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Upadhyay M, Nair D, Moseley GW, Srivastava S, Kondabagil K. Giant Virus Global Proteomics Innovation: Comparative Evaluation of In-Gel and In-Solution Digestion Methods. OMICS 2024; 28:170-181. [PMID: 38621149 DOI: 10.1089/omi.2024.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
With their unusually large genome and particle sizes, giant viruses (GVs) defy the conventional definition of viruses. Although most GVs isolated infect unicellular protozoans, such as amoeba, studies in the last decade have established their much wider prevalence infecting most eukaryotic supergroups and some giant viral families with the potential to be human pathogens. Their complexity, almost autonomous life cycle, and enigmatic evolution necessitate the study of GVs. The accurate assessment of GV proteome is a veritable challenge. We have compared the coverage of global protein identification using different methods for GVs isolated in Mumbai, Mimivirus Bombay (MVB), Powai Lake Megavirus (PLMV), and Kurlavirus (KV), along with two previously studied GVs, Acanthamoeba polyphaga Mimivirus (APMV) and Marseillevirus (MV). Our study shows that the simultaneous use of in-gel and in-solution digestion methods can significantly increase the coverage of protein identification in the global proteome analysis of purified GV particles. Combining the two methods of analyses, we identified an additional 72 proteins in APMV and 114 in MV compared with what have been previously reported. Similarly, proteomes of MVB, PLMV, and KV were analyzed, and a total of 242 proteins in MVB, 287 proteins in PLMV, and 174 proteins in KV were identified. Our results suggest that a combined methodology of in-gel and in-solution methods is more efficient and opens up new avenues for innovation in global proteome analysis of GVs. Future planetary health research on GVs can benefit from consideration of a broader range of proteomics methodologies as illustrated by the present study.
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Affiliation(s)
- Monica Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Gregory W Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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2
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Pinto N, Nissa MU, Yashwanth BS, Sathiyanarayanan A, Pai MGJ, Srivastava S, Goswami M. Proteomics analysis of differentially abundant proteins in the rohu kidney infected with Edwardsiella tarda. Comp Biochem Physiol Part D Genomics Proteomics 2024; 50:101221. [PMID: 38430708 DOI: 10.1016/j.cbd.2024.101221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
Edwardsiella tarda (Et) is a zoonotic gram-negative pathogen with a diverse host range, including fish. However, the in-depth molecular mechanisms underlying the response of Labeo rohita (rohu) kidney to Et are poorly understood. A proteomic and histopathological analysis was performed for the rohu kidney after Et infection. The histopathology of the infected rohu kidney showed vacuolation and necrosis. After LC-MS/MS analysis, ~1240 proteins were identified with ≥2 unique peptides. A total of 96 differentially abundant proteins (DAPs) were observed between the control and Et infected group (ET). Metascape and STRING analysis were used for the gene ontology (GO), and protein-protein interaction network (PPI) for the significant pathways of DAPs. In PPI, low-abundant proteins were mapped to metabolic pathways and oxidative phosphorylation (cox5ab, uqcrfs1). High-abundance proteins were mapped to ribosomes (rplp2), protein process in the ER (hspa8), and immune system (ptgdsb.1, muc2). Our label-free proteomic approach in the rohu kidney revealed abundant enriched proteins involved in vesicle coat (ehd4), complement activation (c3a.1, c9, c7a), phagosome (thbs4, mapk1), metabolic reprogramming (hao1, glud1a), wound healing (vim, alox5), and the immune system (psap) after Et infection. A targeted proteomics approach of multiple reaction monitoring (MRM) validated the DAPs (nprl3, ambp, vmo1a, hspg2, muc2, hao1 and glud1a) between control and ET. Overall, the current analysis of histology and proteome in the rohu kidney provides comprehensive data on pathogenicity and the potential immune proteins against Et.
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Affiliation(s)
- Nevil Pinto
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India. https://twitter.com/pintonevil8
| | - Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - B S Yashwanth
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India
| | - A Sathiyanarayanan
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India. https://twitter.com/Sanjeeva_IITB
| | - Mukunda Goswami
- Indian Council of Agricultural Research - Central Institute of Fisheries Education, Versova, Mumbai, Maharashtra 400061, India.
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Verma A, Patel R, Mahale A, Thorat RV, Rath SL, Sridhar E, Moiyadi A, Srivastava S. Multitarget Potential Drug Candidates for High-Grade Gliomas Identified by Multiple Reaction Monitoring Coupled with In Silico Drug Repurposing. OMICS 2024; 28:59-75. [PMID: 38320249 DOI: 10.1089/omi.2023.0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
High-grade gliomas (HGGs) are extremely aggressive primary brain tumors with high mortality rates. Despite notable progress achieved by clinical research and biomarkers emerging from proteomics studies, efficacious drugs and therapeutic targets are limited. This study used targeted proteomics, in silico molecular docking, and simulation-based drug repurposing to identify potential drug candidates for HGGs. Importantly, we performed multiple reaction monitoring (MRM) on differentially expressed proteins with putative roles in the development and progression of HGGs based on our previous work and the published literature. Furthermore, in silico molecular docking-based drug repurposing was performed with a customized library of FDA-approved drugs to identify multitarget-directed ligands. The top drug candidates such as Pazopanib, Icotinib, Entrectinib, Regorafenib, and Cabozantinib were explored for their drug-likeness properties using the SwissADME. Pazopanib exhibited binding affinities with a maximum number of proteins and was considered for molecular dynamic simulations and cell toxicity assays. HGG cell lines showed enhanced cytotoxicity and cell proliferation inhibition with Pazopanib and Temozolomide combinatorial treatment compared to Temozolomide alone. To the best of our knowledge, this is the first study combining MRM with molecular docking and simulation-based drug repurposing to identify potential drug candidates for HGG. While the present study identified five multitarget-directed potential drug candidates, future clinical studies in larger cohorts are crucial to evaluate the efficacy of these molecular candidates. The research strategy and methodology used in the present study offer new avenues for innovation in drug discovery and development which may prove useful, particularly for cancers with low cure rates.
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Affiliation(s)
- Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Rushda Patel
- Sinhgad College of Pharmacy, Savitribai Phule Pune University, Pune, India
| | - Atharva Mahale
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Rujuta Vijay Thorat
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Epari Sridhar
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Aliasgar Moiyadi
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Dhamija B, Marathe S, Sawant V, Basu M, Attrish D, Mukherjee D, Kumar S, Pai MGJ, Wad S, Sawant A, Nayak C, Venkatesh KV, Srivastava S, Barthel SR, Purwar R. IL-17A Orchestrates Reactive Oxygen Species/HIF1α-Mediated Metabolic Reprogramming in Psoriasis. J Immunol 2024; 212:302-316. [PMID: 38019129 DOI: 10.4049/jimmunol.2300319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023]
Abstract
Immune cell-derived IL-17A is one of the key pathogenic cytokines in psoriasis, an immunometabolic disorder. Although IL-17A is an established regulator of cutaneous immune cell biology, its functional and metabolic effects on nonimmune cells of the skin, particularly keratinocytes, have not been comprehensively explored. Using multiomics profiling and systems biology-based approaches, we systematically uncover significant roles for IL-17A in the metabolic reprogramming of human primary keratinocytes (HPKs). High-throughput liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance spectroscopy revealed IL-17A-dependent regulation of multiple HPK proteins and metabolites of carbohydrate and lipid metabolism. Systems-level MitoCore modeling using flux-balance analysis identified IL-17A-mediated increases in HPK glycolysis, glutaminolysis, and lipid uptake, which were validated using biochemical cell-based assays and stable isotope-resolved metabolomics. IL-17A treatment triggered downstream mitochondrial reactive oxygen species and HIF1α expression and resultant HPK proliferation, consistent with the observed elevation of these downstream effectors in the epidermis of patients with psoriasis. Pharmacological inhibition of HIF1α or reactive oxygen species reversed IL-17A-mediated glycolysis, glutaminolysis, lipid uptake, and HPK hyperproliferation. These results identify keratinocytes as important target cells of IL-17A and reveal its involvement in multiple downstream metabolic reprogramming pathways in human skin.
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Affiliation(s)
- Bhavuk Dhamija
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Soumitra Marathe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Vinanti Sawant
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Moumita Basu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Diksha Attrish
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ditipriya Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sushant Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Siddhi Wad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Abhijeet Sawant
- Plastic Surgery Department, Topiwala National Medical College and B.Y.L. Nair Charitable Hospital, Mumbai, India
| | - Chitra Nayak
- Skin and Venereal Diseases Department, Topiwala National Medical College and B.Y.L. Nair Charitable Hospital, Mumbai, India
| | | | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Steven R Barthel
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Rahul Purwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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5
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Rajoria S, Kavuru SR, Pyda HS, Bihani S, Borishetty D, Biswas D, Prajapati J, Paladi H, Srivastava S. CoVProt: Toward a Mass Spectrometry Data Portal for COVID-19 Proteomics Research and Development. OMICS 2024; 28:24-31. [PMID: 38193774 DOI: 10.1089/omi.2023.0274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has wreaked havoc globally. Beyond the pandemic, the long-term effects of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in multiple organ systems are yet to be deciphered. This calls for continued systems science research. Moreover, the host response to SARS-CoV-2 varies person-to-person and gives rise to different degrees of morbidity and mortality. Mass spectrometry (MS) has been a proven asset in studies of the SARS-CoV-2 from an omics systems science lens. To strengthen the proteomics research dedicated to COVID-19, we introduce here a web-based portal, CoVProt. The portal is work in progress and aims for a comprehensive curation of MS-based proteomics data of COVID-19 clinical samples for deep proteomic investigations, data visualization, and easy data accessibility for life sciences innovations and planetary health research community. Currently, CoVProt contains information on 2725 different proteins and 37,125 different peptides from six data sets covering a total of 202 clinical samples. Moreover, all pertinent data sets extracted from the literature have been reanalyzed using a common analysis pipeline developed by combining multiple tools. Going forward, we anticipate that the CoVProt portal will also provide access to the clinical parameters of the patients. The CoVProt (v1.0) portal addresses an existing significant gap to study COVID-19 host proteomics, which, to the best of our knowledge, is the first effort in this direction. We believe that CoVProt is poised to make contributions as a community resource for proteomic applications and aims to broadly support clinical studies to facilitate the discovery of COVID-19 biomarkers and therapeutics with translational potential.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sai Rohith Kavuru
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Hari Sundar Pyda
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai- Indian Oil Odisha Campus, Bhubaneswar, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Dhanush Borishetty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptrup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Jeel Prajapati
- Department of Biotechnology and Bioengineering, Institute of Advanced Research, Gandhinagar, India
| | - Harshith Paladi
- Department of Computer Science, School of Computing, SASTRA Deemed to be University, Thanjavur, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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6
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Srivastava S, Basak U, Naghibi M, Vijayakumar V, Parihar R, Patel J, Jadon PS, Pandit A, Dargad RR, Khanna S, Kumar S, Day R. A randomized double-blind, placebo-controlled trial to evaluate the safety and efficacy of live Bifidobacterium longum CECT 7347 (ES1) and heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) in participants with diarrhea-predominant irritable bowel syndrome. Gut Microbes 2024; 16:2338322. [PMID: 38630015 PMCID: PMC11028008 DOI: 10.1080/19490976.2024.2338322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
To determine the efficacy of the probiotic Bifidobacterium longum CECT 7347 (ES1) and postbiotic heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) in improving symptom severity in adults with diarrhea-predominant irritable bowel syndrome (IBS-D), a randomised, double-blind, placebo-controlled trial with 200 participants split into three groups was carried out. Two capsules of either ES1, HT-ES1 or placebo were administered orally, once daily, for 84 days (12 weeks). The primary outcome was change in total IBS-Symptom Severity Scale (IBS-SSS) score from baseline, compared to placebo. Secondary outcome measures were stool consistency, quality of life, abdominal pain severity and anxiety scores. Safety parameters and adverse events were also monitored. The change in IBS-SSS scores from baseline compared to placebo, reached significance in the ES1 and HT-ES1 group, on Days 28, 56 and 84. The decrease in mean IBS-SSS score from baseline to Day 84 was: ES1 (-173.70 [±75.60]) vs placebo (-60.44 [±65.5]) (p < .0001) and HT-ES1 (-177.60 [±79.32]) vs placebo (-60.44 [±65.5]) (p < .0001). Secondary outcomes included changes in IBS-QoL, APS-NRS, stool consistency and STAI-S and STAI-T scores, with changes from baseline to Day 84 being significant in ES1 and HT-ES1 groups, compared to the placebo group. Both ES1 and HT-ES1 were effective in reducing IBS-D symptom severity, as evaluated by measures such as IBS-SSS, IBS-QoL, APS-NRS, stool consistency, and STAI, in comparison to the placebo. These results are both statistically significant and clinically meaningful, representing, to the best of the authors' knowledge, the first positive results observed for either a probiotic or postbiotic from the same strain, in this particular population.
