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Zhang Y, Xiang G, Jiang AY, Lynch A, Zeng Z, Wang C, Zhang W, Fan J, Kang J, Gu SS, Wan C, Zhang B, Liu XS, Brown M, Meyer CA. MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment. Nat Commun 2023; 14:2634. [PMID: 37149682 PMCID: PMC10164163 DOI: 10.1038/s41467-023-38333-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/26/2023] [Indexed: 05/08/2023] Open
Abstract
Recent advances in single-cell RNA sequencing have shown heterogeneous cell types and gene expression states in the non-cancerous cells in tumors. The integration of multiple scRNA-seq datasets across tumors can indicate common cell types and states in the tumor microenvironment (TME). We develop a data driven framework, MetaTiME, to overcome the limitations in resolution and consistency that result from manual labelling using known gene markers. Using millions of TME single cells, MetaTiME learns meta-components that encode independent components of gene expression observed across cancer types. The meta-components are biologically interpretable as cell types, cell states, and signaling activities. By projecting onto the MetaTiME space, we provide a tool to annotate cell states and signature continuums for TME scRNA-seq data. Leveraging epigenetics data, MetaTiME reveals critical transcriptional regulators for the cell states. Overall, MetaTiME learns data-driven meta-components that depict cellular states and gene regulators for tumor immunity and cancer immunotherapy.
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Affiliation(s)
- Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Guanjue Xiang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Alva Yijia Jiang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Allen Lynch
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Chenfei Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Wubing Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Jingyu Fan
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Jiajinlong Kang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Shengqing Stan Gu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Changxin Wan
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Boning Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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152
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Guo Q, Wang Y, Wang Q, Qian Y, Jiang Y, Dong X, Chen H, Chen X, Liu X, Yu S, Zhu J, Shan S, Wu B, Zhou W, Wang H. In the developing cerebral cortex: axonogenesis, synapse formation, and synaptic plasticity are regulated by SATB2 target genes. Pediatr Res 2023; 93:1519-1527. [PMID: 36028553 DOI: 10.1038/s41390-022-02260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/23/2022] [Accepted: 07/29/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Special AT-rich sequence-binding protein 2 is essential for the development of cerebral cortex and key molecular node for the establishment of proper neural circuitry and function. Mutations in the SATB2 gene lead to SATB2-associated syndrome, which is characterized by abnormal development of skeleton and central nervous systems. METHODS We generated Satb2 knockout mouse model through CRISPR-Cas9 technology and performed RNA-seq and ChIP-seq of embryonic cerebral cortex. We conducted RT-qPCR, western blot, immunofluorescence staining, luciferase reporter assay and behavioral analysis for experimental verification. RESULTS We identified 1363 downstream effector genes of Satb2 and correlation analysis of Satb2-targeted genes and neurological disease genes showed that Satb2 contribute to cognitive and mental disorders from the early developmental stage. We found that Satb2 directly regulate the expression of Ntng1, Cdh13, Kitl, genes important for axon guidance, synaptic formation, neuron migration, and Satb2 directly activates the expression of Mef2c. We also showed that Satb2 heterozygous knockout mice showed impaired spatial learning and memory. CONCLUSIONS Taken together, our study supportsroles of Satb2 in the regulation of axonogenesis and synaptic formation at the early developmental stage and provides new insights into the complicated regulatory mechanism of Satb2 and new evidence to elucidate the pathogen of SATB2-associated syndrome. IMPACT 1363 downstream effector genes of Satb2 were classified into 5 clusters with different temporal expression patterns. We identified Plxnd1, Ntng1, Efnb2, Ephb1, Plxna2, Epha3, Plxna4, Unc5c, and Flrt2 as axon guidance molecules to regulate axonogenesis. 168 targeted genes of Satb2 were found to regulate synaptic formation in the early development of the cerebral cortex. Transcription factor Mef2c is positively regulated by Satb2, and 28 Mef2c-targeted genes can be directly regulated by Satb2. In the Morris water maze test, Satb2+/- mice showed impaired spatial learning and memory, further strengthening that Satb2 can regulate synaptic functions.
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Affiliation(s)
- Qiufang Guo
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
- Berry Genomics Co, 102206, Beijing, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Qing Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yinmo Jiang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xiang Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xiuyun Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Sha Yu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Jitao Zhu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Shifang Shan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Key Laboratory of Neonatal Diseases, Ministry of Health, 201102, Shanghai, China.
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
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153
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Wang Y, Li Y, Skuland T, Zhou C, Li A, Hashim A, Jermstad I, Khan S, Dalen KT, Greggains GD, Klungland A, Dahl JA, Au KF. The RNA m 6A landscape of mouse oocytes and preimplantation embryos. Nat Struct Mol Biol 2023; 30:703-709. [PMID: 37081317 DOI: 10.1038/s41594-023-00969-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/16/2023] [Indexed: 04/22/2023]
Abstract
Despite the significance of N6-methyladenosine (m6A) in gene regulation, the requirement for large amounts of RNA has hindered m6A profiling in mammalian early embryos. Here we apply low-input methyl RNA immunoprecipitation and sequencing to map m6A in mouse oocytes and preimplantation embryos. We define the landscape of m6A during the maternal-to-zygotic transition, including stage-specifically expressed transcription factors essential for cell fate determination. Both the maternally inherited transcripts to be degraded post fertilization and the zygotically activated genes during zygotic genome activation are widely marked by m6A. In contrast to m6A-marked zygotic ally-activated genes, m6A-marked maternally inherited transcripts have a higher tendency to be targeted by microRNAs. Moreover, RNAs derived from retrotransposons, such as MTA that is maternally expressed and MERVL that is transcriptionally activated at the two-cell stage, are largely marked by m6A. Our results provide a foundation for future studies exploring the regulatory roles of m6A in mammalian early embryonic development.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yanjiao Li
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trine Skuland
- Department of Reproductive Medicine, Oslo University Hospital, Oslo, Norway
- Division of Gynaecology and Obstetrics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Chengjie Zhou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Aifu Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Adnan Hashim
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ingunn Jermstad
- Norwegian Transgenic Centre, Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Shaista Khan
- Norwegian Transgenic Centre, Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Knut Tomas Dalen
- Norwegian Transgenic Centre, Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gareth D Greggains
- Department of Reproductive Medicine, Oslo University Hospital, Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
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154
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Lee J, Møller AF, Chae S, Bussek A, Park TJ, Kim Y, Lee HS, Pers TH, Kwon T, Sedzinski J, Natarajan KN. A single-cell, time-resolved profiling of Xenopus mucociliary epithelium reveals nonhierarchical model of development. SCIENCE ADVANCES 2023; 9:eadd5745. [PMID: 37027470 PMCID: PMC10081853 DOI: 10.1126/sciadv.add5745] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
The specialized cell types of the mucociliary epithelium (MCE) lining the respiratory tract enable continuous airway clearing, with its defects leading to chronic respiratory diseases. The molecular mechanisms driving cell fate acquisition and temporal specialization during mucociliary epithelial development remain largely unknown. Here, we profile the developing Xenopus MCE from pluripotent to mature stages by single-cell transcriptomics, identifying multipotent early epithelial progenitors that execute multilineage cues before specializing into late-stage ionocytes and goblet and basal cells. Combining in silico lineage inference, in situ hybridization, and single-cell multiplexed RNA imaging, we capture the initial bifurcation into early epithelial and multiciliated progenitors and chart cell type emergence and fate progression into specialized cell types. Comparative analysis of nine airway atlases reveals an evolutionary conserved transcriptional module in ciliated cells, whereas secretory and basal types execute distinct function-specific programs across vertebrates. We uncover a continuous nonhierarchical model of MCE development alongside a data resource for understanding respiratory biology.
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Affiliation(s)
- Julie Lee
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Andreas Fønss Møller
- Danish Institute of Advanced Study (DIAS) and Functional Genomics and Metabolism Research Unit, University of Southern Denmark, Odense, Denmark
- Sino-Danish College (SDC), University of Chinese Academy of Sciences, Beijing, China
| | - Shinhyeok Chae
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Alexandra Bussek
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Tae Joo Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Youni Kim
- KNU-Center for Nonlinear Dynamics, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyun-Shik Lee
- KNU-Center for Nonlinear Dynamics, School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Tune H. Pers
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jakub Sedzinski
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Kedar Nath Natarajan
- Danish Institute of Advanced Study (DIAS) and Functional Genomics and Metabolism Research Unit, University of Southern Denmark, Odense, Denmark
- DTU Bioengineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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155
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LPCAT1 is transcriptionally regulated by FOXA1 to promote breast cancer progression and paclitaxel resistance. Oncol Lett 2023; 25:134. [PMID: 36909375 PMCID: PMC9996177 DOI: 10.3892/ol.2023.13720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/09/2023] [Indexed: 02/17/2023] Open
Abstract
Bioinformatics analysis indicates that lysophosphatidylcholine acyltransferase 1 (LPCAT1) and forkhead box A1 (FOXA1) are highly expressed in breast cancer tissues and their expression levels are correlated. Therefore, the aim of the present study was to investigate their involvement in the malignant progression and drug resistance of breast cancer. The clinical significance of LPCAT1 was analyzed using The Cancer Genome Atlas data. The enrichment of LPCAT1 in breast cancer cells was determined and the effects of LPCAT1 knockdown on cell proliferation, colony formation, migration, invasion and paclitaxel (PTX) resistance were evaluated. The association between LPCAT1 and FOXA1 was verified using luciferase reporter and chromatin immunoprecipitation assays. Thereafter, the ability of FOXA1 overexpression to regulate LPCAT1 regulation was evaluated. The results revealed that a high LPCAT1 level was associated with poor overall survival in patients with breast cancer. Furthermore, LPCAT1 was found to be highly expressed in breast cancer cells, and its knockdown resulted in suppressed proliferation, colony formation, migration and invasion, and weakened PTX resistance. Furthermore, FOXA1 overexpression attenuated the effects of LPCAT1 knockdown on cells, indicating that FOXA1 transcriptionally regulates LPCAT1. In summary, the present study reveals that LPCAT1 is transcriptionally regulated by FOXA1, which influences breast cancer cell proliferation, metastatic potential and PTX resistance.
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156
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Ren N, Dai S, Ma S, Yang F. Strategies for activity analysis of single nucleotide polymorphisms associated with human diseases. Clin Genet 2023; 103:392-400. [PMID: 36527336 DOI: 10.1111/cge.14282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Genome-wide association studies (GWAS) have identified a large number of single nucleotide polymorphism (SNP) sites associated with human diseases. In the annotation of human diseases, especially cancers, SNPs, as an important component of genetic factors, have gained increasing attention. Given that most of the SNPs are located in non-coding regions, the functional verification of these SNPs is a great challenge. The key to functional annotation for risk SNPs is to screen SNPs with regulatory activity from thousands of disease associated-SNPs. In this review, we systematically recapitulate the characteristics and functional roles of SNP sites, discuss three parallel reporter screening strategies in detail based on barcode tag classification, and recommend the common in silico strategies to help supplement the annotation of SNP sites with epigenetic activity analysis, prediction of target genes and trans-acting factors. We hope that this review will contribute to this exuberant research field by providing robust activity analysis strategies that can facilitate the translation of GWAS results into personalized diagnosis and prevention measures for human diseases.
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Affiliation(s)
- Naixia Ren
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Shangkun Dai
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Shumin Ma
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Fengtang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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157
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Zhao JY, Yuan XK, Luo RZ, Wang LX, Gu W, Yamane D, Feng H. Phospholipase A and acyltransferase 4/retinoic acid receptor responder 3 at the intersection of tumor suppression and pathogen restriction. Front Immunol 2023; 14:1107239. [PMID: 37063830 PMCID: PMC10102619 DOI: 10.3389/fimmu.2023.1107239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Phospholipase A and acyltransferase (PLAAT) 4 is a class II tumor suppressor with phospholipid metabolizing abilities. It was characterized in late 2000s, and has since been referred to as ‘tazarotene-induced gene 3’ (TIG3) or ‘retinoic acid receptor responder 3’ (RARRES3) as a key downstream effector of retinoic acid signaling. Two decades of research have revealed the complexity of its function and regulatory roles in suppressing tumorigenesis. However, more recent findings have also identified PLAAT4 as a key anti-microbial effector enzyme acting downstream of interferon regulatory factor 1 (IRF1) and interferons (IFNs), favoring protection from virus and parasite infections. Unveiling the molecular mechanisms underlying its action may thus open new therapeutic avenues for the treatment of both cancer and infectious diseases. Herein, we aim to summarize a brief history of PLAAT4 discovery, its transcriptional regulation, and the potential mechanisms in tumor prevention and anti-pathogen defense, and discuss potential future directions of PLAAT4 research toward the development of therapeutic approaches targeting this enzyme with pleiotropic functions.
