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De Mori R, Tardivo S, Pollara L, Giliani SC, Ali E, Giordano L, Leuzzi V, Fischetto R, Gener B, Diprima S, Morelli MJ, Monti MC, Sottile V, Valente EM. Joubert syndrome-derived induced pluripotent stem cells show altered neuronal differentiation in vitro. Cell Tissue Res 2024; 396:255-267. [PMID: 38502237 PMCID: PMC11055696 DOI: 10.1007/s00441-024-03876-9] [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: 08/04/2023] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Joubert syndrome (JS) is a recessively inherited congenital ataxia characterized by hypotonia, psychomotor delay, abnormal ocular movements, intellectual disability, and a peculiar cerebellar and brainstem malformation, the "molar tooth sign." Over 40 causative genes have been reported, all encoding for proteins implicated in the structure or functioning of the primary cilium, a subcellular organelle widely present in embryonic and adult tissues. In this paper, we developed an in vitro neuronal differentiation model using patient-derived induced pluripotent stem cells (iPSCs), to evaluate possible neurodevelopmental defects in JS. To this end, iPSCs from four JS patients harboring mutations in distinct JS genes (AHI1, CPLANE1, TMEM67, and CC2D2A) were differentiated alongside healthy control cells to obtain mid-hindbrain precursors and cerebellar granule cells. Differentiation was monitored over 31 days through the detection of lineage-specific marker expression by qRT-PCR, immunofluorescence, and transcriptomics analysis. All JS patient-derived iPSCs, regardless of the mutant gene, showed a similar impairment to differentiate into mid-hindbrain and cerebellar granule cells when compared to healthy controls. In addition, analysis of primary cilium count and morphology showed notable ciliary defects in all differentiating JS patient-derived iPSCs compared to controls. These results confirm that patient-derived iPSCs are an accessible and relevant in vitro model to analyze cellular phenotypes connected to the presence of JS gene mutations in a neuronal context.
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Affiliation(s)
- Roberta De Mori
- Induced Pluripotent Stem Cells Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Silvia Tardivo
- Neurogenetics Lab, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Lidia Pollara
- Neurogenetics Research Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Silvia Clara Giliani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Eltahir Ali
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Lucio Giordano
- Paediatric Neurology and Psychiatry Unit, Spedali Civili Children's Hospital, University of Brescia, Brescia, Italy
| | - Vincenzo Leuzzi
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, University of Rome La Sapienza, Rome, Italy
| | - Rita Fischetto
- Clinical Genetics Unit, Department of Pediatric Medicine, XXIII Children's Hospital, Bari, Giovanni, Italy
| | - Blanca Gener
- Department of Genetics, Cruces University Hospital, BioBizkaia Health Research Institute, 48903 Barakaldo, Cruces PlazaBizkaia, Spain
| | - Santo Diprima
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Maria Cristina Monti
- Unit of Biostatistics and Clinical Epidemiology, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Virginie Sottile
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
| | - Enza Maria Valente
- Neurogenetics Research Unit, IRCCS Mondino Foundation, Pavia, Italy.
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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2
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Teng X, Yang T, Yuan B, Yang Y, Liu J, Wang X, Wang Y, Ma T, Yin X, Yu H, Wang S, Huang W. Prognostic analysis of patients with breast cancer based on tumor mutational burden and DNA damage repair genes. Front Oncol 2023; 13:1177133. [PMID: 37350936 PMCID: PMC10282748 DOI: 10.3389/fonc.2023.1177133] [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: 03/01/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
Background Breast cancer has a high tumor-specific death rate and poor prognosis. In this study, we aimed to provide a basis for the prognostic risk in patients with breast cancer using significant gene sets selected by analyzing tumor mutational burden (TMB) and DNA damage repair (DDR). Methods Breast cancer genomic and transcriptomic data were obtained from The Cancer Genome Atlas (TCGA). Breast cancer samples were dichotomized into high- and low-TMB groups according to TMB values. Differentially expressed DDR genes between high- and low-TMB groups were incorporated into univariate and multivariate cox regression model to build prognosis model. Performance of the prognosis model was validated in an independently new GEO dataset and evaluated by time-dependent ROC curves. Results Between high- and low-TMB groups, there were 6,424 differentially expressed genes, including 67 DDR genes. Ten genes associated with prognosis were selected by univariate cox regression analysis, among which seven genes constituted a panel to predict breast cancer prognosis. The seven-gene prognostic model, as well as the gene copy numbers are closely associated with tumor-infiltrating immune cells. Conclusion We established a seven-gene prognostic model comprising MDC1, PARP3, PSMB1, PSMB9, PSMD2, PSMD7, and PSMD14 genes, which provides a basis for further exploration of a population-based prediction of prognosis and immunotherapy response in patients with breast cancer.
