Biological Procedures Online最新文献

{"title":"YTHDF2 exerts tumor-suppressor roles in gastric cancer via up-regulating PPP2CA independently of m⁶A modification.","authors":"Ying Zhou,&nbsp;Kailing Fan,&nbsp;Ning Dou,&nbsp;Li Li,&nbsp;Jialin Wang,&nbsp;Jingde Chen,&nbsp;Yandong Li,&nbsp;Yong Gao","doi":"10.1186/s12575-023-00195-1","DOIUrl":"https://doi.org/10.1186/s12575-023-00195-1","url":null,"abstract":"<p><strong>Background: </strong>YTHDF2 is one of important readers of N6-methyladenosine (m⁶A) modification on RNA. Growing evidence implicates that YTHDF2 takes an indispensable part in the regulation of tumorigenesis and metastasis in different cancers, but its biological functions and underlying mechanisms remain elusive in gastric cancer (GC).</p><p><strong>Aim: </strong>To investigate the clinical relevance and biological function of YTHDF2 in GC.</p><p><strong>Results: </strong>Compared with matched normal stomach tissues, YTHDF2 expression was markedly decreased in gastric cancer tissues. The expression level of YTHDF2 was inversely associated with gastric cancer patients' tumor size, AJCC classification and prognosis. Functionally, YTHDF2 reduction facilitated gastric cancer cell growth and migration in vitro and in vivo, whereas YTHDF2 overexpression exhibited opposite phenotypes. Mechanistically, YTHDF2 enhanced expression of PPP2CA, the catalytic subunit of PP2A (Protein phosphatase 2A), in an m⁶A-independent manner, and silencing of PPP2CA antagonized the anti-tumor effects caused by overexpression of YTHDF2 in GC cells.</p><p><strong>Conclusion: </strong>These findings demonstrate that YTHDF2 is down-regulated in GC and its down-regulation promotes GC progression via a possible mechanism involving PPP2CA expression, suggesting that YTHDF2 may be a hopeful biomarker for diagnosis and an unrevealed treatment target for GC.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"25 1","pages":"6"},"PeriodicalIF":6.4,"publicationDate":"2023-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9985201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10847149","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":"Influence of Exosomes on Astrocytes in the Pre-Metastatic Niche of Lung Cancer Brain Metastases.","authors":"Lingyun Ye,&nbsp;Yinfei Wu,&nbsp;Juan Zhou,&nbsp;Mengqing Xie,&nbsp;Zhemin Zhang,&nbsp;Chunxia Su","doi":"10.1186/s12575-023-00192-4","DOIUrl":"https://doi.org/10.1186/s12575-023-00192-4","url":null,"abstract":"<p><strong>Background: </strong>Lung cancer is the most common cause of cancer-related death globally. There are several reasons for this high mortality rate, including metastasis to multiple organs, especially the brain. Exosomes play a pivotal role in tumor metastasis by remodeling the microenvironment of remote target organs and promoting the pre-metastatic niche's formation. Since astrocytes are indispensable for maintaining the homeostasis of brain microenvironment, it's of great interest to explore the influence of lung cancer cell-derived exosomes on astrocytes to further understand the mechanism of lung cancer brain metastasis.</p><p><strong>Results: </strong>Twenty four h after co-culture of H1299 cell-derived exosomes and SVG P12 cells, the viability of astrocytes decreased and the apoptosis increased. The levels of cytokines in the supernatant including GROα/CXCL1, IFN-γ, IL-3, IL-5, IL-15, LIF, M-CSF, NGF, PDGF, and VEGF were significantly enhanced, while IL-7 secretion was significantly reduced. Meanwhile, apoptosis-related proteins MAP2K1, TUBA1C, RELA, and CASP6 were up-regulated. And the differentially expressed proteins were involved in regulating metabolic pathways.</p><p><strong>Conclusion: </strong>Exosomes of H1299 could induce apoptosis of astrocytes as well as promote their secretion of cytokines that were conducive to the formation of the inflammatory microenvironment and immunosuppressive microenvironment, and affect their metabolic pathways, thus facilitating the formation of pre-metastatic niche in lung cancer brain metastases.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"25 1","pages":"5"},"PeriodicalIF":6.4,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9976367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10826181","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":"A 3D human co-culture to model neuron-astrocyte interactions in tauopathies.","authors":"Kevin L Batenburg,&nbsp;Claudia Sestito,&nbsp;Paulien Cornelissen-Steijger,&nbsp;Jan R T van Weering,&nbsp;Leo S Price,&nbsp;Vivi M Heine,&nbsp;Wiep Scheper","doi":"10.1186/s12575-023-00194-2","DOIUrl":"https://doi.org/10.1186/s12575-023-00194-2","url":null,"abstract":"<p><strong>Background: </strong>Intraneuronal tau aggregation is the major pathological hallmark of neurodegenerative tauopathies. It is now generally acknowledged that tau aggregation also affects astrocytes in a cell non-autonomous manner. However, mechanisms involved are unclear, partly because of the lack of models that reflect the situation in the human tauopathy brain. To accurately model neuron-astrocyte interaction in tauopathies, there is a need for a model that contains both human neurons and human astrocytes, intraneuronal tau pathology and mimics the three-dimensional architecture of the brain.