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Affiliation(s)
- Jian-Yong Zhao
- Hospital of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Cangzhou, Hebei, China
| | - Xiang-Kun Yuan
- Hospital of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Cangzhou, Hebei, China
| | - Rui-Zhen Luo
- Hospital of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Cangzhou, Hebei, China
| | - Li-Xin Wang
- Hospital of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Cangzhou, Hebei, China
| | - Wei Gu
- School of Medicine, Chongqing University, Chongqing, China
| | - Daisuke Yamane
- Department of Diseases and Infection, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- *Correspondence: Hui Feng, ; Daisuke Yamane,
| | - Hui Feng
- School of Medicine, Chongqing University, Chongqing, China
- *Correspondence: Hui Feng, ; Daisuke Yamane,
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158
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Duan M, Liu Y, Zhao D, Li H, Zhang G, Liu H, Wang Y, Fan Y, Huang L, Zhou F. Gender-specific dysregulations of nondifferentially expressed biomarkers of metastatic colon cancer. Comput Biol Chem 2023; 104:107858. [PMID: 37058814 DOI: 10.1016/j.compbiolchem.2023.107858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/12/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023]
Abstract
Colon cancer is a common cancer type in both sexes and its mortality rate increases at the metastatic stage. Most studies exclude nondifferentially expressed genes from biomarker analysis of metastatic colon cancers. The motivation of this study is to find the latent associations of the nondifferentially expressed genes with metastatic colon cancers and to evaluate the gender specificity of such associations. This study formulates the expression level prediction of a gene as a regression model trained for primary colon cancers. The difference between a gene's predicted and original expression levels in a testing sample is defined as its mqTrans value (model-based quantitative measure of transcription regulation), which quantitatively measures the change of the gene's transcription regulation in this testing sample. We use the mqTrans analysis to detect the messenger RNA (mRNA) genes with nondifferential expression on their original expression levels but differentially expressed mqTrans values between primary and metastatic colon cancers. These genes are referred to as dark biomarkers of metastatic colon cancer. All dark biomarker genes were verified by two transcriptome profiling technologies, RNA-seq and microarray. The mqTrans analysis of a mixed cohort of both sexes could not recover gender-specific dark biomarkers. Most dark biomarkers overlap with long non-coding RNAs (lncRNAs), and these lncRNAs might have contributed their transcripts to calculating the dark biomarkers' expression levels. Therefore, mqTrans analysis serves as a complementary approach to identify dark biomarkers generally ignored by conventional studies, and it is essential to separate the female and male samples into two analysis experiments. The dataset and mqTrans analysis code are available at https://figshare.com/articles/dataset/22250536.
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Affiliation(s)
- Meiyu Duan
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China; School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, Guizhou, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yaqing Liu
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Dong Zhao
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, Guizhou, China
| | - Haijun Li
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, Guizhou, China
| | - Gongyou Zhang
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, Guizhou, China
| | - Hongmei Liu
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, Guizhou, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China; Engineering Research Center of Medical Biotechnology, Guizhou Medical University, Guiyang 550025, Guizhou, China
| | - Yueying Wang
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yusi Fan
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China; College of Software, Jilin University, Changchun, Jilin 130012, China.
| | - Lan Huang
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Fengfeng Zhou
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China; School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, Guizhou, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.
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159
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Luan Y, Tang Z, He Y, Xie Z. Intra-Domain Residue Coevolution in Transcription Factors Contributes to DNA Binding Specificity. Microbiol Spectr 2023; 11:e0365122. [PMID: 36943132 PMCID: PMC10100741 DOI: 10.1128/spectrum.03651-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Understanding the basis of the DNA-binding specificity of transcription factors (TFs) has been of long-standing interest. Despite extensive efforts to map millions of putative TF binding sequences, identifying the critical determinants for DNA binding specificity remains a major challenge. The coevolution of residues in proteins occurs due to a shared evolutionary history. However, it is unclear how coevolving residues in TFs contribute to DNA binding specificity. Here, we systematically collected publicly available data sets from multiple large-scale high-throughput TF-DNA interaction screening experiments for the major TF families with large numbers of TF members. These families included the Homeobox, HLH, bZIP_1, Ets, HMG_box, ZF-C4, and Zn_clus TFs. We detected TF subclass-determining sites (TSDSs) and showed that the TSDSs were more likely to coevolve with other TSDSs than with non-TSDSs, particularly for the Homeobox, HLH, Ets, bZIP_1, and HMG_box TF families. By in silico modeling, we showed that mutation of the highly coevolving residues could significantly reduce the stability of the TF-DNA complex. The distant residues from the DNA interface also contributed to TF-DNA binding activity. Overall, our study gave evidence that coevolved residues relate to transcriptional regulation and provided insights into the potential application of engineered DNA-binding domains and proteins. IMPORTANCE While unraveling DNA-binding specificity of TFs is the key to understanding the basis and molecular mechanism of gene expression regulation, identifying the critical determinants that contribute to DNA binding specificity remains a major challenge. In this study, we provided evidence showing that coevolving residues in TF domains contributed to DNA binding specificity. We demonstrated that the TSDSs were more likely to coevolve with other TSDSs than with non-TSDSs. Mutation of the coevolving residue pairs (CRPs) could significantly reduce the stability of THE TF-DNA complex, and even the distant residues from the DNA interface contribute to TF-DNA binding activity. Collectively, our study expands our knowledge of the interactions among coevolved residues in TFs, tertiary contacting, and functional importance in refined transcriptional regulation. Understanding the impact of coevolving residues in TFs will help understand the details of transcription of gene regulation and advance the application of engineered DNA-binding domains and protein.
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Affiliation(s)
- Yizhao Luan
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zehua Tang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Zhong Z, Li J, Zhong J, Huang Y, Hu J, Zhang P, Zhang B, Jin Y, Luo W, Liu R, Zhang Y, Ling F. MAPKAPK2, a potential dynamic network biomarker of α-synuclein prior to its aggregation in PD patients. NPJ Parkinsons Dis 2023; 9:41. [PMID: 36927756 PMCID: PMC10020541 DOI: 10.1038/s41531-023-00479-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
One of the important pathological features of Parkinson's disease (PD) is the pathological aggregation of α-synuclein (α-Syn) in the substantia nigra. Preventing the aggregation of α-Syn has become a potential strategy for treating PD. However, the molecular mechanism of α-Syn aggregation is unclear. In this study, using the dynamic network biomarker (DNB) method, we first identified the critical time point when α-Syn undergoes pathological aggregation based on a SH-SY5Y cell model and found that DNB genes encode transcription factors that regulated target genes that were differentially expressed. Interestingly, we found that these DNB genes and their neighbouring genes were significantly enriched in the cellular senescence pathway and thus proposed that the DNB genes HSF1 and MAPKAPK2 regulate the expression of the neighbouring gene SERPINE1. Notably, in Gene Expression Omnibus (GEO) data obtained from substantia nigra, prefrontal cortex and peripheral blood samples, the expression level of MAPKAPK2 was significantly higher in PD patients than in healthy people, suggesting that MAPKAPK2 has potential as an early diagnostic biomarker of diseases related to pathological aggregation of α-Syn, such as PD. These findings provide new insights into the mechanisms underlying the pathological aggregation of α-Syn.
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Affiliation(s)
- Zhenggang Zhong
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Jiabao Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Jiayuan Zhong
- School of Mathematics, South China University of Technology, Guangzhou, Guangdong, China
| | - Yilin Huang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Jiaqi Hu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Piao Zhang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Baowen Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Yabin Jin
- The First People's Hospital of Foshan, Sun Yat-sen University, Foshan, China
| | - Wei Luo
- The First People's Hospital of Foshan, Sun Yat-sen University, Foshan, China.
| | - Rui Liu
- School of Mathematics, South China University of Technology, Guangzhou, Guangdong, China.
| | - Yuhu Zhang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
| | - Fei Ling
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China.
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161
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Mohammadi MA, Mansouri M, Derakhshani A, Rezaie M, Borhani M, Nasibi S, Mousavi SM, Afgar A, Macchiaroli N, Rosenzvit MC, Harandi MF. MicroRNA-Transcription factor regulatory networks in the early strobilar development of Echinococcus granulosus protoscoleces. BMC Genomics 2023; 24:114. [PMID: 36922762 PMCID: PMC10016175 DOI: 10.1186/s12864-023-09199-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/21/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND Echinococcus granulosus sensu lato has a complex developmental biology with a variety of factors relating to both intermediate and final hosts. To achieve maximum parasite adaptability, the development of the cestode is dependent on essential changes in transcript regulation. Transcription factors (TFs) and miRNAs are known as master regulators that affect the expression of downstream genes through a wide range of metabolic and signaling pathways. In this study, we aimed to develop a regulatory miRNA-Transcription factor (miRNA-TF) network across early developmental stages of E. granulosus protoscoleces by performing in silico analysis, and to experimentally validate TFs expression in protoscoleces obtained from in vitro culture, and from in vivo experiments. RESULTS We obtained list of 394 unique E. granulosus TFs and matched them with 818 differentially expressed genes which identified 41 predicted TFs with differential expression. These TFs were used to predict the potential targets of 31 differentially expressed miRNAs. As a result, eight miRNAs and eight TFs were found, and the predicted network was constructed using Cytoscape. At least four miRNAs (egr-miR-124a, egr-miR-124b-3p, egr-miR-745-3p, and egr-miR-87-3p) and their corresponding differentially expressed TFs (Zinc finger protein 45, Early growth response protein 3, Ecdysone induced protein 78c and ETS transcription factor elf 2) were highlighted in this investigation. The expression of predicted differentially expressed TFs obtained from in vitro and in vivo experiments, were experimentally validated by quantitative polymerase chain reaction. This confirmed findings of RNA-seq data. CONCLUSION miRNA-TF networks presented in this study control some of the most important metabolic and signaling pathways in the development and life cycle of E. granulosus, providing a potential approach for disrupting the early hours of dog infection and preventing the development of the helminth in the final host.
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Affiliation(s)
- Mohammad Ali Mohammadi
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Derakhshani
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Masoud Rezaie
- Student Research Committee, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Borhani
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Jilin, China
| | - Saeid Nasibi
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Seyed Mohammad Mousavi
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Natalia Macchiaroli
- Laboratorio Biología Molecular de Hidatidosis, Facultad de Medicina, Instituto de Microbiología Y Parasitología Médica (IMPaM), Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Mara C. Rosenzvit
- Laboratorio Biología Molecular de Hidatidosis, Facultad de Medicina, Instituto de Microbiología Y Parasitología Médica (IMPaM), Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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Chen J, Wang H, Deng C, Fei M. SLC12A5 as a novel potential biomarker of glioblastoma multiforme. Mol Biol Rep 2023; 50:4285-4299. [PMID: 36917367 DOI: 10.1007/s11033-023-08371-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is the most prevalent and malignant intracranial tumor with significant features of dismal prognosis and limited therapeutic solutions. Consequently, the present studies are committed to exploring potential biomarkers through bioinformatics analysis, which may serve as valuable prognostic predictors or novel therapeutic targets and provide new insights into the pathogenesis of GBM. METHODS We filtered overlapping differentially expressed genes (DEGs) based on expression profilings from three GBM microarray datasets (GSE116520, GSE4290 and GSE68848) and combined RNA sequencing data from The Cancer Genome Atlas and the Genotype-Tissue Expression databases. Hub genes were prioritized from DEGs after performing protein-protein interaction (PPI) network analysis and weighted gene co-expression network analysis (WGCNA). This was followed by survival analysis to identify potential biomarkers among hub genes. Ultimately, the distributions of gene expressions, genetic alterations, upstream regulatory mechanisms and enrichments of gene functions of the identified biomarkers were analysed on public databases. QRT-PCR, immunohistochemical staining and western blotting was also used to confirm the gene expression patterns in GBM and normal brain tissues. CCK-8 assay clarified the effects of the genes on GBM cells. RESULTS A total of 322 common DEGs were determined and nine genes were subsequently considered as hub genes by the combination of PPI network analysis and WGCNA. Only SLC12A5 had prognostic significance, which was deficient in GBM whereas especially enriched in normal neural tissues. SLC12A5 overexpression would inhibit cell proliferation of U251MG. Genetic alterations of SLC12A5 were rarely seen in GBM patients, and there was no apparent association existed between SLC12A5 expression and DNA methylation. SLC12A5 was prominently involved in ion transport, synapse and neurotransmitter. CONCLUSION SLC12A5 shows promise to function as a novel effective biomarker for GBM and deserves further systematic research.
