Article
Biochemistry & Molecular Biology
Denes Tuerei, Alberto Valdeolivas, Lejla Gul, Nicolas Palacio-Escat, Michal Klein, Olga Ivanova, Marton Oelbei, Attila Gabor, Fabian Theis, Tamas Korcsmaros, Julio Saez-Rodriguez
Summary: Molecular knowledge of biological processes is crucial for omics data analysis, with OmniPath providing a comprehensive resource for researchers to access information on both intracellular and intercellular processes. This resource facilitates the study of cell-cell interactions and downstream signaling processes, demonstrated in applications investigating SARS-CoV-2 infection and ulcerative colitis.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biology
Nuzulul Kurniansyah, Danielle A. Wallace, Ying Zhang, Bing Yu, Brian Cade, Heming Wang, Heather M. Ochs-Balcom, Alexander P. Reiner, Alberto R. Ramos, Joshua D. Smith, Jianwen Cai, Martha Daviglus, Phyllis C. Zee, Robert Kaplan, Charles Kooperberg, Stephen S. Rich, Jerome Rotter, Sina A. Gharib, Susan Redline, Tamar Sofer
Summary: Sleep Disordered Breathing (SDB) is a common disease that increases the risk of cardiometabolic, cardiovascular, and cognitive diseases. However, the impact of SDB on the molecular environment is still poorly understood. This study investigates the association between SDB measures and gene expression using RNA-seq in multiple blood tissues. The findings suggest differential gene expression by blood cell type and provide potential markers for intervention development to alleviate the effects of SDB on the human molecular environment.
COMMUNICATIONS BIOLOGY
(2023)
Article
Cell & Tissue Engineering
Katharina Schoenberger, Nadine Obier, Mari Carmen Romero-Mulero, Pierre Cauchy, Julian Mess, Polina Pavlovich, Yu Wei Zhang, Michael Mitterer, Jasmin Rettkowski, Maria-Eleni Lalioti, Karin Jaecklein, Jonathan D. Curtis, Betty Feret, Pia Sommerkamp, Claudia Morganti, Keisuke Ito, Norbert B. Ghyselinck, Eirini Trompouki, Joerg M. Buescher, Erika L. Pearce, Nina Cabezas-Wallscheid
Summary: This study investigates the complex regulatory networks that preserve stemness in hematopoietic stem cells and uncovers a non-classical retinoic acid signaling axis that controls their function. The findings highlight the importance of a single metabolite in controlling stem cell fate through epigenetic and transcriptional attributes.
Article
Biotechnology & Applied Microbiology
Laura A. Cox, Jeannie Chan, Prahlad Rao, Zeeshan Hamid, Jeremy P. Glenn, Avinash Jadhav, Vivek Das, Genesio M. Karere, Ellen Quillen, Kylie Kavanagh, Michael Olivier
Summary: The study on vervet monkeys fed with a high fructose diet for 6 weeks showed alterations in sirtuin signaling and the peroxisome proliferator activated receptor alpha (PPARA) regulatory network in hepatic response to HFr. Integration of three types of omics data enhanced confidence in identifying relevant pathways and networks, providing insights into molecular mechanisms for altered hepatic gluconeogenesis caused by consumption of a HFr diet.
Review
Chemistry, Multidisciplinary
Tae Hwan Shin, Saraswathy Nithiyanandam, Da Yeon Lee, Do Hyeon Kwon, Ji Su Hwang, Seok Gi Kim, Yong Eun Jang, Shaherin Basith, Sungsu Park, Jung-Soon Mo, Gwang Lee
Summary: Nanoparticles in biomedical applications offer advantages due to their small size, but evaluating their potential adverse effects on health is necessary and challenging. Omics approaches, in combination with machine learning techniques, provide a more comprehensive and sensitive way to assess nanotoxicity. Additionally, mechanobiology methods can be applied to evaluate the biophysical changes induced by nanoparticles, enhancing the overall understanding of their safety implications.
Article
Multidisciplinary Sciences
Natalie M. Clark, Trevor M. Nolan, Ping Wang, Gaoyuan Song, Christian Montes, Conner T. Valentine, Hongqing Guo, Rosangela Sozzani, Yanhai Yin, Justin W. Walley
Summary: This study analyzed the BR signaling in Arabidopsis by integrating multiple omics datasets and inferring networks, identifying a BR-regulated transcription factor BRONTOSAURUS that affects cell division in roots. The research provides insights into the molecular signaling events during BR response through integrative network analysis applied to multi-omic data.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Immunology
Sweta B. Patel, Eric M. Pietras
Summary: B-cell-derived acetylcholine initiates a circuit that prompts bone marrow stromal cells to secrete factors that restrain the blood-forming activity of hematopoietic stem cells in response to cardiovascular dysfunction.
