1
|
Kannan V, Srimadh Bhagavatham SK, Dandamudi RB, Kunchala H, Challa S, Almansour AI, Pargaonkar A, Pulukool SK, Sharma A, Sivaramakrishnan V. Integrated clinical and metabolomic analysis identifies molecular signatures, biomarkers, and therapeutic targets in primary angle closure glaucoma. Front Mol Biosci 2024; 11:1421030. [PMID: 39184151 PMCID: PMC11341363 DOI: 10.3389/fmolb.2024.1421030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/17/2024] [Indexed: 08/27/2024] Open
Abstract
Background Glaucoma is the leading cause of permanent blindness. Primary angle closure glaucoma (PACG) is diagnosed only after the onset of symptoms and can result in irreversible blindness despite the standard intraocular pressure (IOP) reduction therapy. The identification of potential biomarkers associated with prognosis will help improve disease management. This study aimed to identify mechanisms associated with disease progression, potential biomarkers, and therapeutic targets of PACG. Methods The clinical data assessment of IOP, cup/disc ratio (CDR), Retinal Nerve Fiber Layer (RNFL) thickness of control, and PACG group were collected and analyzed for significant differences. The ATP levels were estimated, and targeted metabolomic analysis was performed on aqueous humor and cytokines in plasma. The pathways obtained from the metabolomics data set were compared with those obtained for data sets from the literature. Clinical parameters were correlated with cytokine levels. Targeted metabolomic analysis of cell culture supernatant from TNFα-treated N9 microglia was carried out, and overlap analysis was performed with data obtained from PACG patients. Results Elevated IOP, CDR, ATP, cytokines, and reduced RNFL thickness were found in PACG compared to controls. Analysis of PACG and TNFα-treated N9 microglial cell culture supernatant shows activation of immuno-metabolites. The metabolic pathways of PACG, TNFα, and ATP-treated microglia from the literature show considerable overlap. Biomarker analysis identified clinical parameters, ATP, cytokines, and immuno-metabolites. Conclusion This study shows an association between elevated levels of ATP, cytokines, immuno-metabolism, and potential microglial inflammation with disease progression, rendering these levels potential biomarkers. P2 receptors, cytokines, and IDO1/2 could be potential therapeutic targets.
Collapse
Affiliation(s)
- Vishnu Kannan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh, India
| | - Sai Krishna Srimadh Bhagavatham
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh, India
| | - Rajesh Babu Dandamudi
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh, India
| | - Haripriya Kunchala
- Department of Ophthalmology, Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthi Gram, Andhra Pradesh, India
| | - Sivateja Challa
- Department of Ophthalmology, Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthi Gram, Andhra Pradesh, India
| | | | | | - Sujith Kumar Pulukool
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh, India
| | - Anuj Sharma
- Department of Ophthalmology, Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthi Gram, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh, India
| |
Collapse
|
2
|
Li Y, Tu H, Zhang S, Ding Z, Wu G, Piao J, Lv D, Hu L, Li F, Wang Q. P2Y6 Receptor Activation Aggravates NLRP3-dependent Microglial Pyroptosis via Downregulation of the PI3K/AKT Pathway in a Mouse Model of Intracerebral Hemorrhage. Mol Neurobiol 2024; 61:4259-4277. [PMID: 38079109 DOI: 10.1007/s12035-023-03834-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/22/2023] [Indexed: 07/11/2024]
Abstract