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Affiliation(s)
- S Srivastava
- Clinical Development & Science Communications, Vedic Lifesciences Pvt Ltd, Mumbai, India
| | - U Basak
- Clinical Development & Science Communications, Vedic Lifesciences Pvt Ltd, Mumbai, India
| | - M Naghibi
- Medical Department, ADM Health & Wellness, London, UK
| | - V Vijayakumar
- Medical Department, ADM Health & Wellness, London, UK
| | - R Parihar
- Gastroenterology Department, Gastroplus Digestive Disease Centre, Ahmedabad, India
| | - J Patel
- Gastroenterology Department, Apex Gastro Clinic and Hospital, Ahmedabad, India
| | - PS Jadon
- Medicine Department, Jaipur National University Institute for Medical Science & Research Centre, Jaipur, India
| | - A Pandit
- General Surgery Department, United Multispeciality Hospital, Maharashtra, India
| | - RR Dargad
- Medicine Department, Lilavati Hospital & Research Centre, Maharashtra, India
| | - S Khanna
- Gastroenterology Department, Criticare Asia Multispeciality hospital, Maharashtra, India
| | - S Kumar
- Independent Biostatistical Consultant, Delhi, India
| | - R Day
- Medical Department, ADM Health & Wellness, London, UK
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Sharma G, Banerjee R, Srivastava S. Molecular Mechanisms and the Interplay of Important Chronic Obstructive Pulmonary Disease Biomarkers Reveals Novel Therapeutic Targets. ACS Omega 2023; 8:46376-46389. [PMID: 38107961 PMCID: PMC10719921 DOI: 10.1021/acsomega.3c07480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/02/2023] [Indexed: 12/19/2023]
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a progressive, age-dependent, and unmet chronic inflammatory disease of the peripheral airways, leading to difficulty in exhalation. Several biomarkers have been tested in general towards the resolution for a long time, but no apparent success was achieved. Ongoing therapies of COPD have only symptomatic relief but no cure. Reactive oxygen species (ROS) are highly reactive species which include oxygen radicals and nonradical derivatives, and are the prominent players in COPD. They are produced as natural byproducts of cellular metabolism, but their levels can vary due to exposure to indoor air pollution, occupational pollution, and environmental pollutants such as cigarette smoke. In COPD, the lungs are continuously exposed to high levels of ROS thus leading to oxidative stress. ROS can cause damage to cells, proteins, lipids, and DNA which further contributes to the chronic inflammation in COPD and exacerbates the disease condition. Excessive ROS production can overwhelm cellular antioxidant systems and act as signaling molecules that regulate cellular processes, including antioxidant defense mechanisms involving glutathione and sirtuins which further leads to cellular apoptosis, cellular senescence, inflammation, and sarcopenia. In this review paper, we focused on COPD from different perspectives including potential markers and different cellular processes such as apoptosis, cellular senescence, inflammation, sirtuins, and sarcopenia, and tried to connect the dots between them so that novel therapeutic strategies to evaluate and target the possible underlying mechanisms in COPD could be explored.
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Affiliation(s)
- Gautam Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Maharashtra 400076, India
| | | | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Maharashtra 400076, India
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8
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Ghantasala S, Bhat A, Epari S, Moiyadi A, Srivastava S. High-Grade Gliomas from Subventricular Zone: Proteomic Drivers of Aggressiveness Using Fluorescence-Guided Multiple Sampling. OMICS 2023; 27:598-606. [PMID: 38055199 DOI: 10.1089/omi.2023.0124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
High-grade gliomas (HGGs) are among the most aggressive brain tumors and are characterized by dismally low median survival time. Of the many factors influencing the survival of patients with HGGs, proximity to the subventricular zone (SVZ) is one of the key influencers. In this context, 5-amino levulinic acid fluorescence-guided multiple sampling (FGMS) offers the prospect of understanding patient-to-patient molecular heterogeneity driving the aggressiveness of these tumors. Using high-resolution liquid chromatography-mass spectrometry (MS)/MS proteomics for HGGs from seven patients (four SVZ associated and three SVZ nonassociated), this study aimed to uncover the mechanisms driving the aggressiveness in SVZ-associated (SVZ+) HGGs. Differential proteomics analysis revealed significant dysregulation of 11 proteins, of which 9 proteins were upregulated and 2 were downregulated in SVZ+ HGGs compared to SVZ-non-associated (SVZ-) HGGs. The gene set enrichment analysis (GSEA) of the proteomics dataset revealed enrichment of MYC targets V1 and V2, G2M checkpoints, and E2F targets in SVZ+ HGGs. With GSEA, we also compared the pathways enriched in glioma stem cell subpopulations and observed a similar expression trend for most pathways in our data. In conclusion, this study reveals new and emerging insights on pathways that may potentially contribute to greater aggressiveness in SVZ+ HGGs. Future studies using FGMS in larger cohorts are recommended to help uncover the proteomics and molecular basis of aggressiveness and stemness in HGGs.
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Affiliation(s)
- Saicharan Ghantasala
- Centre for Research in Nano Technology and Science, Indian Institute of Technology Bombay, Powai, India
| | - Amruth Bhat
- Department of Bioengineering, Indian Institute of Science, Bengaluru, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre's-Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Aliasgar Moiyadi
- Homi Bhabha National Institute, Mumbai, India
- Department of Neurosurgery, Tata Memorial Centre's-Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, India
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9
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Jin L, Xie Z, Lorkiewicz P, Srivastava S, Bhatnagar A, Conklin DJ. Endothelial-dependent relaxation of α-pinene and two metabolites, myrtenol and verbenol, in isolated murine blood vessels. Am J Physiol Heart Circ Physiol 2023; 325:H1446-H1460. [PMID: 37889254 DOI: 10.1152/ajpheart.00380.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023]
Abstract
Epidemiological evidence shows that residential proximity to greenspaces is associated with lower risk of all-cause and cardiovascular mortality; however, the mechanism(s) underlying this link remains unclear. Plants emit biogenic volatile organic compounds such as α-pinene that could elicit beneficial cardiovascular effects. To explore the role of α-pinene more directly, we studied the metabolism and the vascular effects of α-pinene. We found that exposure of mice to α-pinene (1 ppm, 6 h) generated two phase I oxidation metabolites, cis- and trans-verbenol [(1R,2R,5R)-verbenol and (1 R,2S,5R)-verbenol)] and myrtenol [(1S,5R)-(+)-myrtenol] that were identified in urine by GC-MS. Precontracted naïve murine male and female aorta and superior mesenteric artery (SMA) were relaxed robustly (60% tension reduction) by increasing concentrations of α-pinene, myrtenol, and verbenol to 0.3 mM, whereas 1 mM α-pinene was vasotoxic. The SMA was six times more sensitive than the aorta to α-pinene. Both myrtenol and verbenol were equally potent and efficacious as parent α-pinene in male and female SMA. The sensitive portion of the α-pinene-, myrtenol-, and verbenol-induced relaxations in male SMA was mediated by 1) endothelium, 2) eNOS-derived NO, and 3) guanylyl cyclase (GC) activity. Moreover, α-pinene activated the transient receptor potential ankyrin-1 (TRPA1) channel whereas the metabolites did not. Endothelial-derived NO regulates blood flow, blood pressure, and thrombosis, and it is plausible that inhaled (and ingested) α-pinene (or its metabolites) augments NO release to mediate the cardiovascular benefits of exposure to greenness.NEW & NOTEWORTHY A common plant-derived biogenic volatile organic compound, α-pinene, and two of its metabolites, myrtenol and verbenol, stimulate vasorelaxation in murine superior mesenteric artery. Both α-pinene- and its metabolites induce vasorelaxation by activation of the endothelium, nitric oxide, and guanylyl cyclase. α-Pinene also activates the transient receptor potential ankyrin-1. Positive associations between greenness exposure and human cardiovascular health may be a result of the vascular action of α-pinene and its metabolites, a novel consideration.
