Omics A Journal of Integrative Biology最新文献

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Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning. 超越疾病孤岛的思考:系统生物学和机器学习发现的肺结核和肺癌中常见的失调基因》(Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning)。
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-07-01 Epub Date: 2024-06-10 DOI: 10.1089/omi.2024.0116
Sanjukta Dasgupta
{"title":"Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning.","authors":"Sanjukta Dasgupta","doi":"10.1089/omi.2024.0116","DOIUrl":"10.1089/omi.2024.0116","url":null,"abstract":"<p><p>The traditional way of thinking about human diseases across clinical and narrow phenomics silos often masks the underlying shared molecular substrates across human diseases. One Health and planetary health fields particularly address such complexities and invite us to think across the conventional disease nosologies. For example, tuberculosis (TB) and lung cancer (LC) are major pulmonary diseases with significant planetary health implications. Despite distinct etiologies, they can coexist in a given community or patient. This is both a challenge and an opportunity for preventive medicine, diagnostics, and therapeutics innovation. This study reports a bioinformatics analysis of publicly available gene expression data, identifying overlapping dysregulated genes, downstream regulators, and pathways in TB and LC. Analysis of NCBI-GEO datasets (GSE83456 and GSE103888) unveiled differential expression of <i>CEACAM6</i>, <i>MUC1</i>, <i>ADM</i>, <i>DYSF</i>, <i>PLOD2</i>, and <i>GAS6</i> genes in both diseases, with pathway analysis indicating association with lysine degradation pathway. Random forest, a machine-learning-based classification, achieved accuracies of 84% for distinguishing TB from controls and 83% for discriminating LC from controls using these specific genes. Additionally, potential drug targets were identified, with molecular docking confirming the binding affinity of warfarin to <i>GAS6</i>. Taken together, the present study speaks of the pressing need to rethink clinical diagnostic categories of human diseases and that TB and LC might potentially share molecular substrates. Going forward, planetary health and One Health scholarship are poised to cultivate new ways of thinking about diseases not only across medicine and ecology but also across traditional diagnostic conventions.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141296504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Etiologically Significant microRNAs in Hepatitis B Virus-Induced Hepatocellular Carcinoma. 乙型肝炎病毒诱导的肝细胞癌中具有重要病因学意义的 microRNA。
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-06-01 Epub Date: 2024-05-31 DOI: 10.1089/omi.2024.0071
Krishnapriya Ramakrishnan, Riya Vishwakarma, Radul R Dev, Rajesh Raju, Niyas Rehman
{"title":"Etiologically Significant microRNAs in Hepatitis B Virus-Induced Hepatocellular Carcinoma.","authors":"Krishnapriya Ramakrishnan, Riya Vishwakarma, Radul R Dev, Rajesh Raju, Niyas Rehman","doi":"10.1089/omi.2024.0071","DOIUrl":"10.1089/omi.2024.0071","url":null,"abstract":"<p><p>Hepatitis B virus (HBV) infection has been causally linked to hepatocellular carcinoma (HCC) in more than 50% cases. MicroRNAs (miRNAs) play cross-cutting mechanistic roles in the complex interplay between viral pathogenesis, host survival, and clinical outcomes. The present study set out to identify etiologically significant human miRNAs associated with HBV infection in liver-related pathologies leading to HCC. In diverse tissue types, we assembled 573 miRNAs differentially expressed in HBV-associated liver pathologies, HBV infection, fibrosis, cirrhosis, acute on chronic liver failure, and HCC. Importantly, 43 human differentially expressed miRNAs (hDEmiRs) were regulated in serum/plasma and liver tissue of patients with HBV-positive conditions. However, only two hDEmiRs, hsa-miR-21-5p and hsa-miR-143-3p, were regulated across all disease conditions. To shortlist the functional miRNAs in HBV-induced