Functional & Integrative Genomics最新文献

{"title":"Beyond green and red: unlocking the genetic orchestration of tomato fruit color and pigmentation","authors":"Muhammad Naeem,&nbsp;Weihua Zhao,&nbsp;Naveed Ahmad,&nbsp;Lingxia Zhao","doi":"10.1007/s10142-023-01162-5","DOIUrl":"10.1007/s10142-023-01162-5","url":null,"abstract":"<div><p>Fruit color is a genetic trait and a key factor for consumer acceptability and is therefore receiving increasing importance in several breeding programs. Plant pigments offer plants with a variety of colored organs that attract animals for pollination, favoring seed dispersers and conservation of species. The pigments inside plant cells not only play a light-harvesting role but also provide protection against light damage and exhibit nutritional and ecological value for health and visual pleasure in humans. Tomato (<i>Solanum lycopersicum</i>) is a leading vegetable crop; its fruit color formation is associated with the accumulation of several natural pigments, which include carotenoids in the pericarp, flavonoids in the peel, as well as the breakdown of chlorophyll during fruit ripening. To improve tomato fruit quality, several techniques, such as genetic engineering and genome editing, have been used to alter fruit color and regulate the accumulation of secondary metabolites in related pathways. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)-based systems have been extensively used for genome editing in many crops, including tomatoes, and promising results have been achieved using modified CRISPR systems, including CAS9 (CRISPR/CRISPR-associated-protein) and CRISPR/Cas12a systems. These advanced tools in biotechnology and whole genome sequencing of various tomato species will certainly advance the breeding of tomato fruit color with a high degree of precision. Here, we attempt to summarize the current advancement and effective application of genetic engineering techniques that provide further flexibility for fruit color formation. Furthermore, we have also discussed the challenges and opportunities of genetic engineering and genome editing to improve tomato fruit color.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4612843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resveratrol plays an anti-fibrotic and anti-autophagy role by stimulating miR-192-5p expression in urethral fibrosis","authors":"Jin Lv,&nbsp;Rui Zhang,&nbsp;DaoYuan Li,&nbsp;Yan Liu","doi":"10.1007/s10142-023-01173-2","DOIUrl":"10.1007/s10142-023-01173-2","url":null,"abstract":"<div><h3>Background</h3><p>Resveratrol (RSV) exerts anti-fibrotic effects on various fibrotic diseases. Whereas the biological role of RSV on urethral fibrosis remains to be elucidated. This study aimed to determine the mechanisms by which RSV affects urethral fibrosis and autophagy.</p><h3>Methods</h3><p>Sprague‒Dawley rats and primary fibroblasts were treated with transforming growth factor-β1 (TGFβ1) to generate in vivo<i> and </i>in vitro fibrosis models. Then, those were treated with RSV, and autophagy and fibrosis-related indicators were tested.</p><h3>Results</h3><p>Firstly, we found that RSV reversed the upregulation of indicators related to TGFβ1-induced fibrosis (TGFβ1, α-smooth muscle actin, collagen type I, and collagen type III), autophagy (TFEB and LC3), and TGFβR1/Smad4 pathway, as well as the downregulation of p62 and <i>miR-192-5p</i> expression both in vivo<i> and </i>in vitro. Overexpression of <i>miR-192-5p</i> suppressed the upregulation of fibrosis-related markers expression, as well as TFEB and LC3 expression, induced by TGFβ1, while the expression trend of p62 was the opposite. Inhibiting <i>miR-192-5p</i> reversed the effects of RSV on the model group cells. It was also shown that RSV combined with sh-Smad4 inhibited autophagy more effectively than RSV alone.</p><h3>Conclusion</h3><p>These results suggest that RSV inhibits urinary fibrosis and autophagy via the <i>miR-192-5p</i>/TGFβR1/Smad4 pathway. RAV may be a potential drug for alleviating urethral fibrosis.