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Affiliation(s)
- Xu Teng
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Tianshu Yang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Baowen Yuan
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yunkai Yang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaxiang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Wang
- Department of Ultrasound, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianyu Ma
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Yin
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Hefen Yu
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shuang Wang
- Department of Cardio Surgery Center, Shandong Second Provincial General Hospital, Jinan, China
| | - Wei Huang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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Long noncoding RNA PM maintains cerebellar synaptic integrity and Cbln1 activation via Pax6/Mll1-mediated H3K4me3. PLoS Biol 2021; 19:e3001297. [PMID: 34111112 PMCID: PMC8219131 DOI: 10.1371/journal.pbio.3001297] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/22/2021] [Accepted: 05/24/2021] [Indexed: 01/30/2023] Open
Abstract
Recent studies have shown that long noncoding RNAs (lncRNAs) are critical regulators in the central nervous system (CNS). However, their roles in the cerebellum are currently unclear. In this work, we identified the isoform 204 of lncRNA Gm2694 (designated as lncRNA-Promoting Methylation (lncRNA-PM)) is highly expressed in the cerebellum and derived from the antisense strand of the upstream region of Cerebellin-1 (Cbln1), a well-known critical cerebellar synaptic organizer. LncRNA-PM exhibits similar spatiotemporal expression pattern as Cbln1 in the postnatal mouse cerebellum and activates the transcription of Cbln1 through Pax6/Mll1-mediated H3K4me3. In mouse cerebellum, lncRNA-PM, Pax6/Mll1, and H3K4me3 are all associated with the regulatory regions of Cbln1. Knockdown of lncRNA-PM in cerebellum causes deficiencies in Cbln1 expression, cerebellar synaptic integrity, and motor function. Together, our work reveals an lncRNA-mediated transcriptional activation of Cbln1 through Pax6-Mll1-H3K4me3 and provides novel insights of the essential roles of lncRNA in the cerebellum. The long non-coding RNA lncRNA-PM activates transcription of the cerebellar synaptic organizer Cbln1 by promoting Pax6-Mll1-mediated H3K4me3 methylation, thereby helping to maintain cerebellar synaptic integrity and motor function.
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Yu P, Wang Y, Yang WT, Li Z, Zhang XJ, Zhou L, Gui JF. Upregulation of the PPAR signaling pathway and accumulation of lipids are related to the morphological and structural transformation of the dragon-eye goldfish eye. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1031-1049. [PMID: 33428077 DOI: 10.1007/s11427-020-1814-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
Goldfish comprise around 300 different strains with drastically altered and aesthetical morphologies making them suitable models for evolutionary developmental biology. The dragon-eye strain is characterized by protruding eyes (analogous to those of Chinese dragons). Although the strain has been selected for about 400 years, the mechanism of its eye development remains unclear. In this study, a stable dragon-eye goldfish strain with a clear genetic background was rapidly established and studied. We found that upregulation of the PPAR signaling pathway accompanied by an increase in lipid accumulation might trigger the morphological and structural transformation of the eye in dragon-eye goldfish. At the developmental stage of proptosis (eye protrusion), downregulation of the phototransduction pathway was consistent with the structural defects and myopia of the dragon-eye strain. With the impairment of retinal development, cytokine-induced inflammation was activated, especially after proptosis, similar to the pathologic symptoms of many human ocular diseases. In addition, differentially expressed transcription factors were significantly enriched in the PAX and homeobox families, two well-known transcription factor families involved in eye development. Therefore, our findings reveal the dynamic changes in key pathways during eye development in dragon-eye goldfish, and provide insights into the molecular mechanisms underlying drastically altered eyes in goldfish and human ocular disease.
