Hereditas最新文献

{"title":"Identification of the prognostic value of Th1/Th2 ratio and a novel prognostic signature in basal-like breast cancer.","authors":"Yu Xiao, Yi Huang, Jianping Jiang, Yan Chen, Changyuan Wei","doi":"10.1186/s41065-023-00265-0","DOIUrl":"10.1186/s41065-023-00265-0","url":null,"abstract":"<p><strong>Background: </strong>Breast cancer is a heterogeneous group of diseases. The polarization of CD4+ T helper (Th) lymphocytes (mainly Th1 and Th2) may differ in breast cancers with different outcomes, but this has not been fully validated.</p><p><strong>Methods: </strong>This study is a bioinformatic analysis, in which differentially expressed genes (DEGs) were identified in patients with low and high Th1/Th2 ratios. And then, DEG functions, hub genes and independent predictors were determined.</p><p><strong>Results: </strong>Low Th1/Th2 ratio was associated with poor outcome in Luminal A and basal-like breast cancer (p < 0.05). GSEA and KEGG analysis of DEGs obtained from comparing low and high Th1/Th2 ratios illuminated downregulation of immune-related gene sets and pathways affecting Th1/Th2 balance toward Th2 polarization (p < 0.05). Survival and Cox analyses of all the DEGs confirmed CCL1 and MYH6 were independent protective factors and IFNK and SOAT2 were independent risk factors for basal-like breast cancer (95%CI: 1.06-2.5, p = 0.026). Then a four-gene signature was constructed and achieved a promising prognostic value (C-index = 0.82; AUC = 0.826).</p><p><strong>Conclusions: </strong>Low Th1/Th2 ratio predicts poor outcome in Luminal A and Basal-like breast cancer, and downregulation of immune-related gene sets and pathways contribute to Th1/Th2 balance toward Th2 polarization. CCL1, MYH6, IFNK, and SOAT2 have an independent prognostic value of survival outcome and might be novel markers in basal-like breast cancer.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"160 1","pages":"2"},"PeriodicalIF":2.7,"publicationDate":"2023-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9875389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9142881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Upregulation of CENPM is associated with poor clinical outcome and suppression of immune profile in clear cell renal cell carcinoma.","authors":"Zhi-Cheng Zhang,&nbsp;Yi-Fu Liu,&nbsp;Ping Xi,&nbsp;Ye-Chen Nie,&nbsp;Ting Sun,&nbsp;Bin-Bin Gong","doi":"10.1186/s41065-023-00262-3","DOIUrl":"https://doi.org/10.1186/s41065-023-00262-3","url":null,"abstract":"<p><strong>Background: </strong>The response of advanced clear cell renal cell carcinoma (ccRCC) to immunotherapy is still not durable, suggesting that the immune landscape of ccRCC still needs to be refined, especially as some molecules that have synergistic effects with immune checkpoint genes need to be explored.</p><p><strong>Methods: </strong>The expression levels of CENPM and its relationship with clinicopathological features were explored using the ccRCC dataset from TCGA and GEO databases. Quantitative polymerase chain reaction (qPCR) analysis was performed to validate the expression of CENPM in renal cancer cell lines. Kaplan-Meier analysis, COX regression analysis and Nomogram construction were used to systematically evaluate the prognostic potential of CENPM in ccRCC. Besides, single gene correlation analysis, protein-protein interaction (PPI) network, genetic ontology (GO), kyoto encyclopedia of genes and genomes (KEGG) and gene set enrichment analysis (GSEA) were used to predict the biological behaviour of CENPM and the possible signalling pathways involved. Finally, a comprehensive analysis of the crosstalk between CENPM and immune features in the tumor microenvironment was performed based on the ssGSEA algorithm, the tumor immune dysfunction and exclusion (TIDE) algorithm, the TIMER2.0 database and the TISIDB database.