Omics A Journal of Integrative Biology最新文献_第2页

A Paradigm to Identify Biomarkers with Tissue Specificity and Disease Causality. 鉴定具有组织特异性和疾病因果性的生物标记物的范例。

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2025-01-01 Epub Date: 2024-12-16 DOI: 10.1089/omi.2024.0194

Biaoyang Lin, Yingying Ma, Hongyun Yang, Xixiong Kang

引用次数: 0

Multiplexed Molecular Endophenotypes Help Identify Hub Genes in Non-Small Cell Lung Cancer: Unlocking Next-Generation Cancer Phenomics. 多重分子内表型有助于识别非小细胞肺癌的中心基因：解锁下一代癌症表型组学

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2025-01-01 DOI: 10.1089/omi.2024.0179

Sanjukta Dasgupta

{"title":"Multiplexed Molecular Endophenotypes Help Identify Hub Genes in Non-Small Cell Lung Cancer: Unlocking Next-Generation Cancer Phenomics.","authors":"Sanjukta Dasgupta","doi":"10.1089/omi.2024.0179","DOIUrl":"https://doi.org/10.1089/omi.2024.0179","url":null,"abstract":"Next-generation cancer phenomics by deployment of multiple molecular endophenotypes coupled with high-throughput analyses of gene expression offer veritable opportunities for triangulation of discovery findings in non-small cell lung cancer (NSCLC) research. This study reports differentially expressed genes in NSCLC using publicly available datasets (GSE18842 and GSE229253), uncovering 130 common genes that may potentially represent crucial molecular signatures of NSCLC. Additionally, network analyses by GeneMANIA and STRING revealed significant coexpression and interaction patterns among these genes, with four notable hub genes-GRK5, CAV1, PPARG, and CXCR2-identified as pivotal in NSCLC progression. Validation of these hub genes indicated their consistent downregulation in tumor tissues compared to normal counterparts. Gene expression across the endophenotypes representing pathological stages revealed distinct downregulation trends, emphasizing their putative roles as biomarkers for cancer progression. Moreover, three miRNAs (hsa-miR-429, hsa-miR-335-5p, and hsa-miR-126-3p) showed strong associations with these hub genes, while SREBF1 emerged as a relevant transcription factor. Pathway enrichment analysis identified the chemokine signaling pathway as significantly associated with these genes, highlighting its role in tumor progression and immune evasion. Cell-type enrichment analysis indicated that endothelial cells may play a significant role in NSCLC pathogenesis. Finally, survival analysis demonstrated that GRK5 is a potential oncogenic marker, whereas CAV1 may have a protective effect. These findings collectively underscore the critical molecular interactions in NSCLC and suggest novel paths for translational research, targeted therapies, and prognostic markers in clinical settings. They also attest to the promises of next-generation cancer phenomics using multiple endophenotypes for discovery and triangulation of novel findings.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":"29 1","pages":"8-17"},"PeriodicalIF":2.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143009126","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

Artificial Intelligence and Environmental Impact: Moving Beyond Humanizing Vocabulary and Anthropocentrism. 人工智能与环境影响：超越人性化词汇和人类中心主义。

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2025-01-01 Epub Date: 2024-12-17 DOI: 10.1089/omi.2024.0197

Ümit Karakaş, Vural Özdemir

{"title":"Artificial Intelligence and Environmental Impact: Moving Beyond Humanizing Vocabulary and Anthropocentrism.","authors":"Ümit Karakaş, Vural Özdemir","doi":"10.1089/omi.2024.0197","DOIUrl":"10.1089/omi.2024.0197","url":null,"abstract":"Artificial intelligence (AI) and its applications in digital health, bioengineering, and society have significant material impacts on the environment owing to AI's vast energy demands and energy consumption, carbon footprints, and water usage to cool data centers and generate electricity to power the data centers. Yet, the environmental footprints of AI remain underappreciated and inadequately acknowledged. This is significant, particularly in this era of climate emergency and ongoing threats to planetary energy and water supplies. The vocabulary attached to AI often aims to mimic positive human capacities such as \"warmness\" and \"care.\" However, these attempts to humanize AI and digital technology come with an anthropocentric gaze and blind spots that bracket out the environmental impacts and footprints of AI and privilege humans and technology over nonhuman animals and planetary ecological limits. In medicine, the environmental impacts of large language models range from water consumption and carbon emission to rare mineral usage. This commentary and innovation analysis question and queer the popular imagination of AI and digital technology as things that only exist in the immaterial world of cyberspace. In the course of research on AI in planetary health, we must be cognizant of its materiality, ecological impacts, and massive energy and water demands. We argue that moving away from anthropocentric narratives and vocabulary in AI design and praxis would bode well to live within planetary ecological limits so that AI and emerging digital technologies best serve robust and responsible science and all life on the planet Earth.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"2-4"},"PeriodicalIF":2.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847170","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

