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Yang F, Zhao Z, Zhang D, Xiong Y, Dong X, Wang Y, Yang M, Pan T, Liu C, Liu K, Lin Y, Liu Y, Tu Q, Dang Y, Xia M, Mi D, Zhou W, Xu Z. Single-cell multi-omics analysis of lineage development and spatial organization in the human fetal cerebellum. Cell Discov 2024; 10:22. [PMID: 38409116 PMCID: PMC10897198 DOI: 10.1038/s41421-024-00656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Abstract
Human cerebellum encompasses numerous neurons, exhibiting a distinct developmental paradigm from cerebrum. Here we conducted scRNA-seq, scATAC-seq and spatial transcriptomic analyses of fetal samples from gestational week (GW) 13 to 18 to explore the emergence of cellular diversity and developmental programs in the developing human cerebellum. We identified transitory granule cell progenitors that are conserved across species. Special patterns in both granule cells and Purkinje cells were dissected multidimensionally. Species-specific gene expression patterns of cerebellar lobes were characterized and we found that PARM1 exhibited inconsistent distribution in human and mouse granule cells. A novel cluster of potential neuroepithelium at the rhombic lip was identified. We also resolved various subtypes of Purkinje cells and unipolar brush cells and revealed gene regulatory networks controlling their diversification. Therefore, our study offers a valuable multi-omics landscape of human fetal cerebellum and advances our understanding of development and spatial organization of human cerebellum.
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Affiliation(s)
- Fuqiang Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ziqi Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Dan Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yu Xiong
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yuchen Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Min Yang
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | | | - Chuanyu Liu
- BGI-Beijing, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Kaiyi Liu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Yifeng Lin
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Yongjie Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qiang Tu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yashan Dang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, China
| | - Mingyang Xia
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.
| | - Da Mi
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Wenhao Zhou
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
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Liu B, Li C, Feng C, Wang H, Zhang H, Tu C, He S, Li Z. Integrative profiling analysis reveals prognostic significance, molecular characteristics, and tumor immunity of angiogenesis-related genes in soft tissue sarcoma. Front Immunol 2023; 14:1178436. [PMID: 37377953 PMCID: PMC10291125 DOI: 10.3389/fimmu.2023.1178436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Background Soft tissue sarcoma (STS) is a class of malignant tumors originating from mesenchymal stroma with a poor prognosis. Accumulating evidence has proved that angiogenesis is an essential hallmark of tumors. Nevertheless, there is a paucity of comprehensive research exploring the association of angiogenesis-related genes (ARGs) with STS. Methods The ARGs were extracted from previous literature, and the differentially expressed ARGs were screened for subsequent analysis. Next, the least absolute shrinkage and selection operator (LASSO) and Cox regression analyses were conducted to establish the angiogenesis-related signature (ARSig). The predictive performance of the novel ARSig was confirmed using internal and external validation, subgroup survival, and independent analysis. Additionally, the association of the ARSig with the tumor immune microenvironment, tumor mutational burden (TMB), and therapeutic response in STS were further investigated. Notably, we finally conducted in vitro experiments to verify the findings from the bioinformatics analysis. Results A novel ARSig is successfully constructed and validated. The STS with a lower ARSig risk score in the training cohort has an improved prognosis. Also, consistent results were observed in the internal and external cohorts. The receiver operating characteristic (ROC) curve, subgroup survival, and independent analysis further indicate that the novel ARSig is a promising independent prognostic predictor for STS. Furthermore, it is proved that the novel ARSig is relevant to the immune landscape, TMB, immunotherapy, and chemotherapy sensitivity in STS. Encouragingly, we also validate that the signature ARGs are significantly dysregulated in STS, and ARDB2 and SRPK1 are closely connected with the malignant progress of STS cells. Conclusion In sum, we construct a novel ARSig for STS, which could act as a promising prognostic factor for STS and give a strategy for future clinical decisions, immune landscape, and personalized treatment of STS.