HCC pathogenesis, a reverse bioinformatics analysis was performed using eight GEO datasets and the TCGA database containing the list of differentially regulated mRNAs in HCC. A comparative study using these data with the identified targets of hDEmiRs, a set of unidirectionally regulated hDEmiRs with the potential to modulate mRNAs in HCC, were found. Moreover, our study identified five miRNAs; hsa-miR-98-5p, hsa-miR-193b-3p, hsa-miR-142-5p, hsa-miR-522-5p, and hsa-miR-370-3p targeting <i>PIGC</i>, <i>KNTC1</i>, <i>CSTF2</i>, <i>SLC41A2</i>, and <i>RAB17</i>, respectively, in HCC. These hDEmiRs and their targets could be pivotal in HBV infection and subsequent liver pathologies modulating HCC clinical progression. HBV infection is the largest contributor to HCC, and the present study comprises the first of its kind compendium of hDEmiRs related to HBV-related pathologies.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141180173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Major Genetic Drivers of Statin Treatment Response in African Populations and Pharmacogenetics of Dyslipidemia Through a One Health Lens. 非洲人群中他汀类药物治疗反应的主要遗传驱动因素和血脂异常的药物遗传学
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-06-01 Epub Date: 2023-11-14 DOI: 10.1089/omi.2023.0122
Zizo Lusiki, Dirk Blom, Nyarai D Soko, Smangele Malema, Erika Jones, Brian Rayner, Jonathan Blackburn, Phumla Sinxadi, Michelle T Dandara, Collet Dandara
{"title":"Major Genetic Drivers of Statin Treatment Response in African Populations and Pharmacogenetics of Dyslipidemia Through a One Health Lens.","authors":"Zizo Lusiki, Dirk Blom, Nyarai D Soko, Smangele Malema, Erika Jones, Brian Rayner, Jonathan Blackburn, Phumla Sinxadi, Michelle T Dandara, Collet Dandara","doi":"10.1089/omi.2023.0122","DOIUrl":"10.1089/omi.2023.0122","url":null,"abstract":"<p><p>A One Health lens is increasingly significant to address the intertwined challenges in planetary health concerned with the health of humans, nonhuman animals, plants, and ecosystems. A One Health approach can benefit the public health systems in Africa that are overburdened by noncommunicable, infectious, and environmental diseases. Notably, the COVID-19 pandemic revealed the previously overlooked two-fold importance of pharmacogenetics (PGx), for individually tailored treatment of noncommunicable diseases and environmental pathogens. For example, dyslipidemia, a common cardiometabolic risk factor, has been identified as an independent COVID-19 severity risk factor. Observational data suggest that patients with COVID-19 infection receiving lipid-lowering therapy may have better outcomes. However, among African patients, the response to these drugs varies from patient to patient, pointing to the possible contribution of genetic variation in important pharmacogenes. The PGx of lipid-lowering therapies may underlie differences in treatment responses observed among dyslipidemia patients as well as patients comorbid with COVID-19 and dyslipidemia. Genetic variations in <i>APOE, ABCB1, CETP, CYP2C9, CYP3A4, CYP3A5, HMGCR, LDLR, NPC1L1,</i> and <i>SLCO1B1 g</i>enes affect the pharmacogenomics of statins, and they have individually been linked to differential responses to dyslipidemia and COVID-19 treatment. African populations are underrepresented in PGx research. This leads to poor accounting of additional diverse genetic variants that could be important in understanding interindividual and between-population variations in therapeutic responses to dyslipidemia and COVID-19. This expert review examines and synthesizes the salient and priority PGx variations, as seen through a One Health lens in Africa, to improve and inform personalized medicine in both dyslipidemia and COVID-19.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92155942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Pomegranate Rhizosphere Microbial Diversity Revealed by Metagenomics: Toward Organic Farming, Plant Growth Promotion and Biocontrol? 元基因组学揭示的石榴根瘤微生物多样性:实现有机农业、植物生长促进和生物防治?
