various databases. A total number of 138 variant-level, 262 protein-level and 103 genome-level features were extracted for constructing the models of VPatho. The development of VPatho consists of two stages: (i) a random under-sampling multi-scale residual neural network (ResNet) with a newly defined weighted-loss function (RUS-Wg-MSResNet) was proposed to predict variants' pathogenicity on the gnomAD_NV + GOF/LOF dataset; and (ii) an XGBOD model was constructed to predict the functional impact of the given variants. Benchmarking experiments demonstrated that RUS-Wg-MSResNet achieved the highest prediction performance with the weights calculated based on the ratios of neutral versus pathogenic variants. Independent tests showed that both RUS-Wg-MSResNet and XGBOD achieved outstanding performance. Moreover, assessed using variants from the CAGI6 competition, RUS-Wg-MSResNet achieved superior performance compared to state-of-the-art predictors. The fine-trained XGBOD models were further used to blind test the whole LOF data downloaded from gnomAD and accordingly, we identified 31 nonLOF variants that were previously labeled as LOF/uncertain variants. As an implementation of the developed approach, a webserver of VPatho is made publicly available at http://csbio.njust.edu.cn/bioinf/vpatho/ to facilitate community-wide efforts for profiling and prioritizing the query variants with respect to their pathogenicity and functional impact.
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Affiliation(s)
- Fang Ge
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China.,School of Computer Science and Information Engineering, Bengbu University, 1866 Caoshan Road, Bengbu, 233030, China
| | - Chen Li
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Shahid Iqbal
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Arif Muhammad
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Fuyi Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.,College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Maha A Thafar
- Department of Computer Science, College of Computers and Information Technology, Taif University, P.O.Box 110099, Taif 21944, Saudi Arabia
| | - Zihao Yan
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
| | - Apilak Worachartcheewan
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Xiaofeng Xu
- School of Computer and Information, Anhui Polytechnic University, Beijingzhong Road, Wuhu 241000, China
| | - Jiangning Song
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
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Meng F, Li X, Zhang J, Gao Z, Yang X, Liu Z, Liu Y, Guo T, Wang L, Yang L, Wang Z. Single amino acid variation in MAB21L1 is dominantly associated with congenital eye defects. J Med Genet 2022:jmg-2022-108506. [DOI: 10.1136/jmg-2022-108506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022]
Abstract
BackgroundDiagnosis of a genetic disease and determination of the causative molecular lesion rely on the availability of the disease-associated pedigrees. Microphthalmia is a congenital eye defect due to an insufficiently developed visual system; its prevalence is 1–3 in 10 000 live births.ObjectiveWe analysed a pedigree exhibiting autosomal dominant inheritance of microphthalmia to determine the genetic lesion; used AlphaFold2 to predict the changes in the protein’s 3-Dimensional structure; and compared wild-type and variant proteins in cultured cells or Drosophila model was used to explore the cellular or developmental function of the encoded product.ResultsWe identified a novel missense variation, F52L, in MAB21L1 that is absent in population databases and present exclusively in the individuals diagnosed with microphthalmia in this pedigree. Common structural changes were predicted for the disease-associated variants clustered at amino acids 49–52, and these variant products were also predominantly trapped in the cytoplasm of cultured human lens epithelia. To recapitulate its dominant effect in development, we expressed the Drosophila homologue corresponding to MAB21L1F52Land caused malformation of sensory organs.ConclusionMutations at the residues 49–52 of MAB21L1 compromise eye development. We recommend includingMAB21L1in the genetic testing panel for congenital eye disorders.
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Ferre-Fernández JJ, Muheisen S, Thompson S, Semina EV. CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements. Hum Genomics 2022; 16:49. [PMID: 36284357 PMCID: PMC9597995 DOI: 10.1186/s40246-022-00423-x] [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: 07/08/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
FOXC1 encodes a forkhead-domain transcription factor associated with several ocular disorders. Correct FOXC1 dosage is critical to normal development, yet the mechanisms controlling its expression remain unknown. Together with FOXQ1 and FOXF2, FOXC1 is part of a cluster of FOX genes conserved in vertebrates. CRISPR-Cas9-mediated dissection of genomic sequences surrounding two zebrafish orthologs of FOXC1 was performed. This included five zebrafish-human conserved regions, three downstream of foxc1a and two remotely upstream of foxf2a/foxc1a or foxf2b/foxc1b clusters, as well as two intergenic regions between foxc1a/b and foxf2a/b lacking sequence conservation but positionally corresponding to the area encompassing a previously reported glaucoma-associated SNP in humans. Removal of downstream sequences altered foxc1a expression; moreover, zebrafish carrying deletions of two or three downstream elements demonstrated abnormal phenotypes including enlargement of the anterior chamber of the eye reminiscent of human congenital glaucoma. Deletions of distant upstream conserved elements influenced the expression of foxf2a/b or foxq1a/b but not foxc1a/b within each cluster. Removal of either intergenic sequence reduced foxc1a or foxc1b expression during late development, suggesting a role in transcriptional regulation despite the lack of conservation at the nucleotide level. Further studies of the identified regions in human patients may explain additional individuals with developmental ocular disorders.
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Affiliation(s)
- Jesús-José Ferre-Fernández
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Sanaa Muheisen
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Samuel Thompson
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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Xiao Y, Xiang JW, Gao Q, Bai YY, Huang ZX, Hu XH, Wang L, Li DWC. MAB21L1 promotes survival of lens epithelial cells through control of αB-crystallin and ATR/CHK1/p53 pathway. Aging (Albany NY) 2022; 14:6128-6148. [PMID: 35951367 PMCID: PMC9417230 DOI: 10.18632/aging.204203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022]
Abstract
The male abnormal gene family 21 (mab21), was initially identified in C. elegans. Since its identification, studies from different groups have shown that it regulates development of ocular tissues, brain, heart and liver. However, its functional mechanism remains largely unknown. Here, we demonstrate that Mab21L1 promotes survival of lens epithelial cells. Mechanistically, Mab21L1 upregulates expression of αB-crystallin. Moreover, our results show that αB-crystallin prevents stress-induced phosphorylation of p53 at S-20 and S-37 through abrogating the activation of the upstream kinases, ATR and CHK1. As a result of suppressing p53 activity by αB-crystallin, Mab21L1 downregulates expression of Bak but upregulates Mcl-1 during stress insult. Taken together, our results demonstrate that Mab21L1 promotes survival of lens epithelial cells through upregulation of αB-crystallin to suppress ATR/CHK1/p53 pathway.
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Affiliation(s)
- Yuan Xiao
- College of Life Sciences, Hunan Normal University, Changsha 410080, Hunan, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Tianhe, Guangzhou 510230, Guangdong, China
| | - Jia-Wen Xiang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Tianhe, Guangzhou 510230, Guangdong, China
| | - Qian Gao
- College of Life Sciences, Hunan Normal University, Changsha 410080, Hunan, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Tianhe, Guangzhou 510230, Guangdong, China
| | - Yue-Yue Bai
- College of Life Sciences, Hunan Normal University, Changsha 410080, Hunan, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Tianhe, Guangzhou 510230, Guangdong, China
| | - Zhao-Xia Huang
- Department of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang 121212, Guizhou, China
| | - Xiao-Hui Hu
- College of Life Sciences, Hunan Normal University, Changsha 410080, Hunan, China
| | - Ling Wang
- The Academician Work Station, Changsha Medical University, Changsha 410219, Hunan, China
| | - David Wan-Cheng Li
- College of Life Sciences, Hunan Normal University, Changsha 410080, Hunan, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Tianhe, Guangzhou 510230, Guangdong, China
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