</p><p><strong>Results: </strong>CENPM was significantly upregulated in ccRCC tissues and renal cancer cell lines and was closely associated with poor clinicopathological features and prognosis. Pathway enrichment analysis revealed that CENPM may be involved in the regulation of the cell cycle in ccRCC and may have some crosstalk with the immune microenvironment in tumors. The ssGSEA algorithm, CIBERSOPT algorithm suggests that CENPM is associated with suppressor immune cells in ccRCC such as regulatory T cells. The ssGSEA algorithm, CIBERSOPT algorithm suggests that CENPM is associated with suppressor immune cells in ccRCC such as regulatory T cells. Furthermore, the TISIDB database provides evidence that not only CENPM is positively associated with immune checkpoint genes such as CTLA4, PDCD1, LAG3, TIGIT, but also chemokines and receptors (such as CCL5, CXCL13, CXCR3, CXCR5) may be responsible for the malignant phenotype of CENPM in ccRCC. Meanwhile, predictions based on the TIDE algorithm support that patients with high CENPM expression have a worse response to immunotherapy.</p><p><strong>Conclusions: </strong>The upregulation of CENPM in ccRCC predicts a poor clinical outcome, and this malignant phenotype may be associated with its exacerbation of the immunosuppressive state in the tumor microenvironment.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"160 1","pages":"1"},"PeriodicalIF":2.7,"publicationDate":"2023-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9837903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10538871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stages of preadipocyte differentiation: biomarkers and pathways for extracellular structural remodeling.","authors":"Zhihan Hu,&nbsp;Yi Liu,&nbsp;Zongjiang Yao,&nbsp;Liming Chen,&nbsp;Gang Wang,&nbsp;Xiaohui Liu,&nbsp;Yafei Tian,&nbsp;Guangtong Cao","doi":"10.1186/s41065-022-00261-w","DOIUrl":"https://doi.org/10.1186/s41065-022-00261-w","url":null,"abstract":"<p><strong>Background: </strong>This study utilized bioinformatics to analyze the underlying biological mechanisms involved in adipogenic differentiation, synthesis of the extracellular matrix (ECM), and angiogenesis during preadipocyte differentiation in human Simpson-Golabi-Behmel syndrome at different time points and identify targets that can potentially improve fat graft survival.</p><p><strong>Results: </strong>We analyzed two expression profiles from the Gene Expression Omnibus and identified differentially expressed genes (DEGs) at six different time points after the initiation of preadipocyte differentiation. Related pathways were identified using Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analyses and Gene Set Enrichment Analysis (GSEA). We further constructed a protein-protein interaction (PPI) network and its central genes. The results showed that upregulated DEGs were involved in cell differentiation, lipid metabolism, and other cellular activities, while downregulated DEGs were associated with angiogenesis and development, ECM tissue synthesis, and intercellular and intertissue adhesion. GSEA provided a more comprehensive basis, including participation in and positive regulation of key pathways of cell metabolic differentiation, such as the \"peroxisome proliferator-activated receptor signaling pathway\" and the \"adenylate-activated protein kinase signaling pathway,\" a key pathway that negatively regulates pro-angiogenic development, ECM synthesis, and adhesion.</p><p><strong>Conclusions: </strong>We identified the top 20 hub genes in the PPI network, including genes involved in cell differentiation, ECM synthesis, and angiogenesis development, providing potential targets to improve the long-term survival rate of fat grafts. Additionally, we identified drugs that may interact with these targets to potentially improve fat graft survival.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"159 1","pages":"47"},"PeriodicalIF":2.7,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9793557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10449401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variations in the TAS2R38 gene among college students in Hubei.","authors":"Xiaojun Wang,&nbsp;Lin Wang,&nbsp;Mengwei Xia,&nbsp;Feng Teng,&nbsp;Xuejiao Chen,&nbsp;Rufeng Huang,&nbsp;Jiahao Zhou,&nbsp;Juan Xiao,&nbsp;Lihong Zhai","doi":"10.1186/s41065-022-00260-x","DOIUrl":"https://doi.org/10.1186/s41065-022-00260-x","url":null,"abstract":"<p><strong>Background: </strong>The bitter taste receptor gene TAS2R38 is a member of the human TAS2R gene family. Polymorphisms in TAS2R38 affect the ability to taste the bitterness of phenylthiourea (PTC) compounds, thus affecting an individual's food preference and health status.