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Affiliation(s)
- Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Tao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Ha TJ, Zhang PGY, Robert R, Yeung J, Swanson DJ, Mathelier A, Wasserman WW, Im S, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest ARR, Goldowitz D. Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. BMC Genomics 2019; 20:718. [PMID: 31533632 PMCID: PMC6751898 DOI: 10.1186/s12864-019-6063-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 08/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background The work of the FANTOM5 Consortium has brought forth a new level of understanding of the regulation of gene transcription and the cellular processes involved in creating diversity of cell types. In this study, we extended the analysis of the FANTOM5 Cap Analysis of Gene Expression (CAGE) transcriptome data to focus on understanding the genetic regulators involved in mouse cerebellar development. Results We used the HeliScopeCAGE library sequencing on cerebellar samples over 8 embryonic and 4 early postnatal times. This study showcases temporal expression pattern changes during cerebellar development. Through a bioinformatics analysis that focused on transcription factors, their promoters and binding sites, we identified genes that appear as strong candidates for involvement in cerebellar development. We selected several candidate transcriptional regulators for validation experiments including qRT-PCR and shRNA transcript knockdown. We observed marked and reproducible developmental defects in Atf4, Rfx3, and Scrt2 knockdown embryos, which support the role of these genes in cerebellar development. Conclusions The successful identification of these novel gene regulators in cerebellar development demonstrates that the FANTOM5 cerebellum time series is a high-quality transcriptome database for functional investigation of gene regulatory networks in cerebellar development. Electronic supplementary material The online version of this article (10.1186/s12864-019-6063-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas J Ha
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Peter G Y Zhang
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Remi Robert
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Douglas J Swanson
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Mathelier
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0372, Oslo, Norway
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sujin Im
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Masayoshi Itoh
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Hideya Kawaji
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Timo Lassmann
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan.,Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, Western Australia, 6008, Australia
| | - Carsten O Daub
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Erik Arner
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | | | - Piero Carninci
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Alistair R R Forrest
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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6
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López JM, Morona R, Moreno N, Lozano D, Jiménez S, González A. Pax6 expression highlights regional organization in the adult brain of lungfishes, the closest living relatives of land vertebrates. J Comp Neurol 2019; 528:135-159. [PMID: 31299095 DOI: 10.1002/cne.24744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/27/2019] [Accepted: 07/05/2019] [Indexed: 12/15/2022]
Abstract
The Pax6 gene encodes a regulatory transcription factor that is key in brain development. The molecular structure of Pax6, the roles it plays and its patterns of expression in the brain have been highly conserved during vertebrate evolution. As neurodevelopment proceeds, the Pax6 expression changes from the mitotic germinal zone in the ventricular zone to become distributed in cell groups in the adult brain. Studies in various vertebrates, from fish to mammals, found that the Pax6 expression is maintained in adults in most regions that express it during development. Specifically, in amphibians, Pax6 is widely expressed in the adult brain and its distribution pattern serves to highlight regional organization of the brain. In the present study, we analyzed the detailed distribution of Pax6 cells in the adult central nervous system of lungfishes, the closest living relatives of all tetrapods. Immunohistochemistry performed using double labeling techniques with several neuronal markers of known distribution patterns served to evaluate the actual location of Pax6 cells. Our results show that the Pax6 expression is maintained in the adult brain of lungfishes, in distinct regions of the telencephalon (pallium and subpallium), diencephalon, mesencephalon, hindbrain, spinal cord, and retina. The pattern of Pax6 expression is largely shared with amphibians and helps to understand the primitive condition that would have characterized the common ancestors to all sarcopterygians (lobe-finned fishes and tetrapods), in which Pax6 would be needed to maintain specific entities of subpopulations of neurons.