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-06-01 Epub Date: 2024-05-28 DOI: 10.1089/omi.2023.0272
Renuka Ravinath, Talambedu Usha, Anupam J Das, Aditya Narayan Sarangi, Neelakanta Sarvashiva Kiran, Arvind Kumar Goyal, Mothukapalli Krishnareddy Prasannakumar, Nijalingappa Ramesh, Sushil Kumar Middha
{"title":"Pomegranate Rhizosphere Microbial Diversity Revealed by Metagenomics: Toward Organic Farming, Plant Growth Promotion and Biocontrol?","authors":"Renuka Ravinath, Talambedu Usha, Anupam J Das, Aditya Narayan Sarangi, Neelakanta Sarvashiva Kiran, Arvind Kumar Goyal, Mothukapalli Krishnareddy Prasannakumar, Nijalingappa Ramesh, Sushil Kumar Middha","doi":"10.1089/omi.2023.0272","DOIUrl":"10.1089/omi.2023.0272","url":null,"abstract":"<p><p>Food production must undergo systems change to meet the sustainable development goals (SDGs). For example, organic farming can be empowered by soil microorganisms with plant growth promotion (PGP) and biocontrol features. In this context, there have been limited studies on pomegranate. We investigated microbial diversity in rhizosphere of the pomegranate \"Bhagwa\" variety and its potential role in PGP and biocontrol. Both bulk and rhizosphere soil samples were analyzed for their physicochemical properties. Whole metagenome sequencing was conducted using the Illumina NovaSeq6000 platform. Surprisingly, we found that bulk and rhizosphere soil samples had comparable microbial diversity. Metagenome sequencing revealed the abundance of <i>Streptomyces indicus, Bradyrhizobium kalamazoonesis,</i> and <i>Pseudomonas cellulosum</i> in the rhizosphere that are reported here for the first time in agricultural literature. Pathway prediction analysis using KEGG (Kyoto Encyclopedia for Genes and Genomes) and COG (clusters of orthologous genes) databases identified metabolic pathways associated with biocontrol properties against pathogens. We confirmed the metagenome data <i>in vitro</i>, which demonstrated their PGP potential and antimicrobial properties. For instance, <i>S. indicus</i> produced high concentration of indole-3-acetic acid, a PGP phytohormone, that can stimulate plant growth. In addition, an antimicrobial susceptibility assay suggested that bacterial extracts displayed activity against <i>Xanthomonas</i>, a primary pathogen causing the pomegranate wilt disease. In conclusion, this study suggests that <i>S. indicus, B. kalamazoonesis</i>, and <i>P. cellulosum</i> can potentially be PGP and biocontrol agents that may contribute to increased crop productivity in pomegranate cultivation. These agents and their combinations warrant future research with an eye on SDGs and so as to enable and innovate organic farming and pomegranate agricultural practices.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
A Quadruple Revolution: Deciphering Biological Complexity with Artificial Intelligence, Multiomics, Precision Medicine, and Planetary Health. 四重革命:用人工智能、多组学、精准医学和行星健康破解生物复杂性。
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-06-01 Epub Date: 2024-05-30 DOI: 10.1089/omi.2024.0110
Yi Cong, Toshinori Endo
{"title":"A Quadruple Revolution: Deciphering Biological Complexity with Artificial Intelligence, Multiomics, Precision Medicine, and Planetary Health.","authors":"Yi Cong, Toshinori Endo","doi":"10.1089/omi.2024.0110","DOIUrl":"10.1089/omi.2024.0110","url":null,"abstract":"<p><p>A quiet quadruple revolution has been in the making in systems science with convergence of (1) artificial intelligence, machine learning, and other digital technologies; (2) multiomics big data integration; (3) growing interest in the \"variability science\" of precision/personalized medicine that aims to account for patient-to-patient and between-population differences in disease susceptibilities and responses to health interventions such as drugs, nutrition, vaccines, and radiation; and (4) planetary health scholarship that both scales up and integrates biological, clinical, and ecological contexts of health and disease. Against this overarching background, this article presents and highlights some of the salient challenges and prospects of multiomics research, emphasizing the attendant pivotal role of systems medicine and systems biology. In addition, we emphasize the rapidly growing importance of planetary health research for systems medicine, particularly amid climate emergency, ecological degradation, and loss of planetary biodiversity. Looking ahead, we anticipate that the integration and utilization of multiomics big data and artificial intelligence will drive further progress in systems medicine and systems biology, heralding a promising future for both human and planetary health.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Can Microbiome Modulate Regenerative Capacity? A Comparative Microbiome Study Reveals a Dominant Presence of Flavobacteriaceae in Blastema Tissue During Axolotl Limb Regeneration. 微生物组能否调节再生能力?微生物组比较研究揭示了在轴足类肢体再生过程中泡组织中主要存在黄杆菌。
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-06-01 Epub Date: 2024-05-29 DOI: 10.1089/omi.2024.0075
Turan Demircan, Sultan Gül, Ebru Altuntaş Taşçı
{"title":"Can Microbiome Modulate Regenerative Capacity? A Comparative Microbiome Study Reveals a Dominant Presence of Flavobacteriaceae in Blastema Tissue During Axolotl Limb Regeneration.","authors":"Turan Demircan, Sultan Gül, Ebru Altuntaş Taşçı","doi":"10.1089/omi.2024.0075","DOIUrl":"10.1089/omi.2024.0075","url":null,"abstract":"<p><p>The axolotl (<i>Ambystoma mexicanum</i>) is renowned for its remarkable regenerative capabilities, which are not diminished by the transition from a neotenic to a metamorphic state. This study explored the microbiome dynamics in axolotl limb regeneration by examining the microbial communities present in neotenic and metamorphic axolotls at two critical stages of limb regeneration: pre-amputation and during blastema formation. Utilizing 16S rRNA amplicon sequencing, we investigated the variations in microbiome profiles associated with different developmental and regenerative states. Our findings reveal a distinct separation in the microbiome profiles of neotenic and metamorphic samples, with a clear demarcation in microbial composition at both the phylum and genus levels. In neotenic 