Functional & Integrative Genomics最新文献

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AC092100.1 promotes angiogenesis in pre-eclampsia through YTHDC2/VEGFA signaling AC092100.1 通过 YTHDC2/VEGFA 信号传导促进先兆子痫的血管生成。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-06 DOI: 10.1007/s10142-024-01428-6
Wenjing Yong, Yu Jian, Qi Wang, Kuilin Fei, Ping Li
{"title":"AC092100.1 promotes angiogenesis in pre-eclampsia through YTHDC2/VEGFA signaling","authors":"Wenjing Yong,&nbsp;Yu Jian,&nbsp;Qi Wang,&nbsp;Kuilin Fei,&nbsp;Ping Li","doi":"10.1007/s10142-024-01428-6","DOIUrl":"10.1007/s10142-024-01428-6","url":null,"abstract":"<div><p>Aberrant long non-coding RNA (lncRNA) expression has been shown to be involved in the pathological process of pre-eclampsia (PE), yet only a small portion of lncRNAs has been characterized concerning the function and molecular mechanisms involved in PE. This study aimed to investigate the regulatory mechanism of the lncRNA AC092100.1 (AC092100.1) in angiogenesis in PE. In our study, bioinformatics analysis was performed to screen for differentially expressed lncRNAs between normal subjects and PE patients. The levels of AC092100.1 in placental tissues of patients with or without PE were validated using qRT-PCR. The effect of AC092100.1 overexpression on the proliferation, migration, and tube formation of human umbilical vein endothelial cells (HUVECs) was investigated. The binding of AC092100.1 and YT521-B homology domain-containing 2 (YTHDC2) was predicted and verified. The effect of AC092100.1/YTHDC2 on the expression of vascular endothelial growth factor-A (VEGFA) in HUVECs was determined. Finally, a PE mice model was conducted. Fetal mouse growth, the abundance of mesenchymal morphology markers, including hypoxia-inducible factor 1-alpha (HIF-1α), soluble fms-like tyrosine kinase-1 (sFlt-1), soluble endoglin (sEng), Slug, and Vimentin, and endothelial markers, including placental growth factor (PLGF), CD31, and vascular endothelial (VE)-cadherin, in placental tissues were assessed. Here, we found that AC092100.1 was abnormally downregulated in placental tissues from PE patients. We established that AC092100.1 overexpression promoted HUVEC proliferation, migration, and tube formation in vitro. Mechanistically, AC092100.1 induced the accumulation of YTHDC2 and VEGFA through binding to YTHDC2 in HUVECs. Inhibition of YTHDC2 or VEGFA reversed AC092100.1-promoted tube formation. AC092100.1 overexpression contributed to alleviating fetal growth disorder, decreased levels of sEng, HIF-1α, sFlt-1, Slug, and Vimentin, and increased levels of VEGFA, PLGF, CD31, and VE-cadherin in PE mice. Our findings provided evidence supporting the role of the AC092100.1/YTHDC2/VEGFA axis in regulating angiogenesis, which demonstrated a therapeutic pathway for PE targeting angiogenesis.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138950","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}
引用次数: 0
Biotechnological frontiers in harnessing allelopathy for sustainable crop production 利用等位基因促进可持续作物生产的生物技术前沿。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-04 DOI: 10.1007/s10142-024-01418-8
Nazish Akhtar, Mo Shadab, Nourien Bhatti, Moh Sajid Ansarì, M. B. Siddiqui
{"title":"Biotechnological frontiers in harnessing allelopathy for sustainable crop production","authors":"Nazish Akhtar,&nbsp;Mo Shadab,&nbsp;Nourien Bhatti,&nbsp;Moh Sajid Ansarì,&nbsp;M. B. Siddiqui","doi":"10.1007/s10142-024-01418-8","DOIUrl":"10.1007/s10142-024-01418-8","url":null,"abstract":"<div><p>Allelopathy, the phenomenon in which plants release biochemical compounds that influence the growth and development of neighbouring plants, presents promising opportunities for revolutionizing agriculture towards sustainability. This abstract explores the role of biotechnological advancements in unlocking the potential of allelopathy for sustainable crop production and its applications in agriculture, ecology, and natural resource management. By combining molecular, genetic, biochemical, and bioinformatic tools, researchers can unravel the complexities of allelopathic interactions and their potential for sustainable crop production and environmental stewardship. The development of novel management methods for weed control is getting a lot of attention with the introduction of new genetic technologies such as Gene drive, Transgene technologies, Gene silencing, Marker-assisted selection (MAS), and Clustered regularly interspaced short palindromic repeats (CRISPR-Cas9). By strengthening competitive characteristics these tools hold great promise for boosting crops’ ability to compete with weeds. Considering recent literature, this review highlights the genetic, transcriptomics, and metabolomics approaches to allelopathy. Employing allelopathic properties in agriculture offer sustainable benefits like natural weed management, pest management, and reduced chemical pollution, but challenges include environmental factors, toxicity, regulatory hurdles, and limited resources. Effective integration requires continued research, regulatory support, and farmer education​. Also, we aimed to identify the biotechnological domains requiring more investigation and to provide the basis for future advances through this assessment.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124482","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}