Article
Developmental Biology
Laura F. Bennett, Melanie D. Mumau, Yan Li, Nancy A. Speck
Summary: The study reveals that MyD88-dependent toll like receptor (TLR) signaling regulates the numbers of lympho-myeloid biased progenitors (LMPs) and adult-repopulating hematopoietic stem cells (HSCs) in hemogenic endothelial cells and intra-arterial hematopoietic clusters.
Review
Cell Biology
Clovis H. T. Seumen, Tanja M. Grimm, Christof R. Hauck
Summary: Toll-like receptors (TLRs) play a crucial role in immune response, but exaggerated activation can lead to inflammatory diseases. This review discusses the impact of protein phosphorylation on TLR signaling, highlighting the role of phosphatases as negative regulators. Understanding phosphatase-mediated regulation could offer new approaches to modulate immune signaling.
CELL COMMUNICATION AND SIGNALING
(2021)
Review
Immunology
Tobias Kull, Timm Schroeder
Summary: Cells constantly adapt their behavior to changing needs by sensing their environment, and compute fine-tuned responses to complex inputs through signaling pathways. Despite progress, our understanding of the precise implementation, relevance, and manipulation of cellular signaling remains limited.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Medicine, Research & Experimental
Kang Mi Lee, Qiang Fu, Guoli Huai, Kevin Deng, Ji Lei, Lisa Kojima, Divyansh Agarwal, Peter van Galen, Shoko Kimura, Naoki Tanimine, Laura Washburn, Heidi Yeh, Ali Naji, Charles G. Rickert, Christian LeGuern, James F. Markmann
Summary: B lymphocytes play important roles in adaptive immunity and self-tolerance. Activated B cells through TLR4/TLR9 receptors acquire regulatory properties, inhibiting T cell proliferation and preventing allograft rejection.
Article
Biochemistry & Molecular Biology
Peng Zhou, Li Wang, Hai Liu, Chunyan Li, Zhimin Li, Jinxiang Wang, Xiaoming Tan
Summary: CyanoOmicsDB is a database aiming to provide comprehensive functional information for cyanobacterial genes, with over 8 million entries from 928 genomes. It integrates transcriptional and translational profiles, gene function predictions, protein sequences, homologs, and more, offering researchers in this field a convenient way to access functional information on cyanobacterial genes. Compared to other existing databases, CyanoOmicsDB stands out for its extensive datasets and comprehensive functional information.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Muta Tah Hira, M. A. Razzaque, Claudio Angione, James Scrivens, Saladin Sawan, Mosharraf Sarkar
Summary: The research focused on integrated multi-omics analysis of cancer data using VAE and MMD-VAE. The results indicated that MMD-VAE outperformed VAE in most omics datasets, and the compressed features could be used for cancer prognosis.
SCIENTIFIC REPORTS
(2021)
Article
Immunology
Qiaoke Li, Mingze Sun, Qi Zhou, Yulong Li, Jinmei Xu, Hong Fan
Summary: This study used gene set enrichment analysis to analyze the transcriptome of sepsis patients and identified 84 differentially expressed KEGG pathways. Among them, 10 pathways were associated with 28-day survival. Some pathways were correlated with immune cell abundance, and five pathways could be used to distinguish systemic inflammatory response syndrome, bacterial sepsis, and viral sepsis with an AUC above 0.80. Furthermore, seven related drugs were screened using survival-related pathways.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Judith Canto-Santos, Laura Valls-Roca, Ester Tobias, Clara Oliva, Francesc Josep Garcia-Garcia, Mariona Guitart-Mampel, Felix Andujar-Sanchez, Anna Esteve-Codina, Beatriz Martin-Mur, Joan Padrosa, Raquel Aranega, Pedro J. Moreno-Lozano, Jose Cesar Milisenda, Rafael Artuch, Josep M. Grau-Junyent, Gloria Garrabou
Summary: In this study, an omics analysis of multiple samples from IBM patients was conducted to gain insights into the pathophysiology of the disease. The presence of amyloid beta peptide 1-42, imbalanced organic acid profile, and abnormal expression of metabolites and gene regulators were observed in various samples. The findings reported in this study provide novel insights into IBM and suggest potential biomarkers that need to be validated in larger cohorts.