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Affiliation(s)
- Binfeng Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chenbei Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chengyao Feng
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hua Wang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haixia Zhang
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shasha He
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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He Z, Chang T, Chen Y, Wang H, Dai L, Zeng H. PARM1 Drives Smooth Muscle Cell Proliferation in Pulmonary Arterial Hypertension via AKT/FOXO3A Axis. Int J Mol Sci 2023; 24:ijms24076385. [PMID: 37047359 PMCID: PMC10094810 DOI: 10.3390/ijms24076385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/25/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a group of severe, progressive, and debilitating diseases with limited therapeutic options. This study aimed to explore novel therapeutic targets in PAH through bioinformatics and experiments. Weighted gene co-expression network analysis (WGCNA) was applied to detect gene modules related to PAH, based on the GSE15197, GSE113439, and GSE117261. GSE53408 was applied as validation set. Subsequently, the validated most differentially regulated hub gene was selected for further ex vivo and in vitro assays. PARM1, TSHZ2, and CCDC80 were analyzed as potential intervention targets for PAH. Consistently with the bioinformatic results, our ex vivo and in vitro data indicated that PARM1 expression increased significantly in the lung tissue and/or pulmonary artery of the MCT-induced PAH rats and hypoxia-induced PAH mice in comparison with the respective controls. Besides, a similar expression pattern of PARM1 was found in the hypoxia- and PDGF--treated isolated rat primary pulmonary arterial smooth muscle cells (PASMCs). In addition, hypoxia/PDGF--induced PARM1 protein expression could promote the elevation of phosphorylation of AKT, phosphorylation of FOXO3A and PCNA, and finally the proliferation of PASMCs in vitro, whereas PARM1 siRNA treatment inhibited it. Mechanistically, PARM1 promoted PAH via AKT/FOXO3A/PCNA signaling pathway-induced PASMC proliferation.
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Ding L, Sishc BJ, Polsdofer E, Yordy JS, Facoetti A, Ciocca M, Saha D, Pompos A, Davis AJ, Story MD. Evaluation of the Response of HNSCC Cell Lines to γ-Rays and 12C Ions: Can Radioresistant Tumors Be Identified and Selected for 12C Ion Radiotherapy? Front Oncol 2022; 12:812961. [PMID: 35280731 PMCID: PMC8914432 DOI: 10.3389/fonc.2022.812961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Thirty percent of patients will experience locoregional recurrence for which median survival is less than 1 year. Factors contributing to treatment failure include inherent resistance to X-rays and chemotherapy, hypoxia, epithelial to mesenchymal transition, and immune suppression. The unique properties of 12C radiotherapy including enhanced cell killing, a decreased oxygen enhancement ratio, generation of complex DNA damage, and the potential to overcome immune suppression make its application well suited to the treatment of HNSCC. We examined the 12C radioresponse of five HNSCC cell lines, whose surviving fraction at 3.5 Gy ranged from average to resistant when compared with a larger panel of 38 cell lines to determine if 12C irradiation can overcome X-ray radioresistance and to identify biomarkers predictive of 12C radioresponse. Cells were irradiated with 12C using a SOBP with an average LET of 80 keV/μm (CNAO: Pavia, Italy). RBE values varied depending upon endpoint used. A 37 gene signature was able to place cells in their respective radiosensitivity cohort with an accuracy of 86%. Radioresistant cells were characterized by an enrichment of genes associated with radioresistance and survival mechanisms including but not limited to G2/M Checkpoint MTORC1, HIF1α, and PI3K/AKT/MTOR signaling. These data were used in conjunction with an in silico-based modeling approach to evaluate tumor control probability after 12C irradiation that compared clinically used treatment schedules with fixed RBE values vs. the RBEs determined for each cell line. Based on the above analysis, we present the framework of a strategy to utilize biological markers to predict which HNSCC patients would benefit the most from 12C radiotherapy.