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Affiliation(s)
- Jiakai Chen
- Department of Neurosurgery, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Handong Wang
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China.
| | - Chulei Deng
- Department of Neurosurgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, Jiangsu, China
| | - Maoxing Fei
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
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163
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Gene Self-Expressive Networks as a Generalization-Aware Tool to Model Gene Regulatory Networks. Biomolecules 2023; 13:biom13030526. [PMID: 36979461 PMCID: PMC10046116 DOI: 10.3390/biom13030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
Self-expressiveness is a mathematical property that aims at characterizing the relationship between instances in a dataset. This property has been applied widely and successfully in computer-vision tasks, time-series analysis, and to infer underlying network structures in domains including protein signaling interactions and social-networks activity. Nevertheless, despite its potential, self-expressiveness has not been explicitly used to infer gene networks. In this article, we present Generalizable Gene Self-Expressive Networks, a new, interpretable, and generalization-aware formalism to model gene networks, and we propose two methods: GXN•EN and GXN•OMP, based respectively on ElasticNet and OMP (Orthogonal Matching Pursuit), to infer and assess Generalizable Gene Self-Expressive Networks. We evaluate these methods on four Microarray datasets from the DREAM5 benchmark, using both internal and external metrics. The results obtained by both methods are comparable to those obtained by state-of-the-art tools, but are fast to train and exhibit high levels of sparsity, which make them easier to interpret. Moreover we applied these methods to three complex datasets containing RNA-seq informations from different mammalian tissues/cell-types. Lastly, we applied our methodology to compare a normal vs. a disease condition (Alzheimer), which allowed us to detect differential expression of genes’ sub-networks between these two biological conditions. Globally, the gene networks obtained exhibit a sparse and modular structure, with inner communities of genes presenting statistically significant over/under-expression on specific cell types, as well as significant enrichment for some anatomical GO terms, suggesting that such communities may also drive important functional roles.
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164
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Berns HM, Watkins-Chow DE, Lu S, Louphrasitthiphol P, Zhang T, Brown KM, Moura-Alves P, Goding CR, Pavan WJ. Loss of MC1R signaling implicates TBX3 in pheomelanogenesis and melanoma predisposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.532018. [PMID: 37090624 PMCID: PMC10120706 DOI: 10.1101/2023.03.10.532018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The human Red Hair Color (RHC) trait is caused by increased pheomelanin (red-yellow) and reduced eumelanin (black-brown) pigment in skin and hair due to diminished melanocortin 1 receptor (MC1R) function. In addition, individuals harboring the RHC trait are predisposed to melanoma development. While MC1R variants have been established as causative of RHC and are a well-defined risk factor for melanoma, it remains unclear mechanistically why decreased MC1R signaling alters pigmentation and increases melanoma susceptibility. Here, we use single-cell RNA-sequencing (scRNA-seq) of melanocytes isolated from RHC mouse models to reveal a Pheomelanin Gene Signature (PGS) comprising genes implicated in melanogenesis and oncogenic transformation. We show that TBX3, a well-known anti-senescence transcription factor implicated in melanoma progression, is part of the PGS and binds both E-box and T-box elements to regulate genes associated with melanogenesis and senescence bypass. Our results provide key insights into mechanisms by which MC1R signaling regulates pigmentation and how individuals with the RHC phenotype are predisposed to melanoma.
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Affiliation(s)
- H. Matthew Berns
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Dawn E. Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sizhu Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, 13 USA
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, 13 USA
| | - Pedro Moura-Alves
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, PT
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, PT
| | - Colin R. Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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Zheng J, Wang Y, Hu J. Study of the shared gene signatures of polyarticular juvenile idiopathic arthritis and autoimmune uveitis. Front Immunol 2023; 14:1048598. [PMID: 36969183 PMCID: PMC10030950 DOI: 10.3389/fimmu.2023.1048598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
ObjectiveTo explore the shared gene signatures and potential molecular mechanisms of polyarticular juvenile idiopathic arthritis (pJIA) and autoimmune uveitis (AU).MethodThe microarray data of pJIA and AU from the Gene Expression Omnibus (GEO) database were downloaded and analyzed. The GEO2R tool was used to identify the shared differentially expressed genes (DEGs) and genes of extracellular proteins were identified among them. Then, weighted gene co-expression network analysis (WGCNA) was used to identify the shared immune-related genes (IRGs) related to pJIA and AU. Moreover, the shared transcription factors (TFs) and microRNAs (miRNAs) in pJIA and AU were acquired by comparing data from HumanTFDB, hTFtarget, GTRD, HMDD, and miRTarBase. Finally, Metascape and g: Profiler were used to carry out function enrichment analyses of previously identified gene sets.ResultsWe found 40 up-regulated and 15 down-regulated shared DEGs via GEO2R. Then 24 shared IRGs in positivity-related modules, and 18 shared IRGs in negatively-related modules were found after WGCNA. After that, 3 shared TFs (ARID1A, SMARCC2, SON) were screened. And the constructed TFs-shared DEGs network indicates a central role of ARID1A. Furthermore, hsa-miR-146 was found important in both diseases. The gene sets enrichment analyses suggested up-regulated shared DEGs, TFs targeted shared DEGs, and IRGs positivity-correlated with both diseases mainly enriched in neutrophil degranulation process, IL-4, IL-13, and cytokine signaling pathways. The IRGs negatively correlated with pJIA and AU mainly influence functions of the natural killer cell, cytotoxicity, and glomerular mesangial cell proliferation. The down-regulated shared DEGs and TFs targeted shared DEGs did not show particular functional enrichment.ConclusionOur study fully demonstrated the flexibility and complexity of the immune system disorders involved in pJIA and AU. Neutrophil degranulation may be considered the shared pathogenic mechanism, and the roles of ARID1A and MiR-146a are worthy of further in-depth study. Other than that, the importance of periodic inspection of kidney function is also noteworthy.
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Balagannavar G, Basavaraju K, Bajpai AK, Davuluri S, Kannan S, S Srini V, S Chandrashekar D, Chitturi N, K Acharya K. Transcriptomic analysis of the Non-Obstructive Azoospermia (NOA) to address gene expression regulation in human testis. Syst Biol Reprod Med 2023; 69:196-214. [PMID: 36883778 DOI: 10.1080/19396368.2023.2176268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
There is a need to understand the molecular basis of testes under Non-Obstructive Azoospermia (NOA), a state of failed spermatogenesis. There has been a lack of attention to the transcriptome at the level of alternatively spliced mRNAs (iso-mRNAs) and the mechanism of gene expression regulation. Hence, we aimed to establish a reliable iso-mRNA profile of NOA-testes, and explore molecular mechanisms - especially those related to gene expression regulation. We sequenced mRNAs from testicular samples of donors with complete spermatogenesis (control samples) and a failure of spermatogenesis (NOA samples). We identified differentially expressed genes and their iso-mRNAs via standard NGS data analyses. We then listed these iso-mRNAs hierarchically based on the extent of consistency of differential quantities across samples and groups, and validated the lists via RT-qPCRs (for 80 iso-mRNAs). In addition, we performed extensive bioinformatic analysis of the splicing features, domains, interactions, and functions of differentially expressed genes and iso-mRNAs. Many top-ranking down-regulated genes and iso-mRNAs, i.e., those down-regulated more consistently across the NOA samples, are associated with mitosis, replication, meiosis, cilium, RNA regulation, and post-translational modifications such as ubiquitination and phosphorylation. Most down-regulated iso-mRNAs correspond to full-length proteins that include all expected domains. The predominance of alternative promoters and termination sites in these iso-mRNAs indicate their gene expression regulation via promoters and UTRs. We compiled a new, comprehensive list of human transcription factors (TFs) and used it to identify TF-'TF gene' interactions with potential significance in down-regulating genes under the NOA condition. The results indicate that RAD51 suppression by HSF4 prevents SP1-activation, and SP1, in turn, could regulate multiple TF genes. This potential regulatory axis and other TF interactions identified in this study could explain the down-regulation of multiple genes in NOA-testes. Such molecular interactions may also have key regulatory roles during normal human spermatogenesis.
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Affiliation(s)
- Govindkumar Balagannavar
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,Research Scholar, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kavyashree Basavaraju
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Akhilesh Kumar Bajpai
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Sravanthi Davuluri
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Shruthi Kannan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Vasan S Srini
- Manipal Fertility, Manipal Hospital, Bengaluru, Karnataka, India
| | | | - Neelima Chitturi
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Kshitish K Acharya
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
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Zhang Y, Bao S, Wang D, Lu W, Xu S, Zhou W, Wang X, Xu X, Ding X, Zhao S. Downregulation of KLF10 contributes to the regeneration of survived renal tubular cells in cisplatin-induced acute kidney injury via ZBTB7A-KLF10-PTEN axis. Cell Death Discov 2023; 9:82. [PMID: 36878898 PMCID: PMC9988960 DOI: 10.1038/s41420-023-01381-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023] Open
Abstract
Acute kidney injury (AKI) is a common clinical dysfunction with complicated pathophysiology and limited therapeutic methods. Renal tubular injury and the following regeneration process play a vital role in the course of AKI, but the underlining molecular mechanism remains unclear. In this study, network-based analysis of online transcriptional data of human kidney found that KLF10 was closely related to renal function, tubular injury and regeneration in various renal diseases. Three classical mouse models confirmed the downregulation of KLF10 in AKI and its correlation with tubular regeneration and AKI outcome. The 3D renal tubular model in vitro and fluorescent visualization system of cellular proliferation were constructed to show that KLF10 declined in survived cells but increased during tubular formation or conquering proliferative impediment. Furthermore, overexpression of KLF10 significantly inhibited, whereas knockdown of KLF10 extremely promoted the capacity of proliferation, injury repairing and lumen-formation of renal tubular cells. In mechanism, PTEN/AKT pathway were validated as the downstream of KLF10 and participated in its regulation of tubular regeneration. By adopting proteomic mass spectrum and dual-luciferase reporter assay, ZBTB7A were found to be the upstream transcription factor of KLF10. Our findings suggest that downregulation of KLF10 positively contributed to tubular regeneration in cisplatin induced acute kidney injury via ZBTB7A-KLF10-PTEN axis, which gives insight into the novel therapeutic and diagnostical target of AKI.
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Affiliation(s)
- Yang Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Siyu Bao
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daxi Wang
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Lu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sujuan Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Weiran Zhou
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaoyan Wang
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xialian Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China. .,Shanghai Medical Center of Kidney Disease, Shanghai, China. .,Kidney and Dialysis Institute of Shanghai, Shanghai, China. .,Kidney and Blood Purification Key Laboratory of Shanghai, Shanghai, China.
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China. .,Shanghai Medical Center of Kidney Disease, Shanghai, China. .,Kidney and Dialysis Institute of Shanghai, Shanghai, China. .,Kidney and Blood Purification Key Laboratory of Shanghai, Shanghai, China.
| | - Shuan Zhao
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China. .,Shanghai Medical Center of Kidney Disease, Shanghai, China. .,Kidney and Dialysis Institute of Shanghai, Shanghai, China. .,Kidney and Blood Purification Key Laboratory of Shanghai, Shanghai, China.
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Nishanth MJ, Jha S. Computational analysis of crosstalk between transcriptional regulators and RNA-binding proteins suggests mutual regulation of polycomb proteins and SRSF1 influencing adult hippocampal neurogenesis. DISCOVER MENTAL HEALTH 2023; 3:7. [PMID: 37861946 PMCID: PMC10501017 DOI: 10.1007/s44192-023-00034-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/28/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Adult hippocampal neurogenesis (AHN) is a clinically significant neural phenomenon. Understanding its molecular regulation would be important. In this regard, most studies have focused on transcriptional regulators (TRs), epigenetic modifiers, or non-coding RNAs. RNA-binding proteins (RBPs) have emerged as dominant molecular regulators. It would be significant to understand the potential cross-talk between RBPs and TRs, which could influence AHN. METHODS The present study employed computational analyses to identify RBPs and TRs regulating AHN, followed by the analysis of their interaction networks and detection of hub proteins. Next, the potential mutual regulation of hub TRs and RBPs was analyzed. Additionally, hippocampal genes differentially expressed upon exercise were analyzed for potential regulation by the identified TRs and RBPs. RESULTS 105 TRs and 26 RBPs were found to influence AHN, which could also form interactive networks. Polycomb complex proteins were among the TR network hubs, while HNRNP and SRSF family members were among the hub RBPs. Further, the polycomb complex proteins and SRSF1 could have a mutual regulatory relationship, suggesting a cross-talk between epigenetic/transcriptional and post-transcriptional regulatory pathways. A number of exercise-induced hippocampal genes were also found to be potential targets of the identified TRs and RBPs. CONCLUSION SRSF1 may influence post-transcriptional stability, localization, and alternative splicing patterns of polycomb complex transcripts, and the polycomb proteins may in turn epigenetically influence the SRSF1. Further experimental validation of these regulatory loops/networks could provide novel insights into the molecular regulation of AHN, and unravel new targets for disease-treatment.