Article
Biochemical Research Methods
Aliabbas A. Husain, Sneha M. Pinto, Yashwanth Subbannayya, Saketh Kapoor, Payal Khulkhule, Nidhi Bhartiya, T. S. Keshava Prasad, Hatim F. Daginawala, Lokendra R. Singh, Rajpal Singh Kashyap
Summary: In this study, a high throughput targeted multiple reaction monitoring-mass spectrometry (MRM-MS) approach was developed to screen and identify protein biomarkers for brucellosis in humans and livestock. By generating in silico tryptic peptides of the Brucella proteome, specific peptides were selected for further analysis. The experimental results showed that the corresponding peptides to B. abortus proteins could be accurately detected in clinically confirmed serum samples of both humans and livestock. This study provides a sensitive detection method for accurately diagnosing brucellosis.
PROTEOMICS CLINICAL APPLICATIONS
(2023)
Article
Cell Biology
D. A. B. Rex, Shobha Dagamajalu, Mahesh Manjunath Gouda, G. P. Suchitha, Jaikanth Chanderasekaran, Rajesh Raju, T. S. Keshava Prasad, Yashodhar Prabhakar Bhandary
Summary: IL-17A, a member of the IL-17 family, is implicated in the pathogenesis of autoimmune diseases. Activation of the IL-17A/IL-17RA system regulates multiple signaling pathways and leads to the release of pro-inflammatory cytokines, promoting neutrophil-mediated immune response.
JOURNAL OF CELL COMMUNICATION AND SIGNALING
(2023)
Article
Microbiology
Aliabbas A. Husain, Sneha M. Pinto, Nupur Agarwal, Santosh K. Behera, Payal R. Khulkhule, Nidhi M. Bhartiya, Yashwanth Subbannayya, T. S. Keshava Prasad, Lokendra R. Singh, Hatim F. Daginawala, Rajpal S. Kashyap
Summary: In this study, we conducted a comprehensive proteomic analysis of Brucella melitensis strain ATCC23457 to investigate proteome changes in response to in vitro-induced nutrient stress. We identified 2440 proteins, including hypothetical and potentially secretory proteins, representing approximately 77.8% of the B. melitensis proteome. Through proteogenomics and label-free quantitative proteomic analysis, we gained new insights into the cellular processes governed by nutrient stress and identified enrichment of survival and homeostasis maintenance pathways. Our findings highlight the importance of in-depth proteomic analysis in improving genome annotation and provide insights into the metabolic adaptations of B. melitensis during nutrient stress.
CURRENT MICROBIOLOGY
(2023)
Article
Cell Biology
Shobha Dagamajalu, D. A. B. Rex, G. P. Suchitha, Akhila B. B. Rai, Shreya Kumar, Shreya Joshi, Rajesh Raju, T. S. Keshava Prasad
Summary: DDR1, a non-integrin collagen receptor, is mainly found in epithelial and smooth muscle cells, playing a role in organogenesis. However, it is also overexpressed in pathological conditions like cancer and inflammation. DDR1 activates through various pathways and regulates downstream signaling molecules in diseases. Unfortunately, a consolidated network map of the DDR1 signaling pathway is currently lacking.
JOURNAL OF CELL COMMUNICATION AND SIGNALING
(2023)
Article
Multidisciplinary Sciences
Sneha M. Pinto, Yashwanth Subbannayya, Hera Kim, Lars Hagen, Maria W. Gorna, Anni I. Nieminen, Magnar Bjoras, Terje Espevik, Denis Kainov, Richard K. Kandasamy
Summary: The COVID-19 pandemic remains a global health concern due to the emergence of new variants. Extensive evidence from multi-Omics studies has revealed host-pathogen interactions and potential therapeutic targets. Understanding the regulation of host signaling networks by post-translational modifications and their impact on cellular dynamics is crucial for advancing knowledge on SARS-CoV-2 infections.
Article
Biochemistry & Molecular Biology
Poornima Ramesh, Santosh Kumar Behera, Chinmaya Narayana Kotimoole, Varshasnata Mohanty, Rajesh Raju, T. S. Keshava Prasad, Jalaluddin Akbar Kandel Codi
Summary: Gastric cancers are characterized by late diagnosis and poor prognosis, and protein post-translational modifications (PTMs) have been associated with cancer development and metastasis. However, limited data is available on PTMs in gastric cancers. This study used an iterative searching strategy to analyze mass spectrometry data and identified 21,710 unique modification sites on 16,364 modified peptides. The majority of the altered PTMs/proteins were found in cytoskeletal and extracellular matrix proteins, which are known to be perturbed in gastric cancer.