Pro-inflammatory signals generated after intracerebral hemorrhage (ICH) trigger a form of regulated cell death known as pyroptosis in microglia. White matter injury (WMI) refers to the condition where the white matter area of the brain suffers from mechanical, ischemic, metabolic, or inflammatory damage. Although the p2Y purinoceptor 6 (P2Y6R) plays a significant role in the control of inflammatory reactions in central nervous system diseases, its roles in the development of microglial pyroptosis and WMI following ICH remain unclear. In this study, we sought to clarify the role of P2Y6R in microglial pyroptosis and WMI by using an experimental mouse model of ICH. Type IV collagenase was injected into male C57BL/6 mice to induce ICH. Mice were then treated with MRS2578 and LY294002 to inhibit P2Y6R and phosphatidylinositol 3-kinase (PI3K), respectively. Bio-conductivity analysis was performed to examine PI3K/AKT pathway involvement in microglial pyroptosis. Quantitative Real-Time PCR, immunofluorescence staining, and western blot were conducted to examine microglial pyroptosis and WMI following ICH. A modified Garcia test, corner turning test, and forelimb placement test were used to assess neurobehavior. Hematoxylin-eosin staining (HE) was performed to detect cells damage around hematoma. Increases in the expression of P2Y6R, NLRP3, ASC, Caspase-1, and GSDMD were observed after ICH. P2Y6R was only expressed on microglia. MRS2578, a specific inhibitor of P2Y6R, attenuated short-term neurobehavioral deficits, brain edema and hematoma volume while improving both microglial pyroptosis and WMI. These changes were accompanied by decreases in pyroptosis-related proteins and pro-inflammatory cytokines both in vivo and vitro. Bioinformatic analysis revealed an association between the PI3K/AKT pathway and P2Y6R-mediated microglial pyroptosis. The effects of MRS2578 were partially reversed by treatment with LY294002, a specific PI3K inhibitor. P2Y6R inhibition alleviates microglial pyroptosis and WMI and ameliorates neurological deficits through the PI3K/AKT pathway after ICH. Consequently, targeting P2Y6R might be a promising approach for ICH treatment.
Collapse
Affiliation(s)
- Yulong Li
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Huiru Tu
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Shengfan Zhang
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Zhiquan Ding
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Guiwei Wu
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Jifeng Piao
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Dingyi Lv
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Libin Hu
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Feng Li
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China.
| | - Qinghua Wang
- Neurosurgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China.
| |
Collapse
|
3
|
Golshan-Tafti A, Bahrami M, Mohsenzadeh-Yazdi R, Dastgheib SA, Aghasipour M, Shiri A, Alijanpour K, Asadian F, Aghili K, Manzourolhojeh M, Neamatzadeh H. Consolidating data on the association of IL-6 and IL-10 polymorphisms with the development of glaucoma: a meta-analysis. Ophthalmic Genet 2024:1-11. [PMID: 38602069 DOI: 10.1080/13816810.2024.2336964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND The study aimed to investigate the association of IL-6 and IL-10 polymorphisms with susceptibility to glaucoma by analyzing all relevant individual studies. MATERIALS AND METHODS Relevant articles were gathered from PubMed, Web of Science, Embase, WanFang, and CNKI databases up to 15 October 2023. Odds ratios (ORs) were used to evaluate the association strengths, along with 95% confidence intervals (CIs). RESULTS Seven case-control studies involving 1408 cases and 1789 controls on the IL-6 -174 G>C polymorphism, and three studies with 675 cases and 1100 controls on the IL-6 -572 G>C were included. Moreover, three separate studies, each comprising 442 cases and 672 controls, investigated the IL-10 -592C>A, -819T>C, and -1082A>G polymorphisms. The combined data indicated a significant association between -592C>A, -819T>C, and -1082A>G at IL-10 gene and IL-6 -572 G>C with glaucoma susceptibility, with no correlation found for IL-6 -174 G>C. CONCLUSIONS The study found that IL-10 -592C>A, -819T>C, -1082A>G, and IL-6 -572 G>C polymorphisms were linked to glaucoma risk. However, no significant association was observed for IL-6 -174 G>C. These findings imply a possible connection between genetic variations in these genes and glaucoma risk. Further research is crucial to fully understand the underlying mechanisms and their significance in managing and preventing glaucoma.
