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Liu S, Nam HS, Zeng Z, Deng X, Pashaei E, Zang Y, Yang L, Li C, Huang J, Wendt MK, Lu X, Huang R, Wan J. CDHu40: a novel marker gene set of neuroendocrine prostate cancer. Brief Bioinform 2024; 25:bbae471. [PMID: 39318189 PMCID: PMC11422505 DOI: 10.1093/bib/bbae471] [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: 04/01/2024] [Revised: 07/22/2024] [Accepted: 09/10/2024] [Indexed: 09/26/2024] Open
Abstract
Prostate cancer (PCa) is the most prevalent cancer affecting American men. Castration-resistant prostate cancer (CRPC) can emerge during hormone therapy for PCa, manifesting with elevated serum prostate-specific antigen levels, continued disease progression, and/or metastasis to the new sites, resulting in a poor prognosis. A subset of CRPC patients shows a neuroendocrine (NE) phenotype, signifying reduced or no reliance on androgen receptor signaling and a particularly unfavorable prognosis. In this study, we incorporated computational approaches based on both gene expression profiles and protein-protein interaction networks. We identified 500 potential marker genes, which are significantly enriched in cell cycle and neuronal processes. The top 40 candidates, collectively named CDHu40, demonstrated superior performance in distinguishing NE PCa (NEPC) and non-NEPC samples based on gene expression profiles. CDHu40 outperformed most of the other published marker sets, excelling particularly at the prognostic level. Notably, some marker genes in CDHu40, absent in the other marker sets, have been reported to be associated with NEPC in the literature, such as DDC, FOLH1, BEX1, MAST1, and CACNA1A. Importantly, elevated CDHu40 scores derived from our predictive model showed a robust correlation with unfavorable survival outcomes in patients, indicating the potential of the CDHu40 score as a promising indicator for predicting the survival prognosis of those patients with the NE phenotype. Motif enrichment analysis on the top candidates suggests that REST and E2F6 may serve as key regulators in the NEPC progression.
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Affiliation(s)
- Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th Street, Indianapolis, IN 46202, United States
| | - Hye Seung Nam
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, United States
| | - Ziyu Zeng
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, 100 Galvin Life Science Center, Notre Dame, IN 46556, United States
| | - Xuehong Deng
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, United States
| | - Elnaz Pashaei
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th Street, Indianapolis, IN 46202, United States
| | - Yong Zang
- Department of Biostatistics & Health Data Science, Indiana University School of Medicine, 410 W 10th Street, Indianapolis, IN 46202, United States
| | - Lei Yang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 W Walnut St, Indianapolis, IN 46202, United States
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Dr Room P3-12, Gainesville, FL 32603, United States
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Davison Building, 40 Duke Medicine, Durham, NC 27710, United States
| | - Michael K Wendt
- Department of Internal Medicine, Division of Hematology and Oncology, University of Iowa, 200 Hawkins Dr, Iowa City, IA 52242, United States
- Holden Comprehensive Cancer Center, University of Iowa, 200 Hawkins Dr, Iowa City, IA, 52242, United States
| | - Xin Lu
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, 100 Galvin Life Science Center, Notre Dame, IN 46556, United States
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 535 Barnhill Dr, Indianapolis, IN 46202, United States
| | - Rong Huang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, United States
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th Street, Indianapolis, IN 46202, United States
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 535 Barnhill Dr, Indianapolis, IN 46202, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W 10th Street, Indianapolis, IN 46202, United States
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2
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Ruscu M, Capitanescu B, Rupek P, Dandekar T, Radu E, Hermann DM, Popa-Wagner A. The post-stroke young adult brain has limited capacity to re-express the gene expression patterns seen during early postnatal brain development. Brain Pathol 2024; 34:e13232. [PMID: 38198833 PMCID: PMC11328347 DOI: 10.1111/bpa.13232] [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: 06/07/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The developmental origins of the brain's response to injury can play an important role in recovery after a brain lesion. In this study, we investigated whether the ischemic young adult brain can re-express brain plasticity genes that were active during early postnatal development. Differentially expressed genes in the cortex of juvenile post-natal day 3 and the peri-infarcted cortical areas of young, 3-month-old post-stroke rats were identified using fixed-effects modeling within an empirical Bayes framework through condition-specific comparison. To further analyze potential biological processes, upregulated and downregulated genes were assessed for enrichment using GSEA software. The genes showing the highest expression changes were subsequently verified through RT-PCR. Our findings indicate that the adult brain partially recapitulates the gene expression profile observed in the juvenile brain but fails to upregulate many genes and pathways necessary for brain plasticity. Of the upregulated genes in post-stroke brains, specific roles have not been assigned to Apobec1, Cenpf, Ect2, Folr2, Glipr1, Myo1f, and Pttg1. New genes that failed to upregulate in the adult post-stroke brain include Bex4, Cd24, Klhl1/Mrp2, Trim67, and St8sia2. Among the upregulated pathways, the largest change was observed in the KEGG pathway "One carbon pool of folate," which is necessary for cellular proliferation, followed by the KEGG pathway "Antifolate resistance," whose genes mainly encode the family of ABC transporters responsible for the efflux of drugs that have entered the brain. We also noted three less-described downregulated KEGG pathways in experimental models: glycolipid biosynthesis, oxytocin, and cortisol pathways, which could be relevant as therapeutic targets. The limited brain plasticity of the adult brain is illustrated through molecular and histological analysis of the axonal growth factor, KIF4. Collectively, these results strongly suggest that further research is needed to decipher the complex genetic mechanisms that prevent the re-expression of brain plasticity-associated genes in the adult brain.