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Affiliation(s)
- Jesús M López
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Madrid, Spain
| | - Ruth Morona
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Madrid, Spain
| | - Nerea Moreno
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Madrid, Spain
| | - Daniel Lozano
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Madrid, Spain
| | - Sara Jiménez
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Madrid, Spain
| | - Agustín González
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Madrid, Spain
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7
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Nayler SP, Becker EBE. The Use of Stem Cell-Derived Neurons for Understanding Development and Disease of the Cerebellum. Front Neurosci 2018; 12:646. [PMID: 30319335 PMCID: PMC6168705 DOI: 10.3389/fnins.2018.00646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022] Open
Abstract
The cerebellum is a fascinating brain structure, containing more neurons than the rest of the brain combined. The cerebellum develops according to a highly orchestrated program into a well-organized laminar structure. Much has been learned about the underlying genetic networks controlling cerebellar development through the study of various animal models. Cerebellar development in humans however, is significantly protracted and more complex. Given that the cerebellum regulates a number of motor and non-motor functions and is affected in a wide variety of neurodevelopmental and neurodegenerative disorders, a better understanding of human cerebellar development is highly desirable. Pluripotent stem cells offer an exciting new tool to unravel human cerebellar development and disease by providing a dynamic and malleable platform, which is amenable to genetic manipulation and temporally unrestricted sampling. It remains to be seen, however, whether in vitro neuronal cultures derived from pluripotent stem cells fully recapitulate the formation and organization of the developing nervous system, with many reports detailing the functionally immature nature of these cultures. Nevertheless, recent advances in differentiation protocols, cell-sampling methodologies, and access to informatics resources mean that the field is poised for remarkable discoveries. In this review, we provide a general overview of the field of neuronal differentiation, focusing on the cerebellum and highlighting conceptual advances in understanding neuronal maturity, including a discussion of both current and emerging methods to classify, and influence neuroanatomical identity and maturation status.
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Affiliation(s)
- Samuel P Nayler
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Esther B E Becker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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8
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Kiselev Y, Andersen S, Johannessen C, Fjukstad B, Standahl Olsen K, Stenvold H, Al-Saad S, Donnem T, Richardsen E, Bremnes RM, Rasmussen Busund LT. Transcription factor PAX6 as a novel prognostic factor and putative tumour suppressor in non-small cell lung cancer. Sci Rep 2018; 8:5059. [PMID: 29568088 PMCID: PMC5864921 DOI: 10.1038/s41598-018-23417-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 03/09/2018] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is the leading cause of cancer deaths. Novel predictive biomarkers are needed to improve treatment selection and more accurate prognostication. PAX6 is a transcription factor with a proposed tumour suppressor function. Immunohistochemical staining was performed on tissue microarrays from 335 non-small cell lung cancer (NSCLC) patients for PAX6. Multivariate analyses of clinico-pathological variables and disease-specific survival (DSS) was carried out, and phenotypic changes of two NSCLC cell lines with knockdown of PAX6 were characterized. While PAX6 expression was only associated with a trend of better disease-specific survival (DSS) (p = 0.10), the pN+ subgroup (N = 103) showed significant correlation between high PAX6 expression and longer DSS (p = 0.022). Median survival for pN + patients with high PAX6 expression was 127.4 months, versus 22.9 months for patients with low PAX6 expression. In NCI-H661 cells, knockdown of PAX6 strongly activated serum-stimulated migration. In NCI-H460 cells, PAX6 knockdown activated anchorage-independent growth. We did not observe any significant effect of PAX6 on proliferation in either of cell lines. Our findings strongly support the proposition of PAX6 as a valid and positive prognostic marker in NSCLC in node-positive patients. There is a need for further studies, which should provide mechanistical explanation for the role of PAX6 in NSCLC.
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Affiliation(s)
- Yury Kiselev
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway. .,Department of Pharmacy, UiT The Arctic University of Norway, Tromso, Norway. .,Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway.