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Affiliation(s)
- M J Nishanth
- Department of Biotechnology, School of Lifesciences, St Joseph's University, Bengaluru, India
| | - Shanker Jha
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India.
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169
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Yermakovich D, Pankratov V, Võsa U, Yunusbayev B, Dannemann M. Long-range regulatory effects of Neandertal DNA in modern humans. Genetics 2023; 223:6957427. [PMID: 36560850 PMCID: PMC9991505 DOI: 10.1093/genetics/iyac188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/13/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
The admixture between modern humans and Neandertals has resulted in ∼2% of the genomes of present-day non-Africans being composed of Neandertal DNA. Introgressed Neandertal DNA has been demonstrated to significantly affect the transcriptomic landscape in people today and via this molecular mechanism influence phenotype variation as well. However, little is known about how much of that regulatory impact is mediated through long-range regulatory effects that have been shown to explain ∼20% of expression variation. Here we identified 60 transcription factors (TFs) with their top cis-eQTL SNP in GTEx being of Neandertal ancestry and predicted long-range Neandertal DNA-induced regulatory effects by screening for the predicted target genes of those TFs. We show that the TFs form a significantly connected protein-protein interaction network. Among them are JUN and PRDM5, two brain-expressed TFs that have their predicted target genes enriched in regions devoid of Neandertal DNA. Archaic cis-eQTLs for the 60 TFs include multiple candidates for local adaptation, some of which show significant allele frequency increases over the last ∼10,000 years. A large proportion of the cis-eQTL-associated archaic SNPs have additional associations with various immune traits, schizophrenia, blood cell type composition and anthropometric measures. Finally, we demonstrate that our results are consistent with those of Neandertal DNA-associated empirical trans-eQTLs. Our results suggest that Neandertal DNA significantly influences regulatory networks, that its regulatory reach goes beyond the 40% of genomic sequence it still covers in present-day non-Africans and that via the investigated mechanism Neandertal DNA influences the phenotypic variation in people today.
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Affiliation(s)
- Danat Yermakovich
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Vasili Pankratov
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Bayazit Yunusbayev
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | | | - Michael Dannemann
- Centre for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
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170
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Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn Macrobrachium rosenbergii. Biomolecules 2023; 13:biom13030460. [PMID: 36979395 PMCID: PMC10046887 DOI: 10.3390/biom13030460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Macrobrachium rosenbergii is an important aquaculture prawn that exhibits sexual dimorphism in growth, with males growing much faster than females. However, the mechanisms controlling these complex traits are not well understood. The nervous system plays an important role in regulating life functions. In the present work, we applied PacBio RNA-seq to obtain and characterize the full-length transcriptomes of the brains and thoracic ganglia of female and male prawns, and we performed comparative transcriptome analysis of female and male prawns. A total of 159.1-Gb of subreads were obtained with an average length of 2175 bp and 93.2% completeness. A total of 84,627 high-quality unigenes were generated and annotated with functional databases. A total of 6367 transcript factors and 6287 LncRNAs were predicted. In total, 5287 and 6211 significantly differentially expressed genes (DEGs) were found in the brain and thoracic ganglion, respectively, and confirmed by qRT-PCR. Of the 435 genes associated with protein processing pathways in the endoplasmic reticula, 42 DEGs were detected, and 21/26 DEGs with upregulated expression in the male brain/thoracic ganglion. The DEGs in this pathway are regulated by multiple LncRNAs in polypeptide folding and misfolded protein degradation in the different organs and sexes of the prawn. Our results provide novel theories and insights for studying the nervous system, sexual control, and growth dimorphism.
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171
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Du Z, Huang T, Uversky VN, Li J. Predicting TF Proteins by Incorporating Evolution Information Through PSSM. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1319-1326. [PMID: 35981062 DOI: 10.1109/tcbb.2022.3199758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Transcription factors (TFs) are DNA binding proteins involved in the regulation of gene expression. They exist in all organisms and activate or repress transcription by binding to specific DNA sequences. Traditionally, TFs have been identified by experimental methods that are time-consuming and costly. In recent years, various computational methods have been developed to identify TF to overcome these limitations. However, there is a room for further improvement in the predictive performance of these tools in terms of accuracy. We report here a novel computational tool, TFnet, that provides accurate and comprehensive TF predictions from protein sequences. The accuracy of these predictions is substantially better than the results of the existing TF predictors and methods. Especially, it outperforms comparable methods significantly when sequence similarity to other known sequences in the database drops below 40%. Ablation tests reveal that the high predictive performance stems from innovative ways used in TFnet to derive sequence Position-Specific Scoring Matrix (PSSM) and encode inputs.
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172
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Frias A, Di Leo L, Antoranz A, Nazerai L, Carretta M, Bodemeyer V, Pagliuca C, Dahl C, Claps G, Mandelli GE, Andhari MD, Pacheco MP, Sauter T, Robert C, Guldberg P, Madsen DH, Cecconi F, Bosisio FM, De Zio D. Ambra1 modulates the tumor immune microenvironment and response to PD-1 blockade in melanoma. J Immunother Cancer 2023; 11:jitc-2022-006389. [PMID: 36868570 PMCID: PMC9990656 DOI: 10.1136/jitc-2022-006389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Loss of Ambra1 (autophagy and beclin 1 regulator 1), a multifunctional scaffold protein, promotes the formation of nevi and contributes to several phases of melanoma development. The suppressive functions of Ambra1 in melanoma are mediated by negative regulation of cell proliferation and invasion; however, evidence suggests that loss of Ambra1 may also affect the melanoma microenvironment. Here, we investigate the possible impact of Ambra1 on antitumor immunity and response to immunotherapy. METHODS This study was performed using an Ambra1-depleted BrafV600E /Pten-/ - genetically engineered mouse (GEM) model of melanoma, as well as GEM-derived allografts of BrafV600E /Pten-/ - and BrafV600E /Pten-/ -/Cdkn2a-/ - tumors with Ambra1 knockdown. The effects of Ambra1 loss on the tumor immune microenvironment (TIME) were analyzed using NanoString technology, multiplex immunohistochemistry, and flow cytometry. Transcriptome and CIBERSORT digital cytometry analyses of murine melanoma samples and human melanoma patients (The Cancer Genome Atlas) were applied to determine the immune cell populations in null or low-expressing AMBRA1 melanoma. The contribution of Ambra1 on T-cell migration was evaluated using a cytokine array and flow cytometry. Tumor growth kinetics and overall survival analysis in BrafV600E /Pten-/ -/Cdkn2a-/ - mice with Ambra1 knockdown were evaluated prior to and after administration of a programmed cell death protein-1 (PD-1) inhibitor. RESULTS Loss of Ambra1 was associated with altered expression of a wide range of cytokines and chemokines as well as decreased infiltration of tumors by regulatory T cells, a subpopulation of T cells with potent immune-suppressive properties. These changes in TIME composition were associated with the autophagic function of Ambra1. In the BrafV600E /Pten-/ -/Cdkn2a-/ - model inherently resistant to immune checkpoint blockade, knockdown of Ambra1 led to accelerated tumor growth and reduced overall survival, but at the same time conferred sensitivity to anti-PD-1 treatment. CONCLUSIONS This study shows that loss of Ambra1 affects the TIME and the antitumor immune response in melanoma, highlighting new functions of Ambra1 in the regulation of melanoma biology.
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Affiliation(s)
- Alex Frias
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Luca Di Leo
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Asier Antoranz
- Lab of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Loulieta Nazerai
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Marco Carretta
- National Center for Cancer Immunotherapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Valérie Bodemeyer
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Chiara Pagliuca
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Christina Dahl
- Molecular Diagnostics Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Giuseppina Claps
- INSERM U981 and Department of Oncologic Medicine, Gustave Roussy Institute and Paris Saclay University, Villejuif, France
| | | | | | - Maria Pires Pacheco
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Caroline Robert
- INSERM U981 and Department of Oncologic Medicine, Gustave Roussy Institute and Paris Saclay University, Villejuif, France
| | - Per Guldberg
- Molecular Diagnostics Group, Danish Cancer Society Research Center, Copenhagen, Denmark.,Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Daniel Hargbøl Madsen
- National Center for Cancer Immunotherapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Francesco Cecconi
- Cell Stress and Survival, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | | | - Daniela De Zio
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark .,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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173
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Wang ZH, Jiang S, Xu WH. ROS downregulate TCA activity to modulate energy metabolism via the HIF/miR-34/ACS-PK pathway for lifespan extension in Helicoverpa armigera. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119414. [PMID: 36535371 DOI: 10.1016/j.bbamcr.2022.119414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/09/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Previous studies have shown that high levels of reactive oxygen species (ROS) and low tricarboxylic acid (TCA) activity in the brain promote pupal diapause, which is characterized by metabolic depression and lifespan extension. However, it is unclear whether ROS are associated with TCA activity. In this study, we demonstrate that ROS downregulate TCA activity and acetyl-CoA and pyruvate levels in the brains of diapause-destined pupae in the moth Helicoverpa armigera, as well as the protein levels of acetyl-CoA synthetase (ACS) and pyruvate kinase (PK), two proteins involved in the biosynthesis of acetyl-CoA and pyruvate, respectively. Interestingly, miR-34, which is highly expressed in the brains of diapause-destined pupae, can respond to ROS signaling. Furthermore, we show that miR-34 can reduce the expression of ACS and PK by directly targeting their mRNAs. Additionally, hypoxia-inducible factor (HIF), a transcription factor, can be activated by ROS and then promotes miR-34 transcription by binding a cis-element in its promoter. Moreover, we observed delayed pupal development after treatment with a ROS activator paraquat and a HIF activator dimethyloxallyl glycine. Taken together, these results suggest that a novel pathway ROS/HIF/miR-34/ACS-PK was found to negatively regulate TCA activity to promote insect diapause for lifespan extension.
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Affiliation(s)
- Zheng-Hao Wang
- State Key Laboratory of Biocontrol and Institute of Entomology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Songshan Jiang
- State Key Laboratory of Biocontrol and Institute of Entomology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China.
| | - Wei-Hua Xu
- State Key Laboratory of Biocontrol and Institute of Entomology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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174
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Wang H, Yuan H, Guo Q, Zeng X, Liu M, Ji R, Chen Z, Guan Q, Zheng Y, Wang Y, Zhou Y. A novel circRNA, hsa_circ_0069382, regulates gastric cancer progression. Cancer Cell Int 2023; 23:35. [PMID: 36841760 PMCID: PMC9960672 DOI: 10.1186/s12935-023-02871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 02/27/2023] Open
Abstract
Aberrant expression of circRNAs is closely associated with the progression of gastric cancer; however, the specific mechanisms involved remain unclear. Our aim was to identify new gastric cancer biomarkers and explore the molecular mechanisms of gastric cancer progression. Therefore, we analyzed miRNA and circRNA microarrays of paired early-stage gastric cancer samples. Our study identified a new circRNA called hsa_circ_0069382, that had not been reported before and was expressed at low levels in gastric cancer tissues. Our study also included bioinformatics analyses which determined that the high expression of hsa_circ_0069382 regulated the BTG anti-proliferation factor 2 (BTG2)/ focal adhesion kinase (FAK) axis in gastric cancer lines by sponging for miR-15a-5p. Therefore, proliferation, invasion, and migration of gastric cancer is impacted. miR-15a-5p overexpression partially restored the effects of hsa_circ_0069382. This study provides potential new therapeutic options and a future direction to explore for gastric cancer treatment, and biomarkers.
