Molecular omics最新文献_第10页

Correction: Generation of β-like cell subtypes from differentiated human induced pluripotent stem cells in 3D spheroids 更正：3D球体中分化的人类诱导多能干细胞产生β样细胞亚型。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-10-06 DOI: 10.1039/D3MO90033A

Lisa Morisseau, Fumiya Tokito, Stéphane Poulain, Valérie Plaisance, Valérie Pawlowski, Soo Hyeon Kim, Cécile Legallais, Rachid Jellali, Yasuyuki Sakai, Amar Abderrahmani and Eric Leclerc

引用次数: 0

Cronobacter sakazakii infection implicates multifaceted neuro-immune regulatory pathways of Caenorhabditis elegans† 阪崎克罗诺杆菌感染涉及秀丽隐杆线虫的多方面神经免疫调节途径。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-09-28 DOI: 10.1039/D3MO00167A

Lappasi Mohanram VenkataKrishna, Boopathi Balasubramaniam, T. J. Sushmitha, V. Ravichandiran and Krishnaswamy Balamurugan

{"title":"Cronobacter sakazakii infection implicates multifaceted neuro-immune regulatory pathways of Caenorhabditis elegans†","authors":"Lappasi Mohanram VenkataKrishna, Boopathi Balasubramaniam, T. J. Sushmitha, V. Ravichandiran and Krishnaswamy Balamurugan","doi":"10.1039/D3MO00167A","DOIUrl":"10.1039/D3MO00167A","url":null,"abstract":"The neural pathways of Caenorhabditis elegans play a crucial role in regulating host immunity and inflammation during pathogenic infections. To understand the major neuro-immune signaling pathways, this study aimed to identify the key regulatory proteins in the host C. elegans during C. sakazakii infection. We used high-throughput label-free quantitative proteomics and identified 69 differentially expressed proteins. KEGG analysis revealed that C. sakazakii elicited host immune signaling cascades primarily including mTOR signaling, axon regeneration, metabolic pathways (let-363 and acox-1.4), calcium signaling (mlck-1), and longevity regulating pathways (ddl-2), respectively. The abrogation in functional loss of mTOR-associated players deciphered that C. sakazakii infection negatively regulated the lifespan of mutant worms (akt-1, let-363 and dlk-1), including physiological aberrations, such as reduced pharyngeal pumping and egg production. Additionally, the candidate pathway proteins were validated by transcriptional profiling of their corresponding genes. Furthermore, immunoblotting showed the downregulation of mTORC2/SGK-1 during the later hours of pathogen exposure. Overall, our findings profoundly provide an understanding of the specificity of proteome imbalance in affecting neuro-immune regulations during C. sakazakii infection.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 48-63"},"PeriodicalIF":2.9,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41206541","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

Generation of β-like cell subtypes from differentiated human induced pluripotent stem cells in 3D spheroids† 在3D球体中从分化的人类诱导多能干细胞产生β样细胞亚型。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-09-12 DOI: 10.1039/D3MO00050H

Lisa Morisseau, Fumiya Tokito, Stéphane Poulain, Valerie Plaisance, Valerie Pawlowski, Soo Hyeon Kim, Cécile Legallais, Rachid Jellali, Yasuyuki Sakai, Amar Abderrahmani and Eric Leclerc