| | - Sigve Andersen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Charles Johannessen
- Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Bjørn Fjukstad
- Department of Computer Science, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromso, Norway
| | - Karina Standahl Olsen
- Department of Community Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromso, Norway
| | - Helge Stenvold
- Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Samer Al-Saad
- Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Tom Donnem
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Elin Richardsen
- Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Roy M Bremnes
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway.,Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Lill-Tove Rasmussen Busund
- Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
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9
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Adorjan I, Ahmed B, Feher V, Torso M, Krug K, Esiri M, Chance SA, Szele FG. Calretinin interneuron density in the caudate nucleus is lower in autism spectrum disorder. Brain 2017; 140:2028-2040. [PMID: 29177493 DOI: 10.1093/brain/awx131] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 04/18/2017] [Indexed: 02/05/2023] Open
Abstract
Autism spectrum disorder is a debilitating condition with possible neurodevelopmental origins but unknown neuroanatomical correlates. Whereas investigators have paid much attention to the cerebral cortex, few studies have detailed the basal ganglia in autism. The caudate nucleus may be involved in the repetitive movements and limbic changes of autism. We used immunohistochemistry for calretinin and neuropeptide Y in 24 age- and gender-matched patients with autism spectrum disorder and control subjects ranging in age from 13 to 69 years. Patients with autism had a 35% lower density of calretinin+ interneurons in the caudate that was driven by loss of small calretinin+ neurons. This was not caused by altered size of the caudate, as its cross-sectional surface areas were similar between diagnostic groups. Controls exhibited an age-dependent increase in the density of medium and large calretinin+ neurons, whereas subjects with autism did not. Diagnostic groups did not differ regarding ionized calcium-binding adapter molecule 1+ immunoreactivity for microglia, suggesting chronic inflammation did not cause the decreased calretinin+ density. There was no statistically significant difference in the density of neuropeptide Y+ neurons between subjects with autism and controls. The decreased calretinin+ density may disrupt the excitation/inhibition balance in the caudate leading to dysfunctional corticostriatal circuits. The description of such changes in autism spectrum disorder may clarify pathomechanisms and thereby help identify targets for drug intervention and novel therapeutic strategies.
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Affiliation(s)
- Istvan Adorjan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.,Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Bashir Ahmed
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Virginia Feher
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Mario Torso
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Kristine Krug
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Margaret Esiri
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Steven A Chance
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Francis G Szele
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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A Novel and Multivalent Role of Pax6 in Cerebellar Development. J Neurosci 2017; 36:9057-69. [PMID: 27581449 DOI: 10.1523/jneurosci.4385-15.2016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 07/12/2016] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED Pax6 is a prominent gene in brain development. The deletion of Pax6 results in devastated development of eye, olfactory bulb, and cortex. However, it has been reported that the Pax6-null Sey cerebellum only has minor defects involving granule cells despite Pax6 being expressed throughout cerebellar development. The present work has uncovered a requirement of Pax6 in the development of all rhombic lip (RL) lineages. A significant downregulation of Tbr1 and Tbr2 expression is found in the Sey cerebellum, these are cell-specific markers of cerebellar nuclear (CN) neurons and unipolar brush cells (UBCs), respectively. The examination of Tbr1 and Lmx1a immunolabeling and Nissl staining confirmed the loss of CN neurons from the Sey cerebellum. CN neuron progenitors are produced in the mutant but there is an enhanced death of these neurons as shown by increased presence of caspase-3-positive cells. These data indicate that Pax6 regulates the survival of CN neuron progenitors. Furthermore, the analysis of experimental mouse chimeras suggests a cell-extrinsic role of Pax6 in CN neuron survival. For UBCs, using Tbr2 immunolabeling, these cells are significantly reduced in the Sey cerebellum. The loss of UBCs in the mutant is due partly to cell death in the RL and also to the reduced production of progenitors from the RL. These results demonstrate a critical role for Pax6 in regulating the generation and survival of UBCs. This and previous work from our laboratory demonstrate a seminal role of Pax6 in the development of all cerebellar glutamatergic neurons. SIGNIFICANCE STATEMENT Pax6 is a key molecule in development. Pax6 is best known as the master control gene in eye development with mutations causing aniridia in humans. Pax6 also plays important developmental roles in the cortex and olfactory bulb. During cerebellar development, Pax6 is robustly expressed in the germinal zone of all glutamatergic neurons [cerebellar nuclear (CN) neurons, granule cells, and unipolar brush cells (UBCs)]. Past work has not found abnormalities in the CN and UBC populations. Our study reveals that the Pax6-null mutation dramatically affects these cells and identifies Pax6 as a key regulator of cell survival in CN neurons and of cell production in UBCs. The present study shows how Pax6 is key to the development of glutamatergic cells in the cerebellum.