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4869841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Exploration of the potential common pathogenic mechanisms in COVID‑19 and silicosis by using bioinformatics and system biology","authors":"Yunze Tian,&nbsp;Beibei Yu,&nbsp;Yongfeng Zhang,&nbsp;Sanpeng Zhang,&nbsp;Boqiang lv,&nbsp;Shouping Gong,&nbsp;Jianzhong Li","doi":"10.1007/s10142-023-01165-2","DOIUrl":"10.1007/s10142-023-01165-2","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-023-01165-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4573306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis the mechanisms of anti-osteoporosis of desert-living Cistanche herb in ovariectomized rats of postmenopausal osteoporosis","authors":"Shuo Tian,&nbsp;Lin Guo,&nbsp;Yagang Song,&nbsp;Jinxin Miao,&nbsp;Mengfan Peng,&nbsp;Xiaoyan Fang,&nbsp;Ming Bai,&nbsp;Mingsan Miao","doi":"10.1007/s10142-023-01154-5","DOIUrl":"10.1007/s10142-023-01154-5","url":null,"abstract":"<div><p>Desert-living Cistanche herb (DC), as a traditional Chinese medicine for tonifying kidney yang, is often used to treat postmenopausal osteoporosis (PMOP). Total phenylethanoid glycosides are instruction ingredients for discrimination and assay according to the China pharmacopoeia for DC. This research aimed to reveal the anti-osteoporosis mechanism of total phenylethanoid glycosides of DC (PGC) by transcriptomic analysis of ovariectomized rats. Serum levels of BGP were evaluated by ELISA, the bone weight was measured, and transmission electron microscopy was used to examine the ultrastructure of osteoblasts in rats. In addition, micro-CT was used to detect the bone volume (Tb.BS/BV), bone mineral density (Tb.BMD), and bone mineral content (Tb.BMC) in trabecular bone, and the ratio of cortical bone area to total area (Ct.ar/Tt.ar), and the level of bone mineral content (Ct.BMC) in cortical bone. Differential expressed genes (DEGs) after PGC treatment were analyzed by transcriptomics. Then, a bioinformatics analysis of DEGs was carried out through GO enrichment, KEGG enrichment, and selection of the nucleus gene through the protein-protein interaction network. Through qRT-PCR analysis, the DEGs were verified. The analysis results indicated that PGC increased the secretion of osteogenic markers, and ultrastructural characterization of osteoblasts and bone morphology were improved in ovariectomized rats. A total of 269 genes were differentially expressed, including 201 genes that were downregulated and 68 genes that were upregulated between the model group and the PGC group. Bioinformation analysis results prompt the conclusion that PGC could promote the bone metabolism by muscle cell development, myofibril assembly, etc. In addition, our study also found that PGC has a good effect on osteoporosis complicated with cardiomyopathy, and it also provided evidence for the correlation between sarcopenia and osteoporosis.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-023-01154-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4542487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell transcriptome analysis identifies novel biomarkers involved in major liver cancer subtypes","authors":"Asish Kumar Swain,&nbsp;Prashant Pandey,&nbsp;Riddhi Sera,&nbsp;Pankaj Yadav","doi":"10.1007/s10142-023-01156-3","DOIUrl":"10.1007/s10142-023-01156-3","url":null,"abstract":"<div><p>Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are the two aggressive subtypes of liver cancer (LC). Immense cellular heterogeneity and cross-talk between cancer and healthy cells make it challenging to treat these cancer subtypes. To address these challenges, the study aims to systematically characterize the tumor heterogeneity of LC subtypes using single-cell RNA sequencing (scRNA-seq) datasets. The study combined 51,927 single cells from HCC, ICC, and healthy scRNA-seq datasets. After integrating the datasets, cell groups with similar gene expression patterns are clustered and cluster annotation has been performed based on gene markers. Cell-cell communication analysis (CCA) was implemented to understand the cross-talk between various cell types. Further, differential gene expression analysis and enrichment analysis were carried out to identify unique molecular drivers associated with HCC and ICC. Our analysis identified T