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Zhang L, Zheng D, Xu L, Wang H, Zhang S, Shi J, Jin N. A novel variant in GAS2 is associated with autosomal dominant nonsyndromic hearing impairment in a Chinese family. Hum Genomics 2024; 18:73. [PMID: 38956677 PMCID: PMC11218307 DOI: 10.1186/s40246-024-00628-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
Knockout of GAS2 (growth arrest-specific protein 2), causes disorganization and destabilization of microtubule bundles in supporting cells of the cochlear duct, leading to hearing loss in vivo. However, the molecular mechanism through which GAS2 variant results in hearing loss remains unknown. By Whole-exome sequencing, we identified a novel heterozygous splicing variant in GAS2 (c.616-2 A > G) as the only candidate mutation segregating with late-onset and progressive nonsyndromic hearing loss (NSHL) in a large dominant family. This splicing mutation causes an intron retention and produces a C-terminal truncated protein (named GAS2mu). Mechanistically, the degradation of GAS2mu via the ubiquitin-proteasome pathway is enhanced, and cells expressing GAS2mu exhibit disorganized microtubule bundles. Additionally, GAS2mu further promotes apoptosis by increasing the Bcl-xS/Bcl-xL ratio instead of through the p53-dependent pathway as wild-type GAS2 does, indicating that GAS2mu acts as a toxic molecule to exacerbate apoptosis. Our findings demonstrate that this novel variant of GAS2 promotes its own protein degradation, microtubule disorganization and cellular apoptosis, leading to hearing loss in carriers. This study expands the spectrum of GAS2 variants and elucidates the underlying pathogenic mechanisms, providing a foundation for future investigations of new therapeutic strategies to prevent GAS2-associated progressive hearing loss.
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Affiliation(s)
- Luping Zhang
- Institute for Translational Neuroscience, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Nantong University, Affiliated Hospital of Nantong University, Nantong University, Nantong, Jiangsu, 226001, China
| | - Danya Zheng
- Institute for Translational Neuroscience, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Nantong University, Affiliated Hospital of Nantong University, Nantong University, Nantong, Jiangsu, 226001, China
| | - Lian Xu
- Institute for Translational Neuroscience, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Nantong University, Affiliated Hospital of Nantong University, Nantong University, Nantong, Jiangsu, 226001, China
| | - Han Wang
- Institute for Translational Neuroscience, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Nantong University, Affiliated Hospital of Nantong University, Nantong University, Nantong, Jiangsu, 226001, China
| | - Shuqiang Zhang
- Institute for Translational Neuroscience, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Nantong University, Affiliated Hospital of Nantong University, Nantong University, Nantong, Jiangsu, 226001, China
| | - Jianhua Shi
- Institute for Translational Neuroscience, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Nantong University, Affiliated Hospital of Nantong University, Nantong University, Nantong, Jiangsu, 226001, China
| | - Nana Jin
- Institute for Translational Neuroscience, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Nantong University, Affiliated Hospital of Nantong University, Nantong University, Nantong, Jiangsu, 226001, China.
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2
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Xu YY, Bai RX, Zhang QR, Zhang S, Zhang JH, Du SY. A comprehensive analysis of GAS2 family members identifies that GAS2L1 is a novel biomarker and promotes the proliferation of hepatocellular carcinoma. Discov Oncol 2024; 15:220. [PMID: 38858234 PMCID: PMC11164853 DOI: 10.1007/s12672-024-01083-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a common primary liver cancer with a high incidence and mortality. Members of the growth-arresting-specific 2 (GAS2) family are involved in various biological processes in human malignancies. To date, there is only a limited amount of information available about the expression profile and clinical importance of GAS2 family in HCC. In this study, we found that GAS2L1 and GAS2L3 were distinctly upregulated in HCC specimens compared to non-tumor specimens. Pan-cancer assays indicated that GAS2L1 and GAS2L3 were highly expressed in most cancers. The Pearson's correlation revealed that the expressions of GAS2, GAS2L1 and GAS2L2 were negatively associated with methylation levels. Survival assays indicated that GAS2L1 and GAS2L3 were independent prognostic factors for HCC patients. Immune cell infiltration analysis revealed that GAS2, GAS2L1 and GAS2L3 were associated with several immune cells. Finally, we confirmed that GAS2L1 was highly expressed in HCC cells and its knockdown suppressed the proliferation of HCC cells. Taken together, our findings suggested the expression patterns and prognostic values of GAS2 members in HCC, providing insights for further study of the GAS2 family as sensitive diagnostic and prognostic markers for HCC.