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Affiliation(s)
- Mihai Ruscu
- Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
- University of Medicine and Pharmacy Craiova, Craiova, Romania
| | | | - Paul Rupek
- Chair of Bioinformatics, University of Würzburg, Wuerzburg, Germany
| | - Thomas Dandekar
- Chair of Bioinformatics, University of Würzburg, Wuerzburg, Germany
| | - Eugen Radu
- University of Medicine and Pharmacy Carol Davila, Bucharest, Romania
| | - Dirk M Hermann
- Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
- University of Medicine and Pharmacy Craiova, Craiova, Romania
| | - Aurel Popa-Wagner
- Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
- University of Medicine and Pharmacy Craiova, Craiova, Romania
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3
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Pierce SE, van der Schans EJ, Ensink E, Coetzee GA. Gene expression asymmetry in Parkinson's Disease; variation of CCT and BEX gene expression levels are correlated with hemisphere specific severity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601704. [PMID: 39005359 PMCID: PMC11245011 DOI: 10.1101/2024.07.02.601704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Parkinson's Disease (PD) develops unilaterally, which may be related to brain hemispheric differences in gene expression. Here we measured bulk RNA-seq levels in neuronal nuclei obtained from prefrontal cortex postmortem brain samples from males and females with PD and from healthy controls. Left and right hemispheres from each brain were related the side of symptom onset and compared. We employed two a priori approaches; first we identified genes differentially expressed between PD and controls and between left vs right PD brain hemispheres. Second, we examined the presence of, and correlates to, variable asymmetry seen in candidate PD differentially expressed genes. We found large variation among individuals with PD, and PD stratification by gene expression similarity was required for patterns of genetic asymmetry to emerge. For a subset of PD brains, hemispherical variation of CCT and BEX gene levels correlated with the side of PD symptom onset.
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Liu S, Nam HS, Zeng Z, Deng X, Pashaei E, Zang Y, Yang L, Li C, Huang J, Wendt MK, Lu X, Huang R, Wan J. CDHu40: a novel marker gene set of neuroendocrine prostate cancer (NEPC). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587205. [PMID: 38585861 PMCID: PMC10996696 DOI: 10.1101/2024.03.28.587205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Prostate cancer (PCa) is the most prevalent cancer affecting American men. Castration-resistant prostate cancer (CRPC) can emerge during hormone therapy for PCa, manifesting with elevated serum prostate-specific antigen (PSA) levels, continued disease progression, and/or metastasis to the new sites, resulting in a poor prognosis. A subset of CRPC patients shows a neuroendocrine (NE) phenotype, signifying reduced or no reliance on androgen receptor (AR) signaling and a particularly unfavorable prognosis. In this study, we incorporated computational approaches based on both gene expression profiles and protein-protein interaction (PPI) networks. We identified 500 potential marker genes, which are significantly enriched in cell cycle and neuronal processes. The top 40 candidates, collectively named as CDHu40, demonstrated superior performance in distinguishing NE prostate cancer (NEPC) and non-NEPC samples based on gene expression profiles compared to other published marker sets. Notably, some novel marker genes in CDHu40, absent in the other marker sets, have been reported to be associated with NEPC in the literature, such as DDC, FOLH1, BEX1, MAST1, and CACNA1A. Importantly, elevated CDHu40 scores derived from our predictive model showed a robust correlation with unfavorable survival outcomes in patients, indicating the potential of the CDHu40 score as a promising indicator for predicting the survival prognosis of those patients with the NE phenotype. Motif enrichment analysis on the top candidates suggests that REST and E2F6 may serve as key regulators in the NEPC progression. Significance our study integrates gene expression variances in multiple NEPC studies and protein-protein interaction network to pinpoint a specific set of NEPC maker genes namely CDHu40. These genes and scores based on their gene expression levels effectively distinguish NEPC samples and underscore the clinical prognostic significance and potential mechanism.
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Zhao YX, Song JY, Bao XW, Zhang JL, Wu JC, Wang LY, He C, Shao W, Bai XL, Liang TB, Sheng JP. Single-cell RNA sequencing-guided fate-mapping toolkit delineates the contribution of yolk sac erythro-myeloid progenitors. Cell Rep 2023; 42:113364. [PMID: 37922312 DOI: 10.1016/j.celrep.2023.113364] [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: 01/17/2023] [Revised: 09/16/2023] [Accepted: 10/16/2023] [Indexed: 11/05/2023] Open
Abstract
Erythro-myeloid progenitors of the yolk sac that originates during early embryo development has been suggested to generate tissue-resident macrophage, mast cell, and even endothelial cell populations from fetal to adult stages. However, the heterogeneity of erythro-myeloid progenitors (EMPs) is not well characterized. Here, we adapt single-cell RNA sequencing to dissect the heterogeneity of EMPs and establish several fate-mapping tools for each EMP subset to trace the contributions of different EMP subsets. We identify two primitive and one definitive EMP subsets from the yolk sac. In addition, we find that primitive EMPs are decoupled from definitive EMPs. Furthermore, we confirm that primitive and definitive EMPs give rise to microglia and other tissue-resident macrophages, respectively. In contrast, only Kit+ Csf1r- primitive EMPs generate endothelial cells transiently during early embryo development. Overall, our results delineate the contribution of yolk sac EMPs more clearly based on the single-cell RNA sequencing (scRNA-seq)-guided fate-mapping toolkit.
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Affiliation(s)
- Y X Zhao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China
| | - J Y Song
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China
| | - X W Bao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China
| | - J L Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China
| | - J C Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China
| | - L Y Wang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, China
| | - C He
- Infinity Scope Biotechnology Co., Ltd., Hangzhou 311200, China
| | - W Shao
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210000, China.
| | - X L Bai
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China.
| | - T B Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China.
| | - J P Sheng
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310002, China; Zhejiang University Cancer Center, Zhejiang University, Hangzhou 310002, China.