Role of N-Glycosylation in Gastrointestinal Cancers. N 型糖基化在胃肠道癌症中的作用

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2024-12-01 Epub Date: 2024-11-08 DOI: 10.1089/omi.2024.0174

Ruirui Xu, Lois Balmer, Gengzhen Chen, Manshu Song

{"title":"Role of N-Glycosylation in Gastrointestinal Cancers.","authors":"Ruirui Xu, Lois Balmer, Gengzhen Chen, Manshu Song","doi":"10.1089/omi.2024.0174","DOIUrl":"10.1089/omi.2024.0174","url":null,"abstract":"Gastrointestinal cancers pose a significant global health challenge. N-glycosylation modulates various cellular processes, including key cancer-related mechanisms. Elucidating its involvement in the onset and advancement of these cancers can offer critical insights for enhancing diagnostic and therapeutic approaches. This review outlines the core process of protein N-glycosylation and highlights its contribution to the progression of gastrointestinal cancers, encompassing cell proliferation, survival, invasion, metastasis, and immune evasion, mainly through its impact on critical signaling pathways. Notably, aberrant N-glycosylation patterns have emerged as crucial biomarkers for the diagnosis and prognosis of various gastrointestinal cancers, providing the foundation for more personalized therapeutic approaches. Therapeutic strategies targeting N-glycosylation, such as glycosyltransferase inhibitors and glycoengineering, show significant promise in mitigating tumor aggressiveness and enhancing immune recognition. However, the clinical implementation of N-glycosylation biomarkers requires the standardization of glycosylation analysis techniques and solutions to challenges in sample processing and data interpretation. Future research efforts should concentrate on overcoming these obstacles to unlock the full potential of N-glycosylation in enhancing cancer management and advancing patient outcomes.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"596-607"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605851","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

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2024-12-01 Epub Date: 2024-11-25 DOI: 10.1089/omi.2024.0172

Jie Yu, Jingjing Zhu, Hua Zhong, Zicheng Zhang, Jiawen Liu, Xin Lin, Guanghua Zeng, Min Zhang, Chong Wu, Youping Deng, Yanfa Sun, Lang Wu

{"title":"Age-Related Hearing Impairment: Genome and Blood Methylome Data Integration Reveals Candidate Epigenetic Biomarkers.","authors":"Jie Yu, Jingjing Zhu, Hua Zhong, Zicheng Zhang, Jiawen Liu, Xin Lin, Guanghua Zeng, Min Zhang, Chong Wu, Youping Deng, Yanfa Sun, Lang Wu","doi":"10.1089/omi.2024.0172","DOIUrl":"10.1089/omi.2024.0172","url":null,"abstract":"Age-related hearing impairment (ARHI) is a major planetary health burden that is in need of precision medicine for prevention, diagnosis, and treatment. The present study was set out to identify candidate epigenetic markers for ARHI. Associations of genetically predicted DNA methylation levels with ARHI risk were evaluated using two sets of blood DNA methylation genetic prediction models in 147,997 cases and 575,269 controls of European descent. A total of 1314 CpG sites (CpGs) were significantly associated with ARHI risk at a false discovery rate (FDR) <0.05, including 12 putatively causal CpGs based on fine-mapping analysis. Measured methylation levels of 247 of the associated CpGs were significantly correlated with measured expression levels of 127 nearby genes in blood at an FDR <0.05. A total of 37 CpGs and their 18 nearby genes showed consistent association directions for the methylation-gene expression-ARHI risk pathway. Importantly, three genes (PEX6, TCF19, and SPTBN1) were enriched in auditory disease categories. Our results indicate that specific CpGs may modulate ARHI risk by regulating the expression of candidate ARHI target genes. Future precision medicine and biomarker development research on ARHI are called for.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"620-631"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710780","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