Collapse
Affiliation(s)
- Ahmadreza Golshan-Tafti
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Bahrami
- Student Research Committee, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reyhaneh Mohsenzadeh-Yazdi
- Department of Engineering and Public Policy, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Seyed Alireza Dastgheib
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Aghasipour
- Department of Cancer Biology, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Amirmasoud Shiri
- Student Research Committee, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamran Alijanpour
- General Practitioner, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Asadian
- Department of Medical Laboratory Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kazem Aghili
- Department of Radiology, Shahid Rahnemoun Hospital, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Manzourolhojeh
- Mother and Newborn Health Research Center, Shahid Sadoughi Hospital, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hossein Neamatzadeh
- Mother and Newborn Health Research Center, Shahid Sadoughi Hospital, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| |
Collapse
|
4
|
Rathnakumar S, Bhaskar S, Sivaramakrishnan V, Kambhampati NSV, Srinivasan V, Ramamurthy SS. Tecoma stans Floral Extract-Based Biosynthesis for Enhanced Surface Plasmon-Coupled Emission and a Preliminary Study on Fluoroimmunoassay. Anal Chem 2024; 96:4005-4012. [PMID: 38415592 DOI: 10.1021/acs.analchem.3c01441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
We demonstrate the synthesis of biogenic supported silver spiked star architectures and their application to increase the electromagnetic field intensity at its tips that enhance plasmon-coupled emission. Tecoma stans floral extract has been used to synthesize silver nanocubes and spiked stars. We observe ∼445-fold and ∼680-fold enhancements in spacer and cavity configurations, respectively, in the SPCE platform. The hotspot intensity and Purcell factor are evaluated by carrying out finite-difference time-domain (FDTD) simulations. Time-based studies are presented to modulate the sharpness of the edges wherein an increase in the tip sharpness with the increase in reaction time up to 5 h is observed. The unique morphology of the silver architectures allowed us to utilize them in biosensing application. A SPCE-based fluoroimmunoassay was performed, achieving a 1.9 pg/mL limit of detection of TNF-α cytokine. This combination of anisotropic architectures, SPCE and immunoassay prove to be a powerful platform for the ultrasensitive detection of biomarkers in surface-bound assays.
Collapse
Affiliation(s)
- Sriram Rathnakumar
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam Campus, Puttaparthi, 515134, Andhra Pradesh, India
| | - Seemesh Bhaskar
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Venketesh Sivaramakrishnan
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam Campus, Puttaparthi, 515134, Andhra Pradesh, India
| | - Naga Sai Visweswar Kambhampati
- Department of Chemistry, STAR Laboratory, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam Campus, Puttaparthi, 515134, Andhra Pradesh, India
| | - Venkatesh Srinivasan
- Department of Chemistry, STAR Laboratory, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam Campus, Puttaparthi, 515134, Andhra Pradesh, India
| | - Sai Sathish Ramamurthy
- Department of Chemistry, STAR Laboratory, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam Campus, Puttaparthi, 515134, Andhra Pradesh, India
| |
Collapse
|
5
|
Pradhan SS, R SS, Kanikaram SP, V M DD, Pargaonkar A, Dandamudi RB, Sivaramakrishnan V. Metabolic deregulation associated with aging modulates protein aggregation in the yeast model of Huntington's disease. J Biomol Struct Dyn 2023:1-18. [PMID: 37732342 DOI: 10.1080/07391102.2023.2257322] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023]
Abstract
Huntington's disease is associated with increased CAG repeat resulting in an expanded polyglutamine tract in the protein Huntingtin (HTT) leading to its aggregation resulting in neurodegeneration. Previous studies have shown that N-terminal HTT with 46Q aggregated in the stationary phase but not the logarithmic phase in the yeast model of HD. We carried out a metabolomic analysis of logarithmic and stationary phase yeast model of HD expressing different polyQ lengths attached to N-terminal HTT tagged with enhanced green fluorescent protein (EGFP). The results show significant changes in the metabolic profile and deregulated pathways in stationary phase cells compared to logarithmic phase cells. Comparison of metabolic pathways obtained from logarithmic