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Affiliation(s)
- Ying-Ying Xu
- Department of Gastroenterology, China-Japan Friendship Hospital, No. 2, Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Ru-Xue Bai
- Department of Gastroenterology, China-Japan Friendship Hospital, No. 2, Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Qing-Rui Zhang
- Department of Gastroenterology, China-Japan Friendship Hospital, No. 2, Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Shuang Zhang
- Department of Gastroenterology, China-Japan Friendship Hospital, No. 2, Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
- Graduate School, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China
| | - Jun-Hai Zhang
- Department of Gastroenterology, China-Japan Friendship Hospital, No. 2, Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Shi-Yu Du
- Department of Gastroenterology, China-Japan Friendship Hospital, No. 2, Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China.
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3
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Nahalka J. 1-L Transcription of SARS-CoV-2 Spike Protein S1 Subunit. Int J Mol Sci 2024; 25:4440. [PMID: 38674024 PMCID: PMC11049929 DOI: 10.3390/ijms25084440] [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: 02/29/2024] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The COVID-19 pandemic prompted rapid research on SARS-CoV-2 pathogenicity. Consequently, new data can be used to advance the molecular understanding of SARS-CoV-2 infection. The present bioinformatics study discusses the "spikeopathy" at the molecular level and focuses on the possible post-transcriptional regulation of the SARS-CoV-2 spike protein S1 subunit in the host cell/tissue. A theoretical protein-RNA recognition code was used to check the compatibility of the SARS-CoV-2 spike protein S1 subunit with mRNAs in the human transcriptome (1-L transcription). The principle for this method is elucidated on the defined RNA binding protein GEMIN5 (gem nuclear organelle-associated protein 5) and RNU2-1 (U2 spliceosomal RNA). Using the method described here, it was shown that 45% of the genes/proteins identified by 1-L transcription of the SARS-CoV-2 spike protein S1 subunit are directly linked to COVID-19, 39% are indirectly linked to COVID-19, and 16% cannot currently be associated with COVID-19. The identified genes/proteins are associated with stroke, diabetes, and cardiac injury.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska Cesta 9, SK-84538 Bratislava, Slovakia;
- Institute of Chemistry, Centre of Excellence for White-Green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovakia
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4
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Ni L, Yu Q, You R, Chen C, Peng B. Development of the RF-GSEA Method for Identifying Disulfidptosis-Related Genes and Application in Hepatocellular Carcinoma. Curr Issues Mol Biol 2023; 45:9450-9470. [PMID: 38132439 PMCID: PMC10741996 DOI: 10.3390/cimb45120593] [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: 10/17/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Disulfidptosis is a newly discovered cellular programmed cell death mode. Presently, a considerable number of genes related to disulfidptosis remain undiscovered, and its significance in hepatocellular carcinoma remains unrevealed. We have developed a powerful analytical method called RF-GSEA for identifying potential genes associated with disulfidptosis. This method draws inspiration from gene regulation networks and graph theory, and it is implemented through a combination of random forest regression model and Gene Set Enrichment Analysis. Subsequently, to validate the practical application value of this method, we applied it to hepatocellular carcinoma. Based on the RF-GSEA method, we developed a disulfidptosis-related signature. Lastly, we looked into how the disulfidptosis-related signature is connected to HCC prognosis, the tumor microenvironment, the effectiveness of immunotherapy, and the sensitivity of chemotherapy drugs. The RF-GSEA method identified a total of 220 disulfidptosis-related genes, from which 7 were selected to construct the disulfidptosis-related signature. The high-disulfidptosis-related score group had a worse prognosis compared to the low-disulfidptosis-related score group and showed lower infiltration levels of immune-promoting cells. The high-disulfidptosis-related score group had a higher likelihood of benefiting from immunotherapy compared to the low-disulfidptosis-related score group. The RF-GSEA method is a powerful tool for identifying disulfidptosis-related genes. The disulfidptosis-related signature effectively predicts HCC prognosis, immunotherapy response, and drug sensitivity.
