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Sivamaruthi BS, Raghani N, Chorawala M, Bhattacharya S, Prajapati BG, Elossaily GM, Chaiyasut C. NF-κB Pathway and Its Inhibitors: A Promising Frontier in the Management of Alzheimer's Disease. Biomedicines 2023; 11:2587. [PMID: 37761028 PMCID: PMC10526355 DOI: 10.3390/biomedicines11092587] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
The nuclear factor kappa B (NF-κB) pathway has emerged as a pivotal player in the pathogenesis of various diseases, including neurodegenerative illnesses like Alzheimer's disease (AD). The involvement of the NF-κB pathway in immune system responses, inflammation, oxidative stress, and neuronal survival highlights its significance in AD progression. We discuss the advantages of NF-κB pathway inhibition, including the potential to mitigate neuroinflammation, modulate amyloid beta (Aβ) production, and promote neuronal survival. However, we also acknowledge the limitations and challenges associated with this approach. Balancing the fine line between dampening inflammation and preserving physiological immune responses is critical to avoid unintended consequences. This review combines current knowledge on the NF-κB pathway's intricate involvement in AD pathogenesis, emphasizing its potential as a therapeutic target. By evaluating both advantages and limitations, we provide a holistic view of the feasibility and challenges of NF-κB pathway modulation in AD treatment. As the quest for effective AD therapies continues, an in-depth understanding of the NF-κB pathway's multifaceted roles will guide the development of targeted interventions with the potential to improve AD management.
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Affiliation(s)
- Bhagavathi Sundaram Sivamaruthi
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand;
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Neha Raghani
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad 380009, India
| | - Mehul Chorawala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad 380009, India
| | - Sankha Bhattacharya
- School of Pharmacy & Technology Management, SVKM’S NMIMS Deemed-to-be University, Shirpur 425405, India
| | - Bhupendra G. Prajapati
- Shree S. K. Patel College of Pharmaceutical Education and Research, Ganpat University, Mehsana 384012, India
| | - Gehan M. Elossaily
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, P.O. Box 71666, Riyadh 11597, Saudi Arabia
| | - Chaiyavat Chaiyasut
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
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Rex DAB, Chanderasekaran J, Rai AB, Phukan H, Sarma A, Prasad TSK, Madanan MG. Leptospira and Leptospirosis: New Systems Science Insights on Proteome, Posttranslational Modifications, and Pathogen-Host Interaction. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:280-289. [PMID: 35446144 DOI: 10.1089/omi.2022.0007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Leptospirosis is one of the most important zoonotic diseases for planetary health. It is caused by Leptospira spp., which poses a formidable challenge in both rural and urban geographies. Discovery of molecular targets is crucial for developing interventions, including vaccines, against leptospirosis. We report here novel systems science insights on Leptospira proteome, posttranslational modifications (PTMs), and pathogen-host interactions, with an eye to bacterial pathophysiology from a functional standpoint. A systematic reanalysis of unassigned spectra from our previous total proteome identification was used for a multi-PTM search. Notably, we identified 3693 unique high-confidence PTM sites corresponding to 1266 proteins (PTM-profiling probability cutoff value ≥75%). The majority of the phosphorylated peptides were found to be GroEL molecular chaperones. Notably, the molecular docking of PTM-GroEL with STAT3, an important signaling protein in cytokine production, resulted in the prediction of druggable "hotspots." These energetically significant smaller subsets of amino acids (hotspot residues) offer promise for practical applications in planetary health, rational drug design, and peptide engineering. Furthermore, the prediction strategies described here could serve as a starting point for narrowing down the more extensive interface in protein-protein interactions that currently exist. Going forward, systems science approaches and the new insights reported here offer veritable prospects for innovation in preventing and treating leptospirosis.