</p><p><strong>Methods: </strong>We investigated polymorphisms in the TAS2R38 gene and the sensitivity to PTC bitterness among healthy Chinese college students in Hubei province. The association of TAS2R38 polymorphisms and PTC sensitivity with body mass index (BMI), food preference, and health status was also analyzed. A total of 320 healthy college students were enrolled (male: 133, female: 187; aged 18-23 years). The threshold value method was used to measure the perception of PTC bitterness, and a questionnaire was used to analyze dietary preferences and health status. Polymerase chain reaction (PCR) was used to analyze polymorphisms at three common TAS2R38 loci (rs713598, rs1726866, and rs10246939).</p><p><strong>Results: </strong>In our study population, 65.00% of individuals had medium sensitivity to the bitterness of PTC; in contrast, 20.94% were highly sensitive to PTC bitterness, and 14.06% were not sensitive. For the TAS2R38 gene, the PAV/PAV and PAV/AAI diplotypes were the most common (42.19% and 40.63%, respectively), followed by the homozygous AVI/AVI (8.75%) and PAV/AVI (5.00%) diplotypes.</p><p><strong>Conclusion: </strong>There was a significant correlation between the sensitivity to PTC bitterness and sex, but there was no correlation between the common diplotypes of TAS2R38 and gender. Polymorphisms in the TAS2R38 gene were associated with the preference for tea, but not with one's native place, BMI, health status, or other dietary preferences. There was no significant correlation between the perception of PTC bitterness and one's native place, BMI, dietary preference, or health status. We hope to find out the relationship between PTC sensitivity and TAS2R38 gene polymorphisms and dietary preference and health status of Chinese population through this study, providing relevant guidance and suggestions for dietary guidance and prevention of some chronic diseases in Chinese population.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"159 1","pages":"46"},"PeriodicalIF":2.7,"publicationDate":"2022-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9762079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10493604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of GINS1 as a therapeutic target in the cancer patients infected with COVID-19: a bioinformatics and system biology approach.","authors":"Changpeng Hu,&nbsp;Yue Dai,&nbsp;Huyue Zhou,&nbsp;Jing Zhang,&nbsp;Dandan Xie,&nbsp;Rufu Xu,&nbsp;Mengmeng Yang,&nbsp;Rong Zhang","doi":"10.1186/s41065-022-00258-5","DOIUrl":"https://doi.org/10.1186/s41065-022-00258-5","url":null,"abstract":"<p><strong>Background: </strong>Coronavirus disease 2019 (COVID-19) caused a series of biological changes in cancer patients which have rendered the original treatment ineffective and increased the difficulty of clinical treatment. However, the clinical treatment for cancer patients infected with COVID-19 is currently unavailable. Since bioinformatics is an effective method to understand undiscovered biological functions, pharmacological targets, and therapeutic mechanisms. The aim of this study was to investigate the influence of COVID-19 infection in cancer patients and to search the potential treatments.</p><p><strong>Methods: </strong>Firstly, we obtained the COVID-19-associated genes from seven databases and analyzed the cancer pathogenic genes from Gene Expression Omnibus (GEO) databases, respectively. The Cancer/COVID-19-associated genes were shown by Venn analyses. Moreover, we demonstrated the signaling pathways and biological functions of pathogenic genes in Cancer/COVID-19.</p><p><strong>Results: </strong>We identified that Go-Ichi-Ni-San complex subunit 1 (GINS1) is the potential therapeutic target in Cancer/COVID-19 by GEPIA. The high expression of GINS1 was not only promoting the development of cancers but also affecting their prognosis. Furthermore, eight potential compounds of Cancer/COVID-19 were identified from CMap and molecular docking analysis.</p><p><strong>Conclusion: </strong>We revealed the GINS1 is a potential therapeutic target in cancer patients infected with COVID-19 for the first time, as COVID-19 will be a severe and prolonged pandemic. However, the findings have not been verified actually cancer patients infected with COVID-19, and further studies are needed to demonstrate the functions of GINS1 and the clinical treatment of the compounds.