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6
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Zhou S, Zhong H, Wang Y, Wang X, Pan H, Liu X, Hu L. JNK/MAPK pathway regulation by BEX2 gene silencing in alcoholic hepatitis mice: Effects on oxidative stress. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2023; 47:1869-1882. [PMID: 37864534 DOI: 10.1111/acer.15178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Alcoholic hepatitis (AH) is a severe alcoholic-related liver disease that is a leading cause of morbidity and mortality, for which effective treatments are lacking. Brain-expressed X-linked gene 2 (BEX2) has been implicated in various diseases, but its association with AH has received limited attention. Thus, this study investigated BEX2's impact on the progression of AH by affecting the c-Jun NH2-terminal kinase/mitogen-activated protein kinase (JNK/MAPK) pathway. METHODS Microarray dataset GSE28619 from the Gene Expression Omnibus database was used to identify differentially expressed genes in AH. Immunohistochemistry, terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL), Western blot analysis, and flow cytometry were used to measure various factors in the liver tissue of AH mice. RESULTS BEX2 expression was significantly upregulated in the model. BEX2 gene silencing increased the levels of glutathione peroxidase and superoxide dismutase while decreasing malondialdehyde content; phosphorylation of JNK, c-JUN, and p38MAPK; apoptosis rate; and the extent of JNK/MAPK pathway activation. CONCLUSIONS These findings provide valuable insights into the mechanisms underlying AH development and highlight the potential role of BEX2 gene expression as a promising therapeutic target for AH.
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Affiliation(s)
- Shuai Zhou
- Department of General Surgery, Anhui No. 2 Provincial People's Hospital, Anhui Medical University, Hefei, China
| | - Hai Zhong
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yong Wang
- Department of General Surgery, Anhui No. 2 Provincial People's Hospital, Anhui Medical University, Hefei, China
| | - Xiaoguang Wang
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Hongtao Pan
- Department of General Surgery, Anhui No. 2 Provincial People's Hospital, Anhui Medical University, Hefei, China
| | - Xiaolin Liu
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Lingyu Hu
- Department of Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
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Wendorff AA, Aidan Quinn S, Alvarez S, Brown JA, Biswas M, Gunning T, Palomero T, Ferrando AA. Epigenetic reversal of hematopoietic stem cell aging in Phf6-knockout mice. NATURE AGING 2022; 2:1008-1023. [PMID: 37118089 DOI: 10.1038/s43587-022-00304-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 10/03/2022] [Indexed: 04/30/2023]
Abstract
Aging is characterized by an accumulation of myeloid-biased hematopoietic stem cells (HSCs) with reduced developmental potential. Genotoxic stress and epigenetic alterations have been proposed to mediate age-related HSC loss of regenerative and self-renewal potential. However, the mechanisms underlying these changes remain largely unknown. Genetic inactivation of the plant homeodomain 6 (Phf6) gene, a nucleolar and chromatin-associated factor, antagonizes age-associated HSC decline. Immunophenotyping, single-cell transcriptomic analyses and transplantation assays demonstrated markedly decreased accumulation of immunophenotypically defined HSCs, reduced myeloid bias and increased hematopoietic reconstitution capacity with preservation of lymphoid differentiation potential in Phf6-knockout HSCs from old mice. Moreover, deletion of Phf6 in aged mice rejuvenated immunophenotypic, transcriptional and functional hallmarks of aged HSCs. Long-term HSCs from old Phf6-knockout mice showed epigenetic rewiring and transcriptional programs consistent with decreased genotoxic stress-induced HSC aging. These results identify Phf6 as an important epigenetic regulator of HSC aging.
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Affiliation(s)
- Agnieszka A Wendorff
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Calico Life Sciences, South San Francisco, CA, USA.
| | - S Aidan Quinn
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Silvia Alvarez
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Jessie A Brown
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Mayukh Biswas
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Thomas Gunning
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Teresa Palomero
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.
- Regeneron Genetics Center, Tarrytown, NY, USA.
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Bahadar N, Ullah H, Adlat S, Kumar Sah R, Zun Zaw Myint M, Mar Oo Z, Binta Bah F, Hayel Nagi F, Htoo H, Ud Din A, Feng X, Zheng Y. Analyzing differentially expressed genes and pathways of Bex2-deficient mouse lung via RNA-Seq. Turk J Biol 2021; 45:588-598. [PMID: 34803456 PMCID: PMC8574191 DOI: 10.3906/biy-2104-4] [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: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
Bex2 is well known for its role in the nervous system, and is associated with neurological disorders, but its role in the lung’s physiology is still not reported. To elucidate the functional role of Bex2 in the lung, we generated a Bex2 knock-out (KO) mouse model using the CRISPR-Cas9 technology and performed transcriptomic analysis. A total of 652 genes were identified as differentially expressed between Bex2-/- and Bex2+/+ mice, out of which 500 were downregulated, while 152 were upregulated genes. Among these DEGs, Ucp1, Myh6, Coxa7a1, Myl3, Ryr2, RNaset2b, Npy, Enob1, Krt5, Myl2, Hba-a2, and Nrob2 are the most prominent genes. Myl2, was the most downregulated gene, followed by Npy, Hba-a2, Rnaset2b, nr0b2, Klra8, and Ucp1. Tcte3, Eno1b, Zfp990, and Pcdha9 were the most upregulated DEGs. According to gene enrichment analysis, PPAR pathway, cardiac muscle contraction, and cytokine-cytokine receptor interaction were the most enriched pathways. Besides, the nuclear factor-κB signaling pathway and hematopoietic cell linage pathways were also enriched. Chronic obstructive pulmonary disease (COPD) is enriched among KEGG disease pathways. RT-qPCR assays confirmed the RNA-Seq results. This study opens a new window toward the biological functions of Bex2 in different systems.