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Affiliation(s)
- Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Jaikanth Chanderasekaran
- Department of Pharmacology, School of Pharmacy and Technology Management, SVKM'S NMIMS University, Hyderabad, India
| | - Akhila Balakrishna Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Homen Phukan
- Department of Biochemistry, ICMR-Regional Medical Research Centre, Port Blair, India
| | - Abhijit Sarma
- Department of Biochemistry, ICMR-Regional Medical Research Centre, Port Blair, India
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Rex DB, Patil AH, Modi PK, Kandiyil MK, Kasaragod S, Pinto SM, Tanneru N, Sijwali PS, Prasad TSK. Dissecting Plasmodium yoelii Pathobiology: Proteomic Approaches for Decoding Novel Translational and Post-Translational Modifications. ACS OMEGA 2022; 7:8246-8257. [PMID: 35309442 PMCID: PMC8928344 DOI: 10.1021/acsomega.1c03892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Malaria is a vector-borne disease. It is caused by Plasmodium parasites. Plasmodium yoelii is a rodent model parasite, primarily used for studying parasite development in liver cells and vectors. To better understand parasite biology, we carried out a high-throughput-based proteomic analysis of P. yoelii. From the same mass spectrometry (MS)/MS data set, we also captured several post-translational modified peptides by following a bioinformatics analysis without any prior enrichment. Further, we carried out a proteogenomic analysis, which resulted in improvements to some of the existing gene models along with the identification of several novel genes. Analysis of proteome and post-translational modifications (PTMs) together resulted in the identification of 3124 proteins. The identified PTMs were found to be enriched in mitochondrial metabolic pathways. Subsequent bioinformatics analysis provided an insight into proteins associated with metabolic regulatory mechanisms. Among these, the tricarboxylic acid (TCA) cycle and the isoprenoid synthesis pathway are found to be essential for parasite survival and drug resistance. The proteogenomic analysis discovered 43 novel protein-coding genes. The availability of an in-depth proteomic landscape of a malaria pathogen model will likely facilitate further molecular-level investigations on pre-erythrocytic stages of malaria.
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Affiliation(s)
- Devasahayam
Arokia Balaya Rex
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Arun H. Patil
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Prashant Kumar Modi
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Mrudula Kinarulla Kandiyil
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Sandeep Kasaragod
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Sneha M. Pinto
- Center
for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Nandita Tanneru
- CSIR-Centre
for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Puran Singh Sijwali
- CSIR-Centre
for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
- Academy
of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India
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Massanett Aparicio J, Xu Y, Li Y, Colantuoni C, Dastgheyb R, Williams DW, Asahchop EL, McMillian JM, Power C, Fujiwara E, Gill MJ, Rubin LH. Plasma microRNAs are associated with domain-specific cognitive function in people with HIV. AIDS 2021; 35:1795-1804. [PMID: 34074816 PMCID: PMC8524348 DOI: 10.1097/qad.0000000000002966] [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] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Cognitive impairment remains common in people with HIV (PWH) on antiretroviral therapy (ART). The clinical presentation and severity are highly variable in PWH suggesting that the pathophysiological mechanisms of cognitive complications are likely complex and multifactorial. MicroRNA (miRNA) expression changes may be linked to cognition as they are gene regulators involved in immune and stress responses as well as the development, plasticity, and differentiation of neurons. We examined plasma miRNA expression changes in relation to domain-specific and global cognitive function in PWH. DESIGN Cross-sectional observational study. METHODS Thirty-three PWH receiving care at the Southern Alberta Clinic, Canada completed neuropsychological (NP) testing and blood draw. Plasma miRNA extraction was followed by array hybridization. Random forest analysis was used to identify the top 10 miRNAs upregulated and downregulated in relation to cognition. RESULTS Few miRNAs were identified across cognitive domains; however, when evident a miRNA was only associated with two or three domains. Notably, miR-127-3p was related to learning/memory and miR-485-5p to motor function, miRNAs previously identified in CSF or plasma in Alzheimer's and Parkinson's, respectively. Using miRNET 2.0, a software-platform for understanding the biological relevance of the miRNA-targets (genes) relating to cognition through a network-based approach, we identified genes involved in signaling, cell cycle, and transcription relating to executive function, learning/memory, and language. CONCLUSION Findings support the idea that evaluating miRNA expression (or any molecular measure) in the context of global NP function might exclude miRNAs that could be important contributors to the domain-specific mechanisms leading to the variable neuropsychiatric outcomes seen in PWH.