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"159 1","pages":"45"},"PeriodicalIF":2.7,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9713126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10678637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanisms of Cynarine for treatment of non-alcoholic fatty liver disease based on the integration of network pharmacology, molecular docking and cell experiment.","authors":"Chun-Yong Sun,&nbsp;Le-Le Yang,&nbsp;Pan Zhao,&nbsp;Pei-Zheng Yan,&nbsp;Jia Li,&nbsp;Dong-Sheng Zhao","doi":"10.1186/s41065-022-00256-7","DOIUrl":"https://doi.org/10.1186/s41065-022-00256-7","url":null,"abstract":"<p><strong>Background: </strong>Nonalcoholic Fatty Liver Disease (NAFLD) is a chronic Liver Disease prevalent all over the world. It has become more and more common in Japan, China and most western developed countries. The global prevalence rate is 25.24%, and the trend is increasing year by year. Related studies have shown that Cynarine has certain liver protection, lipid lowering and immune intervention effects. So, this study to systematically predict and analyze the mechanism of Cynarine in the treatment of non-alcoholic fatty liver disease (NAFLD) based on the integration of network pharmacology, molecular docking, and cell experiment.</p><p><strong>Methods: </strong>We performed Heatmap and Venn diagram analyses to identify genes and targets in Cynarine treat NAFLD. The network of Cynarine-therapeutic targets and the protein-protein interaction network (PPI) was constructed. We used gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to visualize associated functional pathways. The Sybyl tool was used to dock the Cynarine with key therapeutic targets molecularly. Finally, cell experiments were applied to validate the role of Cynarine in the treatment of NAFLD.</p><p><strong>Results: </strong>The Cynarine could act on 48 targets of NAFLD, and the role of CASP3, TP53, MMP9, ELANE, NOTCH1 were more important. The PPI network showed that immune and inflammation-related targets played a pivotal role. The KEGG analysis found that the PI3K-Akt signaling pathway, cell cycle and MAPK signaling pathway may be the main pathways for Cynarine to prevent and treat NAFLD. Molecular docking studies confirmed that Cynarine has good binding activity with therapeutic targets. Cynarine reduced the fat deposition ability of NAFLD model cells, and effectively reduced the levels of ALT and AST released by liver cells due to excessive lipid accumulation. We also found that Cynarine inhibited the expression of AKT1 and MAPK1.</p><p><strong>Conclusions: </strong>This study revealed that Cynarine could significantly reduce the fat deposition ability of NAFLD model cells, which may be closely related to the effective regulation of AKT1 and MAPK1 expression by Cynarine.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":" ","pages":"44"},"PeriodicalIF":2.7,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9714250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40711499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analysis to identify pseudogenes/lncRNAs-hsa-miR-200b-3p-COL5A2 network as a prognostic biomarker in gastric cancer.","authors":"Peiyuan Li,&nbsp;Wenbin Ji,&nbsp;Zhiwang Wei,&nbsp;Xiulan Wang,&nbsp;Gangjie Qiao,&nbsp;Chao Gao,&nbsp;Yifan Wang,&nbsp;Feng Qi","doi":"10.1186/s41065-022-00257-6","DOIUrl":"https://doi.org/10.1186/s41065-022-00257-6","url":null,"abstract":"<p><strong>Objective: </strong>Gastric cancer is one of the most common and deadly types of cancer. The molecular mechanism of gastric cancer progression remains unclear.</p><p><strong>Materials and methods: </strong>Four hub genes were identified through GEO and TCGA database screening and analysis. Prognostic analysis revealed that COL5A2 was the most likely to affect the prognosis of gastric cancer among the four hub genes. The relationships between COL5A2 and clinical variables and immune cell infiltration were analyzed. Then, COL5A2 was analyzed for single-gene differences and related functional enrichment. Using the starBase database for prediction and analysis, miRNAs and pseudogenes/lncRNAs that might combine with COL5A2 were identified; thus, the ceRNA network was constructed. Finally, the network was verified by Cox analysis and qPCR, and a nomogram was constructed.