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Affiliation(s)
- L Jin
- Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky, United States
| | - Z Xie
- Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky, United States
- Division of Environmental Medicine, Department of Medicine, University of Louisville, Louisville, Kentucky, United States
| | - P Lorkiewicz
- Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky, United States
- Division of Environmental Medicine, Department of Medicine, University of Louisville, Louisville, Kentucky, United States
| | - S Srivastava
- Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky, United States
- Division of Environmental Medicine, Department of Medicine, University of Louisville, Louisville, Kentucky, United States
| | - A Bhatnagar
- Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky, United States
- Division of Environmental Medicine, Department of Medicine, University of Louisville, Louisville, Kentucky, United States
| | - D J Conklin
- Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky, United States
- Division of Environmental Medicine, Department of Medicine, University of Louisville, Louisville, Kentucky, United States
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10
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Dash A, Salkar A, Nissa MU, Makwana P, Athalye A, Parikh S, Srivastava S, Parikh F. Semen proteomics reveals alterations in fertility-related proteins post-recovery from COVID-19. Front Physiol 2023; 14:1212959. [PMID: 38028760 PMCID: PMC10665489 DOI: 10.3389/fphys.2023.1212959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Changes to sperm quality and decline in reproductive function have been reported in COVID-19-recovered males. Further, the emergence of SARS-CoV-2 variants has caused the resurgences of COVID-19 cases globally during the last 2 years. These variants show increased infectivity and transmission along with immune escape mechanisms, which threaten the already burdened healthcare system. However, whether COVID-19 variants induce an effect on the male reproductive system even after recovery remains elusive. Methods: We used mass-spectrometry-based proteomics approaches to understand the post-COVID-19 effect on reproductive health in men using semen samples post-recovery from COVID-19. The samples were collected between late 2020 (1st wave, n = 20), and early-to-mid 2021 (2nd wave, n = 21); control samples were included (n = 10). During the 1st wave alpha variant was prevalent in India, whereas the delta variant dominated the second wave. Results: On comparing the COVID-19-recovered patients from the two waves with control samples, using one-way ANOVA, we identified 69 significantly dysregulated proteins among the three groups. Indeed, this was also reflected by the changes in sperm count, morphology, and motility of the COVID-19- recovered patients. In addition, the pathway enrichment analysis showed that the regulated exocytosis, neutrophil degranulation, antibacterial immune response, spermatogenesis, spermatid development, regulation of extracellular matrix organization, regulation of peptidase activity, and regulations of calcium ion transport were significantly dysregulated. These pathways directly or indirectly affect sperm parameters and function. Our study provides a comprehensive landscape of expression trends of semen proteins related to male fertility in men recovering from COVID-19. Discussion: Our study suggests that the effect of COVID-19 on the male reproductive system persists even after recovery from COVID-19. In addition, these post-COVID-19 complications persist irrespective of the prevalent variants or vaccination status.
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Affiliation(s)
- Ankita Dash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prashant Makwana
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Centre, Jaslok Hospital and Research Centre, Mumbai, India
| | - Arundhati Athalye
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Centre, Jaslok Hospital and Research Centre, Mumbai, India
| | - Swapneil Parikh
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Centre, Jaslok Hospital and Research Centre, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Firuza Parikh
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Centre, Jaslok Hospital and Research Centre, Mumbai, India
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11
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Abad Z, Burgess T, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl J, Verkleij G, Broders K, Schena L, Redford A. Phytophthora : taxonomic and phylogenetic revision of the genus. Stud Mycol 2023; 106:259-348. [PMID: 38298569 PMCID: PMC10825748 DOI: 10.3114/sim.2023.106.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/19/2023] [Indexed: 02/02/2024] Open
Abstract
Many members of the Oomycota genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of regulatory concern around the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for 20 species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani, P. honggalleglyana (Synonym: P. hydropathica), P. megakarya, P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. ×multiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated multigene phylogeny and molecular toolbox with seven genes (ITS rDNA, β-tub, COI, EF1α, HSP90, L10, and YPT1) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 species, are associated with the "IDphy: molecular and morphological identification of Phytophthora based on the types" online resource (https://idtools.org/tools/1056/index.cfm). The first version of the IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic molecular toolbox with seven genes that includes the two metabarcoding genes (ITS and COI) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora, widely considered one of the most important genera of plant pathogens. Taxonomic novelties: New species: Phytophthora cajani K.S. Amin, Baldev & F.J. Williams ex Abad, Phytophthora honggalleglyana Abad, Phytophthora megakarya Brasier & M.J. Griffin ex Abad, Phytophthora pisi Heyman ex Abad, Phytophthora pseudopolonica W.W. Li, W.X. Huai & W.X. Zhao ex Abad & Kasiborski; New combinations: Phytophthora ×multiformis (Brasier & S.A. Kirk) Abad, Phytophthora uniformis (Brasier & S.A. Kirk) Abad; Epitypifications (basionyms): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora inundata Brasier et al., Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Lectotypifications (basionym): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Neotypifications (basionym): Phloeophthora syringae Kleb., Phytophthora meadii McRae Citation: Abad ZG, Burgess TI, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl JC, Verkleij G, Broders K, Schena L, Redford AJ (2023). Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology 106: 259-348. doi: 10.3114/sim.2023.106.05.
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Affiliation(s)
- Z.G. Abad
- USDA APHIS PPQ S&T Plant Pathogen Confirmatory Diagnostics Laboratory, USA;
| | - T.I. Burgess
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, Perth, WA, Australia;
| | - T. Bourret
- Department of Plant Pathology, University of California, Davis, CA, USA,
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8, 3584 CT Utrecht, Netherlands,
| | - S.O. Cacciola
- Department of Agricultural, Food and Environment, University of Catania, Italy;
| | - B. Scanu
- Department of Agricultural Sciences, University of Sassari, Italy;
| | - R. Mathew
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA;
| | - B. Kasiborski
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA;
| | - S. Srivastava
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA;
| | - K. Kageyama
- River Basin Research Center, Gifu University, Japan,
| | - J.C. Bienapfl
- USDA APHIS PPQ S&T Plant Pathogen Confirmatory Diagnostics Laboratory, USA;
| | - G. Verkleij
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8, 3584 CT Utrecht, Netherlands,
| | - K. Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, 61604, USA;
| | - L. Schena
- Dipartimento di Agraria, Mediterranean University of Reggio Calabria, Italy,
| | - A.J. Redford
- USDA APHIS PPQ S&T Identification Technology Program, USA
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Biswas D, Halder A, Barpanda A, Ghosh S, Chauhan A, Bhat L, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S. Integrated Meta-Omics Analysis Unveils the Pathways Modulating Tumorigenesis and Proliferation in High-Grade Meningioma. Cells 2023; 12:2483. [PMID: 37887327 PMCID: PMC10604908 DOI: 10.3390/cells12202483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Meningioma, a primary brain tumor, is commonly encountered and accounts for 39% of overall CNS tumors. Despite significant progress in clinical research, conventional surgical and clinical interventions remain the primary treatment options for meningioma. Several proteomics and transcriptomics studies have identified potential markers and altered biological pathways; however, comprehensive exploration and data integration can help to achieve an in-depth understanding of the altered pathobiology. This study applied integrated meta-analysis strategies to proteomic and transcriptomic datasets comprising 48 tissue samples, identifying around 1832 common genes/proteins to explore the underlying mechanism in high-grade meningioma tumorigenesis. The in silico pathway analysis indicated the roles of extracellular matrix organization (EMO) and integrin binding cascades in regulating the apoptosis, angiogenesis, and proliferation responsible for the pathobiology. Subsequently, the expression of pathway components was validated in an independent cohort of 32 fresh frozen tissue samples using multiple reaction monitoring (MRM), confirming their expression in high-grade meningioma. Furthermore, proteome-level changes in EMO and integrin cell surface interactions were investigated in a high-grade meningioma (IOMM-Lee) cell line by inhibiting integrin-linked kinase (ILK). Inhibition of ILK by administrating Cpd22 demonstrated an anti-proliferative effect, inducing apoptosis and downregulating proteins associated with proliferation and metastasis, which provides mechanistic insight into the disease pathophysiology.
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Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Susmita Ghosh
- Leibniz-Institut für Analytische Wissenschaften—ISAS, 44227 Dortmund, Germany;
| | - Aparna Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
| | - Lipika Bhat
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed-to-be University, Mumbai 400056, India;
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai 400012, India;
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai 400012, India; (P.S.); (A.M.)
| | - Aliasgar Moiyadi
- Department of Neurosurgery, Tata Memorial Centre, Mumbai 400012, India; (P.S.); (A.M.)
| | - Graham Roy Ball
- Medical Technology Research Centre, Anglia Ruskin University, East Rd., Cambridge CB1 1PT, UK;
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; (D.B.); (A.H.); (A.B.); (A.C.)
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13
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Akkerman OW, Dijkwel RDC, Kerstjens HAM, van der Werf TS, Srivastava S, Sturkenboom MGG, Bolhuis MS. Isoniazid and rifampicin exposure during treatment in drug-susceptible TB. Int J Tuberc Lung Dis 2023; 27:772-777. [PMID: 37749836 PMCID: PMC10519386 DOI: 10.5588/ijtld.22.0698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/15/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND: Observational real-world studies on therapeutic drug monitoring (TDM) in relation to pharmacokinetic (PK) target values are lacking. This study aims to describe the PK of rifampicin (RIF) and isoniazid (INH) in a real-world setting of patients with drug-susceptible TB in relation to frequently used threshold values.METHODS: A total of 116 patients with TB using standard doses of RIF and INH and who had TDM as part of clinical care were included. Maximum plasma concentration (Cmax) and 24 h area under the concentration time curve (AUC24) at standard and revised doses were described in relation to the threshold values (Cmax ≥8 mg/L for RIF and ≥3 mg/L for INH).RESULTS: For RIF (100 patients), median Cmax and median AUC24 were respectively 7.9 mg/L (IQR 6.0-11.0) and 35.8 mg*h/L (IQR 27.4-57.3) at the first TDM measurement after a standard dose of 600 mg. For INH (90 patients), median Cmax and median AUC24 were respectively 2.9 mg/L (IQR 1.3-2.5) and 12.5 mg*h/L (IQR 8.7-18.9) at the first TDM after a standard dose 300 mg. Overall, more than 50% of study participants had drug exposure below threshold values at the first TDM.CONCLUSION: Our study shows that the measured Cmax values for both RIF and INH were frequently below the pre-specified targets, emphasising the need for better justification of drug exposure targets. These TDM results highlight the need for validating PK targets of anti-TB drugs associated with clinically relevant outcomes.