引用次数: 0
Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton 长短线程 RNA 测序的综合分析揭示了陆地棉幼苗生长动态的剪接同工酶调控网络。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-04 DOI: 10.1007/s10142-024-01420-0
Kashif Shahzad, Meng Zhang, Iqra Mubeen, Xuexian Zhang, Liping Guo, Tingxiang Qi, Juanjuan Feng, Huini Tang, Xiuqin Qiao, Jianyong Wu, Chaozhu Xing
{"title":"Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton","authors":"Kashif Shahzad,&nbsp;Meng Zhang,&nbsp;Iqra Mubeen,&nbsp;Xuexian Zhang,&nbsp;Liping Guo,&nbsp;Tingxiang Qi,&nbsp;Juanjuan Feng,&nbsp;Huini Tang,&nbsp;Xiuqin Qiao,&nbsp;Jianyong Wu,&nbsp;Chaozhu Xing","doi":"10.1007/s10142-024-01420-0","DOIUrl":"10.1007/s10142-024-01420-0","url":null,"abstract":"<div><p>The polyploid genome of cotton has significantly increased the transcript complexity. Recent advances in full-length transcript sequencing are now widely used to characterize the complete landscape of transcriptional events. Such studies in cotton can help us to explore the genetic mechanisms of the cotton seedling growth. Through long-read single-molecule RNA sequencing, this study compared the transcriptomes of three yield contrasting genotypes of upland cotton. Our analysis identified different numbers of spliced isoforms from 31,166, 28,716, and 28,713 genes in SJ48, Z98, and DT8 cotton genotypes, respectively, most of which were novel compared to previous cotton reference transcriptomes, and showed significant differences in the number of exon structures and coding sequence length due to intron retention. Quantification of isoform expression revealed significant differences in expression in the root and leaf of each genotype. An array of key isoform target genes showed protein kinase or phosphorylation functions, and their protein interaction network contained most of the circadian oscillator proteins. Spliced isoforms from the GIGANTEA (GI) protien were differentially regulated in each genotype and might be expected to regulate translational activities, including the sequence and function of target proteins. In addition, these spliced isoforms generate diurnal expression profiles in cotton leaves, which may alter the transcriptional regulatory network of seedling growth. Silencing of the novel spliced <i>GI</i> isoform <i>Gh_A02G0645_N17</i> significantly affected biomass traits, contributed to variable growth, and increased transcription of the early flowering pathway gene <i>ELF</i> in cotton. Our high-throughput hybrid sequencing results will be useful to dissect functional differences among spliced isoforms in the polyploid cotton genome.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124483","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}
引用次数: 0
Revolutionizing soybean genomics: How CRISPR and advanced sequencing are unlocking new potential 大豆基因组学的革命:CRISPR 和先进测序技术如何释放新潜力。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-03 DOI: 10.1007/s10142-024-01435-7
Muhammad Khuram Razzaq, Muhammad Naveed Babur, Muhammad Jawad Akbar Awan, Ghulam Raza, Mehwish Mobeen, Ali Aslam, Kadambot H. M. Siddique
{"title":"Revolutionizing soybean genomics: How CRISPR and advanced sequencing are unlocking new potential","authors":"Muhammad Khuram Razzaq,&nbsp;Muhammad Naveed Babur,&nbsp;Muhammad Jawad Akbar Awan,&nbsp;Ghulam Raza,&nbsp;Mehwish Mobeen,&nbsp;Ali Aslam,&nbsp;Kadambot H. M. Siddique","doi":"10.1007/s10142-024-01435-7","DOIUrl":"10.1007/s10142-024-01435-7","url":null,"abstract":"<div><p>Soybean <i>Glycine max</i> L., paleopolyploid genome, poses challenges to its genetic improvement. However, the development of reference genome assemblies and genome sequencing has completely changed the field of soybean genomics, allowing for more accurate and successful breeding techniques as well as research. During the single-cell revolution, one of the most advanced sequencing tools for examining the transcriptome landscape is single-cell RNA sequencing (scRNA-seq). Comprehensive resources for genetic improvement of soybeans may be found in the SoyBase and other genomics databases. CRISPR-Cas9 genome editing technology provides promising prospects for precise genetic modifications in soybean. This method has enhanced several soybean traits, including as yield, nutritional value, and resistance to both biotic and abiotic