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Affiliation(s)
- Lianghao Ding
- Univeristy of Texas Southwestern Medical Center, Department of Radiation Oncology, Dallas, TX, United States
| | - Brock J Sishc
- Univeristy of Texas Southwestern Medical Center, Department of Radiation Oncology, Dallas, TX, United States
| | - Elizabeth Polsdofer
- Univeristy of Texas Southwestern Medical Center, Department of Radiation Oncology, Dallas, TX, United States
| | - John S Yordy
- Univeristy of Texas Southwestern Medical Center, Department of Radiation Oncology, Dallas, TX, United States
| | - Angelica Facoetti
- Medical Physics Unit & Research Department, Foundazione Centro Nazionale di Adroterapia Oncologica (CNAO), Pavia, Italy
| | - Mario Ciocca
- Medical Physics Unit & Research Department, Foundazione Centro Nazionale di Adroterapia Oncologica (CNAO), Pavia, Italy
| | - Debabrata Saha
- Univeristy of Texas Southwestern Medical Center, Department of Radiation Oncology, Dallas, TX, United States
| | - Arnold Pompos
- Univeristy of Texas Southwestern Medical Center, Department of Radiation Oncology, Dallas, TX, United States
| | - Anthony J Davis
- Univeristy of Texas Southwestern Medical Center, Department of Radiation Oncology, Dallas, TX, United States
| | - Michael D Story
- Univeristy of Texas Southwestern Medical Center, Department of Radiation Oncology, Dallas, TX, United States
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Feng H, Wang L, Liu J, Wang S. The bioinformatic approach identifies PARM1 as a new potential prognostic factor in osteosarcoma. Front Oncol 2022; 12:1059547. [PMID: 36950314 PMCID: PMC10025378 DOI: 10.3389/fonc.2022.1059547] [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: 10/01/2022] [Accepted: 12/23/2022] [Indexed: 03/08/2023] Open
Abstract
Objective To explore the key factors affecting the prognosis of osteosarcoma patients. Methods Based on the GEO dataset and differential expression analysis of normal and osteosarcoma tissues, the gene modules related to the prognosis of osteosarcoma patients were screened by WGCNA, and intersecting genes were taken with differential genes, and the risk prognosis model of osteosarcoma patients was constructed by LASSO regression analysis of intersecting genes, and the prognosis-related factors of osteosarcoma patients were obtained by survival analysis, followed by target for validation, and finally, the expression of prognostic factors and their effects on osteosarcoma cell migration were verified by cellular assays and lentiviral transfection experiments. Results The prognosis-related gene module of osteosarcoma patients were intersected with differential genes to obtain a total of 9 common genes. PARM1 was found to be a prognostic factor in osteosarcoma patients by LASSO regression analysis, followed by cellular assays to verify that PARM1 was lowly expressed in osteosarcoma cells and that overexpression of PARM1 in osteosarcoma cells inhibited cell migration. Pan-cancer analysis showed that PARM1 was lowly expressed in most cancers and that low expression of PARM1 predicted poor prognosis for patients. Conclusion The data from this study suggest that PARM1 is closely associated with the prognosis of osteosarcoma patients, and PARM1 may serve as a novel potential prognostic target for osteosarcoma, providing a heartfelt direction for the prevention and treatment of osteosarcoma.
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Affiliation(s)
- Haijun Feng
- Department of Orthopedics, Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Liping Wang
- Department of Orthopedics, Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Jie Liu
- Department of Neurosurgery, Liaocheng Second People’s Hospital, Liaocheng, Shandong, China
| | - Shengbao Wang
- Second Hospital of Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Shengbao Wang,
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Glavan D, Gheorman V, Gresita A, Hermann DM, Udristoiu I, Popa-Wagner A. Identification of transcriptome alterations in the prefrontal cortex, hippocampus, amygdala and hippocampus of suicide victims. Sci Rep 2021; 11:18853. [PMID: 34552157 PMCID: PMC8458545 DOI: 10.1038/s41598-021-98210-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/30/2021] [Indexed: 11/09/2022] Open
Abstract
Suicide is one of the leading causes of death globally for all ages, and as such presents a very serious problem for clinicians worldwide. However, the underlying neurobiological pathology remains to a large extent unknown. In order to address this gap, we have carried out a genome-wide investigation of the gene expression in the amygdala, hippocampus, prefrontal cortex and thalamus in post-mortem brain samples obtained from 20 suicide completers and 7 control subjects. By KEGG enrichment analysis indicated we identified novel clusters of downregulated pathways involved in antigen neutralization and autoimmune thyroid disease (amygdala, thalamus), decreased axonal plasticity in the hippocampus. Two upregulated pathways were involved in neuronal death in the hippocampus and olfactory transduction in the thalamus and the prefrontal cortex. Autoimmune thyroid disease pathway was downregulated only in females. Metabolic pathways involved in Notch signaling amino acid metabolism and unsaturated lipid synthesis were thalamus-specific. Suicide-associated changes in the expression of several genes and pseudogenes that point to various functional mechanisms possibly implicated in the pathology of suicide. Two genes (SNORA13 and RNU4-2) involved in RNA processing were common to all brain regions analyzed. Most of the identified gene expression changes were related to region-specific dysregulated manifestation of genetic and epigenetic mechanisms underlying neurodevelopmental disorders (SNORD114-10, SUSd1), motivation, addiction and motor disorders (CHRNA6), long-term depression (RAB3B), stress response, major depression and schizophrenia (GFAP), signal transduction at the neurovascular unit (NEXN) and inhibitory neurotransmission in spatial learning, neural plasticity (CALB2; CLIC6, ENPP1). Some of the differentially expressed genes were brain specific non-coding RNAs involved in the regulation of translation (SNORA13). One, (PARM1) is a potential oncogene and prognostic biomarker for colorectal cancer with no known function in the brain. Disturbed gene expression involved in antigen neutralization, autoimmunity, neural plasticity, stress response, signal transduction at the neurovascular unit, dysregulated nuclear RNA processing and translation and epigenetic imprinting signatures is associated with suicide and point to regulatory non-coding RNAs as potential targets of new drugs development.