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Affiliation(s)
- Haoying Wang
- grid.32566.340000 0000 8571 0482The First Clinical Medical College, Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Hao Yuan
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Qinghong Guo
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Xi Zeng
- grid.32566.340000 0000 8571 0482The First Clinical Medical College, Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Mengxiao Liu
- grid.32566.340000 0000 8571 0482The First Clinical Medical College, Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Rui Ji
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Zhaofeng Chen
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Quanlin Guan
- grid.412643.60000 0004 1757 2902Department of Oncology Surgery, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Ya Zheng
- grid.412643.60000 0004 1757 2902Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.412643.60000 0004 1757 2902Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000 China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000, China. .,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, 730000, China. .,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
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175
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Li T, Feng M, Chi Y, Shi X, Sun Z, Wu Z, Li A, Shi W. Defensive Resistance of Cowpea Vigna unguiculata Control Megalurothrips usitatus Mediated by Jasmonic Acid or Insect Damage. PLANTS (BASEL, SWITZERLAND) 2023; 12:942. [PMID: 36840292 PMCID: PMC9967092 DOI: 10.3390/plants12040942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Vigna unguiculata is a vital vegetable crop in Southeast Asia, and Megalurothrips usitatus can cause huge damage to this crop. Enhancing the resistance of V. unguiculata against M. usitatus is a promising way to protect this crop; however, there is limited information regarding the mechanism underlying the resistance of V. unguiculata against M. usitatus. Here, a behavior assay was performed to explore the resistance of V. unguiculata against M. usitatus after insect damage or treatment by jasmonic acid (JA). Furthermore, transcriptome and metabonomics analysis was used to detect the putative mechanism underlying the resistance of V. unguiculata against M. usitatus. The pre-treatment of Vigna unguiculata with JA or infestation with Megalurothrips usitatus alleviated the damage resulting from the pest insect. We further identified differentially expressed genes and different metabolites involved in flavonoid biosynthesis and alpha-linolenic acid metabolism. Genes of chalcone reductase and shikimate O-hydroxycinnamoyltransferase involved in flavonoid biosynthesis, as well as lipoxygenase and acyl-CoA oxidase involved in alpha-linolenic acid metabolism, were upregulated in plants after herbivory or JA supplementation. The upregulation of these genes contributed to the high accumulation of metabolites involved in flavonoid biosynthesis and the alpha-linolenic acid metabolism pathway. These transcriptional and metabolite changes are potentially responsible for plant defense and a putative regulatory model is thus proposed to illustrate the cowpea defense mechanism against insect attack. Our study provides candidate targets for the breeding of varieties with resistance to insect herbivory by molecular technology.
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Affiliation(s)
- Tao Li
- Department of Entomology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Mingyue Feng
- Department of Entomology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yuanming Chi
- Department of Entomology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xing Shi
- Plant Protection Station of Guangxi Zhuang Autonomous Region, Nanning 530007, China
| | - Zilin Sun
- Department of Entomology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhen Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Aomei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Wangpeng Shi
- Department of Entomology and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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176
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Coffin SL, Durham MA, Nitschke L, Xhako E, Brown AM, Revelli JP, Villavicencio Gonzalez E, Lin T, Handler HP, Dai Y, Trostle AJ, Wan YW, Liu Z, Sillitoe RV, Orr HT, Zoghbi HY. Disruption of the ATXN1-CIC complex reveals the role of additional nuclear ATXN1 interactors in spinocerebellar ataxia type 1. Neuron 2023; 111:481-492.e8. [PMID: 36577402 PMCID: PMC9957872 DOI: 10.1016/j.neuron.2022.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/26/2022] [Accepted: 11/28/2022] [Indexed: 12/28/2022]
Abstract
Spinocerebellar ataxia type 1 (SCA1) is a paradigmatic neurodegenerative disease in that it is caused by a mutation in a broadly expressed protein, ATXN1; however, only select populations of cells degenerate. The interaction of polyglutamine-expanded ATXN1 with the transcriptional repressor CIC drives cerebellar Purkinje cell pathogenesis; however, the importance of this interaction in other vulnerable cells remains unknown. Here, we mutated the 154Q knockin allele of Atxn1154Q/2Q mice to prevent the ATXN1-CIC interaction globally. This normalized genome-wide CIC binding; however, it only partially corrected transcriptional and behavioral phenotypes, suggesting the involvement of additional factors in disease pathogenesis. Using unbiased proteomics, we identified three ATXN1-interacting transcription factors: RFX1, ZBTB5, and ZKSCAN1. We observed altered expression of RFX1 and ZKSCAN1 target genes in SCA1 mice and patient-derived iNeurons, highlighting their potential contributions to disease. Together, these data underscore the complexity of mechanisms driving cellular vulnerability in SCA1.
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Affiliation(s)
- Stephanie L Coffin
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Mark A Durham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Larissa Nitschke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eder Xhako
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Amanda M Brown
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean-Pierre Revelli
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Esmeralda Villavicencio Gonzalez
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Tao Lin
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hillary P Handler
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yanwan Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Alexander J Trostle
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ying-Wooi Wan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Zhandong Liu
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roy V Sillitoe
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harry T Orr
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Huda Y Zoghbi
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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177
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Tellechea-Luzardo J, Stiebritz MT, Carbonell P. Transcription factor-based biosensors for screening and dynamic regulation. Front Bioeng Biotechnol 2023; 11:1118702. [PMID: 36814719 PMCID: PMC9939652 DOI: 10.3389/fbioe.2023.1118702] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Advances in synthetic biology and genetic engineering are bringing into the spotlight a wide range of bio-based applications that demand better sensing and control of biological behaviours. Transcription factor (TF)-based biosensors are promising tools that can be used to detect several types of chemical compounds and elicit a response according to the desired application. However, the wider use of this type of device is still hindered by several challenges, which can be addressed by increasing the current metabolite-activated transcription factor knowledge base, developing better methods to identify new transcription factors, and improving the overall workflow for the design of novel biosensor circuits. These improvements are particularly important in the bioproduction field, where researchers need better biosensor-based approaches for screening production-strains and precise dynamic regulation strategies. In this work, we summarize what is currently known about transcription factor-based biosensors, discuss recent experimental and computational approaches targeted at their modification and improvement, and suggest possible future research directions based on two applications: bioproduction screening and dynamic regulation of genetic circuits.
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Affiliation(s)
- Jonathan Tellechea-Luzardo
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Martin T. Stiebritz
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain,Institute for Integrative Systems Biology I2SysBio, Universitat de València-CSIC, Paterna, Spain,*Correspondence: Pablo Carbonell,
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178
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Upreti A, Padula SL, Tangeman JA, Wagner BD, O’Connell MJ, Jaquish TJ, Palko RK, Mantz CJ, Anand D, Lovicu FJ, Lachke SA, Robinson ML. Lens Epithelial Explants Treated with Vitreous Humor Undergo Alterations in Chromatin Landscape with Concurrent Activation of Genes Associated with Fiber Cell Differentiation and Innate Immune Response. Cells 2023; 12:501. [PMID: 36766843 PMCID: PMC9914805 DOI: 10.3390/cells12030501] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Lens epithelial explants are comprised of lens epithelial cells cultured in vitro on their native basement membrane, the lens capsule. Biologists have used lens epithelial explants to study many different cellular processes including lens fiber cell differentiation. In these studies, fiber differentiation is typically measured by cellular elongation and the expression of a few proteins characteristically expressed by lens fiber cells in situ. Chromatin and RNA was collected from lens epithelial explants cultured in either un-supplemented media or media containing 50% bovine vitreous humor for one or five days. Chromatin for ATAC-sequencing and RNA for RNA-sequencing was prepared from explants to assess regions of accessible chromatin and to quantitatively measure gene expression, respectively. Vitreous humor increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and, surprisingly, an immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had little effect on the accessibility of the genes highly expressed in the lens epithelium despite dramatic reductions in their mRNA transcripts. An unbiased analysis of differentially accessible regions revealed an enrichment of cis-regulatory motifs for RUNX, SOX and TEAD transcription factors that may drive differential gene expression in response to vitreous.
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Affiliation(s)
- Anil Upreti
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Stephanie L. Padula
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Jared A. Tangeman
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Brad D. Wagner
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | | | - Tycho J. Jaquish
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Raye K. Palko
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Courtney J. Mantz
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Frank J. Lovicu
- Molecular and Cellular Biomedicine, School of Medical Sciences, and Save Sight Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Michael L. Robinson
- Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
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179
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Vu HT, Kaur H, Kies KR, Starks RR, Tuteja G. Identifying novel regulators of placental development using time-series transcriptome data. Life Sci Alliance 2023; 6:6/2/e202201788. [PMID: 36622342 PMCID: PMC9748866 DOI: 10.26508/lsa.202201788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
The placenta serves as a connection between the mother and the fetus during pregnancy, providing the fetus with oxygen, nutrients, and growth hormones. However, the regulatory mechanisms and dynamic gene interaction networks underlying early placental development are understudied. Here, we generated RNA-sequencing data from mouse fetal placenta at embryonic days 7.5, 8.5, and 9.5 to identify genes with timepoint-specific expression, then inferred gene interaction networks to analyze highly connected network modules. We determined that timepoint-specific gene network modules were associated with distinct developmental processes, and with similar expression profiles to specific human placental cell populations. From each module, we identified hub genes and their direct neighboring genes, which were predicted to govern placental functions. We confirmed that four novel candidate regulators identified through our analyses regulate cell migration in the HTR-8/SVneo cell line. Overall, we predicted several novel regulators of placental development expressed in specific placental cell types using network analysis of bulk RNA-sequencing data. Our findings and analysis approaches will be valuable for future studies investigating the transcriptional landscape of early development.
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Affiliation(s)
- Ha Th Vu
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Haninder Kaur
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Kelby R Kies
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Rebekah R Starks
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Geetu Tuteja
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA .,Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
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180
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Singh U, Alex R, Chaudhary A, Deb R, Raja TV, Rathod B, Savaliya BD, Kumar S, Das AK. Genetic variants in 5'UTR and exonic region of NPY gene alter the reproduction performance in Indian cattle breeds. Reprod Domest Anim 2023; 58:246-252. [PMID: 36269691 DOI: 10.1111/rda.14281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 11/29/2022]
Abstract
Neuropeptide Y (NPY) is one of the most potent orexigenic factors which can produce diverse effects on behaviour and other physiological functions and is highly conserved in evolution. The present study was aimed to identify and associate SNPs in the 5' UTR and exon2 region of the NPY gene with reproduction and production traits in Kankrej cattle of Indian origin. Three mutations in the 5'-UTR region and one mutation in the exon2 region of the NPY gene were identified by PCR-SSCP and PCR-RFLP, respectively, followed by sequencing. Further, association studies were conducted with reproduction and production traits in Kankrej cattle. The GACCGA genotyped animals based on the 5'UTR variants indicated better dry period and calving interval, whereas with GGCCGG genotypes showed higher total lactation milk yield and 305-day milk yield in comparison to other genotypes. Also, service period and inter calving period varied significantly among the genotypes of exon2, as the GG genotyped animals had significantly longer calving interval. Other traits like age at first heat, age at first service and age at first calving were not affected by the mutations. So, the present study outlined that the bovine NPY gene may be considered to be one of the candidate gene for improvement of reproductive performance of cattle, after validation on large sample size.