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Affiliation(s)
- Noor Bahadar
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Hanif Ullah
- School of medicine, Tsinghua University, Beijing China
| | - Salah Adlat
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Rajiv Kumar Sah
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - May Zun Zaw Myint
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Zin Mar Oo
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Fatoumata Binta Bah
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Farooq Hayel Nagi
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Hsu Htoo
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Ahmad Ud Din
- Drug Discovery Research Center, Southwest Medical University, Luzhou China
| | - Xuechao Feng
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
| | - Yaowu Zheng
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, Jilin China
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Anzai K, Tsuruya K, Ida K, Kagawa T, Inagaki Y, Kamiya A. Kruppel-like factor 15 induces the development of mature hepatocyte-like cells from hepatoblasts. Sci Rep 2021; 11:18551. [PMID: 34535735 PMCID: PMC8448749 DOI: 10.1038/s41598-021-97937-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/01/2021] [Indexed: 11/08/2022] Open
Abstract
The liver is an important metabolic organ that controls homeostasis in the body. Moreover, it functions as a hematopoietic organ, while its metabolic function is low during development. Hepatocytes, which are parenchymal cells of the liver, acquire various metabolic functions by the maturation of hepatic progenitor cells during the fetal period; however, this molecular mechanism is still unclear. In this study, Kruppel-like factor 15 (KLF15) was identified as a new regulator of hepatic maturation through a comprehensive analysis of the expression of transcriptional regulators in mouse fetal and adult hepatocytes. KLF15 is a transcription factor whose expression in the liver increases from the embryonic stage throughout the developmental process. KLF15 induced the overexpression of liver function genes in mouse embryonic hepatocytes. Furthermore, we found that the expression of KLF15 could also induce the expression of liver function genes in hepatoblasts derived from human induced pluripotent stem cells (iPSCs). Moreover, KLF15 increased the promoter activity of tyrosine aminotransferase, a liver function gene. KLF15 also suppressed the proliferation of hepatoblasts. These results suggest that KLF15 induces hepatic maturation through the transcriptional activation of target genes and cell cycle control.
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Affiliation(s)
- Kazuya Anzai
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Kota Tsuruya
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Kinuyo Ida
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Tatehiro Kagawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Yutaka Inagaki
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Department of Innovative Medical Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Akihide Kamiya
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
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10
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Fukushi D, Shibuya-Takahashi R, Mochizuki M, Fujimori H, Kogure T, Sugai T, Iwai W, Wakui Y, Abue M, Murakami K, Nakamura Y, Yasuda J, Yamaguchi K, Sugamura K, Shibata C, Katayose Y, Satoh K, Tamai K. BEX2 is required for maintaining dormant cancer stem cell in hepatocellular carcinoma. Cancer Sci 2021; 112:4580-4592. [PMID: 34424582 PMCID: PMC8586677 DOI: 10.1111/cas.15115] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/12/2021] [Accepted: 08/21/2021] [Indexed: 12/18/2022] Open
Abstract
Cancer stem cells (CSCs) are responsible for therapy resistance and share several properties with normal stem cells. Here, we show that brain‐expressed X‐linked gene 2 (BEX2), which is essential for dormant CSCs in cholangiocarcinoma, is highly expressed in human hepatocellular carcinoma (HCC) lesions compared with the adjacent normal lesions and that in 41 HCC cases the BEX2high expression group is correlated with a poor prognosis. BEX2 localizes to Ki67‐negative (nonproliferative) cancer cells in HCC tissues and is highly expressed in the dormant fraction of HCC cell lines. Knockdown of BEX2 attenuates CSC phenotypes, including sphere formation ability and aldefluor activity, and BEX2 overexpression enhances these phenotypes. Moreover, BEX2 knockdown increases cisplatin sensitivity, and BEX2 expression is induced by cisplatin treatment. Taken together, these data suggest that BEX2 induces dormant CSC properties and affects the prognosis of patients with HCC.
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Affiliation(s)
- Daisuke Fukushi
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan.,Division of Cancer Stem Cell, Tohoku University Graduate School of Medicine, Sendai, Japan.,Division of Gastroenterology, Tohoku Medical and Pharmaceutical University Hospital, Sendai, Japan
| | - Rie Shibuya-Takahashi
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Mai Mochizuki
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Haruna Fujimori
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Takayuki Kogure
- Division of Gastroenterology, Tohoku Medical and Pharmaceutical University Hospital, Sendai, Japan
| | - Takahiro Sugai
- Department of Gastroenterology, Miyagi Cancer Center, Natori, Japan
| | - Wataru Iwai
- Department of Gastroenterology, Miyagi Cancer Center, Natori, Japan
| | - Yuta Wakui
- Department of Gastroenterology, Miyagi Cancer Center, Natori, Japan
| | - Makoto Abue
- Department of Gastroenterology, Miyagi Cancer Center, Natori, Japan
| | - Kazuhiro Murakami
- Division of Pathology, Tohoku Medical and Pharmaceutical University Hospital, Sendai, Japan
| | - Yasuhiro Nakamura
- Division of Pathology, Tohoku Medical and Pharmaceutical University Hospital, Sendai, Japan
| | - Jun Yasuda
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Kazunori Yamaguchi
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Kazuo Sugamura
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Chikashi Shibata
- Gastroenterologic and Hepato-Biliary-Pancreatic Surgery, Tohoku Medical and Pharmaceutical University Hospital, Sendai, Japan
| | - Yu Katayose
- Gastroenterologic and Hepato-Biliary-Pancreatic Surgery, Tohoku Medical and Pharmaceutical University Hospital, Sendai, Japan
| | - Kennichi Satoh
- Division of Gastroenterology, Tohoku Medical and Pharmaceutical University Hospital, Sendai, Japan
| | - Keiichi Tamai
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan.,Division of Cancer Stem Cell, Tohoku University Graduate School of Medicine, Sendai, Japan
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11