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Bubier JA, Phillips CA, Langston MA, Baker EJ, Chesler EJ. GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data. Mamm Genome 2015; 26:556-66. [PMID: 26092690 PMCID: PMC4602068 DOI: 10.1007/s00335-015-9575-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/03/2015] [Indexed: 01/20/2023]
Abstract
A persistent challenge lies in the interpretation of consensus and discord from functional genomics experimentation. Harmonizing and analyzing this data will enable investigators to discover relations of many genes to many diseases, and from many phenotypes and experimental paradigms to many diseases through their genomic substrates. The GeneWeaver.org system provides a platform for cross-species integration and interrogation of heterogeneous curated and experimentally derived functional genomics data. GeneWeaver enables researchers to store, share, analyze, and compare results of their own genome-wide functional genomics experiments in an environment containing rich companion data obtained from major curated repositories, including the Mouse Genome Database and other model organism databases, along with derived data from highly specialized resources, publications, and user submissions. The data, largely consisting of gene sets and putative biological networks, are mapped onto one another through gene identifiers and homology across species. A versatile suite of interactive tools enables investigators to perform a variety of set analysis operations to find consilience among these often noisy experimental results. Fast algorithms enable real-time analysis of large queries. Specific applications include prioritizing candidate genes for quantitative trait loci, identifying biologically valid mouse models and phenotypic assays for human disease, finding the common biological substrates of related diseases, classifying experiments and the biological concepts they represent from empirical data, and applying patterns of genomic evidence to implicate novel genes in disease. These results illustrate an alternative to strict emphasis on replicability, whereby researchers classify experimental results to identify the conditions that lead to their similarity.
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Affiliation(s)
| | - Charles A Phillips
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Michael A Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Erich J Baker
- Computer Science Department, Baylor University, Waco, TX, 76798, USA
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Abstract
Math1 is the defining molecule of the cerebellar rhombic lip and Pax6 is downstream in the Math1 pathway. In the present study, we discover that Wntless (Wls) is a novel molecular marker of the cells in the interior face of the rhombic lip throughout normal mouse cerebellar development. Wls expression is found complementary to the expression of Math1 and Pax6, which are localized to the exterior face of the rhombic lip. To determine the interaction between these molecules, we examine the loss-of-Math1 or loss-of-Pax6 in the cerebellum, i.e., the Math1-null and Pax6-null (Sey) mutant cerebella. The presence of Wls-positive cells in the Math1-null rhombic lip indicates that Wls expression is independent of Math1. In the Sey mutant cerebellum, there is an expansion of Wls-expressing cells into regions that are normally colonized by Pax6-expressing cells. The ectopic expression of Wls in the Pax6-null cerebellum suggests a negative interaction between Wls-expressing cells and Pax6-positive cells. These findings suggest that the rhombic lip is dynamically patterned by the expression of Wls, Math1, and Pax6. We also examine five rhombic lip cell markers (Wls, Math1, Pax6, Lmx1a, and Tbr2) to identify four molecularly distinct compartments in the rhombic lip during cerebellar development. The existence of spatial compartmentation in the rhombic lip and the interplay between Wls, Math1, and Pax6 in the rhombic lip provides novel views of early cerebellar development.
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Ha T, Swanson D, Larouche M, Glenn R, Weeden D, Zhang P, Hamre K, Langston M, Phillips C, Song M, Ouyang Z, Chesler E, Duvvurru S, Yordanova R, Cui Y, Campbell K, Ricker G, Phillips C, Homayouni R, Goldowitz D. CbGRiTS: cerebellar gene regulation in time and space. Dev Biol 2014; 397:18-30. [PMID: 25446528 DOI: 10.1016/j.ydbio.2014.09.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 08/23/2014] [Accepted: 09/27/2014] [Indexed: 01/09/2023]
Abstract
The mammalian CNS is one of the most complex biological systems to understand at the molecular level. The temporal information from time series transcriptome analysis can serve as a potent source of associative information between developmental processes and regulatory genes. Here, we introduce a new transcriptome database called, Cerebellar Gene Regulation in Time and Space (CbGRiTS). This dataset is populated with transcriptome data across embryonic and postnatal development from two standard mouse strains, C57BL/6J and DBA/2J, several recombinant inbred lines and cerebellar mutant strains. Users can evaluate expression profiles across cerebellar development in a deep time series with graphical interfaces for data exploration and link-out to anatomical expression databases. We present three analytical approaches that take advantage of specific aspects of the time series for transcriptome analysis. We demonstrate the use of CbGRiTS dataset as a community resource to explore patterns of gene expression and develop hypotheses concerning gene regulatory networks in brain development.