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Affiliation(s)
| | | | | | | | - Bin Peng
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
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5
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Transcriptome RNA Sequencing Reveals That Circular RNAs Are Abundantly Expressed in Embryonic Breast Muscle of Duck. Vet Sci 2023; 10:vetsci10020075. [PMID: 36851380 PMCID: PMC10004440 DOI: 10.3390/vetsci10020075] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Circular RNAs are widespread in various species and have important roles in myogenesis. However, the circular RNAs involved in breast muscle development in ducks have not yet been studied. Here, to identify circular RNAs during duck skeletal muscle development, three pectorales from Shan Ma ducks at E13 and E19, which represent undifferentiated and differentiated myoblasts, respectively, were collected and subjected to RNA sequencing. A total of 16,622 circular RNAs were identified, of which approximately 80% were exonic circular RNAs and 260 were markedly differentially expressed between E19 and E13. The parental genes of the differentially expressed circular RNAs were significantly enriched in muscle-related biological processes. Moreover, we found that the overexpression of circGAS2-2 promoted cell cycle progression and increased the proliferation viability of duck primary myoblasts; conversely, knockdown of circGAS2-2 retarded the cell cycle and reduced the proliferation viability of myoblasts. Taken together, our results demonstrate that circular RNAs are widespread and variously expressed during the development of duck skeletal muscle and that circGAS2-2 is involved in the regulation of myogenesis.
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6
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Chitre AS, Hebda-Bauer EK, Blandino P, Bimschleger H, Nguyen KM, Maras P, Li F, Ozel AB, Pan Y, Polesskaya O, Cheng R, Flagel SB, Watson SJ, Li J, Akil H, Palmer AA. Genome-wide association study in a rat model of temperament identifies multiple loci for exploratory locomotion and anxiety-like traits. Front Genet 2023; 13:1003074. [PMID: 36712851 PMCID: PMC9873817 DOI: 10.3389/fgene.2022.1003074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/20/2022] [Indexed: 01/12/2023] Open
Abstract
Common genetic factors likely contribute to multiple psychiatric diseases including mood and substance use disorders. Certain stable, heritable traits reflecting temperament, termed externalizing or internalizing, play a large role in modulating vulnerability to these disorders. To model these heritable tendencies, we selectively bred rats for high and low exploration in a novel environment [bred High Responders (bHR) vs. Low Responders (bLR)]. To identify genes underlying the response to selection, we phenotyped and genotyped 538 rats from an F2 cross between bHR and bLR. Several behavioral traits show high heritability, including the selection trait: exploratory locomotion (EL) in a novel environment. There were significant phenotypic and genetic correlations between tests that capture facets of EL and anxiety. There were also correlations with Pavlovian conditioned approach (PavCA) behavior despite the lower heritability of that trait. Ten significant and conditionally independent loci for six behavioral traits were identified. Five of the six traits reflect different facets of EL that were captured by three behavioral tests. Distance traveled measures from the open field and the elevated plus maze map onto different loci, thus may represent different aspects of novelty-induced locomotor activity. The sixth behavioral trait, number of fecal boli, is the only anxiety-related trait mapping to a significant locus on chromosome 18 within which the Pik3c3 gene is located. There were no significant loci for PavCA. We identified a missense variant in the Plekhf1 gene on the chromosome 1:95 Mb QTL and Fancf and Gas2 as potential candidate genes that may drive the chromosome 1:107 Mb QTL for EL traits. The identification of a locomotor activity-related QTL on chromosome 7 encompassing the Pkhd1l1 and Trhr genes is consistent with our previous finding of these genes being differentially expressed in the hippocampus of bHR vs. bLR rats. The strong heritability coupled with identification of several loci associated with exploratory locomotion and emotionality provide compelling support for this selectively bred rat model in discovering relatively large effect causal variants tied to elements of internalizing and externalizing behaviors inherent to psychiatric and substance use disorders.