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Wang X, Zhang W, Yang Y, Wang J, Qiu H, Liao L, Oikawa T, Wauthier E, Sethupathy P, Reid LM, Liu Z, He Z. A MicroRNA-Based Network Provides Potential Predictive Signatures and Reveals the Crucial Role of PI3K/AKT Signaling for Hepatic Lineage Maturation. Front Cell Dev Biol 2021; 9:670059. [PMID: 34141708 PMCID: PMC8204022 DOI: 10.3389/fcell.2021.670059] [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: 02/20/2021] [Accepted: 04/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background Functions of miRNAs involved in tumorigenesis are well reported, yet, their roles in normal cell lineage commitment remain ambiguous. Here, we investigated a specific "transcription factor (TF)-miRNA-Target" regulatory network during the lineage maturation of biliary tree stem cells (BTSCs) into adult hepatocytes (hAHeps). Method Bioinformatic analysis was conducted based on our RNA-seq and microRNA-seq datasets with four human hepatic-lineage cell lines, including hBTSCs, hepatic stem cells (hHpSCs), hepatoblasts (hHBs), and hAHeps. Short time-series expression miner (STEM) analysis was performed to reveal the time-dependent dynamically changed miRNAs and mRNAs. GO and KEGG analyses were applied to reveal the potential function of key miRNAs and mRNAs. Then, the miRDB, miRTarBase, TargetScan, miRWalk, and DIANA-microT-CDS databases were adopted to predict the potential targets of miRNAs while the TransmiR v2.0 database was used to obtain the experimentally supported TFs that regulate miRNAs. The TCGA, Kaplan-Meier Plotter, and human protein atlas (HPA) databases and more than 10 sequencing data, including bulk RNA-seq, microRNA-seq, and scRNA-seq data related to hepatic development or lineage reprogramming, were obtained from both our or other published studies for validation. Results STEM analysis showed that during the maturation from hBTSCs to hAHeps, 52 miRNAs were downwardly expressed and 928 mRNA were upwardly expressed. Enrichment analyses revealed that those 52 miRNAs acted as pluripotency regulators for stem cells and participated in various novel signaling pathways, including PI3K/AKT, MAPK, and etc., while 928 mRNAs played important roles in liver-functional metabolism. With an extensive sorting of those key miRNAs and mRNAs based on the target prediction results, 23 genes were obtained which not only functioned as the targets of 17 miRNAs but were considered critical for the hepatic lineage commitment. A "TF-miRNA-Target" regulatory network for hepatic lineage commitment was therefore established and had been well validated by various datasets. The network revealed that the PI3K/AKT pathway was gradually suppressed during the hepatic commitment. Conclusion A total of 17 miRNAs act as suppressors during hepatic maturation mainly by regulating 23 targets and modulating the PI3K/AKT signaling pathway. The regulatory network uncovers possible signatures and guidelines enabling us to identify or obtain the functional hepatocytes for future study.
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Affiliation(s)
- Xicheng Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai, China.,Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Wencheng Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai, China.,Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Yong Yang
- The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiansong Wang
- Department of Traumatology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hua Qiu
- The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lijun Liao
- Department of Anesthesiology and Pain Management, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tsunekazu Oikawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Eliane Wauthier
- Department of Cell Biology and Physiology, UNC School of Medicine, Chapel Hill, NC, United States
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, United States
| | - Lola M Reid
- Department of Cell Biology and Physiology, UNC School of Medicine, Chapel Hill, NC, United States
| | - Zhongmin Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai, China.,Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Zhiying He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai, China.,Shanghai Engineering Research Center of Stem Cells Translational Medicine, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
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12
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Yamamoto-Shimojima K, Osawa M, Saito MK, Yamamoto T. Induced pluripotent stem cells established from a female patient with Xq22 deletion confirm that BEX2 escapes from X-chromosome inactivation. Congenit Anom (Kyoto) 2021; 61:63-67. [PMID: 33244819 DOI: 10.1111/cga.12403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/30/2020] [Accepted: 11/23/2020] [Indexed: 11/27/2022]
Abstract
Large deletions in Xq22 are responsible for neurodevelopmental disorders, including severe intellectual disability and behavioral abnormalities. Although the deletion regions contain PLP1, the gene related to Pelizaeus-Merzbacher disease (PMD), patients with Xq22 deletions show no clinical features of PMD such as paraplegia and white matter abnormalities. This could be due to skewed X-chromosome inactivation (XCI) occurring predominantly in the affected allele. Isogenic pairs of wild type and mutant induced pluripotent stem cells (iPSCs) were established from the patient. In the iPSC line in which the wild type allele was inactivated, PLP1 was not expressed, but biallelic expression of BEX2 was identified. This suggests that BEX2 escaped from XCI and haploinsufficiency of BEX2 may be related to the phenotype of Xq22 deletions.
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Affiliation(s)
| | - Mitsujiro Osawa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Megumu K Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical genetics, Tokyo, Japan
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13
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Tamai K, Nakamura-Shima M, Shibuya-Takahashi R, Kanno SI, Yasui A, Mochizuki M, Iwai W, Wakui Y, Abue M, Yamamoto K, Miura K, Mizuma M, Unno M, Kawamura S, Sato I, Yasuda J, Yamaguchi K, Sugamura K, Satoh K. BEX2 suppresses mitochondrial activity and is required for dormant cancer stem cell maintenance in intrahepatic cholangiocarcinoma. Sci Rep 2020; 10:21592. [PMID: 33299012 PMCID: PMC7725823 DOI: 10.1038/s41598-020-78539-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer stem cells (CSCs) define a subpopulation of cancer cells that are resistant to therapy. However, little is known of how CSC characteristics are regulated. We previously showed that dormant cancer stem cells are enriched with a CD274low fraction of cholangiocarcinoma cells. Here we found that BEX2 was highly expressed in CD274low cells, and that BEX2 knockdown decreased the tumorigenicity and G0 phase of cholangiocarcinoma cells. BEX2 was found to be expressed predominantly in G0 phase and starvation induced the USF2 transcriptional factor, which induced BEX2 transcription. Comprehensive screening of BEX2 binding proteins identified E3 ubiquitin ligase complex proteins, FEM1B and CUL2, and a mitochondrial protein TUFM, and further demonstrated that knockdown of BEX2 or TUFM increased mitochondria-related oxygen consumption and decreased tumorigenicity in cholangiocarcinoma cells. These results suggest that BEX2 is essential for maintaining dormant cancer stem cells through the suppression of mitochondrial activity in cholangiocarcinoma.