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Affiliation(s)
- Umesh Singh
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Rani Alex
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | | | - Rajib Deb
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | | | - Bharatsingh Rathod
- Livestock Research Station, Sardarkrushinagar Dantiwada Agricultural University, Banaskatha, India
| | | | - Sushil Kumar
- ICAR-Central Institute for Research on Cattle, Meerut, India
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181
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Pan X, Xu X, Wang L, Zhang S, Chen Y, Yang R, Chen X, Cheng B, Xia J, Ren X. BASP1 is a prognostic biomarker associated with immunotherapeutic response in head and neck squamous cell carcinoma. Front Oncol 2023; 13:1021262. [PMID: 36776328 PMCID: PMC9911441 DOI: 10.3389/fonc.2023.1021262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Backgrounds Immunotherapy is effective in a subset of head and neck squamous cell carcinoma (HNSCC). However, the unfavorable response rate and inadequate biomarkers for stratifying patients have primarily limited its clinical application. Considering transcriptional factors (TFs) play essential roles in regulating immune activity during HNSCC progression, we comprehensively analyzed the expression alterations of TFs and their prognostic values. Methods Gene expression datasets and clinical information of HNSCC were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) repository. Then, Brain abundant membrane attached signal protein 1 (BASP1) was screened out of differentially expressed TFs by univariate and multivariate survival analysis. Tumor immune dysfunction and exclusion (TIDE) was applied to analyze the response to immunotherapy of BASP1high/low patients. Meanwhile, GO, KEGG and GSEA analyses were used to enrich the pathways between the BASP1high and BASP1low groups. Single-sample gene set enrichment analysis (ssGSEA), CIBERSORT, EPIC and quanTiseq algorithms were applied to explore immune infiltrations. Also, immune cycle analysis was conducted by ssGSEA. Additionally, lipid peroxidation, glutathione and reactive oxygen species were performed to detect the ferroptosis alternations. Results BASP1 was upregulated and associated with poor survival in HNSCC patients. BASP1high patients exhibited better response rates to anti-PD-1 immunotherapy and higher expressions of immune checkpoint inhibitors. GO, KEGG and GSEA analyses indicated that the expression of BASP1 was related to several immune-related pathways and immunogenic ferroptosis signature. The infiltration of activated CD8+ T cells was authenticated to be decreased in BASP1high patients. Furthermore, BASP1 was identified to be positively correlated with T cell dysfunction and immune escape. Moreover, silencing BASP1 triggered ferroptosis in HNSCC cells, representing as increased LDH, lipid peroxidation and ROS levels, and reduced glutathione synthesis. Conclusions We demonstrated that BASP1 suppressed immunogenic ferroptosis to induce immunosuppressive tumor microenvironment. BASP1 plays a critical role in immune response, and might be a promising classifier for selecting HNSCC patients who benefit from current immunotherapy.
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Affiliation(s)
- Xue Pan
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xun Xu
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Lixuan Wang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Siyuan Zhang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yingyao Chen
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Rongchun Yang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xijuan Chen
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Bin Cheng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China,*Correspondence: Xianyue Ren, ; Juan Xia, ; Bin Cheng,
| | - Juan Xia
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China,*Correspondence: Xianyue Ren, ; Juan Xia, ; Bin Cheng,
| | - Xianyue Ren
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China,*Correspondence: Xianyue Ren, ; Juan Xia, ; Bin Cheng,
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182
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Liu X, Ni G, Zhang P, Li H, Li J, Cavallazzi Sebold B, Wu X, Chen G, Yuan S, Wang T. Single-nucleus RNA sequencing and deep tissue proteomics reveal distinct tumour microenvironment in stage-I and II cervical cancer. J Exp Clin Cancer Res 2023; 42:28. [PMID: 36683048 PMCID: PMC9869594 DOI: 10.1186/s13046-023-02598-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) is the 3rd most common cancer in women and the 4th leading cause of deaths in gynaecological malignancies, yet the exact progression of CC is inconclusive, mainly due to the high complexity of the changing tumour microenvironment (TME) at different stages of tumorigenesis. Importantly, a detailed comparative single-nucleus transcriptomic analysis of tumour microenvironment (TME) of CC patients at different stages is lacking. METHODS In this study, a total of 42,928 and 29,200 nuclei isolated from the tumour tissues of stage-I and II CC patients and subjected to single-nucleus RNA sequencing (snRNA-seq) analysis. The cell heterogeneity and functions were comparatively investigated using bioinformatic tools. In addition, label-free quantitative mass spectrometry based proteomic analysis was carried out. The proteome profiles of stage-I and II CC patients were compared, and an integrative analysis with the snRNA-seq was performed. RESULTS Compared with the stage-I CC (CCI) patients, the immune response relevant signalling pathways were largely suppressed in various immune cells of the stage-II CC (CCII) patients, yet the signalling associated with cell and tissue development was enriched, as well as metabolism for energy production suggested by the upregulation of genes associated with mitochondria. This was consistent with the quantitative proteomic analysis that showed the dominance of proteins promoting cell growth and intercellular matrix development in the TME of CCII group. The interferon-α and γ responses appeared the most activated pathways in many cell populations of the CCI patients. Several collagens, such as COL12A1, COL5A1, COL4A1 and COL4A2, were found significantly upregulated in the CCII group, suggesting their roles in diagnosing CC progression. A novel transcript AC244205.1 was detected as the most upregulated gene in CCII patients, and its possible mechanistic role in CC may be investigated further. CONCLUSIONS Our study provides important resources for decoding the progression of CC and set the foundation for developing novel approaches for diagnosing CC and tackling the immunosuppressive TME.
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Affiliation(s)
- Xiaosong Liu
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
- The First Affiliated Hospital/School of Clinical Medicineof, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
| | - Guoying Ni
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
- The First Affiliated Hospital/School of Clinical Medicineof, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
| | - Pingping Zhang
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Hejie Li
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
| | - Junjie Li
- The First Affiliated Hospital/School of Clinical Medicineof, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
| | | | - Xiaolian Wu
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Guoqiang Chen
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China.
| | - Songhua Yuan
- Department of Gynaecology, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China.
| | - Tianfang Wang
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia.
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183
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Decoding transcriptional regulation via a human gene expression predictor. J Genet Genomics 2023; 50:305-317. [PMID: 36693565 DOI: 10.1016/j.jgg.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
Transcription factors (TFs) regulate cellular activities by controlling gene expression, but a predictive model describing how TFs quantitatively modulate human transcriptomes is lacking. We construct a universal human gene expression predictor and utilize it to decode transcriptional regulation. Using the expression of 1613 TFs, the predictor reconstitutes highly accurate transcriptomes for samples derived from a wide range of tissues and conditions. The broad applicability of the predictor indicates that it recapitulates the quantitative relationships between TFs and target genes ubiquitous across tissues. Significant interacting TF-target gene pairs are extracted from the predictor and enable downstream inference of TF regulators for diverse pathways involved in development, immunity, metabolism, and stress response. A detailed analysis of the hematopoiesis process reveals an atlas of key TFs regulating the development of different hematopoietic cell lineages, and a portion of these TFs are conserved between humans and mice. The results demonstrate that our method is capable of delineating the TFs responsible for fate determination. Compared to other existing tools, our approach shows better performance in recovering the correct TF regulators. Thus, we present a novel approach that can be used to study human transcriptional regulation in general.
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184
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Wang C, Li A, Cong R, Qi H, Wang W, Zhang G, Li L. Cis- and Trans-variations of Stearoyl-CoA Desaturase Provide New Insights into the Mechanisms of Diverged Pattern of Phenotypic Plasticity for Temperature Adaptation in Two Congeneric Oyster Species. Mol Biol Evol 2023; 40:6994358. [PMID: 36661848 PMCID: PMC9949715 DOI: 10.1093/molbev/msad015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/21/2022] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
The evolution of phenotypic plasticity plays an essential role in adaptive responses to climate change; however, its regulatory mechanisms in marine organisms which exhibit high phenotypic plasticity still remain poorly understood. The temperature-responsive trait oleic acid content and its major gene stearoyl-CoA desaturase (Scd) expression have diverged in two allopatric congeneric oyster species, cold-adapted Crassostrea gigas and warm-adapted Crassostrea angulata. In this study, genetic and molecular methods were used to characterize fatty acid desaturation and membrane fluidity regulated by oyster Scd. Sixteen causative single-nucleotide polymorphisms (SNPs) were identified in the promoter/cis-region of the Scd between wild C. gigas and C. angulata. Further functional experiments showed that an SNP (g.-333C [C. gigas allele] >T [C. angulata allele]) may influence Scd transcription by creating/disrupting the binding motif of the positive trans-factor Y-box factor in C. gigas/C. angulata, which mediates the higher/lower constitutive expression of Scd in C. gigas/C. angulata. Additionally, the positive trans-factor sterol-regulatory element-binding proteins (Srebp) were identified to specifically bind to the promoter of Scd in both species, and were downregulated during cold stress in C. gigas compared to upregulated in C. angulata. This partly explains the relatively lower environmental sensitivity (plasticity) of Scd in C. gigas. This study serves as an experimental case to reveal that both cis- and trans-variations shape the diverged pattern of phenotypic plasticity, which provides new insights into the formation of adaptive traits and the prediction of the adaptive potential of marine organisms to future climate change.
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Affiliation(s)
- Chaogang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China,University of Chinese Academy of Sciences, Beijing, China
| | - Ao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China,National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Rihao Cong
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China,National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Haigang Qi
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China,National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China,National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,University of Chinese Academy of Sciences, Beijing, China,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China,National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Li
- Corresponding author: E-mail:
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185
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Li D, Zhong C, Sun Y, Kang L, Jiang Y. Identification of genes involved in chicken follicle selection by ONT sequencing on granulosa cells. Front Genet 2023; 13:1090603. [PMID: 36712880 PMCID: PMC9877231 DOI: 10.3389/fgene.2022.1090603] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/27/2022] [Indexed: 01/15/2023] Open
Abstract
In chickens, follicle selection is an important process affecting laying traits, which is characterized by the differentiation of granulosa cells and the synthesis of progesterone by granulosa cells from hierarchical follicles. By using Oxford Nanopore Technologies (ONT) approach, we compared the transcriptomes of granulosa cells between pre-hierarchical (Pre-GCs) and hierarchical follicles (Post-GCs) to identify genes underlying chicken follicle selection. A total of 2,436 differentially expressed genes (DEGs), 3,852 differentially expressed transcripts (DETs) and 925 differentially expressed lncRNA transcripts were identified between chicken Pre-GCs and Post-GCs. For all of the significant DETs, the alternative 3'splice sites (A3) accounted for a maximum of 23.74% of all alternative splicing events. Three DETs of the 7-dehydrocholesterol reductase gene (DHCR7) named as T1, T3, and T4, differing in 5'untranslated regions (UTRs), increased in Post-GCs with different folds (T1: 1.83, T3: 2.42, T4: 5.06). The expression of the three DHCR7 transcripts was upregulated by estrogen in a dose-dependent manner, while was downregulated by bone morphogenetic protein 15 (BMP15) and transforming growth factor-beta 1 (TGF-β1). Follicle-stimulating hormone (FSH) and bone morphogenetic protein 4 (BMP4) promoted the expression of the three DHCR7 transcripts in Pre-GCs at lower concentrations, while repressed their expression at higher concentrations. The data from this study may provide a reference for better understanding of the genetic mechanisms underlying follicle selection in chicken and other poultry species.
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Affiliation(s)
- Dandan Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Conghao Zhong
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an, China,*Correspondence: Yunliang Jiang,
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186
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Identification and Analysis of Potential Immune-Related Biomarkers in Endometriosis. J Immunol Res 2023; 2023:2975581. [PMID: 36660246 PMCID: PMC9845045 DOI: 10.1155/2023/2975581] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
Background Endometriosis is an inflammatory gynecological disease leading to deep pelvic pain, dyspareunia, and infertility. The pathophysiology of endometriosis is complex and depends on a variety of biological processes and pathways. Therefore, there is an urgent need to identify reliable biomarkers for early detection and accurate diagnosis to predict clinical outcomes and aid in the early intervention of endometriosis. We screened transcription factor- (TF-) immune-related gene (IRG) regulatory networks as potential biomarkers to reveal new molecular subgroups for the early diagnosis of endometriosis. Methods To explore potential therapeutic targets for endometriosis, the Gene Expression Omnibus (GEO), Immunology Database and Analysis Portal (ImmPort), and TF databases were used to obtain data related to the recognition of differentially expressed genes (DEGs), differentially expressed IRGs (DEIRGs), and differentially expressed TFs (DETFs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DETFs and DEIRGs. Then, DETFs and DEIRGs were further validated in the external datasets of GSE51981 and GSE1230103. Then, we used quantitative real-time polymerase chain reaction (qRT-PCR) to verify the hub genes. Simultaneously, the Pearson correlation analysis and protein-protein interaction (PPI) analyses were used to indicate the potential mechanisms of TF-IRGs at the molecular level and obtain hub IRGs. Finally, the receiver operating characteristic (ROC) curve analysis was used to assess the diagnostic value of the hub IRGs. Results We screened a total of 94 DETFs and 121 DEIRGs in endometriosis. Most downregulated DETFs showed decreased expression in the endometria of moderate/severe endometriosis patients. The top-ranked upregulated DEIRGs were upregulated in the endometra of infertile women. Functional analysis showed that DETFs and DEIRGs may be involved in the biological behaviors and pathways of endometriosis. The TF-IRG PPI network was successfully constructed. Compared with the control group, high C3, VCAM1, ITGB2, and C3AR1 expression had statistical significance in endometriosis among the hub DEIRGs. They also showed higher sensitivity and specificity by ROC analysis for the diagnosis of endometriosis. Finally, compared with controls, C3 and VCAM1 were highly expressed in endometriosis tissue samples. In addition, they also showed high specificity and sensitivity for diagnosing endometriosis. Conclusion Overall, we discovered the TF-IRG regulatory network and analyzed 4 hub IRGs that were closely related to endometriosis, which contributes to the diagnosis of endometriosis. Additionally, we verified that DETFs or DEIRGs were associated with the clinicopathological features of endometriosis, and external datasets also confirmed the hub IRGs. Finally, C3 and VCAM1 were highly expressed in endometriosis tissue samples compared with controls and may be potential biomarkers of endometriosis, which are helpful for the early diagnosis of endometriosis.