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Affiliation(s)
- Apurva S. Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Elaine K. Hebda-Bauer
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Peter Blandino
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Hannah Bimschleger
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Khai-Minh Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Pamela Maras
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Fei Li
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - A. Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Shelly B. Flagel
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Stanley J. Watson
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Jun Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States,Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, United States,*Correspondence: Abraham A. Palmer,
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7
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García-Hidalgo MC, Peláez R, González J, Santisteve S, Benítez ID, Molinero M, Perez-Pons M, Belmonte T, Torres G, Moncusí-Moix A, Gort-Paniello C, Aguilà M, Seck F, Carmona P, Caballero J, Barberà C, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Lorente-Balanza JÁ, Menéndez R, Motos A, Peñuelas O, Riera J, Bermejo-Martin JF, Torres A, Barbé F, de Gonzalo-Calvo D, Larráyoz IM. Genome-wide transcriptional profiling of pulmonary functional sequelae in ARDS- secondary to SARS-CoV-2 infection. Biomed Pharmacother 2022; 154:113617. [PMID: 36058144 PMCID: PMC9424524 DOI: 10.1016/j.biopha.2022.113617] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/18/2022] [Accepted: 08/27/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Up to 80% of patients surviving acute respiratory distress syndrome (ARDS) secondary to SARS-CoV-2 infection present persistent anomalies in pulmonary function after hospital discharge. There is a limited understanding of the mechanistic pathways linked to post-acute pulmonary sequelae. AIM To identify the molecular underpinnings associated with severe lung diffusion involvement in survivors of SARS-CoV-2-induced ARDS. METHODS Survivors attended to a complete pulmonary evaluation 3 months after hospital discharge. RNA sequencing (RNA-seq) was performed using Illumina technology in whole-blood samples from 50 patients with moderate to severe diffusion impairment (DLCO<60%) and age- and sex-matched individuals with mild-normal lung function (DLCO≥60%). A transcriptomic signature for optimal classification was constructed using random forest. Transcriptomic data were analyzed for biological pathway enrichment, cellular deconvolution, cell/tissue-specific gene expression and candidate drugs. RESULTS RNA-seq identified 1357 differentially expressed transcripts. A model composed of 14 mRNAs allowed the optimal discrimination of survivors with severe diffusion impairment (AUC=0.979). Hallmarks of lung sequelae involved cell death signaling, cytoskeleton reorganization, cell growth and differentiation and the immune response. Resting natural killer (NK) cells were the most important immune cell subtype for the prediction of severe diffusion impairment. Components of the signature correlated with neutrophil, lymphocyte and monocyte counts. A variable expression profile of the transcripts was observed in lung cell subtypes and bodily tissues. One upregulated gene, TUBB4A, constitutes a target for FDA-approved drugs. CONCLUSIONS This work defines the transcriptional programme associated with post-acute pulmonary sequelae and provides novel insights for targeted interventions and biomarker development.
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Affiliation(s)
- María C. García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Rafael Peláez
- Biomarkers and Molecular Signaling Group, Neurodegenerative Diseases Area Center for Biomedical Research of La Rioja, CIBIR, Logroño, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Sally Santisteve
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Iván D. Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Thalía Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Maria Aguilà
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Faty Seck
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Paola Carmona
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Jesús Caballero
- Grup de Recerca Medicina Intensiva, Intensive Care Department Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Carme Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitari Sagrat Cor, Barcelona, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Servei de Pneumologia, Hospital Clinic; Universitat de Barcelona; IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Intensive Care Department, Vall d’Hebron Hospital Universitari. SODIR Research Group, Vall d’Hebron Institut de Recerca (VHIR), Spain
| | | | - Jose Ángel Lorente-Balanza
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario de Getafe, Madrid, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Servei de Pneumologia, Hospital Clinic; Universitat de Barcelona; IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Intensive Care Department, Vall d’Hebron Hospital Universitari. SODIR Research Group, Vall d’Hebron Institut de Recerca (VHIR), Spain
| | - Jesús F. Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Pneumology Department, Clinic Institute of Thorax (ICT), Hospital Clinic of Barcelona, Insitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), ICREA, University of Barcelona (UB), Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain,Correspondence to: Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Avda. Alcalde Rovira Roure 80, Lleida 25198, Spain
| | - Ignacio M. Larráyoz
- Biomarkers and Molecular Signaling Group, Neurodegenerative Diseases Area Center for Biomedical Research of La Rioja, CIBIR, Logroño, Spain,GRUPAC, Department of Nursing, University of La Rioja, Logroño, Spain,Correspondence to: Biomarkers and Molecular Signaling Group, Neurodegenerative Diseases Area, Center for Biomedical Research of La Rioja, CIBIR. C. Piqueras, 98, Logroño 26006, Spain
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8
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Ma W, Wan Y, Zhang J, Yao J, Wang Y, Lu J, Liu H, Huang X, Zhang X, Zhou H, He Y, Wu D, Wang J, Zhao Y. Growth arrest‐specific protein 2 (
GAS2