cells, hepatocytes, epithelial cells, and monocyte as the major cell types present in the tumor microenvironment. Among them, abundance of natural killer (NK) cells in HCC, epithelial cells, and hepatocytes in ICC was detected. CCA revealed key interaction between T cells to NK cells in HCC and smooth muscle cells to epithelial cells in the ICC. Additionally, SOX4 and DTHD1 are the top differentially expressed genes (DEGs) in HCC, while keratin and CCL4 are in ICC. Enrichment analysis of DEGs reveals major upregulated genes in HCC affect protein folding mechanism and in ICC alter pathways involved in cell adhesion. The findings suggest potential targets for the development of novel therapeutic strategies for the treatment of these two aggressive subtypes of LC.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-023-01156-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4542685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fantastic genes: where and how to find them? Exploiting rice genetic resources for the improvement of yield, tolerance, and resistance to a wide array of stresses in rice","authors":"Vincent Pamugas Reyes","doi":"10.1007/s10142-023-01159-0","DOIUrl":"10.1007/s10142-023-01159-0","url":null,"abstract":"<div><p>Rice production is a critical component of global food security. To date, rice is grown in over 100 countries and is the primary source of food for more than 3 billion people. Despite its importance, rice production is facing numerous challenges that threaten its future viability. One of the primary problems is the advent of climate change. The changing climatic conditions greatly affect the growth and productivity of rice crop and the quality of rice yield. Similarly, biotic stresses brought about by pathogen and pest infestations are greatly affecting the productivity of rice. To address these issues, the utilization of rice genetic resources is necessary to map, identify, and understand the genetics of important agronomic traits. This review paper highlights the role of rice genetic resources for developing high-yielding and stress-tolerant rice varieties. The integration of genetic, genomic, and phenomic tools in rice breeding programs has led to the development of high-yielding and stress-tolerant rice varieties. The collaboration of multidisciplinary teams of experts, sustainable farming practices, and extension services for farmers is essential for accelerating the development of high-yielding and stress-tolerant rice varieties.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4832557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Comprehensive multiomics and in silico approach uncovers prognostic, immunological, and therapeutic roles of ANLN in lung adenocarcinoma","authors":"Prithvi Singh,&nbsp;Shweta Arora,&nbsp;Md Amjad Beg,&nbsp;Sibasis Sahoo,&nbsp;Arnab Nayek,&nbsp;Mohd Mabood Khan,&nbsp;Anuradha Sinha,&nbsp;Md. Zubbair Malik,&nbsp;Fareeda Athar,&nbsp;Mohammad Serajuddin,&nbsp;Ravins Dohare,&nbsp;Mansoor Ali Syed","doi":"10.1007/s10142-023-01174-1","DOIUrl":"10.1007/s10142-023-01174-1","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4540357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural diversity and stress regulation of the plant immunity-associated CALMODULIN-BINDING PROTEIN 60 (CBP60) family of transcription factors in Solanum lycopersicum (tomato)","authors":"Vanessa Shivnauth,&nbsp;Sonya Pretheepkumar,&nbsp;Eric J. R. Marchetta,&nbsp;Christina A. M. Rossi,&nbsp;Keaun Amani,&nbsp;Christian Danve M. Castroverde","doi":"10.1007/s10142-023-01172-3","DOIUrl":"10.1007/s10142-023-01172-3","url":null,"abstract":"<div><p>Cellular signaling generates calcium (Ca²⁺) ions, which are ubiquitous secondary messengers decoded by calcium-dependent protein kinases, calcineurins, calreticulin, calmodulins (CAMs), and CAM-binding proteins. Previous studies in the model plant <i>Arabidopsis thaliana</i> have shown the critical roles of the CAM-BINDING PROTEIN 60 (CBP60) protein family in plant growth, stress responses, and immunity. Certain CBP60 factors can regulate plant immune responses, like pattern-triggered immunity, effector-triggered immunity, and synthesis of major plant