</p><p><strong>Results: </strong>Here we established a novel 100-200 µm thick 3D human neuron/astrocyte co-culture model of tau pathology, comprising homogenous populations of hiPSC-derived neurons and primary human astrocytes in microwell format. Using confocal, electron and live microscopy, we validate the procedures by showing that neurons in the 3D co-culture form pre- and postsynapses and display spontaneous calcium transients within 4 weeks. Astrocytes in the 3D co-culture display bipolar and stellate morphologies with extensive processes that ensheath neuronal somas, spatially align with axons and dendrites and can be found perisynaptically. The complex morphology of astrocytes and the interaction with neurons in the 3D co-culture mirrors that in the human brain, indicating the model's potential to study physiological and pathological neuron-astrocyte interaction in vitro. Finally, we successfully implemented a methodology to introduce seed-independent intraneuronal tau aggregation in the 3D co-culture, enabling study of neuron-astrocyte interaction in early tau pathogenesis.</p><p><strong>Conclusions: </strong>Altogether, these data provide proof-of-concept for the utility of this rapid, miniaturized, and standardized 3D model for cell type-specific manipulations, such as the intraneuronal pathology that is associated with neurodegenerative disorders.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"25 1","pages":"4"},"PeriodicalIF":6.4,"publicationDate":"2023-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9948470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9320089","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":"Ultrasound and microbubble-mediated delivery of miR-424-5p has a therapeutic effect in preeclampsia.","authors":"Xudong Wang,&nbsp;Yan Wu,&nbsp;Qinliang Sun,&nbsp;Zhonghui Jiang,&nbsp;Guoying Che,&nbsp;Yangyang Tao,&nbsp;Jiawei Tian","doi":"10.1186/s12575-023-00191-5","DOIUrl":"https://doi.org/10.1186/s12575-023-00191-5","url":null,"abstract":"<p><strong>Objective: </strong>To determine the influence of ultrasound/microbubble-mediated miR-424-5p delivery on trophoblast cells and the underlying mechanism.</p><p><strong>Methods: </strong>Blood pressure and 24-h proteinuria of patients with preeclampsia (PE) were measured as well as the levels of miR-424-5p and amine oxidase copper containing 1 (AOC1) in placental tissues. HTR-8/Svneo and TEV-1 cells were subjected to cell transfection or ultrasonic microbubble transfection for determination of the expression of miR-424-5p, AOC1, β-catenin and c-Myc as well as cell proliferation, apoptosis, migration and invasiveness. The concentrations of placental growth factor (PLGF), human chorionic gonadotropin (β-hCG) and tumor necrosis factor-α (TNF-α) were measured in HTR-8/Svneo and TEV-1 cells. RNA immunoprecipitation (RIP) and dual luciferase reporter assay detected the binding of miR-424-5p to AOC1. A PE mouse model was induced by subcutaneous injection of L-NAME, where the influence of ultrasound/microbubble-mediated miR-424-5p delivery was evaluated.</p><p><strong>Results: </strong>miR-424-5p was downregulated while AOC1 was upregulated in the placental tissues from PE patients. Overexpression of miR-424-5p activated Wnt/β-catenin signaling pathway and promoted the proliferation of HTR-8/Svneo and TEV-1 cells as well as enhanced the migratory and invasive behaviors. AOC1 overexpression partly eliminated the effects of miR-424-5p on HTR-8/Svneo and TEV-1 cells. Ultrasound and microbubble mediated gene delivery enhanced the transfection efficiency of miR-424-5p and further promoted the effects of miR-424-5p in trophoblast cells. Ultrasound/microbubble-mediated miR-424-5p delivery alleviated experimental PE in mice.</p><p><strong>Conclusion: </strong>Ultrasound and microbubble-mediated miR-424-5p delivery targets AOC1 and activates Wnt/β-catenin signaling pathway, thus promoting the aggressive phenotype of trophoblast cells, which indicating that miR-424-5p/AOC1 axis might be involved with PE pathogenesis.