) interacts with
CXCR4
to promote T‐cell leukemogenesis partially via
c‐MYC. Mol Oncol 2022; 16:3720-3734. [PMID: 36054080 PMCID: PMC9580887 DOI: 10.1002/1878-0261.13306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/08/2022] [Accepted: 08/19/2022] [Indexed: 11/29/2022] Open
Abstract
Although growth arrest‐specific protein 2 (GAS2) promotes the growth of T‐cell acute lymphoblastic leukemia (T‐ALL) cells in culture, the effect of GAS2 on T‐cell leukemogenesis has not been studied, and the mechanism remains unclear. In the present study, xenograft studies showed that GAS2 silencing impaired T‐cell leukemogenesis and decreased leukemic cell infiltration. Mechanistically, GAS2 regulated the protein expression of C‐X‐C chemokine receptor type 4 (CXCR4) rather than its transcript expression. Immunoprecipitation revealed that GAS2 interacted with CXCR4, and confocal analysis showed that GAS2 was partially co‐expressed with CXCR4, which provided a strong molecular basis for GAS2 to regulate CXCR4 expression. Importantly, CXCR4 overexpression alleviated the inhibitory effect of GAS2 silencing on the growth and migration of T‐ALL cells. Moreover, GAS2 or CXCR4 silencing inhibited the expression of NOTCH1 and c‐MYC. Forced expression of c‐MYC rescued the growth suppression induced by GAS2 or CXCR4 silencing. Meanwhile, GAS2 deficiency, specifically in blood cells, had a mild effect on normal hematopoiesis, including T‐cell development, and GAS2 silencing did not affect the growth of normal human CD3+ or CD34+ cells. Overall, our data indicate that GAS2 promotes T‐cell leukemogenesis through its interaction with CXCR4 to activate NOTCH1/c‐MYC, whereas impaired GAS2 expression has a mild effect on normal hematopoiesis. Therefore, our study suggests that targeting the GAS2/CXCR4 axis is a potential therapeutic strategy for T‐ALL.
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Affiliation(s)
- Wenjuan Ma
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
| | - Yan Wan
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
| | - Jianxiang Zhang
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
| | - Jianan Yao
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
| | - Yifei Wang
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
| | - Jinchang Lu
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
| | - Hong Liu
- The First Affiliated Hospital of Soochow University Key Laboratory of Thrombosis and Hemostasis, Ministry of Health Suzhou 215006 China
- National Clinical Research Center for Hematologic Diseases Suzhou 215006 China
| | - Xiaorui Huang
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
| | - Xiuyan Zhang
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
| | - Haixia Zhou
- The First Affiliated Hospital of Soochow University Key Laboratory of Thrombosis and Hemostasis, Ministry of Health Suzhou 215006 China
- National Clinical Research Center for Hematologic Diseases Suzhou 215006 China
| | - Yulong He
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
- National Clinical Research Center for Hematologic Diseases Suzhou 215006 China
- Cam‐Su Genomic Resources Center Soochow University Suzhou 215123 China
- State Key Laboratory of Radiation Medicine and Radioprotection Soochow University Suzhou 215123 China
- MOE Engineering Center of Hematological Disease Soochow University Suzhou 215123 China
| | - Depei Wu
- The First Affiliated Hospital of Soochow University Key Laboratory of Thrombosis and Hemostasis, Ministry of Health Suzhou 215006 China
- National Clinical Research Center for Hematologic Diseases Suzhou 215006 China
- MOE Engineering Center of Hematological Disease Soochow University Suzhou 215123 China
| | - Jianrong Wang
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
- National Clinical Research Center for Hematologic Diseases Suzhou 215006 China
- State Key Laboratory of Radiation Medicine and Radioprotection Soochow University Suzhou 215123 China
- MOE Engineering Center of Hematological Disease Soochow University Suzhou 215123 China
- Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology Suzhou 215123 China
| | - Yun Zhao
- Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology Soochow University Suzhou 215123 China
- National Clinical Research Center for Hematologic Diseases Suzhou 215006 China
- MOE Engineering Center of Hematological Disease Soochow University Suzhou 215123 China
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9
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Lin A, Piehowski PD, Tsai CF, Makushok T, Yi L, Diaz U, Yan C, Summers D, Sood P, Smith RD, Liu T, Marshall WF. Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells. Curr Biol 2022; 32:2300-2308.e4. [PMID: 35447087 PMCID: PMC9133221 DOI: 10.1016/j.cub.2022.03.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/08/2022] [Accepted: 03/30/2022] [Indexed: 12/18/2022]
Abstract
Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell.1-4 Patterning within cells can extend down to the level of individual proteins and mRNA.5,6 But how much of the proteome is actually localized with respect to cell polarity axes? Proteomics combined with cellular fractionation7-11 has shown that most proteins localize to one or more organelles but does not tell us how many proteins have a polarized localization with respect to the large-scale polarity axes of the intact cell. Genome-wide localization studies in yeast12-15 found that only a few percent of proteins have a localized position relative to the cell polarity axis defined by sites of polarized cell growth. Here, we describe an approach for analyzing protein distribution within a cell with a visibly obvious global patterning-the giant ciliate Stentor coeruleus.16,17 Ciliates, including Stentor, have highly polarized cell shapes with visible surface patterning.1,18 A Stentor cell is roughly 2 mm long, allowing a "proteomic dissection" in which microsurgery is used to separate cellular fragments along the anterior-posterior axis, followed by comparative proteomic analysis. In our analysis, 25% of the proteome, including signaling proteins, centrin/SFI proteins, and GAS2 orthologs, shows a polarized location along the cell's anterior-posterior axis. We conclude that a large proportion of all proteins are polarized with respect to global cell polarity axes and that proteomic dissection provides a simple and effective approach for spatial proteomics.