{"title":"Generation of β-like cell subtypes from differentiated human induced pluripotent stem cells in 3D spheroids†","authors":"Lisa Morisseau, Fumiya Tokito, Stéphane Poulain, Valerie Plaisance, Valerie Pawlowski, Soo Hyeon Kim, Cécile Legallais, Rachid Jellali, Yasuyuki Sakai, Amar Abderrahmani and Eric Leclerc","doi":"10.1039/D3MO00050H","DOIUrl":"10.1039/D3MO00050H","url":null,"abstract":"Since the identification of four different pancreatic β-cell subtypes and bi-hormomal cells playing a role in the diabetes pathogenesis, the search for in vitro models that mimics such cells heterogeneity became a key priority in experimental and clinical diabetology. We investigated the potential of human induced pluripotent stem cells to lead to the development of the different β-cells subtypes in honeycomb microwell-based 3D spheroids. The glucose-stimulated insulin secretion confirmed the spheroids functionality. Then, we performed a single cell RNA sequencing of the spheroids. Using a knowledge-based analysis with a stringency on the pancreatic markers, we extracted the β-cells INS+/UCN3+ subtype (11%; β1-like cells), the INS+/ST8SIA1+/CD9− subtype (3%, β3-like cells) and INS+/CD9+/ST8SIA1-subtype (1%; β2-like cells) consistently with literature findings. We did not detect the INS+/ST8SIA1+/CD9+ cells (β4-like cells). Then, we also identified four bi-hormonal cells subpopulations including δ-like cells (INS+/SST+, 6%), γ-like cells (INS+/PPY+, 3%), α-like-cells (INS+/GCG+, 6%) and ε-like-cells (INS+/GHRL+, 2%). Using data-driven clustering, we extracted four progenitors’ subpopulations (with the lower level of INS gene) that included one population highly expressing inhibin genes (INHBA+/INHBB+), one population highly expressing KCNJ3+/TPH1+, one population expressing hepatocyte-like lineage markers (HNF1A+/AFP+), and one population expressing stem-like cell pancreatic progenitor markers (SOX2+/NEUROG3+). Furthermore, among the cycling population we found a large number of REST+ cells and CD9+ cells (CD9+/SPARC+/REST+). Our data confirm that our differentiation leads to large β-cell heterogeneity, which can be used for investigating β-cells plasticity under physiological and pathophysiological conditions.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 10","pages":" 810-822"},"PeriodicalIF":2.9,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10211184","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

Cancer evaluation in dogs using cerumen as a source for volatile biomarker prospection† 狗癌症评估，使用cerumen作为挥发性生物标志物前景的来源。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-09-08 DOI: 10.1039/D3MO00147D

João Marcos G. Barbosa, Engy Shokry, Lurian Caetano David, Naiara Z. Pereira, Adriana R. da Silva, Vilma F. de Oliveira, Maria Clorinda S. Fioravanti, Paulo H. Jorge da Cunha, Anselmo E. de Oliveira and Nelson Roberto Antoniosi Filho

{"title":"Cancer evaluation in dogs using cerumen as a source for volatile biomarker prospection†","authors":"João Marcos G. Barbosa, Engy Shokry, Lurian Caetano David, Naiara Z. Pereira, Adriana R. da Silva, Vilma F. de Oliveira, Maria Clorinda S. Fioravanti, Paulo H. Jorge da Cunha, Anselmo E. de Oliveira and Nelson Roberto Antoniosi Filho","doi":"10.1039/D3MO00147D","DOIUrl":"10.1039/D3MO00147D","url":null,"abstract":"Cancer is one of the deadliest diseases in humans and dogs. Nevertheless, most tumor types spread faster in canines, and early cancer detection methods are necessary to enhance animal survival. Here, cerumen (earwax) was tested as a source of potential biomarkers for cancer evaluation in dogs. Earwax samples from dogs were collected from tumor-bearing and clinically healthy dogs, followed by Headspace/Gas Chromatography-Mass Spectrometry (HS/GC-MS) analyses and multivariate statistical workflow. An evolutionary-based multivariate algorithm selected 18 out of 128 volatile metabolites as a potential cancer biomarker panel in dogs. The candidate biomarkers showed a full discrimination pattern between tumor-bearing dogs and cancer-free canines with high accuracy in the test dataset: an accuracy of 95.0% (75.1–99.9), and sensitivity and specificity of 100.0% and 92.9%, respectively. In summary, this work raises a new perspective on cancer diagnosis in dogs, being carried out painlessly and non-invasive, facilitating sample collection and periodic application in a veterinary routine.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 27-36"},"PeriodicalIF":2.9,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41105027","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

Unraveling the role of intra-cellular metabolites in the lactic acid production by novel Bacillus amyloliquefaciens using sugarcane molasses as a substratum† 揭示细胞内代谢物在以甘蔗糖蜜为基质的新型解淀粉芽孢杆菌产乳酸中的作用。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-08-31 DOI: 10.1039/D3MO00141E

Balasubramanian Vignesh Kumar, Balakrishnan Muthumari, Murugan Kavitha, John Kennedy John Praveen Kumar and Muthuramalingam Jothi Basu

引用次数: 0

Characterization of methionine dependence in melanoma cells† 黑色素瘤细胞蛋氨酸依赖性的特征。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-08-31 DOI: 10.1039/D3MO00087G