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"25 1","pages":"3"},"PeriodicalIF":6.4,"publicationDate":"2023-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10793507","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":"Isolation and characterization of apical papilla cells from root end of human third molar and their differentiation into cementoblast cells: an in vitro study.","authors":"Morvarid Ebadi,&nbsp;Amirfarhang Miresmaeili,&nbsp;Sarah Rajabi,&nbsp;Shahrokh Shojaei,&nbsp;Sareh Farhadi","doi":"10.1186/s12575-023-00190-6","DOIUrl":"https://doi.org/10.1186/s12575-023-00190-6","url":null,"abstract":"<p><strong>Background: </strong>Periodontal regeneration, treatment of periodontal-related diseases and improving the function of implants are global therapeutic challenges. The differentiation of human stem cells from apical papilla into cementoblasts may provide a strategy for periodontitis treatment. This study aimed to evaluate the differentiation of primary human stem cells apical papilla (hSCAPs) to cementoblast cells.</p><p><strong>Material and methods: </strong>SCAPs cells were isolated from human third molar and then incubated for 21 days in a differentiation microenvironment. Alkaline phosphatase (ALP) and Alizarin red S staining assays were performed to evaluate the calcium deposition and formation of hydroxyapatite in the cultured hSCAPs microenvironment. Real-time polymerase chain reaction (RT-PCR) assay was performed for cementum protein 1 (CEMP1), collagen type I (COL1), F-Spondin (SPON1), osteocalcin (OCN), and osteopontin (OPN) as specific markers of cementoblasts and their progenitors.</p><p><strong>Results: </strong>ALP phosphatase activity in day 21 of treatment demonstrated a significant increase in ALP compared to the control. Alizarin red S staining assay showed that the differentiated hSCAPs offered a great amount of calcium deposition nodules compared to the control. The increased expression level of CEMP1, OCN, OPN, COL1 and Spon1 was observed in days 7, 14 and 21 compared to the control, while greatest expression level was observed in day 21.</p><p><strong>Conclusion: </strong>In conclusion, the differentiation microenviroment is convenient and useful for promoting the differentiation of hSCAPs into cementoblast.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"25 1","pages":"2"},"PeriodicalIF":6.4,"publicationDate":"2023-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9869574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9546925","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":"Protocol for Evaluating In Vivo the Activation of the P2RX7 Immunomodulator.","authors":"Serena Janho Dit Hreich,&nbsp;Thierry Juhel,&nbsp;Paul Hofman,&nbsp;Valérie Vouret-Craviari","doi":"10.1186/s12575-022-00188-6","DOIUrl":"https://doi.org/10.1186/s12575-022-00188-6","url":null,"abstract":"<p><strong>Background: </strong>P2RX7 is a purinergic receptor with pleiotropic activities that is activated by high levels of extracellular ATP that are found in inflamed tissues. P2RX7 has immunomodulatory and anti-tumor proprieties and is therefore a therapeutic target for various diseases. Several compounds are developed to either inhibit or enhance its activation. However, studying their effect on P2RX7's activities is limited to in vitro and ex vivo studies that require the use of unphysiological media that could affect its activation. Up to now, the only way to assess the activity of P2RX7 modulators on the receptor in vivo was in an indirect manner.</p><p><strong>Results: </strong>We successfully developed a protocol allowing the detection of P2RX7 activation in vivo in lungs of mice, by taking advantage of its unique macropore formation ability. The protocol is based on intranasal delivery of TO-PRO™-3, a non-permeant DNA intercalating dye, and fluorescence measurement by flow cytometry. We show that ATP enhances TO-PRO™-3 fluorescence mainly in lung immune cells of mice in a P2RX7-dependant manner.</p><p><strong>Conclusions: </strong>The described approach has allowed the successful analysis of P2RX7 activity directly in the lungs of WT and transgenic C57BL6 mice. The provided detailed guidelines and recommendations will support the use of this protocol to study the potency of pharmacologic or biologic compounds targeting P2RX7.