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Affiliation(s)
| | - Yanxun Xu
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore
- Division of Biostatistics and Bioinformatics at The Sidney Kimmel Comprehensive Cancer Center
| | - Yuliang Li
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore
| | - Carlo Colantuoni
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore
- Institute for Genome Sciences, University of Maryland, Baltimore
| | - Raha Dastgheyb
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore
| | - Dionna W Williams
- Department of Molecular and Comparative Pathobiology
- Division of Clinical Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Christopher Power
- Southern Alberta Clinic, Calgary
- Department of Medicine
- Neuroscience and Mental Health Institute
| | - Esther Fujiwara
- Neuroscience and Mental Health Institute
- Department of Psychiatry, University of Alberta, Edmonton, Alberta, Canada
| | - M John Gill
- Cumming School of Medicine, University of Calgary
- Southern Alberta Clinic, Calgary
| | - Leah H Rubin
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Mohamed Asik R, Suganthy N, Aarifa MA, Kumar A, Szigeti K, Mathe D, Gulyás B, Archunan G, Padmanabhan P. Alzheimer's Disease: A Molecular View of β-Amyloid Induced Morbific Events. Biomedicines 2021; 9:biomedicines9091126. [PMID: 34572312 PMCID: PMC8468668 DOI: 10.3390/biomedicines9091126] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/22/2021] [Accepted: 08/27/2021] [Indexed: 12/26/2022] Open
Abstract
Amyloid-β (Aβ) is a dynamic peptide of Alzheimer’s disease (AD) which accelerates the disease progression. At the cell membrane and cell compartments, the amyloid precursor protein (APP) undergoes amyloidogenic cleavage by β- and γ-secretases and engenders the Aβ. In addition, externally produced Aβ gets inside the cells by receptors mediated internalization. An elevated amount of Aβ yields spontaneous aggregation which causes organelles impairment. Aβ stimulates the hyperphosphorylation of tau protein via acceleration by several kinases. Aβ travels to the mitochondria and interacts with its functional complexes, which impairs the mitochondrial function leading to the activation of apoptotic signaling cascade. Aβ disrupts the Ca2+ and protein homeostasis of the endoplasmic reticulum (ER) and Golgi complex (GC) that promotes the organelle stress and inhibits its stress recovery machinery such as unfolded protein response (UPR) and ER-associated degradation (ERAD). At lysosome, Aβ precedes autophagy dysfunction upon interacting with autophagy molecules. Interestingly, Aβ act as a transcription regulator as well as inhibits telomerase activity. Both Aβ and p-tau interaction with neuronal and glial receptors elevate the inflammatory molecules and persuade inflammation. Here, we have expounded the Aβ mediated events in the cells and its cosmopolitan role on neurodegeneration, and the current clinical status of anti-amyloid therapy.
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Affiliation(s)
- Rajmohamed Mohamed Asik
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore; (R.M.A.); (B.G.)
- Cognitive Neuroimaging Centre, 59 Nanyang Drive, Nanyang Technological University, Singapore 636921, Singapore
- Department of Animal Science, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India;
| | - Natarajan Suganthy
- Department of Nanoscience and Technology, Alagappa University, Karaikudi 630003, Tamil Nadu, India;
| | - Mohamed Asik Aarifa
- Department of Animal Science, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India;
| | - Arvind Kumar
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India;
| | - Krisztián Szigeti
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (K.S.); (D.M.)
- CROmed Translational Research Centers, 1094 Budapest, Hungary
| | - Domokos Mathe
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (K.S.); (D.M.)
- CROmed Translational Research Centers, 1094 Budapest, Hungary
- In Vivo Imaging Advanced Core Facility, Hungarian Center of Excellence for Molecular Medicine (HCEMM), 1094 Budapest, Hungary
| | - Balázs Gulyás
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore; (R.M.A.); (B.G.)
- Cognitive Neuroimaging Centre, 59 Nanyang Drive, Nanyang Technological University, Singapore 636921, Singapore
- Department of Clinical Neuroscience, Karolinska Institute, 17176 Stockholm, Sweden
| | - Govindaraju Archunan
- Department of Animal Science, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India;
- Marudupandiyar College, Thanjavur 613403, Tamil Nadu, India
- Correspondence: (G.A.); (P.P.)
| | - Parasuraman Padmanabhan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore; (R.M.A.); (B.G.)
- Cognitive Neuroimaging Centre, 59 Nanyang Drive, Nanyang Technological University, Singapore 636921, Singapore
- Correspondence: (G.A.); (P.P.)