Sarita Garg, Lauren C. Morehead, Jordan T. Bird, Stefan Graw, Allen Gies, Aaron J. Storey, Alan J. Tackett, Rick D. Edmondson, Samuel G. Mackintosh, Stephanie D. Byrum and Isabelle R. Miousse

{"title":"Characterization of methionine dependence in melanoma cells†","authors":"Sarita Garg, Lauren C. Morehead, Jordan T. Bird, Stefan Graw, Allen Gies, Aaron J. Storey, Alan J. Tackett, Rick D. Edmondson, Samuel G. Mackintosh, Stephanie D. Byrum and Isabelle R. Miousse","doi":"10.1039/D3MO00087G","DOIUrl":"10.1039/D3MO00087G","url":null,"abstract":"Dietary methionine restriction is associated with a reduction in tumor growth in preclinical studies and an increase in lifespan in animal models. The mechanism by which methionine restriction inhibits tumor growth while sparing normal cells is incompletely understood. We do know that normal cells can utilize methionine or homocysteine interchangeably (methionine independence) while most cancer cells are strictly dependent on methionine availability. Here, we compared a typical methionine dependent and a rare methionine independent melanoma cell line. We show that replacing methionine, a methyl donor, with its precursor homocysteine generally induced hypomethylation in gene promoters. This decrease was similar in methionine dependent and methionine independent cells. There was only a low level of pathway enrichment, suggesting that the hypomethylation is generalized rather than gene specific. Whole proteome and transcriptome were also analyzed. This analysis revealed that contrarily to the effect on methylation, the replacement of methionine with homocysteine had a much greater effect on the transcriptome and proteome of methionine dependent cells than methionine independent cells. Interestingly, methionine adenosyltransferase 2A (MAT2A), responsible for the synthesis of S-adenosylmethionine from methionine, was equally strongly upregulated in both cell lines. This suggests that the absence of methionine is equally detected but triggers different outcomes in methionine dependent versus independent cells. Our analysis reveals the importance of cell cycle control, DNA damage repair, translation, nutrient sensing, oxidative stress and immune functions in the cellular response to methionine stress in melanoma.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 37-47"},"PeriodicalIF":2.9,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41128976","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

Advancing science through data sharing: a new data policy for Molecular Omics 通过数据共享推进科学:分子组学的新数据政策

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-08-31 DOI: 10.1039/D3MO90028B

引用次数: 0

Single cell proteomics analysis of drug response shows its potential as a drug discovery platform† 药物反应的单细胞蛋白质组学分析显示了其作为药物发现平台的潜力。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-08-16 DOI: 10.1039/D3MO00124E

Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek and Bogdan Budnik

{"title":"Single cell proteomics analysis of drug response shows its potential as a drug discovery platform†","authors":"Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek and Bogdan Budnik","doi":"10.1039/D3MO00124E","DOIUrl":"10.1039/D3MO00124E","url":null,"abstract":"Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling, nanoscale super-resolution microscopy, advances in single cell RNAseq and proteomics technologies, provide more detailed information about biological processes which were not evident with the analysis of bulk material. This new era of single-cell biology provides a better understanding of such complex biological systems as cancer, inflammation, immunity mechanism and aging processes, and opens the door into the field of drug response heterogeneity. The latest discoveries of cellular heterogeneity gives us a unique understanding of complex biological processes, such as disease mechanism, and will lead to new strategies for better and personalized treatment strategies. Recently, single-cell proteomics techniques that allow quantification of thousands of proteins from single mammalian cells have been introduced. Here we present an improved single-cell mass spectrometry-based proteomics platform called SCREEN (Single Cell pRotEomE aNalysis) for deep and high-throughput single-cell proteome coverage with high efficiency, less turnaround time and with an improved ability for protein quantitation across more cells than previously achieved. We applied this new platform to analyze the single-cell proteomic landscape under different drug treatment over time to uncover heterogeneity in cancer cell response, which for the first time, to our knowledge, has been achieved by mass spectrometry based analytical methods. We discuss challenges in single-cell proteomics, future improvements and general trends with the goal to encourage forthcoming technical developments.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 1","pages":" 6-18"},"PeriodicalIF":2.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10185642","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

Integrated proteomic and metabolomic analysis of plasma reveals regulatory pathways and key elements in thyroid cancer† 血浆的综合蛋白质组学和代谢组学分析揭示了甲状腺癌的调节途径和关键因素。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-08-16 DOI: 10.1039/D3MO00142C