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Affiliation(s)
- Athena Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Paul D Piehowski
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Chia-Feng Tsai
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lian Yi
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ulises Diaz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Connie Yan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diana Summers
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pranidhi Sood
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Richard D Smith
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tao Liu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, United States of America.
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10
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Sun D, Li X, Yin Z, Hou Z. The Full-Length Transcriptome Provides New Insights Into the Transcript Complexity of Abdominal Adipose and Subcutaneous Adipose in Pekin Ducks. Front Physiol 2021; 12:767739. [PMID: 34858212 PMCID: PMC8631521 DOI: 10.3389/fphys.2021.767739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/21/2021] [Indexed: 01/12/2023] Open
Abstract
Adipose tissues have a central role in organisms, and adipose content is a crucial economic trait of poultry. Pekin duck is an ideal model to study the mechanism of abdominal and subcutaneous adipose deposition for its high ability of adipose synthesis and deposition. Alternative splicing contributes to functional diversity in abdominal and subcutaneous adipose. However, there has been no systematic analysis of the dynamics of differential alternative splicing of abdominal and subcutaneous adipose in Pekin duck. In our study, the Pacific Biosciences (PacBio) Iso-Seq technology was applied to explore the transcriptional complexity of abdominal and subcutaneous adipose in Pekin ducks. In total, 143,931 and 111,337 full-length non-chimeric transcriptome sequences of abdominal and subcutaneous adipocytes were obtained from 41.78 GB raw data, respectively. These data led us to identify 19,212 long non-coding RNAs (lncRNAs) and 74,571 alternative splicing events. In addition, combined with the next-generation sequencing technology, we correlated the structure and function annotation with the differential expression profiles of abdominal and subcutaneous adipose transcripts. This study identified lots of novel alternative splicing events and major transcripts of transcription factors related to adipose synthesis. STAT3 was reported as a vital gene for adipogenesis, and we found that its major transcript is STAT3-1, which may play a considerable role in the process of adipose synthesis in Pekin duck. This study greatly increases our understanding of the gene models, genome annotations, genome structures, and the complexity and diversity of abdominal and subcutaneous adipose in Pekin duck. These data provide insights into the regulation of alternative splicing events, which form an essential part of transcript diversity during adipogenesis in poultry. The results of this study provide an invaluable resource for studying alternative splicing and tissue-specific expression.
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Affiliation(s)
- Dandan Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaoqin Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhongtao Yin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhuocheng Hou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
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11
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A Novel Toxoplasma Inner Membrane Complex Suture-Associated Protein Regulates Suture Protein Targeting and Colocalizes with Membrane Trafficking Machinery. mBio 2021; 12:e0245521. [PMID: 34634933 PMCID: PMC8510555 DOI: 10.1128/mbio.02455-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The cytoskeleton of Toxoplasma gondii is composed of the inner membrane complex (IMC) and an array of underlying microtubules that provide support at the periphery of the parasite. Specific subregions of the IMC carry out distinct roles in replication, motility, and host cell invasion. Building on our previous in vivo biotinylation (BioID) experiments of the IMC, we identified here a novel protein that localizes to discrete puncta that are embedded in the parasite’s cytoskeleton along the IMC sutures. Gene knockout analysis showed that loss of the protein results in defects in cytoskeletal suture protein targeting, cytoskeletal integrity, parasite morphology, and host cell invasion. We then used deletion analyses to identify a domain in the N terminus of the protein that is critical for both localization and function. Finally, we used the protein as bait for in vivo biotinylation, which identified several other proteins that colocalize in similar spot-like patterns. These putative interactors include several proteins that are implicated in membrane trafficking and are also associated with the cytoskeleton. Together, these data reveal an unexpected link between the IMC sutures and membrane trafficking elements of the parasite and suggest that the suture puncta are likely a portal for trafficking cargo across the IMC.