phase 46Q versus 25Q with those obtained for presymptomatic HD patients from our previous study and drosophila model of HD showed considerable overlap. The arginine biosynthesis pathway emerged as one of the key pathways that is common in stationary phase yeast compared to logarithmic phase and HD patients. Treatment of yeast with arginine led to a significant decrease, while transfer to arginine drop-out media led to a significant increase in the size of protein aggregates in both logarithmic and stationary phase yeast model of HD. Knockout of arginine transporters in the endoplasmic reticulum and vacuole led to a significant decrease in mutant HTT aggregation. Overall our results highlight arginine as a critical metabolite that modulates the aggregation of mutant HTT and disease progression in HD.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Swaroop R
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Phalguna Kanikaram
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru, Karnataka, India
| | | | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| |
Collapse
|
6
|
Rathnakumar S, Kambhampati NSV, Saiswaroop R, Pradhan SS, Ramkumar G, Beeraka N, Muddu GK, Kumar S, Javvaji SK, Parangoankar A, Sivaramakrishnan V, Ramamurthy SS. Integrated clinical and metabolomic analysis of dengue infection shows molecular signatures associated with host-pathogen interaction in different phases of the disease. Metabolomics 2023; 19:47. [PMID: 37130982 DOI: 10.1007/s11306-023-02011-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/20/2023] [Indexed: 05/04/2023]
Abstract
PURPOSE Dengue is a mosquito vector-borne disease caused by the dengue virus, which affects 125 million people globally. The disease causes considerable morbidity. The disease, based on symptoms, is classified into three characteristic phases, which can further lead to complications in the second phase. Molecular signatures that are associated with the three phases have not been well characterized. We performed an integrated clinical and metabolomic analysis of our patient cohort and compared it with omics data from the literature to identify signatures unique to the different phases. METHODS The dengue patients are recruited by clinicians after standard-of-care diagnostic tests and evaluation of symptoms. Blood from the patients was collected. NS1 antigen, IgM, IgG antibodies, and cytokines in serum were analyzed using ELISA. Targeted metabolomics was performed using LC-MS triple quad. The results were compared with analyzed transcriptomic data from the GEO database and metabolomic data sets from the literature. RESULTS The dengue patients displayed characteristic features of the disease, including elevated NS1 levels. TNF-α was found to be elevated in all three phases compared to healthy controls. The metabolic pathways were found to be deregulated compared to healthy controls only in phases I and II of dengue patients. The pathways represent viral replication and host response mediated pathways. The major pathways include nucleotide metabolism of various amino acids and fatty acids, biotin, etc. CONCLUSION: The results show elevated TNF-α and metabolites that are characteristic of viral infection and host response. IL10 and IFN-γ were not significant, consistent with the absence of any complications.
Collapse
Affiliation(s)
- Sriram Rathnakumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India
| | - Naga Sai Visweswar Kambhampati
- STAR Laboratory, Central Research Instruments Facility, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India
| | - R Saiswaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India
| | - G Ramkumar
- Department of General Medicine, Sri Sathya Sai General Hospital, Sri Sathya Sai Institute of Higher Medical Sciences Campus, Whitefield, Bengaluru, Karnataka, 560066, India
| | - Nirmala Beeraka
- Department of General Medicine, Sri Sathya Sai General Hospital, Sri Sathya Sai Institute of Higher Medical Sciences Campus, Whitefield, Bengaluru, Karnataka, 560066, India
| | - Gopi Krishna Muddu
- Department of Pediatrics, Sri Sathya Sai General Hospital, Puttaparthi, Andhra Pradesh, 515134, India
| | - Sandeep Kumar
- Department of General Medicine, Sri Sathya Sai General Hospital, Puttaparthi, Andhra Pradesh, 515134, India
| | - Sai Kiran Javvaji
- Department of Laboratory Medicine and Cardiology, Sri Sathya Sai Institute of Higher Medical Sciences, Whitefield, Bengaluru, Karnataka, 560066, India
| | | | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India.
| | - Sai Sathish Ramamurthy
- STAR Laboratory, Central Research Instruments Facility, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India.