stresses. With base editing techniques that allow for precise DNA modifications, the use of CRISPR-Cas9 is further increased. With the availability of the reference genome for soybeans and the following assembly of wild and cultivated soybeans, significant chromosomal rearrangements and gene duplication events have been identified, offering new perspectives on the complex genomic structure of soybeans. Furthermore, major single nucleotide polymorphisms (SNPs) linked to stachyose and sucrose content have been found through genome-wide association studies (GWAS), providing important tools for enhancing soybean carbohydrate profiles. In order to open up new avenues for soybean genetic improvement, future research approaches include investigating transcriptional divergence processes, enhancing genetic resources, and incorporating CRISPR-Cas9 technologies.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118718","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}
引用次数: 0
Microproteins unveiling new dimensions in cancer 微蛋白揭示癌症新领域
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-03 DOI: 10.1007/s10142-024-01426-8
S. Daisy Precilla, Indrani Biswas, T. S. Anitha, B. Agieshkumar
{"title":"Microproteins unveiling new dimensions in cancer","authors":"S. Daisy Precilla,&nbsp;Indrani Biswas,&nbsp;T. S. Anitha,&nbsp;B. Agieshkumar","doi":"10.1007/s10142-024-01426-8","DOIUrl":"10.1007/s10142-024-01426-8","url":null,"abstract":"<div><p>In the complex landscape of cancer biology, the discovery of microproteins has triggered a paradigm shift, thereby, challenging the conventional conceptions of gene regulation. Though overlooked for years, these entities encoded by the small open reading frames (100–150 codons), have a significant impact on various cellular processes. As precision medicine pioneers delve deeper into the genome and proteome, microproteins have come into the limelight. Typically characterized by a single protein domain that directly binds to the target protein complex and regulates their assembly, these microproteins have been shown to play a key role in fundamental biological processes such as RNA processing, DNA repair, and metabolism regulation. Techniques for identification and characterization, such as ribosome profiling and proteogenomic approaches, have unraveled unique mechanisms by which these microproteins regulate cell signaling or pathological processes in most diseases including cancer. However, the functional relevance of these microproteins in cancer remains unclear. In this context, the current review aims to “rethink the essence of these genes” and explore “how these hidden players-microproteins orchestrate the signaling cascades of cancer, both as accelerators and brakes.”.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118717","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}
引用次数: 0
Genomic profiling of pan-drug resistant proteus mirabilis Isolates reveals antimicrobial resistance and virulence gene landscape 对具有泛耐药性的 mirabilis 蛋白球菌分离物进行基因组分析,揭示抗菌药耐药性和毒力基因图谱。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-03 DOI: 10.1007/s10142-024-01419-7
Sarah Soliman, Salah Abdalla, Amal Zedan, Shymaa Enany
{"title":"Genomic profiling of pan-drug resistant proteus mirabilis Isolates reveals antimicrobial resistance and virulence gene landscape","authors":"Sarah Soliman,&nbsp;Salah Abdalla,&nbsp;Amal Zedan,&nbsp;Shymaa Enany","doi":"10.1007/s10142-024-01419-7","DOIUrl":"10.1007/s10142-024-01419-7","url":null,"abstract":"<div><p><i>Proteus mirabilis</i> is a gram-negative pathogen that caused significant opportunistic infections. In this study we aimed to identify antimicrobial resistance (AMR) genes and virulence determinants in two pan-drug resistant isolate “Bacteria_11” and “Bacteria_27” using whole genome sequencing. <i>Proteus mirabilis</i> “Bacteria_11” and “Bacteria_27” were isolated from two different hospitalized patients in Egypt. Antimicrobial susceptibility determined using Vitek 2 system, then whole genome sequencing (WGS) using MinION nanopore sequencing was done. Antimicrobial resistant genes and virulence determinants were identified using ResFinder, CADR AMR database, Abricate tool and VF analyzer were used respectively. Multiple sequence alignment was performed using MAFFT and FastTree, respectively. All genes were present within bacterial chromosome and no plasmid was detected. “Bacteria_11” and “Bacteria_27” had sizes of approximately 4,128,657 bp and 4,120,646 bp respectively, with GC content of 39.15% and 39.09%. “Bacteria_11” and “Bacteria_27” harbored 43 and 42 antimicrobial resistance genes respectively with different resistance mechanisms, and up to 55 and 59 virulence genes respectively. Different resistance mechanisms were identified: antibiotic inactivation, antibiotic efflux, antibiotic target replacement, and