</p><p><strong>Results: </strong>First, we found that COL5A2, COL12A1, BGN and THBS2 were highly expressed in gastric cancer. COL5A2 had statistical significance in overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) analysis. Immune infiltration analysis suggested that COL5A2 might influence the changes in the tumor immune microenvironment. The StarBase database was used to predict that 3 pseudogenes and 7 lncRNAs might inhibit the hsa-miR-200b-3p-COL5A2 axis in gastric cancer. The pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 ceRNA network was identified and verified using Cox regression analysis and PCR. Finally, we constructed a nomogram.</p><p><strong>Conclusions: </strong>We elucidated the regulatory role of the pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 network in gastric cancer progression and constructed a nomogram. These studies may provide effective treatments and potential prognostic biomarkers for gastric cancer.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":"159 1","pages":"43"},"PeriodicalIF":2.7,"publicationDate":"2022-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9706917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10327207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening of ulcerative colitis biomarkers and potential pathways based on weighted gene co-expression network, machine learning and ceRNA hypothesis.","authors":"Ying Li,&nbsp;Mengyao Tang,&nbsp;Feng Jun Zhang,&nbsp;Yihan Huang,&nbsp;Jing Zhang,&nbsp;Junqi Li,&nbsp;Yunpeng Wang,&nbsp;Jinguang Yang,&nbsp;Shu Zhu","doi":"10.1186/s41065-022-00259-4","DOIUrl":"https://doi.org/10.1186/s41065-022-00259-4","url":null,"abstract":"<p><strong>Background: </strong>Ulcerative colitis (UC) refers to an intractable intestinal inflammatory disease. Its increasing incidence rate imposes a huge burden on patients and society. The UC etiology has not been determined, so screening potential biomarkers is critical to preventing disease progression and selecting optimal therapeutic strategies more effectively.</p><p><strong>Methods: </strong>The microarray datasets of intestinal mucosal biopsy of UC patients were selected from the GEO database, and integrated with R language to screen differentially expressed genes and draw proteins interaction network diagrams. GO, KEGG, DO and GSEA enrichment analyses were performed to explore their biological functions. Through machine learning and WGCNA analysis, targets that can be used as UC potential biomarkers are screened out. ROC curves were drawn to verify the reliability of the results and predicted the mechanism of marker genes from the aspects of immune cell infiltration, co-expression analysis, and competitive endogenous network (ceRNA).</p><p><strong>Results: </strong>Two datasets GSE75214 and GSE87466 were integrated for screening, and a total of 107 differentially expressed genes were obtained. They were mainly related to biological functions such as humoral immune response and inflammatory response. Further screened out five marker genes, and found that they were associated with M0 macrophages, quiescent mast cells, M2 macrophages, and activated NK cells in terms of immune cell infiltration. The co-expression network found significant co-expression relationships between 54 miRNAs and 5 marker genes. According to the ceRNA hypothesis, NEAT1-miR-342-3p/miR-650-SLC6A14, NEAT1-miR-650-IRAK3, and XIST-miR-342-3p-IRAK3 axes were found as potential regulatory pathways in UC.</p><p><strong>Conclusion: </strong>This study screened out five biomarkers that can be used for the diagnosis and treatment of UC, namely SLC6A14, TIMP1, IRAK3, HMGCS2, and APOBEC3B. Confirmed that they play a role in the occurrence and development of UC at the level of immune infiltration, and proposed a potential RNA regulatory pathway that controls the progression of UC.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":" ","pages":"42"},"PeriodicalIF":2.7,"publicationDate":"2022-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9685902/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40702859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation.","authors":"Jun Liu,&nbsp;Tianyu Jin,&nbsp;Lanxi Ran,&nbsp;Ze Zhao,&nbsp;Rui Zhu,&nbsp;Gangcai Xie,&nbsp;Xiaolin Bi","doi":"10.1186/s41065-022-00254-9","DOIUrl":"https://doi.org/10.1186/s41065-022-00254-9","url":null,"abstract":"<p><strong>Background: </strong>ATM (ataxia-telangiectasia mutated) protein kinase is highly conserved in metazoan, and plays a critical role at DNA damage response, oxidative stress, metabolic stress, immunity, RNA biogenesis etc. Systemic profiling of ATM regulated genes, including protein-coding genes, miRNAs, and long non-coding RNAs, will greatly improve our understanding of ATM functions and its regulation.  