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Affiliation(s)
- Daniela Glavan
- Department of Psychiatry, University of Medicine and Pharmacy, Craiova, Romania
| | - Victor Gheorman
- Department of Psychiatry, University of Medicine and Pharmacy, Craiova, Romania
| | - Andrei Gresita
- Griffith University Menzies Health Institute of Queensland, Gold Coast Campus, Brisbane, QLD, 4000, Australia
| | - Dirk M Hermann
- Chair of Vascular Neurology, Dementia and Ageing Research, Department of Neurology, University Hospital Essen, University of Duisburg, Essen, Germany
| | - Ion Udristoiu
- Department of Psychiatry, University of Medicine and Pharmacy, Craiova, Romania.
| | - Aurel Popa-Wagner
- Griffith University Menzies Health Institute of Queensland, Gold Coast Campus, Brisbane, QLD, 4000, Australia. .,Chair of Vascular Neurology, Dementia and Ageing Research, Department of Neurology, University Hospital Essen, University of Duisburg, Essen, Germany.
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Marzec J, Ross-Adams H, Pirrò S, Wang J, Zhu Y, Mao X, Gadaleta E, Ahmad AS, North BV, Kammerer-Jacquet SF, Stankiewicz E, Kudahetti SC, Beltran L, Ren G, Berney DM, Lu YJ, Chelala C. The Transcriptomic Landscape of Prostate Cancer Development and Progression: An Integrative Analysis. Cancers (Basel) 2021; 13:345. [PMID: 33477882 PMCID: PMC7838904 DOI: 10.3390/cancers13020345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing of primary tumors is now standard for transcriptomic studies, but microarray-based data still constitute the majority of available information on other clinically valuable samples, including archive material. Using prostate cancer (PC) as a model, we developed a robust analytical framework to integrate data across different technical platforms and disease subtypes to connect distinct disease stages and reveal potentially relevant genes not identifiable from single studies alone. We reconstructed the molecular profile of PC to yield the first comprehensive insight into its development, by tracking changes in mRNA levels from normal prostate to high-grade prostatic intraepithelial neoplasia, and metastatic disease. A total of nine previously unreported stage-specific candidate genes with prognostic significance were also found. Here, we integrate gene expression data from disparate sample types, disease stages and technical platforms into one coherent whole, to give a global view of the expression changes associated with the development and progression of PC from normal tissue through to metastatic disease. Summary and individual data are available online at the Prostate Integrative Expression Database (PIXdb), a user-friendly interface designed for clinicians and laboratory researchers to facilitate translational research.
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Affiliation(s)
- Jacek Marzec
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Helen Ross-Adams
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Stefano Pirrò
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Jun Wang
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Yanan Zhu
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Xueying Mao
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Emanuela Gadaleta
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Amar S. Ahmad
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK; (A.S.A.); (B.V.N.)
| | - Bernard V. North
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK; (A.S.A.); (B.V.N.)
| | - Solène-Florence Kammerer-Jacquet
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Elzbieta Stankiewicz
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Sakunthala C. Kudahetti
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Luis Beltran
- Department of Pathology, Barts Health NHS, London E1 F1R, UK;
| | - Guoping Ren
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou 310058, China;
| | - Daniel M. Berney
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
- Department of Pathology, Barts Health NHS, London E1 F1R, UK;
| | - Yong-Jie Lu
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Claude Chelala
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University London, London EC1M 6BQ, UK
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Yuan P, Ling L, Fan Q, Gao X, Sun T, Miao J, Yuan X, Liu J, Liu B. A four-gene signature associated with clinical features can better predict prognosis in prostate cancer. Cancer Med 2020; 9:8202-8215. [PMID: 32924329 PMCID: PMC7643642 DOI: 10.1002/cam4.3453] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 01/09/2023] Open
Abstract
Prostate cancer (PCa) is one of the most deadly urinary tumors in men globally, and the 5‐year over survival is poor due to metastasis of tumor. It is significant to explore potential biomarkers for early diagnosis and personalized therapy of PCa. In the present study, we performed an integrated analysis based on multiple microarrays in the Gene Expression Omnibus (GEO) dataset and obtained differentially expressed genes (DEGs) between 510 PCa and 259 benign issues. The weighted correlation network analysis indicated that prognostic profile was the most relevant to DEGs. Then, univariate and multivariate COX regression analyses were conducted and four prognostic genes were obtained to establish a four‐gene prognostic model. And the predictive effect and expression profiles of the four genes were well validated in another GEO dataset, The Cancer Genome Atlas and the Human Protein Atlas datasets. Furthermore, combination of four‐gene model and clinical features was analyzed systematically to guide the prognosis of patients with PCa to a largest extent. In summary, our findings indicate that four genes had important prognostic significance in PCa and combination of four‐gene model and clinical features could achieve a better prediction to guide the prognosis of patients with PCa.