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Affiliation(s)
- Keiichi Tamai
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, 47-1 Nodayama, Medeshima-Shiode, Natori, Miyagi, 981-1293, Japan.
| | - Mao Nakamura-Shima
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Rie Shibuya-Takahashi
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, 47-1 Nodayama, Medeshima-Shiode, Natori, Miyagi, 981-1293, Japan
| | - Shin-Ichiro Kanno
- IDAC Fellow Research Group for DNA Repair and Dynamic Proteome Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, 980-8575, Japan
| | - Akira Yasui
- IDAC Fellow Research Group for DNA Repair and Dynamic Proteome Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, 980-8575, Japan
| | - Mai Mochizuki
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, 47-1 Nodayama, Medeshima-Shiode, Natori, Miyagi, 981-1293, Japan
| | - Wataru Iwai
- Department of Gastroenterology, Miyagi Cancer Center, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Yuta Wakui
- Department of Gastroenterology, Miyagi Cancer Center, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Makoto Abue
- Department of Gastroenterology, Miyagi Cancer Center, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Kuniharu Yamamoto
- Department of Surgery, Miyagi Cancer Center, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan.,Division of Hepatobiliary and Pancreatic Surgery, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi, Japan
| | - Koh Miura
- Department of Surgery, Miyagi Cancer Center, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Masamichi Mizuma
- Department of Surgery, Tohoku University Graduate School of Medicine, 1-1, Seiryo-cho, Aoba-ku, Sendai, Miyagi, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, 1-1, Seiryo-cho, Aoba-ku, Sendai, Miyagi, Japan
| | - Sadafumi Kawamura
- Department of Urology, Miyagi Cancer Center, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Ikuro Sato
- Department of Pathology, Miyagi Cancer Center, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Jun Yasuda
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Kazunori Yamaguchi
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Kazuo Sugamura
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, 47-1, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Kennichi Satoh
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, 47-1 Nodayama, Medeshima-Shiode, Natori, Miyagi, 981-1293, Japan.,Division of Gastroenterology, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi, Japan
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14
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Elmentaite R, Ross ADB, Roberts K, James KR, Ortmann D, Gomes T, Nayak K, Tuck L, Pritchard S, Bayraktar OA, Heuschkel R, Vallier L, Teichmann SA, Zilbauer M. Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease. Dev Cell 2020; 55:771-783.e5. [PMID: 33290721 PMCID: PMC7762816 DOI: 10.1016/j.devcel.2020.11.010] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/04/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023]
Abstract
Human gut development requires the orchestrated interaction of differentiating cell types. Here, we generate an in-depth single-cell map of the developing human intestine at 6–10 weeks post-conception. Our analysis reveals the transcriptional profile of cycling epithelial precursor cells; distinct from LGR5-expressing cells. We propose that these cells may contribute to differentiated cell subsets via the generation of LGR5-expressing stem cells and receive signals from surrounding mesenchymal cells. Furthermore, we draw parallels between the transcriptomes of ex vivo tissues and in vitro fetal organoids, revealing the maturation of organoid cultures in a dish. Lastly, we compare scRNA-seq profiles from pediatric Crohn’s disease epithelium alongside matched healthy controls to reveal disease-associated changes in the epithelial composition. Contrasting these with the fetal profiles reveals the re-activation of fetal transcription factors in Crohn’s disease. Our study provides a resource available at www.gutcellatlas.org, and underscores the importance of unraveling fetal development in understanding disease. Single-cell RNA-seq map of the developing and pediatric human intestine Cycling BEX5+ epithelial precursors are distinct from adult LGR5+ stem cells Human fetal intestinal organoids mature in culture Fetal transcription factors are reactivated in the Crohn’s disease epithelium
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Affiliation(s)
- Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Alexander D B Ross
- Wellcome Trust, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Kylie R James
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Daniel Ortmann
- Wellcome Trust, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Komal Nayak
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals Trust, Cambridge CB2 0QQ, UK
| | - Ludovic Vallier
- Wellcome Trust, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton CB10 1SA, UK.
| | - Matthias Zilbauer
- Wellcome Trust, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals Trust, Cambridge CB2 0QQ, UK.
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15
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Navas-Pérez E, Vicente-García C, Mirra S, Burguera D, Fernàndez-Castillo N, Ferrán JL, López-Mayorga M, Alaiz-Noya M, Suárez-Pereira I, Antón-Galindo E, Ulloa F, Herrera-Úbeda C, Cuscó P, Falcón-Moya R, Rodríguez-Moreno A, D'Aniello S, Cormand B, Marfany G, Soriano E, Carrión ÁM, Carvajal JJ, Garcia-Fernàndez J. Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions. Genome Biol 2020; 21:267. [PMID: 33100228 PMCID: PMC7586669 DOI: 10.1186/s13059-020-02172-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes at the core of key macroevolutionary changes, their origin and organismal function are generally poorly understood. RESULTS Here, we identify several previously unreported transposable element domestication events in the human and mouse genomes. Among them, we find a remarkable molecular domestication that gave rise to a multigenic family in placental mammals, the Bex/Tceal gene cluster. These genes, which act as hub proteins within diverse signaling pathways, have been associated with neurological features of human patients carrying genomic microdeletions in chromosome X. The Bex/Tceal genes display neural-enriched patterns and are differentially expressed in human neurological disorders, such as autism and schizophrenia. Two different murine alleles of the cluster member Bex3 display morphological and physiopathological brain modifications, such as reduced interneuron number and hippocampal electrophysiological imbalance, alterations that translate into distinct behavioral phenotypes. CONCLUSIONS We provide an in-depth understanding of the emergence of a gene cluster that originated by transposon domestication and gene duplication at the origin of placental mammals, an evolutionary process that transformed a non-functional transposon sequence into novel components of the eutherian genome. These genes were integrated into existing signaling pathways involved in the development, maintenance, and function of the CNS in eutherians. At least one of its members, Bex3, is relevant for higher brain functions in placental mammals and may be involved in human neurological disorders.