0DPA samples, Proteobacteria and Firmicutes were the most abundant, whereas in neotenic 7DPA samples, Proteobacteria and Bacteroidetes dominated. Conversely, metamorphic samples displayed a higher abundance of Firmicutes and Bacteroidetes at 0DPA and Proteobacteria and Firmicutes at 7DPA. Alpha and beta diversity analyses, along with dendrogram construction, demonstrated significant variations within and between the sample groups, suggesting a strong influence of both developmental stage and regenerative state on the microbiome. Notably, Flavobacterium and Undibacterium emerged as distinctive microbial entities in neotenic 7DPA samples, highlighting potential key players in the microbial ecology of regeneration. These findings suggest that the axolotl's microbiome is dynamically responsive to blastema formation, and they underscore the potential influence of microbial communities on the regeneration process. This study lays the groundwork for future research into the mechanisms by which the microbiome may modulate regenerative capacity.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Machine Learning Strategies in MicroRNA Research: Bridging Genome to Phenome. MicroRNA 研究中的机器学习策略:连接基因组与表型组
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-05-01 Epub Date: 2024-05-15 DOI: 10.1089/omi.2024.0047
Sonet Daniel Thomas, Krithika Vijayakumar, Levin John, Deepak Krishnan, Niyas Rehman, Amjesh Revikumar, Jalaluddin Akbar Kandel Codi, Thottethodi Subrahmanya Keshava Prasad, Vinodchandra S S, Rajesh Raju
{"title":"Machine Learning Strategies in MicroRNA Research: Bridging Genome to Phenome.","authors":"Sonet Daniel Thomas, Krithika Vijayakumar, Levin John, Deepak Krishnan, Niyas Rehman, Amjesh Revikumar, Jalaluddin Akbar Kandel Codi, Thottethodi Subrahmanya Keshava Prasad, Vinodchandra S S, Rajesh Raju","doi":"10.1089/omi.2024.0047","DOIUrl":"10.1089/omi.2024.0047","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) have emerged as a prominent layer of regulation of gene expression. This article offers the salient and current aspects of machine learning (ML) tools and approaches from genome to phenome in miRNA research. First, we underline that the complexity in the analysis of miRNA function ranges from their modes of biogenesis to the target diversity in diverse biological conditions. Therefore, it is imperative to first ascertain the miRNA coding potential of genomes and understand the regulatory mechanisms of their expression. This knowledge enables the efficient classification of miRNA precursors and the identification of their mature forms and respective target genes. Second, and because one miRNA can target multiple mRNAs and <i>vice versa</i>, another challenge is the assessment of the miRNA-mRNA target interaction network. Furthermore, long-noncoding RNA (lncRNA)and circular RNAs (circRNAs) also contribute to this complexity. ML has been used to tackle these challenges at the high-dimensional data level. The present expert review covers more than 100 tools adopting various ML approaches pertaining to, for example, (1) miRNA promoter prediction, (2) precursor classification, (3) mature miRNA prediction, (4) miRNA target prediction, (5) miRNA- lncRNA and miRNA-circRNA interactions, (6) miRNA-mRNA expression profiling, (7) miRNA regulatory module detection, (8) miRNA-disease association, and (9) miRNA essentiality prediction. Taken together, we unpack, critically examine, and highlight the cutting-edge synergy of ML approaches and miRNA research so as to develop a dynamic and microlevel understanding of human health and diseases.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140945664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Global Governance for Personalized Medicine, Politics of Uncertainty, and Pierre Bourdieu. 个性化医疗的全球治理》、《不确定性政治》和《皮埃尔-布尔迪厄》。
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-05-01 Epub Date: 2024-05-06 DOI: 10.1089/omi.2024.0091
Vural Özdemir
{"title":"Global Governance for Personalized Medicine, Politics of Uncertainty, and Pierre Bourdieu.","authors":"Vural Özdemir","doi":"10.1089/omi.2024.0091","DOIUrl":"10.1089/omi.2024.0091","url":null,"abstract":"<p><p>How we choose to respond to uncertainty matters for robust and responsible science. New laws and consensus reports are popular instruments for global governance of emerging technology and attendant uncertainty. However, the sociologist Pierre Bourdieu noted that \"[t]he judicial situation operates like a <i>neutral space</i> that <i>neutralizes</i> the stakes in any conflict through the de-realization and distancing implicit in the conversion of a direct struggle between parties into a dialogue between mediators.\" Put in other words, while law and legal modes of reasoning are certainly useful for conflict resolution and closure, their overprivileging in emerging technology and uncertainty governance can potentially bring about depoliticization by transforming the struggles and dissent necessary for democratic governance into a \"dialogue between mediators.\" Hence, the critical sociological gaze offered by Bourdieu is particularly relevant for democratization of global governance of multiomics technologies and timely with the current uptake of personalized medicine. For example, in May 2023, the Romanian government introduced a law to give patients the right to personalized medicine. Personalized medicine is related to the larger umbrella concept and field of theranostics, the fusion of therapeutics and diagnostics. It is therefore timely to reflect on a \"right for theranostics in planetary health,\" considering the potential for future pandemics and ecological crises in the 21st century. Rather than forcing consensus or convergence in an innovation ecosystem, dissent grounded in rigorous political theory, sociology of law and critical legal studies can strengthen democratization and global governance for personalized medicine and multiomics technologies.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140863494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Molecular Basis of Cerebral Vasospasm: What Can We Learn from Transcriptome and Temporal Gene Expression Profiling in Intracranial Aneurysm? 脑血管痉挛的分子基础:从颅内动脉瘤的转录组和时相基因表达谱分析中我们能学到什么?