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Affiliation(s)
- O W Akkerman
- Department of Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, Tuberculosis Center Beatrixoord, University of Groningen, University Medical Center Groningen, Haren
| | - R D C Dijkwel
- Departments of Clinical Pharmacy and Pharmacology, and
| | - H A M Kerstjens
- Department of Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen
| | - T S van der Werf
- Department of Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, Departments of Internal Medicine and Infectiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - S Srivastava
- Department of Medicine, The University of Texas Health Science Center at Tyler, Tyler, TX, USA, Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA, Department of Center for Biomedical Research, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | | | - M S Bolhuis
- Departments of Clinical Pharmacy and Pharmacology, and
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14
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Halder A, Biswas D, Chauhan A, Saha A, Auromahima S, Yadav D, Nissa MU, Iyer G, Parihari S, Sharma G, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S. A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors. Clin Proteomics 2023; 20:41. [PMID: 37770851 PMCID: PMC10540342 DOI: 10.1186/s12014-023-09426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Meningiomas are the most prevalent primary brain tumors. Due to their increasing burden on healthcare, meningiomas have become a pivot of translational research globally. Despite many studies in the field of discovery proteomics, the identification of grade-specific markers for meningioma is still a paradox and requires thorough investigation. The potential of the reported markers in different studies needs further verification in large and independent sample cohorts to identify the best set of markers with a better clinical perspective. METHODS A total of 53 fresh frozen tumor tissue and 51 serum samples were acquired from meningioma patients respectively along with healthy controls, to validate the prospect of reported differentially expressed proteins and claimed markers of Meningioma mined from numerous manuscripts and knowledgebases. A small subset of Glioma/Glioblastoma samples were also included to investigate inter-tumor segregation. Furthermore, a simple Machine Learning (ML) based analysis was performed to evaluate the classification accuracy of the list of proteins. RESULTS A list of 15 proteins from tissue and 12 proteins from serum were found to be the best segregator using a feature selection-based machine learning strategy with an accuracy of around 80% in predicting low grade (WHO grade I) and high grade (WHO grade II and WHO grade III) meningiomas. In addition, the discriminant analysis could also unveil the complexity of meningioma grading from a segregation pattern, which leads to the understanding of transition phases between the grades. CONCLUSIONS The identified list of validated markers could play an instrumental role in the classification of meningioma as well as provide novel clinical perspectives in regard to prognosis and therapeutic targets.
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Affiliation(s)
- Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Aparna Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Adrita Saha
- Motilal Nehru National Institute of Technology, Allahabad, 211004, UP, India
| | - Shreeman Auromahima
- Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Deeksha Yadav
- CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, New Delhi, 110025, India
| | - Mehar Un Nissa
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Gayatri Iyer
- Koita Centre for Digital Health, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Shashwati Parihari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Gautam Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai, India
| | | | - Graham Roy Ball
- Medical Technology Research Centre, Anglia Ruskin University, Cambridge Campus, East Rd, Cambridge, CB1 1PT, UK
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 185 Berry St., Suite 290, San Francisco, CA, 94107, USA.
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15
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Lad SB, Upadhyay M, Thorat P, Nair D, Moseley GW, Srivastava S, Pradeepkumar PI, Kondabagil K. Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway. J Mol Biol 2023; 435:168188. [PMID: 37380013 DOI: 10.1016/j.jmb.2023.168188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Abstract
Viruses are believed to be the obligate intracellular parasites that only carry genes essential for infecting and hijacking the host cell machinery. However, a recently discovered group of viruses belonging to the phylum nucleocytovirocota, also known as the nucleo-cytoplasmic large DNA viruses (NCLDVs), possess a number of genes that code for proteins predicted to be involved in metabolism, and DNA replication, and repair. In the present study, first, using proteomics of viral particles, we show that several proteins required for the completion of the DNA base excision repair (BER) pathway are packaged within the virions of Mimivirus as well as related viruses while they are absent from the virions of Marseillevirus and Kurlavirus that are NCLDVs with smaller genomes. We have thoroughly characterized three putative base excision repair enzymes from Mimivirus, a prototype NCLDV and successfully reconstituted the BER pathway using the purified recombinant proteins. The mimiviral uracil-DNA glycosylase (mvUDG) excises uracil from both ssDNA and dsDNA, a novel finding contrary to earlier studies. The putative AP-endonuclease (mvAPE) specifically cleaves at the abasic site created by the glycosylase while also exhibiting the 3'-5' exonuclease activity. The Mimivirus polymerase X protein (mvPolX) can bind to gapped DNA substrates and perform single nucleotide gap-filling followed by downstream strand displacement. Furthermore, we show that when reconstituted in vitro, mvUDG, mvAPE, and mvPolX function cohesively to repair a uracil-containing DNA predominantly by long patch BER and together, may participate in the BER pathway during the early phase of Mimivirus life-cycle.
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Affiliation(s)
- Shailesh B Lad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India. https://twitter.com/shailesh2603
| | - Monica Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India; Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia. https://twitter.com/upadhyaymonica
| | - Pracheta Thorat
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Gregory W Moseley
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India. https://twitter.com/sanjeeva_IITB
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India. https://twitter.com/pradeepkumarpi
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India.
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Bihani S, Gupta A, Mehta S, Rajczewski AT, Johnson J, Borishetty D, Griffin TJ, Srivastava S, Jagtap PD. Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients. J Proteome Res 2023; 22:2608-2619. [PMID: 37450889 DOI: 10.1021/acs.jproteome.3c00040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
During the COVID-19 pandemic, impaired immunity and medical interventions resulted in cases of secondary infections. The clinical difficulties and dangers associated with secondary infections in patients necessitate the exploration of their microbiome. Metaproteomics is a powerful approach to study the taxonomic composition and functional status of the microbiome under study. In this study, the mass spectrometry (MS)-based data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. We have established a robust bioinformatics workflow within the Galaxy platform, which includes (a) generation of a tailored database of the common respiratory tract pathogens, (b) database search using multiple search algorithms, and (c) verification of the detected microbial peptides. The microbial peptides detected in this study, belong to several opportunistic pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Rhizopus microsporus, and Syncephalastrum racemosum. Microbial proteins with a role in stress response, gene expression, and DNA repair were found to be upregulated in severe patients compared to negative patients. Using parallel reaction monitoring (PRM), we confirmed some of the microbial peptides in fresh clinical samples. MS-based clinical metaproteomics can serve as a powerful tool for detection and characterization of potential pathogens, which can significantly impact the diagnosis and treatment of patients.
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Affiliation(s)
- Surbhi Bihani
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Aryan Gupta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-129 MCB, 420 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - Andrew T Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-129 MCB, 420 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - James Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Dhanush Borishetty
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-129 MCB, 420 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - Sanjeeva Srivastava
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-129 MCB, 420 Washington Ave SE, Minneapolis, Minnesota 55455, United States
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Sharma G, Pund S, Govindan R, Nissa MU, Biswas D, Middha S, Ganguly K, Anand MP, Banerjee R, Srivastava S. A Proteomics Investigation of Cigarette Smoke Exposed Wistar Rats Revealed Improved Anti-Inflammatory Effects of the Cysteamine Nanoemulsions Delivered via Inhalation. OMICS 2023; 27:338-360. [PMID: 37581495 DOI: 10.1089/omi.2023.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Cigarette smoking is the major cause of chronic inflammatory diseases such as chronic obstructive pulmonary disease (COPD). It is paramount to develop pharmacological interventions and delivery strategies against the cigarette smoke (CS) associated oxidative stress in COPD. This study in Wistar rats examined cysteamine in nanoemulsions to counteract the CS distressed microenvironment. In vivo, 28 days of CS and 15 days of cysteamine nanoemulsions treatment starting on 29th day consisting of oral and inhalation routes were established in Wistar rats. In addition, we conducted inflammatory and epithelial-to-mesenchymal transition (EMT) studies in vitro in human bronchial epithelial cell lines (BEAS2B) using 5% CS extract. Inflammatory and anti-inflammatory markers, such as tumor necrosis factor-alpha (TNF-α), interleukin (IL)-6, IL-1β, IL-8, IL-10, and IL-13, have been quantified in bronchoalveolar lavage fluid (BALF) to evaluate the effects of the cysteamine nanoemulsions in normalizing the diseased condition. Histopathological analysis of the alveoli and the trachea showed the distorted, lung parenchyma and ciliated epithelial barrier, respectively. To obtain mechanistic insights into the CS COPD rat model, "shotgun" proteomics of the lung tissues have been carried out using high-resolution mass spectrometry wherein genes such as ABI1, PPP3CA, PSMA2, FBLN5, ACTG1, CSNK2A1, and ECM1 exhibited significant differences across all the groups. Pathway analysis showed autophagy, signaling by receptor tyrosine kinase, cytokine signaling in immune system, extracellular matrix organization, and hemostasis, as the major contributing pathways across all the studied groups. This work offers new preclinical findings on how cysteamine taken orally or inhaled can combat CS-induced oxidative stress.
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Affiliation(s)
- Gautam Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Swati Pund
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Biobay, Ahmedabad, India
| | - Rajkumar Govindan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Biomedical Engineering, Hajim School of Engineering & Applied Sciences, University of Rochester, Rochester, New York, USA
| | - Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanniya Middha
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Koustav Ganguly
- Unit of Integrative Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Rinti Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Srivastava S, Bertone MP, Parmar D, Walsh C, De Allegri M. The genesis of the PM-JAY health insurance scheme in India: technical and political elements influencing a national reform towards universal health coverage. Health Policy Plan 2023:czad045. [PMID: 37436821 DOI: 10.1093/heapol/czad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 04/18/2023] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
Many countries are using health insurance to advance progress towards universal health coverage (UHC). India launched the Pradhan Mantri Jan Arogya Yojana (PM-JAY) health insurance scheme in 2018. We examine the political economy context around PM-JAY policy formulation, by examining the perspectives of policy stakeholders shaping decisions around the reform. More specifically, we focus on early policy design at the central (national) level. We use a framework on the politics of UHC reform proposed by Fox and Reich (The politics of universal health coverage in low- and middle-income countries: A framework for evaluation and action. J. Health Polit. Policy Law 2015;40:1023-1060), to categorize the reform into phases and examine the interactions between actors, institutions, interests, ideas and ideology which shaped reform decisions. We interviewed 15 respondents in Delhi between February and April 2019, who were either closely associated with the reform process or subject experts. The ruling centre-right government introduced PM-JAY shortly before national elections, drawing upon policy legacies from prior and state insurance schemes. Empowered policy entrepreneurs within the government focused discourse around ideas of UHC and strategic purchasing, and engaged in institution building leading to the creation of the National Health Authority and State Health Agencies through policy directives, thereby expanding state infrastructural and institutional power for insurance implementation. Indian state inputs were incorporated in scheme design features like mode of implementation, benefit package and provider network, while features like the coverage amount, portability of benefits and branding strategy were more centrally driven. These balanced negotiations opened up political space for a cohesive, central narrative of the reform and facilitated adoption. Our analysis shows that the PM-JAY reform focused on bureaucratic rather than ideological elements and that technical compromises and adjustments accommodating the interests of states enabled the political success of policy formulation. Appreciating these politics, power and structural issues shaping PM-JAY institutional design will be important to understand how PM-JAY is implemented and how it advances UHC in India.