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Affiliation(s)
- Enrique Navas-Pérez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Cristina Vicente-García
- Centro Andaluz de Biología del Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Serena Mirra
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Demian Burguera
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Noèlia Fernàndez-Castillo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, 08950, Barcelona, Spain
| | - José Luis Ferrán
- Department of Human Anatomy, School of Medicine, University of Murcia and IMIB-Arrixaca Institute, 30120, Murcia, Spain
| | - Macarena López-Mayorga
- Centro Andaluz de Biología del Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Marta Alaiz-Noya
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain.,Present Address: Instituto de Neurociencias de Alicante (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Alicante, Spain
| | - Irene Suárez-Pereira
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain.,Present Address: Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Neuropsychopharmacology and psychobiology research group, UCA, INiBICA, Cádiz, Spain
| | - Ester Antón-Galindo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Fausto Ulloa
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Carlos Herrera-Úbeda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Pol Cuscó
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Rafael Falcón-Moya
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Antonio Rodríguez-Moreno
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy
| | - Bru Cormand
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, 08950, Barcelona, Spain
| | - Gemma Marfany
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, 08950, Barcelona, Spain
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Ángel M Carrión
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Jaime J Carvajal
- Centro Andaluz de Biología del Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, 41013, Sevilla, Spain.
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.
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16
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Pei W, Shang F, Wang X, Fanti AK, Greco A, Busch K, Klapproth K, Zhang Q, Quedenau C, Sauer S, Feyerabend TB, Höfer T, Rodewald HR. Resolving Fates and Single-Cell Transcriptomes of Hematopoietic Stem Cell Clones by PolyloxExpress Barcoding. Cell Stem Cell 2020; 27:383-395.e8. [PMID: 32783885 DOI: 10.1016/j.stem.2020.07.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/22/2020] [Accepted: 07/22/2020] [Indexed: 01/08/2023]
Abstract
Lineage tracing reveals hematopoietic stem cell (HSC) fates, while single-cell RNA sequencing identifies snapshots of HSC transcriptomes. To obtain information on fate plus transcriptome in the same cell, we developed the PolyloxExpress allele, enabling Cre-recombinase-dependent RNA barcoding in situ. Linking fates to single HSC transcriptomes provided the information required to identify transcriptional signatures of HSC fates, which were not apparent in single-HSC transcriptomes alone. We find that differentiation-inactive, multilineage, and lineage-restricted HSC clones reside in distinct regions of the transcriptional landscape of hematopoiesis. Differentiation-inactive HSC clones are closer to the origin of the transcriptional trajectory, yet they are not characterized by a quiescent gene signature. Fate-specific gene signatures imply coherence of clonal HSC fates, and HSC output toward short-lived lineage progenitors indicates stability of HSC fates over time. These combined analyses of fate and transcriptome under physiological conditions may pave the way toward identifying molecular determinants of HSC fates.
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Affiliation(s)
- Weike Pei
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Fuwei Shang
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Medicine, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany
| | - Xi Wang
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Division of Theoretical Systems Biology, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Ann-Kathrin Fanti
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Alessandro Greco
- Division of Theoretical Systems Biology, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Katrin Busch
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Kay Klapproth
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Qin Zhang
- Division of Theoretical Systems Biology, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Claudia Quedenau
- Max Delbrück Centrum, Scientific Genomics Platforms (BIMSB/BIH), Hannoversche Straße 28, 10115 Berlin, Germany
| | - Sascha Sauer
- Max Delbrück Centrum, Scientific Genomics Platforms (BIMSB/BIH), Hannoversche Straße 28, 10115 Berlin, Germany
| | - Thorsten B Feyerabend
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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17
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Schwarz BA, Cetinbas M, Clement K, Walsh RM, Cheloufi S, Gu H, Langkabel J, Kamiya A, Schorle H, Meissner A, Sadreyev RI, Hochedlinger K. Prospective Isolation of Poised iPSC Intermediates Reveals Principles of Cellular Reprogramming. Cell Stem Cell 2018; 23:289-305.e5. [PMID: 30017590 DOI: 10.1016/j.stem.2018.06.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 03/29/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022]
Abstract
Cellular reprogramming converts differentiated cells into induced pluripotent stem cells (iPSCs). However, this process is typically very inefficient, complicating mechanistic studies. We identified and molecularly characterized rare, early intermediates poised to reprogram with up to 95% efficiency, without perturbing additional genes or pathways, during iPSC generation from mouse embryonic fibroblasts. Analysis of these cells uncovered transcription factors (e.g., Tfap2c and Bex2) that are important for reprogramming but dispensable for pluripotency maintenance. Additionally, we observed striking patterns of chromatin hyperaccessibility at pluripotency loci, which preceded gene expression in poised intermediates. Finally, inspection of these hyperaccessible regions revealed an early wave of DNA demethylation that is uncoupled from de novo methylation of somatic regions late in reprogramming. Our study underscores the importance of investigating rare intermediates poised to produce iPSCs, provides insights into reprogramming mechanisms, and offers a valuable resource for the dissection of transcriptional and epigenetic dynamics intrinsic to cell fate change.
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Affiliation(s)
- Benjamin A Schwarz
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Murat Cetinbas
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kendell Clement
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan M Walsh
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sihem Cheloufi
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jan Langkabel
- University of Bonn Medical School, Institute of Pathology, Department of Developmental Pathology, Bonn, Germany
| | - Akihide Kamiya
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Hubert Schorle
- University of Bonn Medical School, Institute of Pathology, Department of Developmental Pathology, Bonn, Germany
| | - Alexander Meissner
- Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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18
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Burger LL, Vanacker C, Phumsatitpong C, Wagenmaker ER, Wang L, Olson DP, Moenter SM. Identification of Genes Enriched in GnRH Neurons by Translating Ribosome Affinity Purification and RNAseq in Mice. Endocrinology 2018; 159. [PMID: 29522155 PMCID: PMC6287592 DOI: 10.1210/en.2018-00001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Gonadotropin-releasing hormone (GnRH) neurons are a nexus of fertility regulation. We used translating ribosome affinity purification coupled with RNA sequencing to examine messenger RNAs of GnRH neurons in adult intact and gonadectomized (GDX) male and female mice. GnRH neuron ribosomes were tagged with green fluorescent protein (GFP) and GFP-labeled polysomes isolated by immunoprecipitation, producing one RNA fraction enhanced for GnRH neuron transcripts and one RNA fraction depleted. Complementary DNA libraries were created from each fraction and 50-base, paired-end sequencing done and differential expression (enhanced fraction/depleted fraction) determined with a threshold of >1.5- or <0.66-fold (false discovery rate P ≤ 0.05). A core of ∼840 genes was differentially expressed in GnRH neurons in all treatments, including enrichment for Gnrh1 (∼40-fold), and genes critical for GnRH neuron and/or gonadotrope development. In contrast, non-neuronal transcripts were not enriched or were de-enriched. Several epithelial markers were also enriched, consistent with the olfactory epithelial origins of GnRH neurons. Interestingly, many synaptic transmission pathways were de-enriched, in accordance with relatively low innervation of GnRH neurons. The most striking difference between intact and GDX mice of both sexes was a marked downregulation of genes associated with oxidative phosphorylation and upregulation of glucose transporters in GnRH neurons from GDX mice. This may suggest that GnRH neurons switch to an alternate fuel to increase adenosine triphosphate production in the absence of negative feedback when GnRH release is elevated. Knowledge of the GnRH neuron translatome and its regulation can guide functional studies and can be extended to disease states, such as polycystic ovary syndrome.