immune-activating metabolites salicylic acid (SA) and <i>N</i>-hydroxypipecolic acid (NHP). Although homologous CBP60 sequences have been identified in the plant kingdom, their function and regulation in most species remain unclear. In this paper, we specifically characterized 11 members of the CBP60 family in the agriculturally important crop tomato (<i>Solanum lycopersicum</i>). Protein sequence analyses revealed that three CBP60 homologs have the closest amino acid identity to <i>Arabidopsis</i> CBP60g and SARD1, master transcription factors involved in plant immunity. Strikingly, AlphaFold deep learning–assisted prediction of protein structures highlighted close structural similarity between these tomato and <i>Arabidopsis</i> CBP60 homologs. Conserved domain analyses revealed that they possess CAM-binding domains and DNA-binding domains, reflecting their potential involvement in linking Ca²⁺ signaling and transcriptional regulation in tomato plants. In terms of their gene expression profiles under biotic (<i>Pseudomonas syringae</i> pv. <i>tomato</i> DC3000 pathogen infection) and/or abiotic stress (warming temperatures), five tomato <i>CBP60</i> genes were pathogen-responsive and temperature-sensitive, reminiscent of <i>Arabidopsis CBP60g</i> and <i>SARD1</i>. Overall, we present a genome-wide identification of the CBP60 gene/protein family in tomato plants, and we provide evidence on their regulation and potential function as Ca²⁺-sensing transcriptional regulators.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-023-01172-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4543255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Strigolactone signaling gene from soybean GmMAX2a enhances the drought and salt‑alkaline resistance in Arabidopsis via regulating transcriptional profiles of stress‑related genes","authors":"Zaib‑un Nisa,&nbsp;Yudan Wang,&nbsp;Naila Ali,&nbsp;Chen Chen,&nbsp;Xu Zhang,&nbsp;Xiaoxia Jin,&nbsp;Lijie Yu,&nbsp;Legang Jing,&nbsp;Chao Chen,&nbsp;Hosam O. Elansary","doi":"10.1007/s10142-023-01171-4","DOIUrl":"10.1007/s10142-023-01171-4","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4499982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TRIP 13-dependent pathways promote the development of gastric cancer","authors":"Fengming Ni,&nbsp;Xinmin Liu,&nbsp;Yan Xia,&nbsp;He Zhu,&nbsp;Fudong Li,&nbsp;Nan Zhang,&nbsp;Hong Xu","doi":"10.1007/s10142-023-01160-7","DOIUrl":"10.1007/s10142-023-01160-7","url":null,"abstract":"<div><p>TRIP13 is highly expressed in various human tumors and promotes tumorigenesis. We aimed to explore the biological effect of TRIP13 on gastric cancer. The RNA sequence data were retrieved from TCGA to evaluate TRIP13 mRNA expression in gastric cancer. Paired formalin-fixed paraffin-embedded blocks were further analyzed to verify the relationship between TRIP13 expression and carcinogenic status. The functions of TRIP13 on the proliferation of gastric malignancy were investigated by MTT, flow cytometry, colony formation experiment, and nude mouse tumor formation experiment. Finally, microarray analysis of TRIP13-related pathways was performed to identify the potential underlying mechanism of TRIP13 in gastric cancer. TRIP13 was found to have high expression in tumor samples. TRIP13 expression status was significantly subjective to tumor-node-metastasis (TNM) staging and poor survival. The downregulation of TRIP13 promoted apoptosis and inhibited tumor growth. TRIP13-dependent JAK/STAT and NF-κB signaling cascade were found as two key pathways in the carcinogenesis of GC. In conclusion, TRIP13 participates in the carcinogenesis of stomach cancer, and its overexpression in the cancerous tissues dovetail with advanced stage and survival. Moreover, TRIP13 functions as an upstream regulator of the JAK/STAT and p53 signaling pathways, which play critical roles in developing various malignancies.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"23 3","pages":""},"PeriodicalIF":2.9,"publicationDate":"2023-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-023-01160-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4760979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}