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"25 1","pages":"1"},"PeriodicalIF":6.4,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9811721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10484512","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":"The Critical Biomarkers Identification of Insulin Signaling Involved in Initiating cAMP Signaling Mediated Salivary Secretion in Sjogren Syndrome: Transcriptome Sequencing in NOD Mice Model.","authors":"Bo Chen,&nbsp;Jiannan Zhou,&nbsp;Tianjiao Mao,&nbsp;Tingting Cao,&nbsp;Shilin Hu,&nbsp;Wenqi Zhang,&nbsp;Xueyang Li,&nbsp;Xiuni Qin,&nbsp;Xintong Liu,&nbsp;Nobumoto Watanabe,&nbsp;Jiang Li","doi":"10.1186/s12575-022-00189-5","DOIUrl":"https://doi.org/10.1186/s12575-022-00189-5","url":null,"abstract":"<p><strong>Background: </strong>Sjogren's syndrome (SS) is an autoimmune disorder characterized by the destruction of exocrine glands, resulting in dry mouth and eyes. Currently, there is no effective treatment for SS, and the mechanisms associated with inadequate salivary secretion are poorly understood.</p><p><strong>Methods: </strong>In this study, we used NOD mice model to monitor changes in mice's salivary secretion and water consumption. Tissue morphology of the submandibular glands was examined by H&E staining, and Immunohistochemical detected the expression of AQP5 (an essential protein in salivary secretion). Global gene expression profiling was performed on submandibular gland tissue of extracted NOD mice model using RNA-seq. Subsequently, a series of bioinformatics analyses of transcriptome sequencing was performed, including differentially expressed genes (DEGs) identification, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, PPI network construction, hub gene identification, and the validity of diagnostic indicators using the dataset GSE40611. Finally, IFN-γ was used to treat the cells, the submandibular gland tissue of NOD mice model was extracted, and RT-qPCR was applied to verify the expression of hub genes.</p><p><strong>Results: </strong>We found that NOD mice model had reduced salivary secretion and increased water consumption. H&E staining suggests acinar destruction and basement membrane changes in glandular tissue. Immunohistochemistry detects a decrease in AQP5 immunostaining within acinar. In transcriptome sequencing, 42 overlapping DEGs were identified, and hub genes (REN, A2M, SNCA, KLK3, TTR, and AZGP1) were identified as initiating targets for insulin signaling. In addition, insulin signaling and cAMP signaling are potential pathways for regulating salivary secretion and constructing a regulatory relationship between target-cAMP signaling-salivary secretion.</p><p><strong>Conclusion: </strong>The new potential targets and signal axes for regulating salivary secretion provide a strategy for SS therapy in a clinical setting.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"24 1","pages":"26"},"PeriodicalIF":6.4,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9793606/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10819070","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":"Clinical Prognostic Factors and Integrated Multi-Omics Studies Identify Potential Novel Therapeutic Targets for Pediatric Desmoid Tumor.","authors":"Bo Ning,&nbsp;Peng Huang,&nbsp;Lining Zhu,&nbsp;Zhijie Ma,&nbsp;Xiaoli Chen,&nbsp;Haojun Xu,&nbsp;Ruixue Ma,&nbsp;Chengyun Yao,&nbsp;Pengfei Zheng,&nbsp;Tian Xia,&nbsp;Hongping Xia","doi":"10.1186/s12575-022-00180-0","DOIUrl":"https://doi.org/10.1186/s12575-022-00180-0","url":null,"abstract":"<p><strong>Background: </strong>Desmoid tumor (DT), also known as desmoid-type fibromatosis (DTF) or aggressive fibromatosis (AF) is a rare mesenchymal tumor affecting both children and adults. It is non-metastasis but infiltrative, growing with a high recurrence rate to even cause serious health problems. This study investigates the biology of desmoid tumors through integrated multi-omics studies.</p><p><strong>Methods: </strong>We systematically investigated the clinical data of 98 extra-abdominal cases in our pediatric institute and identified some critical clinical prognostic factors. Moreover, our integrated multi-omics studies (Whole Exome Sequencing, RNA sequencing, and untargeted metabolomics profiling) in the paired PDT tumor/matched normal tissues identified more novel mutations, and potential prognostic markers and therapeutic targets for PDTs.</p><p><strong>Results: </strong>The top mutation genes, such as CTNNB1 (p.T41A and p.S45F) and MUC4 (p.T3775T, p.S3450S, etc.), were observed with a mutation in more than 40% of PDT patients. We also identified a panel of genes that are classed as the FDA-approved drug targets or Wnt/β-catenin signaling pathway-related genes. The integrated analysis identified pathways and key genes/metabolites that may be important for developing potential treatment of PDTs. We also successfully established six primary PDT cell lines for future studies.</p><p><strong>Conclusions: </strong>These studies may promote the development of novel drugs and therapeutic strategies for PDTs.