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Affiliation(s)
- S Srivastava
- Heidelberg Institute of Global Health, Medical Faculty and University Hospital, Heidelberg University, Im Neuenheimer Feld 130.3, Heidelberg, Baden-Württemberg 69120, Germany
| | - M P Bertone
- Institute for Global Health and Development, Queen Margaret University, Edinburgh, Scotland EH21 6UU, UK
| | - D Parmar
- King's Centre for Global Health and Health Partnerships, School of Life Course and Population Sciences, King's College London, Strand, London WC2R 2LS, UK
| | - C Walsh
- Heidelberg Institute of Global Health, Medical Faculty and University Hospital, Heidelberg University, Im Neuenheimer Feld 130.3, Heidelberg, Baden-Württemberg 69120, Germany
| | - M De Allegri
- Heidelberg Institute of Global Health, Medical Faculty and University Hospital, Heidelberg University, Im Neuenheimer Feld 130.3, Heidelberg, Baden-Württemberg 69120, Germany
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Keller SB, Cohen J, Moon-Grady A, Cuneo B, Paul E, Coll AC, Campbell M, Srivastava S. Patterns of endocardial fibroelastosis without atrioventricular block in fetuses exposed to anti-Ro/SSA antibodies. Ultrasound Obstet Gynecol 2023; 62:148-151. [PMID: 36806323 DOI: 10.1002/uog.26181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Anti-Ro/SSA-antibody-mediated endocardial fibroelastosis (EFE) without atrioventricular (AV) block at presentation is a rare cardiac phenotype. We report on 11 fetuses with this rare type of anti-Ro/SSA-antibody-mediated cardiac involvement, presenting with a distinctive echocardiographic pattern of EFE. Eleven fetuses with isolated EFE at presentation were included from four cardiac centers, and experienced fetal cardiologists reached a consensus regarding EFE location on echocardiography at presentation. Interval changes to subsequent fetal and postnatal echocardiograms were assessed to evaluate response to therapy. Echocardiographic markers of cardiac performance, including diastolic function and AV conduction, were reviewed. Ten fetuses were found to have EFE of the aortic root, proximal aorta and/or left ventricular outflow tract. In the same 10 cases, EFE of the pulmonary root, pulmonary artery and/or right ventricular outflow tract was identified. Six cases had atrial EFE and six had EFE of the crux. Four cases were known to be positive for anti-Ro/SSA antibodies prior to diagnosis, whereas, in the remaining seven, echocardiographic findings prompted testing, which was positive in all cases. The AV interval at presentation was normal in all cases, but one fetus subsequently developed AV block. Nine patients were treated with transplacental dexamethasone, five of which also received intravenous immunoglobulin (IVIG), and one received IVIG only. Of the 10 treated cases, six had improvement in EFE as shown by serial imaging and, in four cases, the severity was unchanged. All patients were liveborn. In our cohort, EFE of the aortic and pulmonary arteries and outflow tracts was nearly universal, and involvement of the atria and the crux of the heart was also common. The high survival rate and low burden of AV block are also suggestive of a distinct phenotype of anti-Ro/SSA-antibody-mediated cardiac disease with a favorable prognosis. © 2023 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- S B Keller
- Department of Pediatrics, Division of Cardiology, University of California San Francisco, San Francisco, CA, USA
| | - J Cohen
- Division of Pediatric Cardiology, Department of Pediatrics, Mount Sinai Hospital, New York, NY, USA
| | - A Moon-Grady
- Department of Pediatrics, Division of Cardiology, University of California San Francisco, San Francisco, CA, USA
| | - B Cuneo
- Department of Pediatrics, Division of Cardiology, University of Colorado, Denver, CO, USA
| | - E Paul
- Division of Pediatric Cardiology, Department of Pediatrics, Mount Sinai Hospital, New York, NY, USA
| | - A C Coll
- Department of Pediatrics, Division of Cardiology, University of California San Francisco, San Francisco, CA, USA
| | - M Campbell
- Department of Pediatric Cardiology, Nemours Children's Hospital, Wilmington, DE, USA
| | - S Srivastava
- Department of Pediatric Cardiology, Nemours Children's Hospital, Wilmington, DE, USA
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20
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Singh KP, Carvalho ACC, Centis R, D Ambrosio L, Migliori GB, Mpagama SG, Nguyen BC, Aarnoutse RE, Aleksa A, van Altena R, Bhavani PK, Bolhuis MS, Borisov S, van T Boveneind-Vrubleuskaya N, Bruchfeld J, Caminero JA, Carvalho I, Cho JG, Davies Forsman L, Dedicoat M, Dheda K, Dooley K, Furin J, García-García JM, Garcia-Prats A, Hesseling AC, Heysell SK, Hu Y, Kim HY, Manga S, Marais BJ, Margineanu I, Märtson AG, Munoz Torrico M, Nataprawira HM, Nunes E, Ong CWM, Otto-Knapp R, Palmero DJ, Peloquin CA, Rendon A, Rossato Silva D, Ruslami R, Saktiawati AMI, Santoso P, Schaaf HS, Seaworth B, Simonsson USH, Singla R, Skrahina A, Solovic I, Srivastava S, Stocker SL, Sturkenboom MGG, Svensson EM, Tadolini M, Thomas TA, Tiberi S, Trubiano J, Udwadia ZF, Verhage AR, Vu DH, Akkerman OW, Alffenaar JWC, Denholm JT. Clinical standards for the management of adverse effects during treatment for TB. Int J Tuberc Lung Dis 2023; 27:506-519. [PMID: 37353868 PMCID: PMC10321364 DOI: 10.5588/ijtld.23.0078] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND: Adverse effects (AE) to TB treatment cause morbidity, mortality and treatment interruption. The aim of these clinical standards is to encourage best practise for the diagnosis and management of AE.METHODS: 65/81 invited experts participated in a Delphi process using a 5-point Likert scale to score draft standards.RESULTS: We identified eight clinical standards. Each person commencing treatment for TB should: Standard 1, be counselled regarding AE before and during treatment; Standard 2, be evaluated for factors that might increase AE risk with regular review to actively identify and manage these; Standard 3, when AE occur, carefully assessed and possible allergic or hypersensitivity reactions considered; Standard 4, receive appropriate care to minimise morbidity and mortality associated with AE; Standard 5, be restarted on TB drugs after a serious AE according to a standardised protocol that includes active drug safety monitoring. In addition: Standard 6, healthcare workers should be trained on AE including how to counsel people undertaking TB treatment, as well as active AE monitoring and management; Standard 7, there should be active AE monitoring and reporting for all new TB drugs and regimens; and Standard 8, knowledge gaps identified from active AE monitoring should be systematically addressed through clinical research.CONCLUSION: These standards provide a person-centred, consensus-based approach to minimise the impact of AE during TB treatment.
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Affiliation(s)
- K P Singh
- Department of Infectious diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia, Victorian Infectious Disease Unit, Royal Melbourne Hospital, VIC, Australia
| | - A C C Carvalho
- Laboratório de Inovações em Terapias, Ensino e Bioprodutos (LITEB), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - R Centis
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Tradate, Italy
| | - L D Ambrosio
- Public Health Consulting Group, Lugano, Switzerland
| | - G B Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Tradate, Italy
| | - S G Mpagama
- Kilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania, Kibong´oto Infectious Diseases Hospital, Sanya Juu, Siha, Kilimanjaro, United Republic of Tanzania
| | - B C Nguyen
- Woolcock Institute of Medical Research, Viet Nam and University of Sydney, NSW, Australia
| | - R E Aarnoutse
- Department of Pharmacy, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A Aleksa
- Grodno State Medical University, Grodno, Belarus
| | - R van Altena
- Asian Harm Reduction Network (AHRN) and Medical Action Myanmar (MAM), Yangon, Myanmar
| | - P K Bhavani
- Indian Council of Medical Research-National Institute for Research in Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - M S Bolhuis
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - S Borisov
- Moscow Research and Clinical Center for Tuberculosis Control, Moscow, Russia
| | - N van T Boveneind-Vrubleuskaya
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands, Department of Public Health TB Control, Metropolitan Public Health Services, The Hague, The Netherlands
| | - J Bruchfeld
- Departement of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stokholm, Sweden, Departement of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - J A Caminero
- Department of Pneumology. University General Hospital of Gran Canaria "Dr Negrin", Las Palmas, Spain, ALOSA (Active Learning over Sanitary Aspects) TB Academy, Spain
| | - I Carvalho
- Paediatric Department, Vila Nova de Gaia Hospital Centre, Vila Nova de Gaia Outpatient Tuberculosis Centre, Vila Nova de Gaia, Portugal
| | - J G Cho
- Sydney Infecious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia, Parramatta Chest Clinic, Parramatta, NSW, Australia
| | - L Davies Forsman
- Departement of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Stokholm, Sweden, Departement of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - M Dedicoat
- Department of Infectious Diseases, Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - K Dheda
- Centre for Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Cape Town, South Africa, South African Medical Research Council Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - K Dooley
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - J Furin
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - J M García-García
- Tuberculosis Research Programme, SEPAR (Sociedad Española de Neumología y Cirugía Torácica), Barcelona, Spain
| | - A Garcia-Prats
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa, Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | - A C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa
| | - S K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Y Hu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - H Y Kim
- Sydney Infecious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - S Manga
- Tuberculosis Department Latin American Society of Thoracic Diseases, Lima, Peru
| | - B J Marais
- Sydney Infecious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia, Department of Infectious Diseases and Microbiology, The Children´s Hospital at Westmead, Westmead, NSW, Australia
| | - I Margineanu
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - A-G Märtson
- Centre of Excellence in Infectious Diseases Research, Antimicrobial Pharmacodynamics and Therapeutics Group, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - M Munoz Torrico
- Clínica de Tuberculosis, Instituto Nacional de Enfermedades Respiratorias, México City, Mexico
| | - H M Nataprawira
- Division of Paediatric Respirology, Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Hasan Sadikin Hospital, Bandung, Indonesia
| | - E Nunes
- Department of Pulmonology of Central Hospital of Maputo, Maputo, Mozambique, Faculty of Medicine of Eduardo Mondlane University, Maputo, Mozambique
| | - C W M Ong
- Infectious Disease Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Tradate, Italy, Division of Infectious Diseases, Department of Medicine, National University Hospital, Singapore
| | - R Otto-Knapp
- German Central Committee Against Tuberculosis (DZK), Berlin, Germany
| | - D J Palmero
- Hospital Muniz and Instituto Vaccarezza, Buenos Aires, Argentina
| | - C A Peloquin