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-05-01 Epub Date: 2024-05-07 DOI: 10.1089/omi.2024.0070
Munish Kumar, Tanavi Sharma, Krishna Patel, Shobia Chinnapparaj, Ravi Dixit, Chandrashekhar Gendle, Ashish Aggarwal, Aastha Takkar, Tulika Gupta, Navneet Singla, Arnab Pal, Pravin Salunke, Sivashanmugam Dhandapani, Rajesh Chabra, Aditi Chatterjee, Harsha Gowda, Hemant Bhagat
{"title":"Molecular Basis of Cerebral Vasospasm: What Can We Learn from Transcriptome and Temporal Gene Expression Profiling in Intracranial Aneurysm?","authors":"Munish Kumar, Tanavi Sharma, Krishna Patel, Shobia Chinnapparaj, Ravi Dixit, Chandrashekhar Gendle, Ashish Aggarwal, Aastha Takkar, Tulika Gupta, Navneet Singla, Arnab Pal, Pravin Salunke, Sivashanmugam Dhandapani, Rajesh Chabra, Aditi Chatterjee, Harsha Gowda, Hemant Bhagat","doi":"10.1089/omi.2024.0070","DOIUrl":"10.1089/omi.2024.0070","url":null,"abstract":"<p><p>Cerebral vasospasm (CV) is a significant complication following aneurysmal subarachnoid hemorrhage (aSAH), and lacks a comprehensive molecular understanding. Given the temporal trajectory of intracranial aneurysm (IA) formation, its rupture, and development of CV, altered gene expression might be a molecular substrate that runs through these clinical events, influencing both disease inception and progression. Utilizing RNA-Seq, we analyzed tissue samples from ruptured IAs with and without vasospasm to identify the dysregulated genes. In addition, temporal gene expression analysis was conducted. We identified seven dysregulated genes in patients with ruptured IA with vasospasm when compared with those without vasospasm. We found 192 common genes when the samples of each clinical subset of patients with IA, that is, unruptured aneurysm, ruptured aneurysm without vasospasm, and ruptured aneurysm with vasospasm, were compared with control samples. Among these common genes, <i>TNFSF13B</i>, <i>PLAUR</i>, <i>OSM</i>, and <i>LAMB3</i> displayed temporal expression (progressive increase) with the pathological progression of disease that is formation of aneurysm, its rupture, and consequently the development of vasospasm. We validated the temporal gene expression pattern of <i>OSM</i> at both the transcript and protein levels and <i>OSM</i> emerges as a crucial gene implicated in the pathological progression of disease. In addition, <i>RSAD2</i> and <i>ATP1A2</i> appear to be pivotal genes for CV development. To the best of our knowledge, this is the first study to compare the transcriptome of aneurysmal tissue samples of aSAH patients with and without CV. The findings collectively provide new insights on the molecular basis of IA and CV and new leads for translational research.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140891864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Romania's Pioneering Law: Establishing the Right to Personalized Medicine. 罗马尼亚的先锋法律:确立个性化医疗的权利。
IF 2.2 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2024-05-01 Epub Date: 2024-05-14 DOI: 10.1089/omi.2024.0039
Marius Geanta, Cosmina Cioroboiu, Bianca Cucos, Adriana Boata
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