Next-Generation Cancer Phenomics: A Transformative Approach to Unraveling Lung Cancer Complexity and Advancing Precision Medicine. 下一代癌症表型组学：揭示肺癌复杂性和推进精准医疗的变革性方法》（Next-Generation Cancer Phenomics: A Transformative Approach to Unraveling Lung Cancer Complexity and Advancing Precision Medicine）。

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2024-12-01 Epub Date: 2024-10-22 DOI: 10.1089/omi.2024.0175

Sanjukta Dasgupta

{"title":"Next-Generation Cancer Phenomics: A Transformative Approach to Unraveling Lung Cancer Complexity and Advancing Precision Medicine.","authors":"Sanjukta Dasgupta","doi":"10.1089/omi.2024.0175","DOIUrl":"10.1089/omi.2024.0175","url":null,"abstract":"Lung cancer remains one of the leading causes of cancer-related deaths globally, with its complexity driven by intricate and intertwined genetic, epigenetic, and environmental factors. Despite advances in genomics, transcriptomics, and proteomics, understanding the phenotypic diversity of lung cancer has lagged behind. Next-generation phenomics, which integrates high-throughput phenotypic data with multiomics approaches and digital technologies such as artificial intelligence (AI), offers a transformative strategy for unraveling the complexity of lung cancer. This approach leverages advanced imaging, single-cell technologies, and AI to capture dynamic phenotypic variations at cellular, tissue, and whole organism levels and in ways resolved in temporal and spatial contexts. By mapping the high-throughput and spatially and temporally resolved phenotypic profiles onto molecular alterations, next-generation phenomics provides deeper insights into the tumor microenvironment, cancer heterogeneity, and drug efficacy, safety, and resistance mechanisms. Furthermore, integrating phenotypic data with genomic and proteomic networks allows for the identification of novel biomarkers and therapeutic targets in ways informed by biological structure and function, fostering precision medicine in lung cancer treatment. This expert review examines and places into context the current advances in next-generation phenomics and its potential to redefine lung cancer diagnosis, prognosis, and therapy. It highlights the emerging role of AI and machine learning in analyzing complex phenotypic datasets, enabling personalized therapeutic interventions. Ultimately, next-generation phenomics holds the promise of bridging the gap between molecular alterations and clinical and population health outcomes, providing a holistic understanding of lung cancer biology that could revolutionize its management and improve patient survival rates.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"585-595"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142471533","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

Crosstalk Between Cytokines and IgG N-Glycosylation: Bidirectional Effects and Relevance to Clinical Innovation for Inflammatory Diseases. 细胞因子与 IgG N-糖基化之间的相互影响：双向效应及与炎症性疾病临床创新的相关性。

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2024-12-01 Epub Date: 2024-11-25 DOI: 10.1089/omi.2024.0176

Zhixian Chen, Xiaojia Xu, Manshu Song, Ling Lin

{"title":"Crosstalk Between Cytokines and IgG N-Glycosylation: Bidirectional Effects and Relevance to Clinical Innovation for Inflammatory Diseases.","authors":"Zhixian Chen, Xiaojia Xu, Manshu Song, Ling Lin","doi":"10.1089/omi.2024.0176","DOIUrl":"10.1089/omi.2024.0176","url":null,"abstract":"The crosstalk between cytokines and immunoglobulin G (IgG) N-glycosylation forms a bidirectional regulatory network that significantly impacts inflammation and immune function. This review examines how various cytokines, both pro- and anti-inflammatory, modulate IgG N-glycosylation, shaping antibody activity and influencing inflammatory responses. In addition, we explore how altered IgG N-glycosylation patterns affect cytokine production and immune signaling, either promoting or reducing inflammation. Through a comprehensive analysis of current studies, this review underscores the dynamic relationship between cytokines and IgG N-glycosylation. These insights enhance our understanding of the mechanisms underlying inflammatory diseases and contribute to improved strategies for disease prevention, diagnosis, monitoring, prognosis, and the exploration of novel treatment options. By focusing on this crosstalk, we identify new avenues for developing innovative diagnostic tools and therapies to improve patient outcomes in inflammatory diseases.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"608-619"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710834","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