- Infectious Disease Pharmacokinetics Laboratory, College of Pharmacy and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - A Rendon
- Universidad Autonoma de Nuevo Leon, Facultad de Medicina, Neumología, CIPTIR, Monterrey, Mexico
| | - D Rossato Silva
- Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - R Ruslami
- TB/HIV Research Centre, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia, Department of Biomedical Sciences, Division of Pharmacology and Therapy, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - A M I Saktiawati
- Department of Internal Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia, Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - P Santoso
- Division of Respirology and Critical Care, Department of Internal Medicine, Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, Indonesia
| | - H S Schaaf
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa
| | - B Seaworth
- University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - U S H Simonsson
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - R Singla
- Department of TB & Respiratory Diseases, National Institute of TB & Respiratory Diseases, New Delhi, India
| | - A Skrahina
- Republican Research and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - I Solovic
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Faculty of Health, Catholic University, Ružomberok, Vyšné Hágy, Slovakia
| | - S Srivastava
- University of Texas Health Science Center at Tyler, Tyler, TX, USA, Department of Medicine, The University of Texas at Tyler School of Medicine, TX, USA, Department of Pharmacy Practice, Texas Tech University Health Science Center, Dallas, TX, USA
| | - S L Stocker
- School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia, Department of Clinical Pharmacology and Toxicology, St Vincent´s Hospital, Sydney, NSW, Australia
| | - M G G Sturkenboom
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - E M Svensson
- Department of Pharmacy, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands, Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - M Tadolini
- Infectious Diseases Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico di Sant´Orsola, Bologna, Italy, Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - T A Thomas
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - S Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - J Trubiano
- Department of Infectious diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia, Department of Infectious Diseases, Austin Hospital, Melbourne, VIC, Australia
| | - Z F Udwadia
- P. D. Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - A R Verhage
- Department of Paediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - D H Vu
- National Drug Information and Adverse Drug Reaction Monitoring Centre, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - O W Akkerman
- Department of Pulmonary Diseases and Tuberculosis, Groningen, Haren, the Netherlands, Tuberculosis Center Beatrixoord, University Medical Center Groningen, University of Groningen, Haren, the Netherlands
| | - J W C Alffenaar
- Sydney Infecious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
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Pai MGJ, Biswas D, Verma A, Srivastava S. A proteome-level view of brain tumors for a better understanding of novel diagnosis, prognosis, and therapy. Expert Rev Proteomics 2023; 20:381-395. [PMID: 37970632 DOI: 10.1080/14789450.2023.2283498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023]
Abstract
INTRODUCTION Brain tumors are complex and heterogeneous malignancies with significant challenges in diagnosis, prognosis, and therapy. Proteomics, the large-scale study of proteins and their functions, has emerged as a powerful tool to comprehensively investigate the molecular mechanisms underlying brain tumor regulation. AREAS COVERED This review explores brain tumors from a proteomic standpoint, highlighting recent progress and insights gained through proteomic methods. It delves into the proteomic techniques employed and underscores potential biomarkers for early detection, prognosis, and treatment planning. Recent PubMed Central proteomic studies (2017-present) are discussed, summarizing findings on altered protein expression, post-translational changes, and protein interactions. This sheds light on brain tumor signaling pathways and their significance in innovative therapeutic approaches. EXPERT OPINION Proteomics offers immense potential for revolutionizing brain tumor diagnosis and therapy. To unlock its full benefits, further translational research is crucial. Combining proteomics with other omics data enhances our grasp of brain tumors. Validating and translating proteomic biomarkers are vital for better patient results. Challenges include tumor complexity, lack of curated proteomic databases, and the need for collaboration between researchers and clinicians. Overcoming these challenges requires investment in technology, data sharing, and translational research.
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Affiliation(s)
- Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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22
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Rajoria S, Halder A, Tarnekar I, Pal P, Bansal P, Srivastava S. Detection of Mutant Peptides of SARS-CoV-2 Variants by LC/MS in the DDA Approach Using an In-House Database. J Proteome Res 2023; 22:1816-1827. [PMID: 37093804 PMCID: PMC10152398 DOI: 10.1021/acs.jproteome.2c00819] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 04/25/2023]
Abstract
Equipped with a dramatically high mutation rate, which happens to be a signature of RNA viruses, SARS-CoV-2 trampled across the globe infecting individuals of all ages and ethnicities. As the variants of concern (VOC) loomed large, definitive detection of SARS-CoV-2 strains became a matter of utmost importance in epidemiological and clinical research. Besides, unveiling the disease pathogenesis at the molecular level and deciphering the therapeutic targets became key priorities since the emergence of the pandemic. Mass spectrometry has been largely used in this regard. A critical part of mass spectrometric analyses is the proteome database required for the identification of peptides. Presently, the mutational information on proteins available on SARS-CoV-2 databases cannot be used to analyze data extracted from mass spectrometers. Hence, we developed the novel Mutant Peptide Database (MPD) for the mass spectrometry (MS)-based identification of mutated peptides, which contains information from 11 proteins of SARS-CoV-2 from a total of 21,549 SARS-CoV-2 variants across different regions of India. The database was validated using clinical samples, and its applicability was also demonstrated with the mutated peptides extracted from the literature. We believe that MPD will support broad-spectrum MS-based studies like viral detection, disease pathogenesis, and therapeutics with respect to SARS-CoV-2 and its variants.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Mumbai 400076,
India
| | - Ankit Halder
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Mumbai 400076,
India
| | - Ishita Tarnekar
- Thadomal Shahani Engineering
College, P.G. Kher Marg T.P.S III, Bandra West, Mumbai 400050,
India
| | - Pracheta Pal
- Department of Life Sciences, Presidency
University, 86/1 College Street, Kolkata 700073, West Bengal,
India
| | - Prakhar Bansal
- Department of Electrical Engineering,
Indian Institute of Technology Bombay, Mumbai 400076,
India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Mumbai 400076,
India
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23
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Aggarwal S, Karmakar A, Krishnakumar S, Paul U, Singh A, Banerjee N, Laha N, Roy Ball G, Srivastava S. Advances in Drug Discovery Based on Genomics, Proteomics and Bioinformatics in Malaria. Curr Top Med Chem 2023; 23:551-578. [PMID: 37073654 DOI: 10.2174/1568026623666230418114455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 02/05/2023] [Accepted: 02/22/2023] [Indexed: 04/20/2023]
Abstract
Malaria is one of the neglected infectious diseases, and drugs are the first line of action taken against the onset of malaria as therapeutics. The drugs can be of either natural or artificial origin. Drug development has multiple impediments grouped under three categories, a. drug discovery and screening, b. the drug's action on the host and the pathogen, and c. clinical trials. Drug development takes coon's age from discovery to the market after FDA approval. At the same time, targeted organisms develop drug resistance quicker than drug approval, raising the requirement for advancement in drug development. The approach to explore drug candidates using the classical methods from natural sources, computation-based docking, mathematical and machine learning-based high throughput in silico models or drug repurposing has been investigated and developed. Also, drug development with information about the interaction between Plasmodium species and its host, humans, may facilitate obtaining an efficient drug cohort for further drug discovery or repurposing expedition. However, drugs may have side effects on the host system. Hence, machine learning and systems-based approaches may provide a holistic view of genomic, proteomic, and transcriptomic data and their interaction with the selected drug candidates. This review comprehensively describes the drug discovery workflows using drug and target screening methodologies, followed by possible ways to check the binding affinity of the drug and targets using various docking software.
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Affiliation(s)
- Shalini Aggarwal
- Indian Institute of Technology Bombay Biosciences and Bioengineering Mumbai India
| | - Amit Karmakar
- Visva-Bharati University Botany Sh?nti Niketan India
| | | | - Utpalendu Paul
- Vellore Institute of Technology University Biotechnology Vellore India
| | | | - Nirjhar Banerjee
- Indian Institute of Technology Bombay Biosciences and Bioengineering Mumbai India
| | - Nehashri Laha
- VISVA BHARATI UNIVERSITY Department of Botany Santiniketan India
| | | | - Sanjeeva Srivastava
- Indian Institute of Technology Bombay Biosciences and Bioengineering Mumbai India
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24
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Naik A, Srivastava S, Wiita AP. "Cell Surface Capture" Workflow for Label-Free Quantification of the Cell Surface Proteome. J Vis Exp 2023. [PMID: 37036222 DOI: 10.3791/64952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
Abstract
Over the past decade, mass spectrometry-based proteomics has enabled an in-depth characterization of biological systems across a broad array of applications. The cell surface proteome ("surfaceome") in human disease is of significant interest, as plasma membrane proteins are the primary target of most clinically approved therapeutics, as well as a key feature by which to diagnostically distinguish diseased cells from healthy tissues. However, focused characterization of membrane and surface proteins of the cell has remained challenging, primarily due to the complexity of cellular lysates, which mask proteins of interest by other high-abundance proteins. To overcome this technical barrier and accurately define the cell surface proteome of various cell types using mass spectrometry proteomics, it is necessary to enrich the cell lysate for cell surface proteins prior to analysis on the mass spectrometer. This paper presents a detailed workflow for labeling cell surface proteins from cancer cells, enriching these proteins out of the cell lysate, and subsequent sample preparation for mass spectrometry analysis.