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Affiliation(s)
- Penghui Yuan
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Le Ling
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Fan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xintao Gao
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Taotao Sun
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianping Miao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jihong Liu
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Riedel R, Addo R, Ferreira-Gomes M, Heinz GA, Heinrich F, Kummer J, Greiff V, Schulz D, Klaeden C, Cornelis R, Menzel U, Kröger S, Stervbo U, Köhler R, Haftmann C, Kühnel S, Lehmann K, Maschmeyer P, McGrath M, Naundorf S, Hahne S, Sercan-Alp Ö, Siracusa F, Stefanowski J, Weber M, Westendorf K, Zimmermann J, Hauser AE, Reddy ST, Durek P, Chang HD, Mashreghi MF, Radbruch A. Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow. Nat Commun 2020; 11:2570. [PMID: 32444631 PMCID: PMC7244721 DOI: 10.1038/s41467-020-16464-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/03/2020] [Indexed: 12/15/2022] Open
Abstract
At present, it is not clear how memory B lymphocytes are maintained over time, and whether only as circulating cells or also residing in particular tissues. Here we describe distinct populations of isotype-switched memory B lymphocytes (Bsm) of murine spleen and bone marrow, identified according to individual transcriptional signature and B cell receptor repertoire. A population of marginal zone-like cells is located exclusively in the spleen, while a population of quiescent Bsm is found only in the bone marrow. Three further resident populations, present in spleen and bone marrow, represent transitional and follicular B cells and B1 cells, respectively. A population representing 10-20% of spleen and bone marrow memory B cells is the only one qualifying as circulating. In the bone marrow, all cells individually dock onto VCAM1+ stromal cells and, reminiscent of resident memory T and plasma cells, are void of activation, proliferation and mobility.
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Affiliation(s)
- René Riedel
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Evolutionary Genomics Group, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Richard Addo
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Marta Ferreira-Gomes
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Gitta Anne Heinz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Frederik Heinrich
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Jannis Kummer
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Victor Greiff
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH Zürich), CH-4058, Basel, Switzerland
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, 0424, Oslo, Norway
| | - Daniel Schulz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Cora Klaeden
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Rebecca Cornelis
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Ulrike Menzel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH Zürich), CH-4058, Basel, Switzerland
| | - Stefan Kröger
- Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin, 12489, Berlin, Germany
- Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353, Berlin, Germany
| | - Ulrik Stervbo
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Ralf Köhler
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Claudia Haftmann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Institute of Experimental Immunology, Universitätsspital Zürich, 8057, Zürich, Switzerland
| | - Silvia Kühnel
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Katrin Lehmann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Patrick Maschmeyer
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Mairi McGrath
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Sandra Naundorf
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Stefanie Hahne
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Özen Sercan-Alp
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- R&D, TA Immunology & Inflammation Research, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926, Frankfurt am Main, Germany
| | - Francesco Siracusa
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Jonathan Stefanowski
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Melanie Weber
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Kerstin Westendorf
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Jakob Zimmermann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
| | - Anja E Hauser
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH Zürich), CH-4058, Basel, Switzerland
| | - Pawel Durek
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Hyun-Dong Chang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Mir-Farzin Mashreghi
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany.
- BCRT/DRFZ Single-Cell Laboratory for Advanced Cellular Therapies - Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany.
| | - Andreas Radbruch
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany.