Zijian Sun, Dongdong Feng, Liehao Jiang, Jingkui Tian, Jiafeng Wang and Wei Zhu

{"title":"Integrated proteomic and metabolomic analysis of plasma reveals regulatory pathways and key elements in thyroid cancer†","authors":"Zijian Sun, Dongdong Feng, Liehao Jiang, Jingkui Tian, Jiafeng Wang and Wei Zhu","doi":"10.1039/D3MO00142C","DOIUrl":"10.1039/D3MO00142C","url":null,"abstract":"Thyroid cancer (TC) is the most common endocrine malignancy with increasing incidence in recent years. Fine-needle aspiration biopsy (FNAB), as a gold standard for the initial evaluation of thyroid nodules, fails to cover all the cytopathologic conditions resulting in overdiagnosis. There is an urgent need for a better classification of thyroid cancer from benign thyroid nodules (BTNs). Here, data independent acquisition (DIA)-based proteomics and untargeted metabolomics in plasma samples of 10 patients with TC and 15 patients with BTNs were performed. Key proteins and metabolites were identified specific to TC, and an independent cohort was used to validate the potential biomarkers using enzyme-linked immunosorbent assay (ELISA). In total, 1429 proteins and 1172 metabolites were identified. Principal component analysis showed a strong overlap at the proteomic level and a significant discrimination at the metabolomic level between the two groups, indicating a more drastic disturbance in the metabolome of thyroid cancer. Integrated analysis of proteomics and metabolomics shows glycerophospholipid metabolism and arachidonic acid metabolism as key regulatory pathways. Furthermore, a multi-omics biomarker panel was developed consisting of LCAT, GPX3 and leukotriene B4. Based on the AUC value for the discovery set, the classification performance was 0.960. The AUC value of the external validation set was 0.930. Altogether, our results will contribute to the clinical application of potential biomarkers in the diagnosis of thyroid cancer.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 10","pages":" 800-809"},"PeriodicalIF":2.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10111449","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: 1

Association of lipid metabolism-related metabolites with overweight/obesity based on the FTO rs1421085† 基于FTO rs1421085的脂质代谢相关代谢产物与超重/肥胖的相关性。

IF 2.9 4区生物学

Molecular omics Pub Date : 2023-08-04 DOI: 10.1039/D3MO00112A

Sabiha Farooq, Sobia Rana, Amna Jabbar Siddiqui, Ayesha Iqbal, Adil Anwar Bhatti and Syed Ghulam Musharraf

{"title":"Association of lipid metabolism-related metabolites with overweight/obesity based on the FTO rs1421085†","authors":"Sabiha Farooq, Sobia Rana, Amna Jabbar Siddiqui, Ayesha Iqbal, Adil Anwar Bhatti and Syed Ghulam Musharraf","doi":"10.1039/D3MO00112A","DOIUrl":"10.1039/D3MO00112A","url":null,"abstract":"Globally, obesity is a severe health issue. A more precise and practical approach is required to enhance clinical care and drug development. The FTO (fat mass and obesity-associated) gene variant rs1421085 is strongly associated with an increased susceptibility to obesity in numerous populations; however, the precise mechanism behind this association concerning metabolomics is still not understood. This study aims to examine the association between metabolites and obesity-related anthropometric traits based on the variant FTO rs1421085. This study was based on a case-control design involving a total of 542 participants including overweight/obese cases and healthy controls. The blood samples were collected from all the participants. The isolated serum samples were subjected to untargeted metabolomics using GC-MS. The isolated DNA samples were genotyped for the FTO rs1421085 variant. Initially, a total of 42 metabolites were identified on GC-MS, which were subjected to further association analyses. The study observed a significant association of two metabolites, glycerol and 2,3-dihydroxypropyl stearate with FTO gene variant rs1421085 and obesity-related anthropometric traits including % BF, WHtR, WC, and HC. The CT genotype of FTO rs1421085 may greatly increase the risk of overweight/obesity by changing the lipid metabolism-related metabolites. Therefore, this study highlights the significance of biochemical networks in the progression of obesity in carriers of the FTO rs1421085 risk genotype.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 9","pages":" 697-705"},"PeriodicalIF":2.9,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9989111","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