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"24 1","pages":"25"},"PeriodicalIF":6.4,"publicationDate":"2022-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9768966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10417874","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 of Cellular Senescence-Related Genes in Prognosis, Molecular Characterization and Immunotherapy of Hepatocellular Carcinoma.","authors":"Liang Sun,&nbsp;Zitao Liu,&nbsp;Ke Ning,&nbsp;Zhipeng Wu,&nbsp;Zhendong Chen,&nbsp;Zhengyi Wu,&nbsp;Xiangbao Yin","doi":"10.1186/s12575-022-00187-7","DOIUrl":"https://doi.org/10.1186/s12575-022-00187-7","url":null,"abstract":"<p><strong>Background: </strong>Cellular senescence is a tumor suppressive response in which the cell cycle is in a state of permanent arrest and can inhibit tumor cell proliferation. In recent years, induction of cellular senescence has been shown to be important for antitumor therapy, and the link between cellular senescence and clinical prognosis and immunotherapy of hepatocellular carcinoma is still unknown.</p><p><strong>Methods: </strong>We performed enrichment analysis of genes in three cellular senescence gene sets, screened for gene sets significantly enriched in hepatocellular carcinoma and extracted genes from them. Signature were constructed using senescence-related genes, and their expression was verified at the protein and RNA levels. Survival, clinical staging and grading, immune infiltration, immunotherapy, and drug sensitivity were also analyzed between risk groups.</p><p><strong>Results: </strong>The q-PCR and immunohistochemistry results revealed significant differences in the expression of the signature genes between normal and tumor tissues. Significant differences in clinicopathological features, prognosis and immune infiltration were observed between risk groups. In the low-risk group, better OS and lower TMB scores were demonstrated, while the high-risk group had higher immune checkpoint expression, as well as lower risk of immune escape. In addition, we found that the High-risk group was more sensitive to sorafenib.</p><p><strong>Conclusion: </strong>In summary, the signature constructed using aging-related genes can reliably predict patient prognosis and immunotherapy efficacy, providing a new idea for immune system therapy of hepatocellular carcinoma.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"24 1","pages":"24"},"PeriodicalIF":6.4,"publicationDate":"2022-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9761989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10419278","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":"Decoding the Virtual 2D Map of the Chloroplast Proteomes.","authors":"Tapan Kumar Mohanta,&nbsp;Yugal Kishore Mohanta,&nbsp;Ahmed Al-Harrasi","doi":"10.1186/s12575-022-00186-8","DOIUrl":"https://doi.org/10.1186/s12575-022-00186-8","url":null,"abstract":"<p><strong>Background: </strong>The chloroplast is a semi-autonomous organelle having its own genome and corresponding proteome. Although chloroplast genomes have been reported, no reports exist on their corresponding proteomes. Therefore, a proteome-wide analysis of the chloroplast proteomes of 2893 species was conducted, and a virtual 2D map was constructed.</p><p><strong>Results: </strong>The resulting virtual 2D map of the chloroplast proteome exhibited a bimodal distribution. The molecular mass of the chloroplast proteome ranged from 0.448 to 616.334 kDa, and the isoelectric point (pI) ranged from 2.854 to 12.954. Chloroplast proteomes were dominated by basic pI proteins with an average pI of 7.852. The molecular weight and isoelectric point of chloroplast proteome were found to show bimodal distribution. Leu was the most abundant and Cys the least abundant amino acid in the chloroplast proteome. Notably, Trp amino acid was absent in the chloroplast protein sequences of Pilostyles aethiopica. In addition, Selenocysteine (Sec) and Pyrrolysine (Pyl) amino acids were also found to be lacking in the chloroplast proteomes.</p><p><strong>Conclusion: </strong>The virtual 2D map and amino acid composition of chloroplast proteome will enable the researchers to understand the biochemistry of chloroplast protein in detail. Further, the amino acid composition of the chloroplast proteome will also allow us to understand the codon usage bias. The codon usage bias and amino acid usage bias of chloroplast will be crucial to understanding their relationship.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"24 1","pages":"23"},"PeriodicalIF":6.4,"publicationDate":"2022-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9749319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10366754","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}