Article
Biochemistry & Molecular Biology
Rex Devasahayam Arokia Balaya, Jaikanth Chandrasekaran, Saptami Kanekar, Prashant Kumar Modi, Shobha Dagamajalu, Kirthika Gopinathan, Rajesh Raju, T. S. Keshava Prasad
Summary: The CAMKK2 is crucial in regulating intracellular calcium levels and signaling pathways, and dysregulation of its activity is associated with various diseases. The study utilized 'DrugspaceX' for lead identification and repositioned FDA-approved drugs for CAMKK2 inhibition. Through virtual screening, DE273038_5 was identified as a novel candidate with potential inhibitory activity at the CAMKK2 active site.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Oncology
Raviprasad Kuthethur, Maria Sona Jerome, Yashwanth Subbannayya, Sanjiban Chakrabarty
Summary: This study aimed to identify microRNAs associated with DNA repair deficiency in triple-negative breast cancer (TNBC) patients. The results identified 6 miRNAs as potential biomarkers for HR deficiency in TNBC, which could be used for future therapeutic strategies.
Article
Cell Biology
Diya Sanjeev, Shobha Dagamajalu, Vineetha Shaji, Mejo George, Yashwanth Subbannayya, T. S. Keshava Prasad, Rajesh Raju, Rex Devasahayam Arokia Balaya
Summary: MSP is a serum-derived growth factor mainly produced by the liver and associated with various pathological conditions. Activation of MSP/RON system regulates multiple signaling pathways involved in cell proliferation, survival, migration, invasion, angiogenesis, and chemoresistance.
JOURNAL OF CELL COMMUNICATION AND SIGNALING
(2023)
Review
Cell Biology
Riccardo Di Fiore, Sherif Suleiman, Rosa Drago-Ferrante, Yashwanth Subbannayya, Sarah Suleiman, Mariela Vasileva-Slaveva, Angel Yordanov, Francesca Pentimalli, Antonio Giordano, Jean Calleja-Agius
Summary: The FBXW7 protein plays a role in regulating cellular growth and acts as a tumor suppressor. It is a component of the SCF complex and aids in the degradation of oncoproteins via the UPS. FBXW7 mutations are associated with cancer and could potentially serve as diagnostic and prognostic biomarkers. This review aims to provide an update on the role of FBXW7 as a potential biomarker and therapeutic target, particularly in gynecologic cancers.
Article
Biochemical Research Methods
Homen Phukan, Abhijit Sarma, Devasahayam Arokia Balaya Rex, Swamidurai Arul Diana Christie, Sarath Kizhakkemuriyil Sabu, Suneetha Hariharan, Thottethodi Subrahmanya Keshava Prasad, Madathiparambil Gopalakrishnan Madanan
Summary: In this study, the changes in leptospiral proteins under infection-like conditions were investigated using proteomics and bioinformatics. The results revealed significant alterations in proteins at the subcellular level, particularly on the outer membrane, and identified several upregulated proteins exclusively during infection that could be useful for vaccine and diagnostic targets. Furthermore, the differentially expressed proteins were found to be involved in metabolic adaptation and enriched in pathways related to signal transduction and antibiotic biosynthesis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Riaz Abdulla, Jofy Devasia Puthenpurackal, Sneha M. Pinto, Punchappady Devasya Rekha, Yashwanth Subbannayya
Summary: In this study, we identified and evaluated the diagnostic value of autoantibodies in serum samples of OSCC patients using immunome protein array profiling. We found a number of differential autoantibodies associated with OSCC, including NUBP2. Immunohistochemical validation showed positive staining of NUBP2 in the majority of OSCC cases. Overall, the serum autoantibodies identified in this study, including NUBP2, have the potential to serve as biomarkers for early diagnosis or screening of OSCC.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemical Research Methods
Mohammad Arefian, Thottethodi Subrahmanya Keshava Prasad
Summary: Rice, a staple food crop worldwide, is estimated to have its global production reduced by 50% due to salinity stress. However, limited knowledge exists regarding the initial molecular signaling and proteins associated with sensing salinity in crop plants. In this study, we characterized the early effects of salt on the proteome and metabolome of rice tissues and identified numerous signaling pathways induced by salinity. By combining omics data and physiological changes, we identified the most susceptible proteins and metabolites in each pathway, providing potential targets for improving rice's sensitivity to salinity.
JOURNAL OF PROTEOME RESEARCH
(2023)