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Affiliation(s)
- Akul Naik
- Department of Laboratory Medicine, University of California, San Francisco
| | - Sanjeeva Srivastava
- Department of Laboratory Medicine, University of California, San Francisco; Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco; Deptartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco; Chan Zuckerberg Biohub;
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25
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Nissa MU, Pinto N, Ghosh B, Singh U, Goswami M, Srivastava S. Proteomic analysis of liver tissue reveals Aeromonas hydrophila infection mediated modulation of host metabolic pathways in Labeo rohita. J Proteomics 2023; 279:104870. [PMID: 36906258 DOI: 10.1016/j.jprot.2023.104870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
Aeromonas hydrophila (Ah) is a Gram-negative bacterium and a serious global pathogen causing Motile Aeromonas Septicaemia (MAS) in fish leading to global loss in aquaculture. Investigation of the molecular alterations of host tissues such as liver could be a powerful approach to identify mechanistic and diagnostic immune signatures of disease pathogenesis. We performed a proteomic analysis of Labeo rohita liver tissue to examine the protein dynamics in the host cells during Ah infection. The proteomic data was acquired using two strategies; discovery and targeted proteomics. Label-free quantification was performed between Control and challenged group (AH) to identify the differentially expressed proteins (DEPs). A total of 2525 proteins were identified and 157 were DEPs. DEPs include metabolic enzymes (CS, SUCLG2), antioxidative proteins, cytoskeletal proteins and immune related proteins (TLR3, CLEC4E). Pathways like lysosome pathway, apoptosis, metabolism of xenobiotics by cytochrome P450 were enriched by downregulated proteins. However, upregulated proteins majorly mapped to innate immune system, signaling of B cell receptor, proteosome pathway, ribosome, carbon metabolism and protein processing in ER. Our study would help in exploring the role of Toll-like receptors, C-type lectins and, metabolic intermediates like citrate and succinate in Ah pathogenesis to understand the Ah infection in fish. SIGNIFICANCE: Bacterial diseases such as motile aeromonas septicaemia (MAS) are among the most serious problems in aquaculture industry. Small molecules that target the metabolism of the host have recently emerged as potential treatment possibilities in infectious diseases. However, the ability to develop new therapies is hampered due to lack of knowledge about pathogenesis mechanisms and host-pathogen interactions. We examined alterations in the host proteome during MAS caused by Aeromonas hydrophila (Ah) infection, in Labeo rohita liver tissue to find cellular proteins and processes affected by Ah infection. Upregulated proteins belong to innate immune system, signaling of B cell receptor, proteosome pathway, ribosome, carbon metabolism and protein processing. Our work is an important step towards leveraging host metabolism in targeting the disease by providing a bigger picture on proteome pathology correlation during Ah infection.
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Affiliation(s)
- Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nevil Pinto
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India
| | - Biplab Ghosh
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Urvi Singh
- Department of Biochemistry, Sri Venkateswara College, University of Delhi, 110034, India
| | - Mukunda Goswami
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India.
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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26
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Barpanda A, Biswas D, Verma A, Parihari S, Singh A, Kapoor S, Kantharia C, Srivastava S. Integrative Proteomic and Pharmacological Analysis of Colon Cancer Reveals the Classical Lipogenic Pathway with Prognostic and Therapeutic Opportunities. J Proteome Res 2023; 22:871-884. [PMID: 36731020 DOI: 10.1021/acs.jproteome.2c00646] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Despite recent advancements, the high mortality rate remains a concern in colon cancer (CAC). Identification of therapeutic markers could prove to be a great asset in CAC management. Multiple studies have reported hyperactivation of de novo lipogenesis (DNL), but its association with the pathology is unclear. This study aims to establish the importance as well as the prognostic and therapeutic potential of DNL in CAC. The key lipogenic enzymes fatty acid synthase along with ATP citrate lyase were quantified using an LC-MS/MS-based targeted proteomics approach in the samples along with the matched controls. The potential capacity of the proteins to distinguish between the tumor and controls was demonstrated using random forest-based class prediction analysis using the peptide intensities. Furthermore, in-depth proteomics of DNL inhibition in the CAC cell line revealed the significance of the pathway in proliferation and metastasis. DNL inhibition affected the major signaling pathways, including DNA repair, PI3K-AKT-mTOR pathway, membrane trafficking, proteasome, etc. The study revealed the upregulation of 26S proteasome machinery as a result of the treatment with subsequent induction of apoptosis. Again, in silico molecular docking-based drug repurposing was performed to find potential drug candidates. Furthermore, we have demonstrated that blocking DNL could be explored as a therapeutic option in CAC treatment.
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Affiliation(s)
- Abhilash Barpanda
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India.,Centre for Research in Nanotechnology and Science, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Deeptarup Biswas
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Ayushi Verma
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Shashwati Parihari
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Avinash Singh
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Shobhna Kapoor
- Department of Chemistry, IIT Bombay, Mumbai 400076 Maharashtra, India
| | - Chetan Kantharia
- Department of Surgical Gastroenterology, Seth G.S. Medical College and KEM Hospital, Mumbai 400076 Maharashtra, India
| | - Sanjeeva Srivastava
- Proteomics Lab, Department of Biosciences & Bioengineering, IIT Bombay, Mumbai 400076 Maharashtra, India.,Centre for Research in Nanotechnology and Science, IIT Bombay, Mumbai 400076 Maharashtra, India
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27
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Barpanda A, Tuckley C, Ray A, Banerjee A, Duttagupta SP, Kantharia C, Srivastava S. A protein microarray-based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer. Proteomics Clin Appl 2023; 17:e2200062. [PMID: 36408811 DOI: 10.1002/prca.202200062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/18/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
Abstract
PURPOSE Colorectal cancer (CRC) has been reported as the second leading cause of cancer death worldwide. The 5-year annual survival is around 50%, mainly due to late diagnosis, striking necessity for early detection. This study aims to identify autoantibody in patients' sera for early screening of cancer. EXPERIMENTAL DESIGN The study used a high-density human proteome array with approximately 17,000 recombinant proteins. Screening of sera from healthy individuals, CRC from Indian origin, and CRC from middle-east Asia origin were performed. Bio-statistical analysis was performed to identify significant autoantibodies altered. Pathway analysis was performed to explore the underlying mechanism of the disease. RESULTS The comprehensive proteomic analysis revealed dysregulation of 15 panels of proteins including CORO7, KCNAB1, WRAP53, NDUFS6, KRT30, and COLGALT2. Further biological pathway analysis for the top dysregulated autoantigenic proteins revealed perturbation in important biological pathways such as ECM degradation and cytoskeletal remodeling etc. CONCLUSIONS AND CLINICAL RELEVANCE: The generation of an autoimmune response against cancer-linked pathways could be linked to the screening of the disease. The process of immune surveillance can be detected at an early stage of cancer. Moreover, AAbs can be easily extracted from blood serum through the least invasive test for disease screening.
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Affiliation(s)
- Abhilash Barpanda
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Arka Ray
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Siddhartha P Duttagupta
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India
| | - Chetan Kantharia
- Department of surgical gastroenterology at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Sanjeeva Srivastava
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Mumbai, India.,Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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28
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Tadepalli M, Chhaparwal A, Chawla S, Srivastava S, Dao T, Chhaparwal A, Naren S, Sathyamurthy S, Mukkavilli S, Putha P, Reddy B, Vo L, Warrier P. PP01.59 Performance of a Deep Learning Algorithm for the Early Detection of Malignant Lung Nodules. J Thorac Oncol 2023. [DOI: 10.1016/j.jtho.2022.09.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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29
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Aggarwal S, Selvaraj S, Subramanian JN, Vijayalakshmi MA, Patankar S, Srivastava S. Polyclonal Antibody Generation against PvTRAg for the Development of a Diagnostic Assay for Plasmodium vivax. Diagnostics (Basel) 2023; 13:diagnostics13050835. [PMID: 36899977 PMCID: PMC10001162 DOI: 10.3390/diagnostics13050835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/15/2023] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
The World Health Organization (WHO) has set forth a global call for eradicating malaria, caused majorly by the protozoan parasites Plasmodium falciparum and Plasmodium vivax. The lack of diagnostic biomarkers for P. vivax, especially those that differentiate the parasite from P. falciparum, significantly hinders P. vivax elimination. Here, we show that P. vivax tryptophan-rich antigen (PvTRAg) can be a diagnostic biomarker for diagnosing P. vivax in malaria patients. We report that polyclonal antibodies against purified PvTRAg protein show interactions with purified PvTRAg and native PvTRAg using Western blots and indirect enzyme-linked immunosorbent assay (ELISA). We also developed an antibody-antigen-based qualitative assay using biolayer interferometry (BLI) to detect vivax infection using plasma samples from patients with different febrile diseases and healthy controls. The polyclonal anti-PvTRAg antibodies were used to capture free native PvTRAg from the patient plasma samples using BLI, providing a new expansion range to make the assay quick, accurate, sensitive, and high-throughput. The data presented in this report provides a proof of concept for PvTRAg, a new antigen, for developing a diagnostic assay for P. vivax identification and differentiation from the rest of the Plasmodium species and, at a later stage, translating the BLI assay into affordable, point-of-care formats to make it more accessible.
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Affiliation(s)
- Shalini Aggarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel
| | - Selvamano Selvaraj
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore 632014, India
| | | | | | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
- Correspondence: ; Tel.: +91-(22)-2576-7779
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30
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Barpanda A, Halder A, Dhote A, Parihari S, Kantharia C, Srivastava S. Colon Adenocarcinoma Quantitative Proteomics Reveals Dysregulation in Key Cancer Signaling Pathways and a Candidate Protein Marker Panel. OMICS 2023; 27:75-85. [PMID: 36730729 DOI: 10.1089/omi.2022.0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Colorectal cancer (CRC) is reportedly the second leading cause of cancer death worldwide. By the end of the decade, there will likely be more than one million fatalities worldwide from this cancer, with an estimated 2.2 million additional cases. We need new ways of thinking about cancer research. One approach is to deploy systems science using quantitative proteomics to obtain postgenomic and functional insights into cancer. The present study compares the tissue proteome of CRC (n = 10) with the matched peritumoral controls (n = 10) in samples obtained from the Indian subcontinent. When compared with the controls, a list of 22 substantially altered protein candidates was identified, which were associated with the growth, survival, and metastasis of the tumor. A list of the unique peptides from top significant proteins, including olfactomedin-4, alanyl aminopeptidase, and grancalcin was further validated using a parallel reaction monitoring-based targeted proteomics approach. In addition, biological pathway analysis showed perturbation in key biological processes, including dysregulation in purine metabolism, MYC targets in cancer, DNA repair, and replication, and leukocyte transendothelial migration, among others. The protein panel reported herein is also shown to be dysregulated in CRC and warrants further research toward understanding pathobiology, diagnostics, and therapeutics development in CRC.