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Affiliation(s)
- Thomas Ha
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Douglas Swanson
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Matt Larouche
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Randy Glenn
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Dave Weeden
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Peter Zhang
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Kristin Hamre
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Michael Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Charles Phillips
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Mingzhou Song
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
| | - Zhengyu Ouyang
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
| | | | | | | | - Yan Cui
- Department of Molecular Science, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kate Campbell
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Greg Ricker
- Department of Biology, Bowdoin College, Brunswick, ME, USA
| | - Carey Phillips
- Department of Biology, Bowdoin College, Brunswick, ME, USA
| | - Ramin Homayouni
- Bioinformatics Program, Department of Biology, University of Memphis, Memphis, TN, USA
| | - Dan Goldowitz
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4.
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Abstract
Math1 is the defining molecule of the cerebellar rhombic lip and Pax6 is downstream in the Math1 pathway. In the present study, we discover that Wntless (Wls) is a novel molecular marker of the cells in the interior face of the rhombic lip throughout normal mouse cerebellar development. Wls expression is found complementary to the expression of Math1 and Pax6, which are localized to the exterior face of the rhombic lip. To determine the interaction between these molecules, we examine the loss-of-Math1 or loss-of-Pax6 in the cerebellum, i.e., the Math1-null and Pax6-null (Sey) mutant cerebella. The presence of Wls-positive cells in the Math1-null rhombic lip indicates that Wls expression is independent of Math1. In the Sey mutant cerebellum, there is an expansion of Wls-expressing cells into regions that are normally colonized by Pax6-expressing cells. The ectopic expression of Wls in the Pax6-null cerebellum suggests a negative interaction between Wls-expressing cells and Pax6-positive cells. These findings suggest that the rhombic lip is dynamically patterned by the expression of Wls, Math1, and Pax6. We also examine five rhombic lip cell markers (Wls, Math1, Pax6, Lmx1a, and Tbr2) to identify four molecularly distinct compartments in the rhombic lip during cerebellar development. The existence of spatial compartmentation in the rhombic lip and the interplay between Wls, Math1, and Pax6 in the rhombic lip provides novel views of early cerebellar development.
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Visualized gene network reveals the novel target transcripts Sox2 and Pax6 of neuronal development in trans-placental exposure to bisphenol A. PLoS One 2014; 9:e100576. [PMID: 25051057 PMCID: PMC4106758 DOI: 10.1371/journal.pone.0100576] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/26/2014] [Indexed: 12/12/2022] Open
Abstract
Background Bisphenol A (BPA) is a ubiquitous endocrine disrupting chemical in our daily life, and its health effect in response to prenatal exposure is still controversial. Early-life BPA exposure may impact brain development and contribute to childhood neurological disorders. The aim of the present study was to investigate molecular target genes of neuronal development in trans-placental exposure to BPA. Methodology A meta-analysis of three public microarray datasets was performed to screen for differentially expressed genes (DEGs) in exposure to BPA. The candidate genes of neuronal development were identified from gene ontology analysis in a reconstructed neuronal sub-network, and their gene expressions were determined using real-time PCR in 20 umbilical cord blood samples dichotomized into high and low BPA level groups upon the median 16.8 nM. Principal Findings Among 36 neuronal transcripts sorted from DAVID ontology clusters of 457 DEGs using the analysis of Bioconductor limma package, we found two neuronal genes, sex determining region Y-box 2 (Sox2) and paired box 6 (Pax6), had preferentially down-regulated expression (Bonferroni correction p-value <10−4 and log2-transformed fold change ≤−1.2) in response to BPA exposure. Fetal cord blood samples had the obviously attenuated gene expression of Sox2 and Pax6 in high BPA group referred to low BPA group. Visualized gene network of Cytoscape analysis showed that Sox2 and Pax6 which were contributed to neural precursor cell proliferation and neuronal differentiation might be down-regulated through sonic hedgehog (Shh), vascular endothelial growth factor A (VEGFA) and Notch signaling. Conclusions These results indicated that trans-placental BPA exposure down-regulated gene expression of Sox2 and Pax6 potentially underlying the adverse effect on childhood neuronal development.
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