antibiotic target change. We identified several genes associated with aminoglycoside resistance, sulfonamide resistance. trimethoprim resistance tetracycline resistance proteins. Also, those responsible for chloramphenicol resistance. For beta-lactam resistance, only bla<i>VEB</i> and bla<i>CMY-2</i> genes were detected. Genome analysis revealed several virulence factors contribution in isolates pathogenicity and bacterial adaptation. As well as numerous typical secretion systems (TSSs) were present in the two isolates, including T6SS and T3SS. Whole genome sequencing of both isolates identify their genetic context of antimicrobial resistant genes and virulence determinants. This genomic analysis offers detailed representation of resistant mechanisms. Also, it clarifies <i>P. mirabilis</i> ability to acquire resistance and highlights the emergence of extensive drug resistant (XDR) and pan-drug resistant (PDR) strains. This may help in choosing the most appropriate antibiotic treatment and limiting broad spectrum antibiotic use.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369002/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118716","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}
引用次数: 0
Biotechnological studies towards improvement of finger millet using multi-omics approaches 利用多组学方法改良小米的生物技术研究。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-02 DOI: 10.1007/s10142-024-01438-4
Rushikesh Sanjay Mane, Bishun Deo Prasad, Sangita Sahni, Zeba Quaiyum, V. K. Sharma
{"title":"Biotechnological studies towards improvement of finger millet using multi-omics approaches","authors":"Rushikesh Sanjay Mane,&nbsp;Bishun Deo Prasad,&nbsp;Sangita Sahni,&nbsp;Zeba Quaiyum,&nbsp;V. K. Sharma","doi":"10.1007/s10142-024-01438-4","DOIUrl":"10.1007/s10142-024-01438-4","url":null,"abstract":"<div><p>A plethora of studies have uncovered numerous important genes with agricultural significance in staple crops. However, when it comes to orphan crops like minor millet, genomic research lags significantly behind that of major crops. This situation has promoted a focus on exploring research opportunities in minor millets, particularly in finger millet, using cutting-edge methods. Finger millet, a coarse cereal known for its exceptional nutritional content and ability to withstand environmental stresses represents a promising climate-smart and nutritional crop in the battle against escalating environmental challenges. The existing traditional improvement programs for finger millet are insufficient to address global hunger effectively. The lack of utilization of high-throughput platforms, genome editing, haplotype breeding, and advanced breeding approaches hinders the systematic multi-omics studies on finger millet, which are essential for pinpointing crucial genes related to agronomically important and various stress responses. The growing environmental uncertainties have widened the gap between the anticipated and real progress in crop improvement. To overcome these challenges a combination of cutting-edge multi-omics techniques such as high-throughput sequencing, speed breeding, mutational breeding, haplotype-based breeding, genomic selection, high-throughput phenotyping, pangenomics, genome editing, and more along with integration of deep learning and artificial intelligence technologies are essential to accelerate research efforts in finger millet. The scarcity of multi-omics approaches in finger millet leaves breeders with limited modern tools for crop enhancement. Therefore, leveraging datasets from previous studies could prove effective in implementing the necessary multi-omics interventions to enrich the genetic resource in finger millet.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103188","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}
引用次数: 0
Correction to: Single‑cell analysis identified PDIA3 as regulator of malignant characteristics and macrophage function in human cancers 更正为单细胞分析发现 PDIA3 是人类癌症恶性特征和巨噬细胞功能的调节因子。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-02 DOI: 10.1007/s10142-024-01439-3
Wantao Wu, Gang Peng, Kaiyue Wang, Yijian Yang, Zhikun Liu, Gelei Xiao
{"title":"Correction to: Single‑cell analysis identified PDIA3 as regulator of malignant characteristics and macrophage function in human cancers","authors":"Wantao Wu,&nbsp;Gang Peng,&nbsp;Kaiyue Wang,&nbsp;Yijian Yang,&nbsp;Zhikun Liu,&nbsp;Gelei Xiao","doi":"10.1007/s10142-024-01439-3","DOIUrl":"10.1007/s10142-024-01439-3","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103190","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}
引用次数: 0
Modulatory effects of miRNAs in doxorubicin resistance: A mechanistic view miRNA 在多柔比星耐药性中的调节作用:从机理角度看
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-02 DOI: 10.1007/s10142-024-01431-x