| |
Collapse
|
7
|
Kodam P, Sai Swaroop R, Pradhan SS, Sivaramakrishnan V, Vadrevu R. Integrated multi-omics analysis of Alzheimer's disease shows molecular signatures associated with disease progression and potential therapeutic targets. Sci Rep 2023; 13:3695. [PMID: 36879094 PMCID: PMC9986671 DOI: 10.1038/s41598-023-30892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by the formation of amyloid plaques implicated in neuronal death. Genetics, age, and sex are the risk factors attributed to AD. Though omics studies have helped to identify pathways associated with AD, an integrated systems analysis with the available data could help to understand mechanisms, potential biomarkers, and therapeutic targets. Analysis of transcriptomic data sets from the GEO database, and proteomic and metabolomic data sets from literature was performed to identify deregulated pathways and commonality analysis identified overlapping pathways among the data sets. The deregulated pathways included those of neurotransmitter synapses, oxidative stress, inflammation, vitamins, complement, and coagulation pathways. Cell type analysis of GEO data sets showed microglia, endothelial, myeloid, and lymphoid cells are affected. Microglia are associated with inflammation and pruning of synapses with implications for memory and cognition. Analysis of the protein-cofactor network of B2, B6, and pantothenate shows metabolic pathways modulated by these vitamins which overlap with the deregulated pathways from the multi-omics analysis. Overall, the integrated analysis identified the molecular signature associated with AD. Treatment with anti-oxidants, B2, B6, and pantothenate in genetically susceptible individuals in the pre-symptomatic stage might help in better management of the disease.
Collapse
Affiliation(s)
- Pradeep Kodam
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad, Telangana, 500078, India
| | - R Sai Swaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India.
| | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad, Telangana, 500078, India.
| |
Collapse
|
8
|
Srimadh Bhagavatham SK, Pulukool SK, Pradhan SS, R S, Ashok Naik A, V M DD, Sivaramakrishnan V. Systems biology approach delineates critical pathways associated with disease progression in rheumatoid arthritis. J Biomol Struct Dyn 2022:1-22. [PMID: 36047508 DOI: 10.1080/07391102.2022.2115555] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Rheumatoid Arthritis (RA) is a chronic systemic autoimmune disease leading to inflammation, cartilage cell death, synoviocyte proliferation, and increased and impaired differentiation of osteoclasts and osteoblasts leading to joint erosions and deformities. Transcriptomics, proteomics, and metabolomics datasets were analyzed to identify the critical pathways that drive the RA pathophysiology. Single nucleotide polymorphisms (SNPs) associated with RA were analyzed for the functional implications, clinical outcomes, and blood parameters later validated by literature. SNPs associated with RA were grouped into pathways that drive the immune response and cytokine production. Further gene set enrichment analysis (GSEA) was performed on gene expression omnibus (GEO) data sets of peripheral blood mononuclear cells (PBMCs), synovial macrophages, and synovial biopsies from RA patients showed enrichment of Th1, Th2, Th17 differentiation, viral and bacterial infections, metabolic signalling and immunological pathways with potential implications for RA. The proteomics data analysis presented pathways with genes involved in immunological signaling and metabolic pathways, including vitamin B12 and folate metabolism. Metabolomics datasets analysis showed significant pathways like amino-acyl tRNA biosynthesis, metabolism of amino acids (arginine, alanine aspartate, glutamate, glutamine, phenylalanine, and tryptophan), and nucleotide metabolism. Furthermore, our commonality analysis of multi-omics datasets identified common pathways with potential implications for joint remodeling in RA. Disease-modifying anti-rheumatic drugs (DMARDs) and biologics treatments were found to modulate many of the pathways that were deregulated in RA. Overall, our analysis identified molecular signatures associated with the observed symptoms, joint erosions, potential biomarkers, and therapeutic targets in RA. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Sujith Kumar Pulukool
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Saiswaroop R
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Ashwin Ashok Naik
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| |
Collapse
|