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187
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Udani S, Langerman J, Koo D, Baghdasarian S, Cheng B, Kang S, Soemardy C, de Rutte J, Plath K, Carlo DD. Secretion encoded single-cell sequencing (SEC-seq) uncovers gene expression signatures associated with high VEGF-A secretion in mesenchymal stromal cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.523110. [PMID: 36711480 PMCID: PMC9881958 DOI: 10.1101/2023.01.07.523110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cells secrete numerous bioactive molecules essential for the function of healthy organisms. However, there are no scalable methods to link individual cell secretions to their transcriptional state. By developing and using secretion encoded single-cell sequencing (SEC-seq), which exploits hydrogel nanovials to capture individual cells and their secretions, we simultaneously measured the secretion of vascular endothelial growth factor A (VEGF-A) and the transcriptome for thousands of individual mesenchymal stromal cells (MSCs). We found that VEGF-A secretion is heterogeneous across the cell population and lowly correlated with the VEGFA transcript level. While there is a modest population-wide increase in VEGF-A secretion by hypoxic induction, highest VEGF-A secretion across normoxic and hypoxic culture conditions occurs in a subpopulation of MSCs characterized by a unique gene expression signature. Taken together, SEC-seq enables the identification of specific genes involved in the control of secretory states, which may be exploited for developing means to modulate cellular secretion for disease treatment.
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Affiliation(s)
- Shreya Udani
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Doyeon Koo
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Sevana Baghdasarian
- Department of Chemical and Biomolecular Engineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Brian Cheng
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Simran Kang
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Citradewi Soemardy
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | | | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California - Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, University of California - Los Angeles, Los Angeles, CA 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
- Partillion Bioscience, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California - Los Angeles, Los Angeles, CA 90095, USA
- Department of Mechanical and Aerospace Engineering, University of California - Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute (CNSI), University of California - Los Angeles, Los Angeles, CA 90095, USA
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188
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Karri K, Waxman DJ. TCDD dysregulation of lncRNA expression, liver zonation and intercellular communication across the liver lobule. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.523119. [PMID: 36711947 PMCID: PMC9881922 DOI: 10.1101/2023.01.07.523119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The persistent environmental aryl hydrocarbon receptor agonist and hepatotoxin TCDD (2,3,7,8-tetrachlorodibenzo- p -dioxin) induces hepatic lipid accumulation (steatosis), inflammation (steatohepatitis) and fibrosis. Thousands of liver-expressed, nuclear-localized lncRNAs with regulatory potential have been identified; however, their roles in TCDD-induced hepatoxicity and liver disease are unknown. We analyzed single nucleus (sn)RNA-seq data from control and chronic TCDD-exposed mouse liver to determine liver cell-type specificity, zonation and differential expression profiles for thousands of IncRNAs. TCDD dysregulated >4,000 of these lncRNAs in one or more liver cell types, including 684 lncRNAs specifically dysregulated in liver non-parenchymal cells. Trajectory inference analysis revealed major disruption by TCDD of hepatocyte zonation, affecting >800 genes, including 121 IncRNAs, with strong enrichment for lipid metabolism genes. TCDD also dysregulated expression of >200 transcription factors, including 19 Nuclear Receptors, most notably in hepatocytes and Kupffer cells. TCDD-induced changes in cellâ€"cell communication patterns included marked decreases in EGF signaling from hepatocytes to non-parenchymal cells and increases in extracellular matrix-receptor interactions central to liver fibrosis. Gene regulatory networks constructed from the snRNA-seq data identified TCDD-exposed liver network-essential lncRNA regulators linked to functions such as fatty acid metabolic process, peroxisome and xenobiotic metabolic. Networks were validated by the striking enrichments that predicted regulatory IncRNAs showed for specific biological pathways. These findings highlight the power of snRNA-seq to discover functional roles for many xenobiotic-responsive lncRNAs in both hepatocytes and liver non-parenchymal cells and to elucidate novel aspects of foreign chemical-induced hepatotoxicity and liver disease, including dysregulation of intercellular communication within the liver lobule.
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Körbelin J, Klein J, Matuszcak C, Runge J, Harbaum L, Klose H, Hennigs JK. Transcription factors in the pathogenesis of pulmonary arterial hypertension-Current knowledge and therapeutic potential. Front Cardiovasc Med 2023; 9:1036096. [PMID: 36684555 PMCID: PMC9853303 DOI: 10.3389/fcvm.2022.1036096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/21/2022] [Indexed: 01/09/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a disease characterized by elevated pulmonary vascular resistance and pulmonary artery pressure. Mortality remains high in severe cases despite significant advances in management and pharmacotherapy. Since currently approved PAH therapies are unable to significantly reverse pathological vessel remodeling, novel disease-modifying, targeted therapeutics are needed. Pathogenetically, PAH is characterized by vessel wall cell dysfunction with consecutive remodeling of the pulmonary vasculature and the right heart. Transcription factors (TFs) regulate the process of transcribing DNA into RNA and, in the pulmonary circulation, control the response of pulmonary vascular cells to macro- and microenvironmental stimuli. Often, TFs form complex protein interaction networks with other TFs or co-factors to allow for fine-tuning of gene expression. Therefore, identification of the underlying molecular mechanisms of TF (dys-)function is essential to develop tailored modulation strategies in PAH. This current review provides a compendium-style overview of TFs and TF complexes associated with PAH pathogenesis and highlights their potential as targets for vasculoregenerative or reverse remodeling therapies.
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Affiliation(s)
- Jakob Körbelin
- ENDomics Lab, Department of Medicine, Center of Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,*Correspondence: Jakob Körbelin,
| | - Julius Klein
- ENDomics Lab, Department of Medicine, Center of Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,Division of Pneumology and Center for Pulmonary Arterial Hypertension Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christiane Matuszcak
- ENDomics Lab, Department of Medicine, Center of Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,Division of Pneumology and Center for Pulmonary Arterial Hypertension Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Runge
- ENDomics Lab, Department of Medicine, Center of Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,Division of Pneumology and Center for Pulmonary Arterial Hypertension Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lars Harbaum
- Division of Pneumology and Center for Pulmonary Arterial Hypertension Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hans Klose
- Division of Pneumology and Center for Pulmonary Arterial Hypertension Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan K. Hennigs
- ENDomics Lab, Department of Medicine, Center of Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,Division of Pneumology and Center for Pulmonary Arterial Hypertension Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,Jan K. Hennigs,
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A 3-Gene Random Forest Model to Diagnose Non-obstructive Azoospermia Based on Transcription Factor-Related Henes. Reprod Sci 2023; 30:233-246. [PMID: 35715550 DOI: 10.1007/s43032-022-01008-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/10/2022] [Indexed: 01/11/2023]
Abstract
Non-obstructive azoospermia (NOA) is one of the most severe forms of male infertility, but its diagnosis biomarkers with high sensitivity and specificity are largely unknown. Transcription factors (TFs) play essential roles in many pathological processes in different diseases. Herein, we aimed to identify the TFs showing high diagnosis ability for NOA through machine learning algorithms. The transcriptome data of the testicular tissue from 11 control and 47 NOA subjects were set as the training dataset; meanwhile, 1665 TFs were retrieved from the HumanTFDB. Through the feature extraction methods, including genomic difference analysis, Lasso, Boruta, SVM-RFE, and logistic regression, ETV2, TBX2, and ZNF689 were ultimately screened and then were included in the random forest (RF) diagnosis model. The RF model displayed high predictive power in the training (F-measure = 1) and two external validation (n = 31, F-measure = 0.902; n = 20, F-measure = 0.941) cohorts. The seminal plasma and testicular biopsy samples of 20 control and 20 NOA patients were collected from the local hospital, and the expression levels of ETV2, TBX2, and ZNF689 were measured via RT-qPCR and immunohistochemistry. The RF model could also distinguish the NOA samples in the local cohort (F-measure = 0.741). Single-cell RNA sequencing analysis, which was based on the 432 testicular cell samples from an NOA patient, showed that ETV2, TBX2, and ZNF689 were all significantly associated with spermatogenesis. In all, a 3-TF random forest diagnosis model was successfully established, providing novel insights into the latent mechanisms of NOA.
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191
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Chow CN, Yang CW, Chang WC. Databases and prospects of dynamic gene regulation in eukaryotes: A mini review. Comput Struct Biotechnol J 2023; 21:2147-2159. [PMID: 37013004 PMCID: PMC10066511 DOI: 10.1016/j.csbj.2023.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/18/2023] [Accepted: 03/19/2023] [Indexed: 04/05/2023] Open
Abstract
In eukaryotes, dynamic regulation enables DNA polymerases to catalyze a variety of RNA products in spatial and temporal patterns. Dynamic gene expression is regulated by transcription factors (TFs) and epigenetics (DNA methylation and histone modification). The applications of biochemical technology and high-throughput sequencing enhance the understanding of mechanisms of these regulations and affected genomic regions. To provide a searchable platform for retrieving such metadata, numerous databases have been developed based on the integration of genome-wide maps (e.g., ChIP-seq, whole-genome bisulfite sequencing, RNA-seq, ATAC-seq, DNase-seq, and MNase-seq data) and functionally genomic annotation. In this mini review, we summarize the main functions of TF-related databases and outline the prevalent approaches used in inferring epigenetic regulations, their associated genes, and functions. We review the literature on crosstalk between TF and epigenetic regulation and the properties of non-coding RNA regulation, which are challenging topics that promise to pave the way for advances in database development.
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192
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Lesha E, George H, Zaki MM, Smith CJ, Khoshakhlagh P, Ng AHM. A Survey of Transcription Factors in Cell Fate Control. Methods Mol Biol 2023; 2594:133-141. [PMID: 36264493 DOI: 10.1007/978-1-0716-2815-7_10] [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] [Indexed: 06/16/2023]
Abstract
Transcription factors (TFs) play a cardinal role in the development and maintenance of human physiology by acting as mediators of gene expression and cell state control. Recent advancements have broadened our knowledge on the potency of TFs in governing cell physiology and have deepened our understanding of the mechanisms through which they exert this control. The ability of TFs to program cell fates has gathered significant interest in recent decades, and high-throughput technologies now allow for the systematic discovery of forward programming factors to convert pluripotent stem cells into numerous differentiated cell types. The next generation of these technologies has the potential to improve our understanding and control of cell fates and states and provide advanced therapeutic modalities to address many medical conditions.
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Affiliation(s)
- Emal Lesha
- GC Therapeutics Inc., Cambridge, MA, USA
- Department of Neurosurgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Haydy George
- GC Therapeutics Inc., Cambridge, MA, USA
- School of Medicine, St. George's University, West Indies, Grenada
| | - Mark M Zaki
- GC Therapeutics Inc., Cambridge, MA, USA
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA
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193
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Identification of key adipogenic transcription factors for the pork belly parameters via the association weight matrix. Meat Sci 2023; 195:109015. [DOI: 10.1016/j.meatsci.2022.109015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
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194
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Wang Y, Wu Y, Yang S, Chen Y. Comparison of Plasma Exosome Proteomes Between Obese and Non-Obese Patients with Type 2 Diabetes Mellitus. Diabetes Metab Syndr Obes 2023; 16:629-642. [PMID: 36915396 PMCID: PMC10008006 DOI: 10.2147/dmso.s396239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
PURPOSE Obesity is considered a promoter of type 2 diabetes mellitus (T2DM). However, the underlying mechanism remains unclear. This study aimed to identify plasma exosome differentially expressed proteins (DEPs) that are potentially involved in the development of obesity-related T2DM. METHODS Exosomes were isolated from the plasma of obese and non-obese T2DM patients (n = 10 for each group). A label-free quantitative mass spectrometry analysis was applied to identify plasma exosome DEPs in obese patients compared with non-obese patients, followed by bioinformatics analysis including GO annotation, KEGG analysis, subcellular localization prediction, transcription factor analysis, and protein-protein interaction (PPI) prediction. RESULTS We identified 2 significantly upregulated proteins (C9 and PON1) and 5 significantly downregulated proteins (HPX, A1BG, CFHR1, ANG, and CALM) in obese patients compared with those in non-obese patients. KEGG analysis demonstrated that the insulin signaling pathway was one of the pathways that significantly correlated with the DEPs. The DEPs were primarily localized in the extracellular space (5 out of 7). HMG-box and NF-Y beta might regulate the transcription of the DEPs. C9, PON1, HPX, and CFHR1 were present in the PPI network. CONCLUSION The plasma exosome DEPs are potentially responsible for the development of obesity-related T2DM possibly through the insulin signaling pathway and the interaction with other proteins. Our study may guide future research direction toward the pathogenesis of obesity-related T2DM.