Unique and Shared Molecular Mechanisms of Alcoholic and Non-Alcoholic Liver Cirrhosis Identified Through Transcriptomics Data Integration. 通过转录组学数据整合发现酒精性和非酒精性肝硬化的独特和共同分子机制

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2024-11-01 Epub Date: 2024-10-17 DOI: 10.1089/omi.2024.0168

Ki-Hoon Park, Hwajin Lee, Ji Hyun Lee, Dong Keon Yon, Young-Il Choi, Hyung-Joo Chung, Junyang Jung, Na Young Jeong

{"title":"Unique and Shared Molecular Mechanisms of Alcoholic and Non-Alcoholic Liver Cirrhosis Identified Through Transcriptomics Data Integration.","authors":"Ki-Hoon Park, Hwajin Lee, Ji Hyun Lee, Dong Keon Yon, Young-Il Choi, Hyung-Joo Chung, Junyang Jung, Na Young Jeong","doi":"10.1089/omi.2024.0168","DOIUrl":"10.1089/omi.2024.0168","url":null,"abstract":"Liver cirrhosis is a severe chronic disease that results from various etiological factors and leads to substantial morbidity and mortality. Alcoholic cirrhosis (AC) and non-AC (NAC) arise from prolonged and excessive consumption of alcohol and metabolic syndromes, respectively. Precise molecular mechanisms of AC and NAC are yet to be comprehensively understood for diagnostics and therapeutic advances to materialize. This study reports novel findings to this end by utilizing high-throughput RNA sequencing and microarray data from the Gene Expression Omnibus (GEO). We performed a meta-analysis of transcriptomics data to identify the differentially expressed genes specific to AC and NAC. Functional enrichment and protein-protein interaction network analyses uncovered novel hub genes and transcription factors (TFs) critical to AC and NAC. We found that AC is primarily driven by metabolic dysregulation and oxidative stress, with key TFs such as RELA, NFKB1, and STAT3. NAC was characterized by fibrosis and tissue remodeling associated with metabolic dysfunction, with TFs including USF1, MYCN, and HIF1A. Key hub genes such as ESR1, JUN, FOS, and PKM in AC, and CD8A, MAPK3, CCND1, and CXCR4 in NAC were identified, along with their associated TFs, pointing to potential therapeutic targets. Our results underscore the unique and shared molecular mechanisms that underlie AC and NAC and inform the efforts toward precision medicine and improved patient outcomes in liver cirrhosis.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"537-547"},"PeriodicalIF":2.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142471535","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

Autism Spectrum Disorder and Atypical Brain Connectivity: Novel Insights from Brain Connectivity-Associated Genes by Combining Random Forest and Support Vector Machine Algorithm. 自闭症谱系障碍与非典型性脑连接：结合随机森林和支持向量机算法，从大脑连接性相关基因中获得新见解

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2024-11-01 Epub Date: 2024-10-17 DOI: 10.1089/omi.2024.0167