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Deolankar SC, Patil AH, Rex DAB, Subba P, Mahadevan A, Prasad TSK. Mapping Post-Translational Modifications in Brain Regions in Alzheimer's Disease Using Proteomics Data Mining. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:525-536. [PMID: 34255573 DOI: 10.1089/omi.2021.0054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is a leading cause of dementia and a neurodegenerative disease. Proteomics and post-translational modification (PTM) analyses offer new opportunities for a comprehensive understanding of pathophysiology of brain in AD. We report here multiple PTMs in patients with AD, harnessing publicly available proteomics data from nine brain regions and at three different Braak stages of disease progression. Specifically, we identified 7190 peptides with PTMs, corresponding to 2545 proteins from brain regions with intermediate tangles, and 6864 peptides with PTMs corresponding to 2465 proteins from brain regions with severe tangles. A total of 103 proteins with PTMs were expressed uniquely to intermediate tangles and severe tangles compared to no tangles. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis suggested the association of these proteins in AD progression through platelet activation. These modified proteins were also found to be enriched for the tricarboxylic acid (TCA) cycle, respiratory electron cycle, and detoxification of reactive oxygen species. The multi-PTM data reported here contribute to our understanding of the neurobiology of AD and highlight the prospects of omics systems science research in neurodegenerative diseases. The present study provides a region-wise classification for the proteins with PTMs along with their differential expression patterns, providing insights into the localization of these proteins upon modification. The catalog of multi-PTMs identified in the context of AD from different brain regions provides a unique platform for generating newer hypotheses in understanding the putative role of specific PTMs in AD pathogenesis.
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Affiliation(s)
- Sayali Chandrashekhar Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Arun H Patil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India.,Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore, India
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Rex DAB, Arun Kumar ST, Rai AB, Kotimoole CN, Modi PK, Prasad TSK. Novel Post-Translational Modifications and Molecular Substrates in Glioma Identified by Bioinformatics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:463-473. [PMID: 34227895 DOI: 10.1089/omi.2021.0050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glioma is the most common type of brain cancer that originates from the glial cells. It constitutes about one-third of all brain cancers. Recently, transcriptomics, proteomics, and multiomics approaches have been harnessed to discover potential biomarkers and therapeutic targets in glioma. Moreover, post-translational modifications (PTMs) of proteins play a major role in cell biology and function and offer new avenues of research in cancer. Using unbiased multi-PTM bioinformatics analyses of two proteomic datasets of glioma available in the public domain, we identified 866 proteins with common PTMs from both studies. Out of these 866 proteins, 19 proteins were identified with the common PTMs, with the same site modifications pertaining to glioma. Importantly, the identified PTMs belonged to proteins involved in integrin PI3K/Akt/mTOR, JAK/STAT, and Ras/Raf/MAPK pathways. These pathways are essential for cell proliferation in tumor cells and thus involved in glioma progression. Taken together, these findings call for validation in larger datasets in glioma and brain cancers and with an eye to future drug discovery and diagnostic innovation. Bioinformatics-guided discovery of novel PTMs from the publicly available proteomic data can offer new avenues for innovation in cancer research.
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Affiliation(s)
- Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sumaithangi Thattai Arun Kumar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Akhila Balakrishna Rai
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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Palollathil A, Aravind A, Vijayakumar M, Kotimoole CN, Mohanty V, Behera SK, Kashyap V, Kiran Kumar KM, Shetty R, Codi JAK, Raju R, Prasad TSK. Omics Data Mining for multiPTMs in Oral Cancer: Cellular Proteome and Secretome of Chronic Tobacco-Treated Oral Keratinocytes. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:450-462. [PMID: 34191607 DOI: 10.1089/omi.2021.0047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Oral cancer is common worldwide but lacks robust diagnostics and therapeutics. Lifestyle factors, such as tobacco chewing and smoking, are significantly associated with oral cancers. Mapping the changes in the global proteome, secretome and post-translational modifications (PTMs) during tobacco exposure of oral keratinocytes hold great potential for understanding the mechanisms of oral carcinogenesis, not to mention for innovation toward clinical interventions in the future. On the other hand, although advances in mass spectrometry (MS)-based techniques have enabled the deep mining of complex proteomes, a large portion of the mass spectrometric data remains unassigned. These unassigned spectral data can be researched for multiple post-translational modifications (multiPTMs). Using data mining of publicly available proteomics data, we report, in this study, a multiPTM analysis of high-resolution MS-derived datasets on cellular proteome and secretome of chronic tobacco-treated oral keratinocytes. We identified 800 PTM sites in 496 proteins. Among them, 43 PTM sites in 37 proteins were found to be differentially expressed, accounting for their protein-level expression. Enrichment analysis of the proteins with altered phosphosite expression and the known kinases of these phosphosites discovered the overrepresentation of certain biological processes such as splicing and hemidesmosome assembly. These findings contribute to a deeper understanding of omics level changes in chronic tobacco-treated oral keratinocytes, and by extension, pathophysiology of oral cancers.