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10
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Laing EE, Möller-Levet CS, Dijk DJ, Archer SN. Identifying and validating blood mRNA biomarkers for acute and chronic insufficient sleep in humans: a machine learning approach. Sleep 2019; 42:5106128. [PMID: 30247731 PMCID: PMC6335875 DOI: 10.1093/sleep/zsy186] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Indexed: 12/18/2022] Open
Abstract
Acute and chronic insufficient sleep are associated with adverse health outcomes and risk of accidents. There is therefore a need for biomarkers to monitor sleep debt status. None are currently available. We applied elastic net and ridge regression to transcriptome samples collected in 36 healthy young adults during acute total sleep deprivation and following 1 week of either chronic insufficient (<6 hr) or sufficient sleep (~8.6 hr) to identify panels of mRNA biomarkers of sleep debt status. The size of identified panels ranged from 9 to 74 biomarkers. Panel performance, assessed by leave-one-subject-out cross-validation and independent validation, varied between sleep debt conditions. Using between-subject assessments based on one blood sample, the accuracy of classifying "acute sleep loss" was 92%, but only 57% for classifying "chronic sleep insufficiency." A reasonable accuracy for classifying "chronic sleep insufficiency" could only be achieved by a within-subject comparison of blood samples. Biomarkers for sleep debt status showed little overlap with previously identified biomarkers for circadian phase. Biomarkers for acute and chronic sleep loss also showed little overlap but were associated with common functions related to the cellular stress response, such as heat shock protein activity, the unfolded protein response, protein ubiquitination and endoplasmic reticulum-associated protein degradation, and apoptosis. This characteristic response of whole blood to sleep loss can further aid our understanding of how sleep insufficiencies negatively affect health. Further development of these novel biomarkers for research and clinical practice requires validation in other protocols and age groups.
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Affiliation(s)
- Emma E Laing
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Carla S Möller-Levet
- Bioinformatics Core Facility, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Derk-Jan Dijk
- Surrey Sleep Research Centre, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Simon N Archer
- Surrey Sleep Research Centre, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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11
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Liu YR, Hu Y, Zeng Y, Li ZX, Zhang HB, Deng JL, Wang G. Neurexophilin and PC-esterase domain family member 4 (NXPE4) and prostate androgen-regulated mucin-like protein 1 (PARM1) as prognostic biomarkers for colorectal cancer. J Cell Biochem 2019; 120:18041-18052. [PMID: 31297877 DOI: 10.1002/jcb.29107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/18/2019] [Indexed: 12/24/2022]
Abstract
Owing to the high morbidity and mortality, novel biomarkers in the occurrence and development of colorectal cancer (CRC) are needed nowadays. In this study, the CRC-related datasets were downloaded from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. After screening the differentially expressed genes (DEGs) in R software, a total of 238 upregulated and 199 downregulated DEGs were revealed simultaneously. Then the Kaplan-Meier survival analysis and Cox regression analysis were used to reveal the prognostic function of these DEGs. Neurexophilin and PC-esterase domain family member 4 (NXPE4) and prostate androgen-regulated mucin-like protein 1 (PARM1) were two outstanding independent overall survival (OS) and relapse-free survival (RFS) prognostic genes of CRC in TCGA database. We next verified the expression of NXPE4 and PARM1 messenger RNA (mRNA) levels were significantly lower in CRC tumor tissue than in the adjacent noncancerous tissue in our clinical samples, and NXPE4 mRNA expression level was related to the tumor location and tumor size, while PARM1 was related to tumor location, lymph nodes metastasis, and tumor size. This study demonstrated that NXPE4 and PARM1 might be two potential novel prognostic biomarkers for CRC.