RESULTS: 1) differentially expressed protein-coding genes, miRNAs, and long non-coding RNAs in atm mutated flies were identified at physiological condition and after X-ray irradiation. 2) functions of differentially expressed genes in atm mutated flies, regardless of protein-coding genes or non-coding RNAs, are closely related with metabolic process, immune response, DNA damage response or oxidative stress. 3) these phenomena are persistent after irradiation. 4) there is a cross-talk regulation towards miRNAs by ATM, E2f1, and p53 during development and after irradiation. 5) knock-out flies or knock-down flies of most irradiation-induced miRNAs were sensitive to ionizing radiation.</p><p><strong>Conclusions: </strong>We provide a valuable resource of protein-coding genes, miRNAs, and long non-coding RNAs, for understanding ATM functions and regulations. Our work provides the new evidence of inter-dependence among ATM-E2F1-p53 for the regulation of miRNAs.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":" ","pages":"41"},"PeriodicalIF":2.7,"publicationDate":"2022-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9587650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40563358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative analyses of genes related to liver ischemia reperfusion injury.","authors":"Hang-Pin Wang,&nbsp;Chu-Hong Chen,&nbsp;Ben-Kai Wei,&nbsp;Ying-Lei Miao,&nbsp;Han-Fei Huang,&nbsp;Zhong Zeng","doi":"10.1186/s41065-022-00255-8","DOIUrl":"https://doi.org/10.1186/s41065-022-00255-8","url":null,"abstract":"<p><strong>Background: </strong>Liver ischemia reperfusion injury (LIRI) is not only a common injury during liver transplantation and major hepatic surgery, but also one of the primary factors that affect the outcome of postoperative diseases. However, there are still no reliable ways to tackle the problem. Our study aimed to find some characteristic genes associated with immune infiltration that affect LIRI, which can provide some insights for future research in the future. Therefore, it is essential for the treatment of LIRI, the elucidation of the mechanisms of LIRI, and exploring the potential biomarkers. Efficient microarray and bioinformatics analyses can promote the understanding of the molecular mechanisms of disease occurrence and development.</p><p><strong>Method: </strong>Data from GSE151648 were downloaded from GEO data sets, and we performed a comprehensive analysis of the differential expression, biological functions and interactions of LIRI-associated genes. Then we performed Gene ontology (GO) analysis and Kyotoencydlopedia of genes and genomes (KEGG) enrichment analysis of DEGs. At last, we performed a protein-protein interaction network to screen out hub genes.</p><p><strong>Results: </strong>A total of 161 differentially expressed genes (DEGs) were identified. GO analysis results revealed that the changes in the modules were mostly enriched in the neutrophil degranulation, neutrophil activation involved in immune response, and neutrophil mediated immunity. KEGG enrichment analysis of DEGs demonstrated that LIRI mainly involved the cytokine-cytokine receptor interaction. Our data indicated that macrophages and neutrophils are closely related to LIRI. 9 hub genes were screened out in the protein-protein interaction network.</p><p><strong>Conclusions: </strong>In summary, our data indicated that neutrophil degranulation, neutrophil activation involved in immune response, neutrophil mediated immunity and cytokine-cytokine receptor interaction may play a key role in LIRI, HRH1, LRP2, P2RY6, PKD1L1, SLC8A3 and TNFRSF8, which were identified as potential biomarkers in the occurrence and development of LIRI. However, further studies are needed to validate these findings and explore the molecular mechanism of these biomarkers in LIRI.</p>","PeriodicalId":12862,"journal":{"name":"Hereditas","volume":" ","pages":"39"},"PeriodicalIF":2.7,"publicationDate":"2022-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9578272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40250738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}