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Affiliation(s)
- Akhina Palollathil
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Anjana Aravind
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Manavalan Vijayakumar
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Vivek Kashyap
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Kenkere M Kiran Kumar
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, India
| | - Rohan Shetty
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
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9
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Kumar A, Doan VM, Kunkli B, Csősz É. Construction of Unified Human Antimicrobial and Immunomodulatory Peptide Database and Examination of Antimicrobial and Immunomodulatory Peptides in Alzheimer's Disease Using Network Analysis of Proteomics Datasets. Front Genet 2021; 12:633050. [PMID: 33995478 PMCID: PMC8113759 DOI: 10.3389/fgene.2021.633050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/17/2021] [Indexed: 12/26/2022] Open
Abstract
The reanalysis of genomics and proteomics datasets by bioinformatics approaches is an appealing way to examine large amounts of reliable data. This can be especially true in cases such as Alzheimer's disease, where the access to biological samples, along with well-defined patient information can be challenging. Considering the inflammatory part of Alzheimer's disease, our aim was to examine the presence of antimicrobial and immunomodulatory peptides in human proteomic datasets deposited in the publicly available proteomics database ProteomeXchange (http://www.proteomexchange.org/). First, a unified, comprehensive human antimicrobial and immunomodulatory peptide database, containing all known human antimicrobial and immunomodulatory peptides was constructed and used along with the datasets containing high-quality proteomics data originating from the examination of Alzheimer's disease and control groups. A throughout network analysis was carried out, and the enriched GO functions were examined. Less than 1% of all identified proteins in the brain were antimicrobial and immunomodulatory peptides, but the alterations characteristic of Alzheimer's disease could be recapitulated with their analysis. Our data emphasize the key role of the innate immune system and blood clotting in the development of Alzheimer's disease. The central role of antimicrobial and immunomodulatory peptides suggests their utilization as potential targets for mechanistic studies and future therapies.
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Affiliation(s)
- Ajneesh Kumar
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Vo Minh Doan
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Balázs Kunkli
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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10
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Deolankar SC, Modi PK, Subbannayya Y, Pervaje R, Prasad TSK. Molecular Targets from Traditional Medicines for Neuroprotection in Human Neurodegenerative Diseases. ACTA ACUST UNITED AC 2020; 24:394-403. [DOI: 10.1089/omi.2020.0033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sayali Chandrashekhar Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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Ramesha KP, Mol P, Kannegundla U, Thota LN, Gopalakrishnan L, Rana E, Azharuddin N, Mangalaparthi KK, Kumar M, Dey G, Patil A, Saravanan K, Behera SK, Jeyakumar S, Kumaresan A, Kataktalware MA, Prasad TSK. Deep Proteome Profiling of Semen of Indian Indigenous Malnad Gidda (Bos indicus) Cattle. J Proteome Res 2020; 19:3364-3376. [DOI: 10.1021/acs.jproteome.0c00237] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kerekoppa P. Ramesha
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore 560030, India
| | - Praseeda Mol
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690525, India
| | - Uday Kannegundla
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore 560030, India
| | | | - Lathika Gopalakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
- Manipal Academy of Higher Education, Madhav Nagar, Manipal 576104, India
| | - Ekta Rana
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore 560030, India
| | - Nizamuddin Azharuddin
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore 560030, India
| | - Kiran K Mangalaparthi
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690525, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Arun Patil
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Kumar Saravanan
- Proteomics Facility, Thermo Fisher Scientific India Pvt. Ltd., Bangalore 560066, India
| | - Santosh Kumar Behera
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Sakthivel Jeyakumar
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore 560030, India
| | - Arumugam Kumaresan
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore 560030, India
| | - Mukund A. Kataktalware
- Southern Regional Station, ICAR-National Dairy Research Institute, Bangalore 560030, India
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Wisniewski T, Drummond E. Future horizons in Alzheimer's disease research. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:223-241. [PMID: 31699317 DOI: 10.1016/bs.pmbts.2019.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There are growing genetic, transcriptomic and proteomic data pointing to the complexity of Alzheimer's disease (AD) pathogenesis. Unbiased "omics" approaches are essential for the future development of effective AD research, which will need to be combined and personalized, given that multiple distinct pathways can drive AD pathology. It is essential to gain a better understanding of the AD pathogenesis subtype variety and to develop several distinct therapeutic approaches tailored to address this diversity, as well as the common presence of mixed pathologies. These nonmutually exclusive therapeutic approaches include the targeting of multiple toxic oligomeric species concurrently, targeting the apolipoprotein E/amyloid β interaction and the modulation of innate immunity, as well as more "out of the box" ideas such as targeting infectious agents that may play a role in AD.
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Affiliation(s)
- Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, United States.
| | - Eleanor Drummond
- Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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