Pelin Gelmez, Talha Emir Karakoc, Ozlem Ulucan

{"title":"Autism Spectrum Disorder and Atypical Brain Connectivity: Novel Insights from Brain Connectivity-Associated Genes by Combining Random Forest and Support Vector Machine Algorithm.","authors":"Pelin Gelmez, Talha Emir Karakoc, Ozlem Ulucan","doi":"10.1089/omi.2024.0167","DOIUrl":"10.1089/omi.2024.0167","url":null,"abstract":"It is estimated that approximately one in every 100 children is diagnosed with autism spectrum disorder (ASD) around the globe. Currently, there are no curative pharmacological treatments for ASD. Discoveries on key molecular mechanisms of ASD are essential for precision medicine strategies. Considering that atypical brain connectivity patterns have been observed in individuals with ASD, this study examined the brain connectivity-associated genes and their putatively distinct expression patterns in brain samples from individuals diagnosed with ASD and using an iterative strategy based on random forest and support vector machine algorithms. We discovered a potential gene signature capable of differentiating ASD from control samples with a 92% accuracy. This gene signature comprised 14 brain connectivity-associated genes exhibiting enrichment in synapse-related terms. Of these genes, 11 were previously associated with ASD in varying degrees of evidence. Notably, NFKBIA, WNT10B, and IFT22 genes were identified as ASD-related for the first time in this study. Subsequent clustering analysis revealed the existence of two distinct ASD subtypes based on our gene signature. The expression levels of signature genes have the potential to influence brain connectivity patterns, potentially contributing to the manifestation of ASD. Further studies on the omics of ASD are called for so as to elucidate the molecular basis of ASD and for diagnostic and therapeutic innovations. Finally, we underscore that advances in ASD research can benefit from integrative bioinformatics and data science approaches.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"563-572"},"PeriodicalIF":2.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142471615","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

Alterations in Hurler-Scheie Syndrome Revealed by Mass Spectrometry-Based Proteomics and Phosphoproteomics Analysis. 基于质谱的蛋白质组学和磷蛋白组学分析揭示了赫勒-谢伊综合征的变化

IF 2.2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2024-11-01 Epub Date: 2024-10-29 DOI: 10.1089/omi.2024.0171

Madan Gopal Ramarajan, K T Shreya Parthasarathy, Kiran Bharat Gaikwad, Neha Joshi, Kishore Garapati, Richard K Kandasamy, Jyoti Sharma, Akhilesh Pandey

{"title":"Alterations in Hurler-Scheie Syndrome Revealed by Mass Spectrometry-Based Proteomics and Phosphoproteomics Analysis.","authors":"Madan Gopal Ramarajan, K T Shreya Parthasarathy, Kiran Bharat Gaikwad, Neha Joshi, Kishore Garapati, Richard K Kandasamy, Jyoti Sharma, Akhilesh Pandey","doi":"10.1089/omi.2024.0171","DOIUrl":"10.1089/omi.2024.0171","url":null,"abstract":"Hurler-Scheie syndrome (MPS IH/S), also known as mucopolysaccharidosis type I-H/S (MPS IH/S), is a lysosomal storage disorder caused by deficiency of the enzyme alpha-L-iduronidase (IDUA) leading to the accumulation of glycosaminoglycans (GAGs) in various tissues, resulting in a wide range of symptoms affecting different organ systems. Postgenomic omics technologies offer the promise to understand the changes in proteome, phosphoproteome, and phosphorylation-based signaling in MPS IH/S. Accordingly, we report here a large dataset and the proteomic and phosphoproteomic analyses of fibroblasts derived from patients with MPS IH/S (n = 8) and healthy individuals (n = 8). We found that protein levels of key lysosomal enzymes such as cathepsin D, prosaposin, arylsulfatases (arylsulfatase A and arylsulfatase B), and IDUA were downregulated. We identified 16,693 unique phosphopeptides, corresponding to 4,605 proteins, in patients with MPS IH/S. We found that proteins related to the cell cycle, mitotic spindle assembly, apoptosis, and cytoskeletal organization were differentially phosphorylated in MPS IH/S. We identified 12 kinases that were differentially phosphorylated, including hyperphosphorylation of cyclin-dependent kinases 1 and 2, hypophosphorylation of myosin light chain kinase, and calcium/calmodulin-dependent protein kinases. Taken together, the findings of the present study indicate significant alterations in proteins involved in cytoskeletal changes, cellular dysfunction, and apoptosis. These new observations significantly contribute to the current understanding of the pathophysiology of MPS IH/S specifically, and the molecular mechanisms involved in the storage of GAGs in MPS more generally. Further translational clinical omics studies are called for to pave the way for diagnostics and therapeutics innovation for patients with MPS IH/S.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"548-562"},"PeriodicalIF":2.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522605","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