Fatemeh Ebadi Meinag, Mina Fatahi, Vahid Vahedian, Nazila Fathi Maroufi, Bashir Mosayyebi, Elham Ahmadi, Mohammad Rahmati
{"title":"Modulatory effects of miRNAs in doxorubicin resistance: A mechanistic view","authors":"Fatemeh Ebadi Meinag,&nbsp;Mina Fatahi,&nbsp;Vahid Vahedian,&nbsp;Nazila Fathi Maroufi,&nbsp;Bashir Mosayyebi,&nbsp;Elham Ahmadi,&nbsp;Mohammad Rahmati","doi":"10.1007/s10142-024-01431-x","DOIUrl":"10.1007/s10142-024-01431-x","url":null,"abstract":"<div><p>MicroRNAs (miRNAs) are a group of small non-coding RNAs and play an important role in controlling vital biological processes, including cell cycle control, apoptosis, metabolism, and development and differentiation, which lead to various diseases such as neurological, metabolic disorders, and cancer. Chemotherapy consider as gold treatment approaches for cancer patients. However, chemotherapeutic is one of the main challenges in cancer management. Doxorubicin (DOX) is an anti-cancer drug that interferes with the growth and spread of cancer cells. DOX is used to treat various types of cancer, including breast, nervous tissue, bladder, stomach, ovary, thyroid, lung, bone, muscle, joint and soft tissue cancers. Also recently, miRNAs have been identified as master regulators of specific genes responsible for the mechanisms that initiate chemical resistance. miRNAs have a regulatory effect on chemotherapy resistance through the regulation of apoptosis process. Also, the effect of miRNAs p53 gene as a key tumor suppressor was confirmed via studies. miRNAs can affect main biological pathways include PI3K pathway. This review aimed to present the current understanding of the mechanisms and effects of miRNAs on apoptosis, p53 and PTEN/PI3K/Akt signaling pathway related to DOX resistance.</p><h3>Graphical Abstract</h3><p>miRNAs involve in DOX resistance according to effecting pathways.</p><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103192","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}
引用次数: 0
Milletomics: a metabolomics centered integrated omics approach toward genetic progression 小米组学:一种以代谢组学为中心、面向遗传进展的综合组学方法。
IF 3.9 4区 生物学
Functional & Integrative Genomics Pub Date : 2024-09-02 DOI: 10.1007/s10142-024-01430-y
Saikat Mazumder, Debasmita Bhattacharya, Dibyajit Lahiri, Moupriya Nag
{"title":"Milletomics: a metabolomics centered integrated omics approach toward genetic progression","authors":"Saikat Mazumder,&nbsp;Debasmita Bhattacharya,&nbsp;Dibyajit Lahiri,&nbsp;Moupriya Nag","doi":"10.1007/s10142-024-01430-y","DOIUrl":"10.1007/s10142-024-01430-y","url":null,"abstract":"<div><p>Producing alternative staple foods like millet will be essential to feeding ten billion people by 2050. The increased demand for millet is driving researchers to improve its genetic variation. Millets include protein, dietary fiber, phenolic substances, and flavonoid components. Its climate resilience makes millet an appealing crop for agronomic sustainability. Integrative omics technologies could potentially identify and develop millets with desirable phenotypes that may have high agronomic value. Millets’ salinity and drought tolerance have been enhanced using transcriptomics. In foxtail, finger, and pearl millet, proteomics has discovered salt-tolerant protein, phytohormone-focused protein, and drought tolerance. Metabolomics studies have revealed that certain metabolic pathways including those involving lignin, flavonoids, phenylpropanoid, and lysophospholipids are critical for many processes, including seed germination, photosynthesis, energy metabolism, and the synthesis of bioactive chemicals necessary for drought tolerance. Metabolomics integration with other omics revealed metabolome engineering and trait-specific metabolite creation. Integrated metabolomics and ionomics are still in the development stage, but they could potentially assist in comprehending the pathway of ionomers to control nutrient levels and biofortify millet. Epigenomic analysis has shown alterations in DNA methylation patterns and chromatin structure in foxtail and pearl millets in response to abiotic stress. Whole-genome sequencing utilizing next-generation sequencing is the most proficient method for finding stress-induced phytoconstituent genes. New genome sequencing enables novel biotechnological interventions including genome-wide association, mutation-based research, and other omics approaches. Millets can breed more effectively by employing next-generation sequencing and genotyping by sequencing, which may mitigate climate change. Millet marker-assisted breeding has advanced with high-throughput markers and combined genotyping technologies.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"24 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103191","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}
引用次数: 0
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