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Affiliation(s)
- Laura L Burger
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
| | - Charlotte Vanacker
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
| | | | - Elizabeth R Wagenmaker
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
| | - Luhong Wang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
| | - David P Olson
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Suzanne M Moenter
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
- Department of Internal Medicine, University of Michigan, Ann Arbor,
Michigan
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor,
Michigan
- Correspondence: Laura L. Burger, PhD, University of Michigan, 7725 Med Sci II, 1137 E. Catherine
Street, Ann Arbor, Michigan 48109-5622. E-mail:
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19
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Nguyen LT, Reverter A, Cánovas A, Venus B, Anderson ST, Islas-Trejo A, Dias MM, Crawford NF, Lehnert SA, Medrano JF, Thomas MG, Moore SS, Fortes MRS. STAT6, PBX2, and PBRM1 Emerge as Predicted Regulators of 452 Differentially Expressed Genes Associated With Puberty in Brahman Heifers. Front Genet 2018; 9:87. [PMID: 29616079 PMCID: PMC5869259 DOI: 10.3389/fgene.2018.00087] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/02/2018] [Indexed: 12/17/2022] Open
Abstract
The liver plays a central role in metabolism and produces important hormones. Hepatic estrogen receptors and the release of insulin-like growth factor 1 (IGF1) are critical links between liver function and the reproductive system. However, the role of liver in pubertal development is not fully understood. To explore this question, we applied transcriptomic analyses to liver samples of pre- and post-pubertal Brahman heifers and identified differentially expressed (DE) genes and genes encoding transcription factors (TFs). Differential expression of genes suggests potential biological mechanisms and pathways linking liver function to puberty. The analyses identified 452 DE genes and 82 TF with significant contribution to differential gene expression by using a regulatory impact factor metric. Brain-derived neurotrophic factor was observed as the most down-regulated gene (P = 0.003) in post-pubertal heifers and we propose this gene influences pubertal development in Brahman heifers. Additionally, co-expression network analysis provided evidence for three TF as key regulators of liver function during pubertal development: the signal transducer and activator of transcription 6, PBX homeobox 2, and polybromo 1. Pathway enrichment analysis identified transforming growth factor-beta and Wnt signaling pathways as significant annotation terms for the list of DE genes and TF in the co-expression network. Molecular information regarding genes and pathways described in this work are important to further our understanding of puberty onset in Brahman heifers.
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Affiliation(s)
- Loan T Nguyen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Bronwyn Venus
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Stephen T Anderson
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alma Islas-Trejo
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Marina M Dias
- Departamento de Zootecnia, Faculdade de Ciências Agráìrias e Veterináìrias, Universidade Estadual Paulista Júlio de Mesquita Filho, São Paulo, Brazil
| | - Natalie F Crawford
- Department of Animal Science, Colorado State University, Fort Collins, CO, United States
| | - Sigrid A Lehnert
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Juan F Medrano
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Milt G Thomas
- Department of Animal Science, Colorado State University, Fort Collins, CO, United States
| | - Stephen S Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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20
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Kazi JU, Kabir NN, Rönnstrand L. Brain-Expressed X-linked (BEX) proteins in human cancers. Biochim Biophys Acta Rev Cancer 2015; 1856:226-33. [PMID: 26408910 DOI: 10.1016/j.bbcan.2015.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/20/2015] [Accepted: 09/22/2015] [Indexed: 01/08/2023]
Abstract
The Brain-Expressed X-linked (BEX) family proteins are comprised of five human proteins including BEX1, BEX2, BEX3, BEX4 and BEX5. BEX family proteins are expressed in a wide range of tissues and are known to play a role in neuronal development. Recent studies suggest a role of BEX family proteins in cancers. BEX1 expression is lost in a subgroup of patients with acute myeloid leukemia (AML) and chronic myeloid leukemia (CML). Expression of BEX1 controls cell surface receptor signaling and restores imatinib response in resistant cells. BEX2 is overexpressed in a group of breast cancer patients and also in gliomas. Increased BEX2 expression led to enhanced NF-κB signaling as well as cell proliferation. Although BEX2 acts as tumor promoter in a subset of breast cancer, BEX3 expression displayed an opposite role. Overexpression of BEX3 resulted in inhibition of tumor formation in breast cancer mouse xenograft models. The role of BEX4 and BEX5 in cancer has not yet been defined. Collectively this suggests that BEX family members have distinct roles in cancers. While BEX1 and BEX3 act as tumor suppressors, BEX2 seems to act as an oncogene.
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Affiliation(s)
- Julhash U Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village 404 ,Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden; Laboratory of Computational Biochemistry, KN Biomedical Research Institute, Barisal, Bangladesh.
| | - Nuzhat N Kabir
- Laboratory of Computational Biochemistry, KN Biomedical Research Institute, Barisal, Bangladesh
| | - Lars Rönnstrand
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village 404 ,Lund, Sweden; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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