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12
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Gao X, Zhao C, Zhang N, Cui X, Ren Y, Su C, Wu S, Yao Z, Yang J. Genetic expression and mutational profile analysis in different pathologic stages of hepatocellular carcinoma patients. BMC Cancer 2021; 21:786. [PMID: 34238242 PMCID: PMC8268469 DOI: 10.1186/s12885-021-08442-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The clinical pathologic stages (stage I, II, III-IV) of hepatocellular carcinoma (HCC) are closely linked to the clinical prognosis of patients. This study aims at investigating the gene expression and mutational profile in different clinical pathologic stages of HCC. METHODS Based on the TCGA-LIHC cohort, we utilized a series of analytical approaches, such as statistical analysis, random forest, decision tree, principal component analysis (PCA), to identify the differential gene expression and mutational profiles. The expression patterns of several targeting genes were also verified by analyzing the Chinese HLivH060PG02 HCC cohort, several GEO datasets, HPA database, and diethylnitrosamine-induced HCC mouse model. RESULTS We identified a series of targeting genes with copy number variation, which is statistically associated with gene expression. Non-synonymous mutations mainly existed in some genes (e.g.,TTN, TP53, CTNNB1). Nevertheless, no association between gene mutation frequency and pathologic stage distribution was detected. The random forest and decision tree modeling analysis data showed a group of genes related to different HCC pathologic stages, including GAS2L3 and SEMA3F. Additionally, our PCA data indicated several genes associated with different pathologic stages, including SNRPA and SNRPD2. Compared with adjacent normal tissues, we observed a highly expressed level of GAS2L3, SNRPA, and SNRPD2 (P = 0.002) genes in HCC tissues of our HLivH060PG02 cohort. We also detected the high expression pattern of GAS2L3, SEMA3F, SNRPA, and SNRPD2 in the datasets of GSE102079, GSE76427, GSE64041, GSE121248, GSE84005, and the qPCR assay using diethylnitrosamine-induced HCC mouse model. Moreover, SEMA3F and SNRPD2 protein were highly stained in the HCC tissues of the HPA database. The high expression level of these four genes was associated with the poor survival prognosis of HCC cases. CONCLUSIONS Our study provides evidence regarding the gene expression and mutational profile in different clinical pathologic stages of TCGA HCC cases. Identifying four targeting genes, including GAS2L3, SNRPA, SNRPD2, and SEMA3F, offers insight into the molecular mechanisms associated with different prognoses of HCC.
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Affiliation(s)
- Xingjie Gao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China.
| | - Chunyan Zhao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Nan Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xiaoteng Cui
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
- Department of Neurosurgery Ministry of Education and Tianjin Municipal Government Laboratory of Neuro-Oncology Key Laboratory of Neurotrauma, Variation, and Regeneration , Tianjin Neurological Institute Tianjin Medical University General Hospital , Tianjin, China
| | - Yuanyuan Ren
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Chao Su
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Shaoyuan Wu
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Zhi Yao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China.
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13
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Novel computational analysis of large transcriptome datasets identifies sets of genes distinguishing chronic obstructive pulmonary disease from healthy lung samples. Sci Rep 2021; 11:10258. [PMID: 33986404 PMCID: PMC8119951 DOI: 10.1038/s41598-021-89762-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/23/2021] [Indexed: 11/08/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) kills over three million people worldwide every year. Despite its high global impact, the knowledge about the underlying molecular mechanisms is still limited. In this study, we aimed to extend the available knowledge by identifying a small set of COPD-associated genes. We analysed different publicly available gene expression datasets containing whole lung tissue (WLT) and airway epithelium (AE) samples from over 400 human subjects for differentially expressed genes (DEGs). We reduced the resulting sets of 436 and 663 DEGs using a novel computational approach that utilises a random depth-first search to identify genes which improve the distinction between COPD patients and controls along the first principle component of the data. Our method identified small sets of 10 and 15 genes in the WLT and AE, respectively. These sets of genes significantly (p < 10–20) distinguish COPD patients from controls with high fidelity. The final sets revealed novel genes like cysteine rich protein 1 (CRIP1) or secretoglobin family 3A member 2 (SCGB3A2) that may underlie fundamental molecular mechanisms of COPD in these tissues.