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Affiliation(s)
- Yanjun Wang
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, People’s Republic of China
| | - You Wu
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, People’s Republic of China
| | - Shuangzhu Yang
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, People’s Republic of China
| | - Yan Chen
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, People’s Republic of China
- Correspondence: Yan Chen, Department of Endocrinology, The Second Hospital of Jilin University, Changchun, 130041, People’s Republic of China, Tel +86 0431-81136436, Email
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195
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Dong F, Ping P, Ma Y, Chen XF. Application of single-cell RNA sequencing on human testicular samples: a comprehensive review. Int J Biol Sci 2023; 19:2167-2197. [PMID: 37151874 PMCID: PMC10158017 DOI: 10.7150/ijbs.82191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/25/2023] [Indexed: 05/09/2023] Open
Abstract
So far there has been no comprehensive review using systematic literature search strategies to show the application of single-cell RNA sequencing (scRNA-seq) in the human testis of the whole life cycle (from embryos to aging males). Here, we summarized the application of scRNA-seq analyses on various human testicular biological samples. A systematic search was conducted in PubMed and Gene Expression Omnibus (GEO), focusing on English researches published after 2009. Articles related to GEO data-series were also retrieved in PubMed or BioRxiv. 81 full-length studies were finally included in the review. ScRNA-seq has been widely used on different human testicular samples with various library strategies, and new cell subtypes such as State 0 spermatogonial stem cells (SSC) and stage_a/b/c Sertoli cells (SC) were identified. For the development of normal testes, scRNA-seq-based evidence showed dynamic transcriptional changes of both germ cells and somatic cells from embryos to adults. And dysregulated metabolic signaling or hedgehog signaling were revealed by scRNA-seq in aged SC or Leydig cells (LC), respectively. For infertile males, scRNA-seq studies revealed profound changes of testes, such as the increased proportion of immature SC/LC of Klinefelter syndrome, the somatic immaturity and altered germline autophagy of patients with non-obstructive azoospermia, and the repressed differentiation of SSC in trans-females receiving testosterone inhibition therapy. Besides, the re-analyzing of public scRNA-seq data made further discoveries such as the potential vulnerability of testicular SARS-CoV-2 infection, and both evolutionary conservatism and divergence among species. ScRNA-seq analyses would unveil mechanisms of testes' development and changes so as to help developing novel treatments for male infertility.
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Affiliation(s)
- Fan Dong
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Ping Ping
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Yi Ma
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
- ✉ Corresponding author: Dr. Xiang-Feng Chen. Address: 845 Lingshan Road, Shanghai, P. R. China, 200135. Telephone: +86-21-20284500; Fax: +86-21-58394262; Email address: . Dr. Yi Ma. Address: 845 Lingshan Road, Shanghai, P. R. China, 200135. Telephone: +86-21-20284500; Fax: +86-21-58394262; Email address:
| | - Xiang-Feng Chen
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
- Shanghai Human Sperm Bank, Shanghai, China
- ✉ Corresponding author: Dr. Xiang-Feng Chen. Address: 845 Lingshan Road, Shanghai, P. R. China, 200135. Telephone: +86-21-20284500; Fax: +86-21-58394262; Email address: . Dr. Yi Ma. Address: 845 Lingshan Road, Shanghai, P. R. China, 200135. Telephone: +86-21-20284500; Fax: +86-21-58394262; Email address:
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Kulka M, Wagner A, Cho JY, Alam SB, Santos JR, Jovel J, Karamchand L, Marcet-Palacios M. Agarose/crystalline nanocellulose (CNC) composites promote bone marrow-derived mast cell integrity, degranulation and receptor expression but inhibit production of de novo synthesized mediators. Front Bioeng Biotechnol 2023; 11:1160460. [PMID: 37113661 PMCID: PMC10126518 DOI: 10.3389/fbioe.2023.1160460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Introduction: Mast cells are highly granulated tissue-resident leukocytes that require a three-dimensional matrix to differentiate and mediate immune responses. However, almost all cultured mast cells rely on two-dimensional suspension or adherent cell culture systems, which do not adequately reflect the complex structure that these cells require for optimal function. Methods: Crystalline nanocellulose (CNC), consisting of rod-like crystals 4-15 nm in diameter and 0.2-1 µm in length, were dispersed in an agarose matrix (12.5% w/v), and bone marrow derived mouse mast cells (BMMC) were cultured on the agarose/CNC composite. BMMC were activated with the calcium ionophore A23187 or immunoglobulin E (IgE) and antigen (Ag) to crosslink high affinity IgE receptors (FcεRI). Results: BMMC cultured on a CNC/agarose matrix remained viable and metabolically active as measured by reduction of sodium 3'-[1-[(phenylamino)-carbony]-3,4-tetrazolium]-bis(4-methoxy-6-nitro) benzene-sulfonic acid hydrate (XTT), and the cells maintained their membrane integrity as analyzed by measuring the release of lactate dehydrogenase (LDH) and propidium iodide exclusion by flow cytometry. Culture on CNC/agarose matrix had no effect on BMMC degranulation in response to IgE/Ag or A23187. However, culture of BMMC on a CNC/agarose matrix inhibited A23187-and IgE/Ag-activated production of tumor necrosis factor (TNF) and other mediators such as IL-1β, IL-4, IL-6, IL-13, MCP-1/CCL2, MMP-9 and RANTES by as much as 95%. RNAseq analysis indicated that BMMC expressed a unique and balanced transcriptome when cultured on CNC/agarose. Discussion: These data demonstrate that culture of BMMCs on a CNC/agarose matrix promotes cell integrity, maintains expression of surface biomarkers such as FcεRI and KIT and preserves the ability of BMMC to release pre-stored mediators in response to IgE/Ag and A23187. However, culture of BMMC on CNC/agarose matrix inhibits BMMC production of de novo synthesized mediators, suggesting that CNC may be altering specific phenotypic characteristics of these cells that are associated with late phase inflammatory responses.
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Affiliation(s)
- Marianna Kulka
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology 6-020 Katz Group Centre, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Marianna Kulka,
| | - Ashley Wagner
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
| | - Jae-Young Cho
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
| | - Syed Benazir Alam
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
| | | | - Juan Jovel
- The Metabolomics Innovation Centre (TMIC), 7-12 Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada
| | - Leshern Karamchand
- Nanotechnology Research Centre, National Research Council Canada, Edmonton, AB, Canada
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Lyu S, Zhai Y, Zhu X, Shi Q, Chen F, Zhang G, Zhang Z, Wang E. Bta-miR-200b promotes endometrial epithelial cell apoptosis by targeting MYB in cattle. Theriogenology 2023; 195:77-84. [DOI: 10.1016/j.theriogenology.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
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Mao L, Zhu Y, Yan J, Zhang L, Zhu S, An L, Meng Q, Zhang Z, Wang X. Full-length transcriptome sequencing analysis reveals differential skin color regulation in snakeheads fish Channa argus. AQUACULTURE AND FISHERIES 2023. [DOI: 10.1016/j.aaf.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Zhu S, Lin D, Ye Z, Chen X, Jiang W, Xu H, Quan S, Zheng B. GOLPH3 modulates expression and alternative splicing of transcription factors associated with endometrial decidualization in human endometrial stromal cells. PeerJ 2023; 11:e15048. [PMID: 36967990 PMCID: PMC10035422 DOI: 10.7717/peerj.15048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Endometrial decidualization is a decidual tissue formed by the proliferation and re-differentiation of endometrial stroma stimulated by decidualization inducing factors. It is very important for the proper maintenance of pregnancy. Previous studies speculated that Golgi phosphoprotein 3 (GOLPH3) may have a regulatory role in the process of endometrial decidualization, while the specific molecular mechanisms of GOLPH3 is unclear. In this part, GOLPH3 was silenced in human endometrial stromal cells (hESCs), and the transcriptome data (RNA-seq) by GOLPH3 knockdown (siGOLPH3) was obtained by high-throughput sequencing technology so as to analyze the potential targets of GOLPH3 at expression and alternative splicing levels in hESCs. Through bioinformatics analysis, we found that siGOLPH3 can significantly affect the overall transcriptional level of hESCs. A total of 6,025 differentially expressed genes (DEGs) and 4,131 differentially alternative splicing events (DASEs) were identified. Through functional cluster analysis of these DEGs and genes where differential alternative splicing events are located, it is found that they are enriched in the PI3K/Akt signaling pathway, RNA splicing and processing, transcription factors and other pathways related to endometrial decidualization and important biological processes, indicating the important biological function of GOLPH3. At the same time, we focused on the analysis of the transcription factors regulated by GOLPH3, including gene expression regulation and the regulation of variable splicing. We found that GOLPH3can regulate the expression of transcription factors such as LD1, FOSL2, GATA2, CSDC2 and CREB3L1. At the same time, it affects the variable splicing mode of FOXM1 and TCF3. The function of these transcription factors is directly related to decidualization of endometrium. Therefore, we infer that GOLPH3 may participate in endometrial de membrane by regulating expression and alternative splicing levels of transcription factors. We further identified the role of GOLPH3 in the transcriptional mechanism. At the same time, it also expands the function mode of GOLPH3 protein molecule, and provides a theoretical basis for downstream targeted drug research and development and clinical application.
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Affiliation(s)
- Suqin Zhu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Dianliang Lin
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Zhoujie Ye
- Medical Research Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaojing Chen
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenwen Jiang
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Huiling Xu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Song Quan
- Department of Obstetrics and Gynecology, Southern Medical University, Guangzhou, Guangdong, China
| | - Beihong Zheng
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
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Porto-Neto LR, Alexandre PA, Hudson NJ, Bertram J, McWilliam SM, Tan AWL, Fortes MRS, McGowan MR, Hayes BJ, Reverter A. Multi-breed genomic predictions and functional variants for fertility of tropical bulls. PLoS One 2023; 18:e0279398. [PMID: 36701372 PMCID: PMC9879470 DOI: 10.1371/journal.pone.0279398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/07/2022] [Indexed: 01/27/2023] Open
Abstract
Worldwide, most beef breeding herds are naturally mated. As such, the ability to identify and select fertile bulls is critically important for both productivity and genetic improvement. Here, we collected ten fertility-related phenotypes for 6,063 bulls from six tropically adapted breeds. Phenotypes were comprised of four bull conformation traits and six traits directly related to the quality of the bull's semen. We also generated high-density DNA genotypes for all the animals. In total, 680,758 single nucleotide polymorphism (SNP) genotypes were analyzed. The genomic correlation of the same trait observed in different breeds was positive for scrotal circumference and sheath score on most breed comparisons, but close to zero for the percentage of normal sperm, suggesting a divergent genetic background for this trait. We confirmed the importance of a breed being present in the reference population to the generation of accurate genomic estimated breeding values (GEBV) in an across-breed validation scenario. Average GEBV accuracies varied from 0.19 to 0.44 when the breed was not included in the reference population. The range improved to 0.28 to 0.59 when the breed was in the reference population. Variants associated with the gene HDAC4, six genes from the spermatogenesis-associated (SPATA) family of proteins, and 29 transcription factors were identified as candidate genes. Collectively these results enable very early in-life selection for bull fertility traits, supporting genetic improvement strategies currently taking place within tropical beef production systems. This study also improves our understanding of the molecular basis of male fertility in mammals.
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Affiliation(s)
| | | | - Nicholas J. Hudson
- School of Animal Studies, The University of Queensland, Gatton, QLD, Australia
| | - John Bertram
- Agriculture Consultant, Livestock Management and Breeding, Toowoomba, QLD, Australia
| | | | - Andre W. L. Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Michael R. McGowan
- School of Veterinary Sciences, The University of Queensland, Gatton, QLD, Australia
| | - Ben J. Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
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