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Affiliation(s)
- Ya-Rui Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Yang Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Ying Zeng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Zhi-Xing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Hai-Bo Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Jun-Li Deng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Guo Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, P. R. China
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, P.R. China
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12
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Zolini AM, Negrón-Pérez VM, Hansen PJ. Importance of prostate androgen-regulated mucin-like protein 1 in development of the bovine blastocyst. BMC DEVELOPMENTAL BIOLOGY 2019; 19:15. [PMID: 31277570 PMCID: PMC6612098 DOI: 10.1186/s12861-019-0195-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/19/2019] [Indexed: 12/22/2022]
Abstract
Background Prostate androgen-regulated mucin-like protein 1 (PARM1) is a pro-proliferative and anti-apoptotic glycoprotein involved in the endoplasmic reticulum (ER) stress response. A single nucleotide polymorphism in the coding region of PARM1 has been associated with competence of bovine embryos to develop to the blastocyst stage. Here we tested the importance of PARM1 for development by evaluating consequences of reducing PARM1 mRNA abundance on embryonic development and differentiation, gene expression and resistance to ER stress. Results Knockdown of PARM1 using an anti-PARM1 GapmeR did not affect competence of embryos to develop into blastocysts but decreased the number of trophectoderm (TE) cells in the blastocyst and tended to increase the number of cells in the blastocyst inner cell mass (ICM). Treatment of embryos with anti-PARM1 GapmeR affected expression of 4 and 3 of 90 genes evaluated at the compact-morula and blastocyst stage of development at days 5.5 and 7.5 after fertilization, respectively. In morulae, treatment increased expression of DAB2, INADL, and STAT3 and decreased expression of CCR2. At the blastocyst stage, knockdown of PARM1 increased expression of PECAM and TEAD4 and decreased expression of CCR7. The potential role of PARM1 in ER stress response was determined by evaluating effects of knockdown of PARM1 on development of embryos after exposure to heat shock or tunicamycin and on expression of ATF6, DDIT3 and EIF2AK3 at the compact morula and blastocyst stages. Both heat shock and tunicamycin reduced the percent of embryos becoming a blastocyst but response was unaffected by PARM1 knockdown. Similarly, there was no effect of knockdown on steady-state amounts of ATF6, DDIT3 or EIF2AK3. Conclusion PARM1 participates in formation of TE and ICM cells in early embryonic development but there is no evidence for the role of PARM1 in the ER stress response. Electronic supplementary material The online version of this article (10.1186/s12861-019-0195-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adriana M Zolini
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, PO Box 110910, Gainesville, Florida, 32611-0910, USA.,Present address: Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Verónica M Negrón-Pérez
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, PO Box 110910, Gainesville, Florida, 32611-0910, USA.,Present address: Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Peter J Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, PO Box 110910, Gainesville, Florida, 32611-0910, USA.
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13
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Carlow DA, Tra MC, Ziltener HJ. A cell-extrinsic ligand acquired by activated T cells in lymph node can bridge L-selectin and P-selectin. PLoS One 2018; 13:e0205685. [PMID: 30379850 PMCID: PMC6209203 DOI: 10.1371/journal.pone.0205685] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 09/29/2018] [Indexed: 01/25/2023] Open
Abstract
P-selectin expressed on activated endothelia and platelets supports recruitment of leukocytes expressing P-selectin ligand to sites of inflammation. While monitoring P-selectin ligand expression on activated CD8+ T cells in murine adoptive transfer models, we observed two distinct ligands on responding donor cells, the canonical cell-intrinsic P-selectin ligand PSGL-1 and a second undocumented P-selectin ligand we provisionally named PSL2. PSL2 is unusual among selectin ligands in that it is cell-extrinsic, loaded onto L-selectin expressed by activated T cells but not L-selectin on resting naïve CD8+ T cells. PSL2 display is highest on activated T cells responding in peripheral lymph nodes and low on T cells responding in spleen suggesting that the original source of PSL2 is high endothelial venules, cells known to produce L-selectin ligands. PSL2 is a ligand for both P-selectin and L-selectin and can physically bridge the two selectins. The L-selectin/PSL2 complex can mediate P-selectin-dependent adherence of activated T cells to immobilized P-selectin or to activated platelets, either independently or cooperatively with PSGL-1. PSL2's capacity to bridge between L-selectin on activated T cells and P-selectin reveals an undocumented and unanticipated activity of cell-extrinsic selectin ligands in mediating selectin-selectin connectivity. The timing and circumstances of PSL2 detection on T cells, together with its capacity to support adherence to P-selectin-bearing substrates, are consistent with P-selectin engagement of both PSGL1 and the L-selectin/PSL2 complex during T cell recruitment. Engagement of PSGL-1 and L-selectin/PSL2 would likely deliver distinct signals known to be relevant in this process.
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Affiliation(s)
- Douglas A. Carlow
- The Biomedical Research Centre, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| | - Michelle C. Tra
- The Biomedical Research Centre, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hermann J. Ziltener
- The Biomedical Research Centre, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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14
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Lee M, Kiefel H, LaJevic MD, Macauley MS, Kawashima H, O'Hara E, Pan J, Paulson JC, Butcher EC. Transcriptional programs of lymphoid tissue capillary and high endothelium reveal control mechanisms for lymphocyte homing. Nat Immunol 2014; 15:982-95. [PMID: 25173345 PMCID: PMC4222088 DOI: 10.1038/ni.2983] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/31/2014] [Indexed: 12/13/2022]
Abstract
Lymphocytes are recruited from blood by high-endothelial venules (HEVs). We performed transcriptomic analyses and identified molecular signatures that distinguish HEVs from capillary endothelium and that define tissue-specific HEV specialization. Capillaries expressed gene programs for vascular development. HEV-expressed genes showed enrichment for genes encoding molecules involved in immunological defense and lymphocyte migration. We identify capillary and HEV markers and candidate mechanisms for regulated recruitment of lymphocytes, including a lymph node HEV-selective transmembrane mucin; transcriptional control of functionally specialized carbohydrate ligands for lymphocyte L-selectin; HEV expression of molecules for transendothelial migration; and metabolic programs for lipid mediators of lymphocyte motility and chemotaxis. We also elucidate a carbohydrate-recognition pathway that targets B cells to intestinal lymphoid tissues, defining CD22 as a lectin-homing receptor for mucosal HEVs.