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14
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Zhao C, Zhang N, Cui X, Zhang X, Ren Y, Su C, He J, Zhang W, Sun X, Yang J, Gao X. Integrative analysis regarding the correlation between GAS2 family genes and human glioma prognosis. Cancer Med 2021; 10:2826-2839. [PMID: 33713047 PMCID: PMC8026934 DOI: 10.1002/cam4.3829] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Background Emerging oncogenes were reportedly linked to the complicated subtypes and pathogenesis of clinical gliomas. Herein, we first comprehensively explored the potential correlation between growth‐arrest‐specific two family genes (GAS2, GAS2L1, GAS2L2, GAS2L3) and gliomas by bioinformatics analysis and cellular experiments. Methods Based on the available datasets of TCGA (The Cancer Genome Atlas), CGGA (Chinese Glioma Genome Atlas), and Oncomine databases, we performed a series of analyses, such as gene expression, survival prognosis, DNA methylation, immune infiltration, and partner enrichment. We also utilized two glioma cell lines to conduct the colony formation and wound‐healing assay. Results GAS2L3 gene was highly expressed in glioma tissues compared to normal brain tissues (p < 0.05). We further observed the relationship between the high expressed GAS2L3 and poor clinical prognosis of brain low‐grade glioma (LGG) cases in our Cox proportional hazard model (hazard ratio [HR] = 0.1715, p < 0.001). Moreover, DNA hypomethylation status of GAS2L3 was correlated with the high expression of GAS2L3 in LGG tissues and the poor clinical prognosis of primary glioma cases (p < 0.05). We also found that the high expression of GAS2L3 was associated with the infiltration level of immune cells, especially the T cells (p < 0.0001). Functional enrichment analysis of GAS2L3‐correlated genes and interaction partners further indicated that GAS2L3 might take part in the occurrence of glioma by influencing a series of biological behaviors, such as cell division, cytoskeleton binding, and cell adhesion. Additionally, our cellular experiment data suggested that a highly expressed GAS2L3 gene contributes to the enhanced proliferation and migration of glioma cells. Conclusion This study first analyzed the potential role of GAS2 family genes, especially GAS2L3, in the clinical prognosis and possible functional mechanisms of glioma, which gives a novel insight into the relationship between GAS2L3 and LGG.
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Affiliation(s)
- Chunyan Zhao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Nan Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xiaoteng Cui
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China.,Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin, China
| | - Xinxin Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Yuanyuan Ren
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Chao Su
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Jinyan He
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Wei Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xiaoming Sun
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
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15
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Zhang N, Zhao C, Zhang X, Cui X, Zhao Y, Yang J, Gao X. Growth arrest-specific 2 protein family: Structure and function. Cell Prolif 2020; 54:e12934. [PMID: 33103301 PMCID: PMC7791176 DOI: 10.1111/cpr.12934] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022] Open
Abstract
Members of the growth arrest–specific 2 (GAS2) protein family consist of a putative actin‐binding (CH) domain and a microtubule‐binding (GAR) domain and are considered miniversions of spectraplakins. There are four members in the GAS2 family, viz. GAS2, GAS2L1, GAS2L2 and GAS2L3. Although GAS2 is defined as a family of growth arrest–specific proteins, the significant differences in the expression patterns, interaction characteristics and biological issues or diseases among the different GAS2 family members have not been systemically reviewed to date. Therefore, we summarized the available evidence on the structures and functions of GAS2 family members. This review facilitates a comprehensive molecular understanding of the involvement of the GAS2 family members in an array of biological processes, including cytoskeleton reorganization, cell cycle, apoptosis and cancer development.
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Affiliation(s)
- Nan Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Chunyan Zhao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xinxin Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xiaoteng Cui
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China.,Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin, China
| | - Yan Zhao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Excellent Talent Project, Tianjin Medical University, Tianjin, China
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