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Affiliation(s)
- Mike Lee
- Laboratory of Immunology and Vascular Biology, Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Helena Kiefel
- Laboratory of Immunology and Vascular Biology, Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Melissa D LaJevic
- Laboratory of Immunology and Vascular Biology, Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew S Macauley
- Departments of Cell and Molecular Biology, Immunology and Microbial Science, and Chemical Physiology, The Scripps Research Institute, La Jolla, California USA
| | | | - Edward O'Hara
- Palo Alto Veterans Institute for Research, Palo Alto, California, USA
| | - Junliang Pan
- Palo Alto Veterans Institute for Research, Palo Alto, California, USA
| | - James C Paulson
- Departments of Cell and Molecular Biology, Immunology and Microbial Science, and Chemical Physiology, The Scripps Research Institute, La Jolla, California USA
| | - Eugene C Butcher
- 1] Laboratory of Immunology and Vascular Biology, Department of Pathology, Stanford University School of Medicine, Stanford, California, USA. [2] Palo Alto Veterans Institute for Research, Palo Alto, California, USA. [3] The Center for Molecular Biology and Medicine, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
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15
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Identification of GPM6A and GPM6B as potential new human lymphoid leukemia-associated oncogenes. Cell Oncol (Dordr) 2014; 37:179-91. [PMID: 24916915 DOI: 10.1007/s13402-014-0171-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Previously, we found that the Graffi murine leukemia virus (MuLV) is able to induce a wide spectrum of hematologic malignancies in vivo. Using high-density oligonucleotide microarrays, we established the gene expression profiles of several of these malignancies, thereby specifically focusing on genes deregulated in the lymphoid sub-types. We observed over-expression of a variety of genes, including Arntl2, Bfsp2, Gfra2, Gpm6a, Gpm6b, Nln, Fbln1, Bmp7, Etv5 and Celsr1 and, in addition, provided evidence that Fmn2 and Parm-1 may act as novel oncogenes. In the present study, we assessed the expression patterns of eight selected human homologs of these genes in primary human B-cell malignancies, and explored the putative oncogenic potential of GPM6A and GPM6B. METHODS The gene expression levels of the selected human homologs were tested in human B-cell malignancies by semi-quantitative RT-PCR. The protein expression profiles of human GPM6A and GPM6B were analyzed by Western blotting. The localization and the effect of GPM6A and GPM6B on the cytoskeleton were determined using confocal and indirect immunofluorescence microscopy. To confirm the oncogenic potential of GPM6A and GPM6B, classical colony formation assays in soft agar and focus forming assays were used. The effects of these proteins on the cell cycle were assessed by flow cytometry analysis. RESULTS Using semi-quantitative RT-PCR, we found that most of the primary B-cell malignancies assessed showed altered expression patterns of the genes tested, including GPM6A and GPM6B. Using confocal microscopy, we found that the GPM6A protein (isoform 3) exhibits a punctate cytoplasmic localization and that the GPM6B protein (isoform 4) exhibits a peri-nuclear and punctate cytoplasmic localization. Interestingly, we found that exogenous over-expression of both proteins in NIH/3T3 cells alters the actin and microtubule networks and induces the formation of long filopodia-like protrusions. Additionally, we found that these over-expressing NIH/3T3 cells exhibit anchorage-independent growth and enhanced proliferation rates. Cellular transformation (i.e., loss of contact inhibition) was, however, only observed after exogenous over-expression of GPM6B. CONCLUSIONS Our results indicate that several human homologs of the genes found to be deregulated in Graffi MuLV experimental mouse models may serve as candidate biomarkers for human B-cell malignancies. In addition, we found that GPM6A and GPM6B may act as novel oncogenes in the development of these malignancies.
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