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Affiliation(s)
- Abhilash Barpanda
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.,Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ankit Halder
- Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ayushi Dhote
- Saint Francis de Sales College, Nagpur, Maharashtra, India
| | - Shashwati Parihari
- Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Chetan Kantharia
- Department of Surgical Gastroenterology, Seth G.S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.,Center for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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31
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Acharjee A, Ray A, Salkar A, Bihani S, Tuckley C, Shastri J, Agrawal S, Duttagupta S, Srivastava S. Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray. Viruses 2023; 15:248. [PMID: 36680289 PMCID: PMC9866125 DOI: 10.3390/v15010248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
The amaranthine scale of the COVID-19 pandemic and unpredictable disease severity is of grave concern. Serological diagnostic aids are an excellent choice for clinicians for rapid and easy prognosis of the disease. To this end, we studied the humoral immune response to SARS-CoV-2 infection to map immunogenic regions in the SARS-CoV-2 proteome at amino acid resolution using a high-density SARS-CoV-2 proteome peptide microarray. The microarray has 4932 overlapping peptides printed in duplicates spanning the entire SARS-CoV-2 proteome. We found 204 and 676 immunogenic peptides against IgA and IgG, corresponding to 137 and 412 IgA and IgG epitopes, respectively. Of these, 6 and 307 epitopes could discriminate between disease severity. The emergence of variants has added to the complexity of the disease. Using the mutation panel available, we could detect 5 and 10 immunogenic peptides against IgA and IgG with mutations belonging to SAR-CoV-2 variants. The study revealed severity-based epitopes that could be presented as potential prognostic serological markers. Further, the mutant epitope immunogenicity could indicate the putative use of these markers for diagnosing variants responsible for the infection.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arka Ray
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | | | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Mumbai 400011, India
| | - Siddhartha Duttagupta
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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32
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Banerjee A, Halder A, Jadhav P, Sarkar A, Hole A, Shastri JS, Agrawal S, Chilakapati MK, Srivastava S. SARS-CoV-2 severity classification from plasma sample using confocal Raman spectroscopy. J Raman Spectrosc 2023; 54:124-132. [PMID: 36713977 PMCID: PMC9874663 DOI: 10.1002/jrs.6461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 06/18/2023]
Abstract
The world is on the brink of facing coronavirus's (COVID-19) fourth wave as the mutant forms of viruses are escaping neutralizing antibodies in spite of being vaccinated. As we have already witnessed that it has encumbered our health system, with hospitals swamped with infected patients observed during the viral outbreak. Rapid triage of patients infected with SARS-CoV-2 is required during hospitalization to prioritize and provide the best point of care. Traditional diagnostics techniques such as RT-PCR and clinical parameters such as symptoms, comorbidities, sex and age are not enough to identify the severity of patients. Here, we investigated the potential of confocal Raman microspectroscopy as a powerful tool to generate an expeditious blood-based test for the classification of COVID-19 disease severity using 65 patients plasma samples from cohorts infected with SARS-CoV-2. We designed an easy manageable blood test where we used a small volume (8 μl) of inactivated whole plasma samples from infected patients without any extra solvent usage in plasma processing. Raman spectra of plasma samples were acquired and multivariate exploratory analysis PC-LDA (principal component based linear discriminant analysis) was used to build a model, which segregated the severe from the non-severe COVID-19 group with a sensitivity of 83.87%, specificity of 70.60% and classification efficiency of 76.92%. Among the bands expressed in both the cohorts, the study led to the identification of Raman fingerprint regions corresponding to lipids (1661, 1742), proteins amide I and amide III (1555, 1247), proteins (Phe) (1006, 1034), and nucleic acids (760) to be differentially expressed in severe COVID-19 patient's samples. In summary, the current study exhibits the potential of confocal Raman to generate simple, rapid, and less expensive blood tests to triage the severity of patients infected with SARS-CoV-2.
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Affiliation(s)
- Arghya Banerjee
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Ankit Halder
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Priyanka Jadhav
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC)Tata Memorial Centre (TMC)Navi MumbaiIndia
- Homi Bhabha National InstituteTraining School Complex, Anushakti NagarMumbaiIndia
| | - Anushka Sarkar
- Department of Life SciencesPresidency University (Main Campus)KolkataIndia
| | - Arti Hole
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC)Tata Memorial Centre (TMC)Navi MumbaiIndia
| | | | | | - Murali Krishna Chilakapati
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC)Tata Memorial Centre (TMC)Navi MumbaiIndia
| | - Sanjeeva Srivastava
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
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Rajoria S, Nair D, Suvarna K, Pai MGJ, Salkar A, Palanivel V, Verma A, Barpanda A, Awasthi G, Doshi H, Dhara V, Burli A, Agrawal S, Shrivastav O, Shastri J, Srivastava S. Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai. Adv Exp Med Biol 2023; 1412:175-195. [PMID: 37378767 DOI: 10.1007/978-3-031-28012-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second wave which led to increased difficulties in understanding the molecular mechanisms behind the disease pathology. Exploring the underlying factors can help to relieve the burden on the medical communities to some extent by prioritizing the patients and, at the same time, opening avenues for improved treatments. In the current study, we have performed a mass-spectrometry-based proteomic analysis to investigate the disease pathology using nasopharyngeal swab samples collected from the COVID-19 patients in the Mumbai region of Maharashtra over the period of March-June 2021, the peak of the second wave. A total of 59 patients, including 32 non-severe and 27 severe cases, were considered for this proteomic study. We identified 23 differentially regulated proteins in severe patients as a host response to infection. In addition to the previously identified innate mechanisms of neutrophil and platelet degranulation, this study revealed significant alterations of anti-microbial peptide pathways in severe conditions, illustrating its role in the severity of the infectious strain of COVID-19 during the second wave. Furthermore, myeloperoxidase, cathepsin G, and profilin-1 were identified as potential therapeutic targets of the FDA-approved drugs dabrafenib, ZINC4097343, and ritonavir. This study has enlightened the role of the anti-microbial peptide pathway associated with the second wave in India and proposed its importance in potential therapeutics for COVID-19.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kruthi Suvarna
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Gaurav Awasthi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Hastyn Doshi
- Department of Computer Science, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vivek Dhara
- Department of Mechanical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ananya Burli
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Om Shrivastav
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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Ghantasala S, Bhat A, Agarwal U, Biswas D, Bhattarai P, Epari S, Moiyadi A, Srivastava S. Deep proteome investigation of high-grade gliomas reveals heterogeneity driving differential metabolism of 5-aminolevulinic acid. Neurooncol Adv 2023; 5:vdad065. [PMID: 37358939 PMCID: PMC10290514 DOI: 10.1093/noajnl/vdad065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Background Fluorescence-guided surgery (FGS) using 5-aminolevulinic acid (5-ALA) as adjunct for high-grade gliomas (HGGs) has been on the rise in recent years. Despite being largely effective, we observed multiple histologically similar sub-regions of the same tumor from a few individuals with varying protoporphyrin IX (PpIX) levels. The current study aims at understanding the proteomic changes driving differential metabolism of 5-ALA in HGGs. Methods Biopsies were histologically and biochemically assayed. Following this, a deep proteomics investigation was carried out using high resolution liquid chromatography-mass spectrometry (HR LC-MS) to identify protein expression in differentially fluorescing regions of HGGs. Results Our analysis identified 5437 proteins with high confidence. Differential analysis in the subgroup with HGGs carrying IDH mutation (IDH mt.) revealed 93 differentially regulated proteins (raw p-value ≤ 0.05 and absolute FC ≥ 1.5). Similar analysis in the IDH wild type (IDH wt.) subgroup revealed 20 differentially regulated proteins. Gene set enrichment analysis (GSEA) identified key pathways like ion channel transport, trafficking of AMPA receptors, and regulation of heme-oxygenase-1 in the IDH wt. subgroup. Pathways such as scavenging of heme, signaling by NOTCH4, negative regulation of PI3-AKT pathway, and iron uptake and transport were observed to be differentially regulated in the IDH mt. subgroup. Conclusions Tumor regions from the same patient exhibiting differential fluorescence following 5-ALA administration were observed to have different proteome profiles. Future studies aimed at a better molecular understanding of 5-ALA metabolism in HGGs hold the potential to increase the efficacy of FGS and the use of 5-ALA as a theragnostic tool.
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Affiliation(s)
- Saicharan Ghantasala
- Centre for Research in Nano Technology and Sciences, Indian Institute of Technology Bombay, Mumbai, India
| | - Amruth Bhat
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Unnati Agarwal
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prawesh Bhattarai
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre’s—Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Aliasgar Moiyadi
- Homi Bhabha National Institute, Mumbai, India
- Department of Neurosurgery, Tata Memorial Centre’s—Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Sanjeeva Srivastava
- Corresponding Author: Sanjeeva Srivastava, PhD, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India ()
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Yadav KK, Chouhan N, Thubstan R, Norlha S, Hariharan J, Borwankar C, Chandra P, Dhar VK, Mankuzhyil N, Godambe S, Sharma M, Venugopal K, Singh KK, Bhatt N, Bhattacharyya S, Chanchalani K, Das MP, Ghosal B, Godiyal S, Khurana M, Kotwal SV, Koul MK, Kumar N, Kushwaha CP, Nand K, Pathania A, Sahayanathan S, Sarkar D, Tolamati A, Koul R, Rannot RC, Tickoo AK, Chitnis VR, Behere A, Padmini S, Manna A, Joy S, Nair PM, Jha KP, Moitra S, Neema S, Srivastava S, Punna M, Mohanan S, Sikder SS, Jain A, Banerjee S, . K, Deshpande J, Sanadhya V, Andrew G, Patil MB, Goyal VK, Gupta N, Balakrishna H, Agrawal A, Srivastava SP, Karn KN, Hadgali PI, Bhatt S, Mishra VK, Biswas PK, Gupta RK, Kumar A, Thul SG, Kalmady R, Sonvane DD, Kumar V, Gaur UK, Chattopadhyay J, Gupta SK, Kiran AR, Parulekar Y, Agrawal MK, Parmar RM, Reddy GR, Mayya YS, Pithawa CK. Commissioning of the MACE gamma-ray telescope at Hanle, Ladakh, India. CURR SCI INDIA 2022. [DOI: 10.18520/cs/v123/i12/1428-1435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Banerjee A, Biswas D, Barpanda A, Halder A, Sibal S, Kattimani R, Shah A, Mahadevan A, Goel A, Srivastava S. The First Pituitary Proteome Landscape From Matched Anterior and Posterior Lobes for a Better Understanding of the Pituitary Gland. Mol Cell Proteomics 2022; 22:100478. [PMID: 36470533 PMCID: PMC9877467 DOI: 10.1016/j.mcpro.2022.100478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
To date, very few mass spectrometry (MS)-based proteomics studies are available on the anterior and posterior lobes of the pituitary. In the past, MS-based investigations have focused exclusively on the whole pituitary gland or anterior pituitary lobe. In this study, for the first time, we performed a deep MS-based analysis of five anterior and five posterior matched lobes to build the first lobe-specific pituitary proteome map, which documented 4090 proteins with isoforms, mostly mapped into chromosomes 1, 2, and 11. About 1446 differentially expressed significant proteins were identified, which were studied for lobe specificity, biological pathway enrichment, protein-protein interaction, regions specific to comparison of human brain and other neuroendocrine glands from Human Protein Atlas to identify pituitary-enriched proteins. Hormones specific to each lobe were also identified and validated with parallel reaction monitoring-based target verification. The study identified and validated hormones, growth hormone and thyroid-stimulating hormone subunit beta, exclusively to the anterior lobe whereas oxytocin-neurophysin 1 and arginine vasopressin to the posterior lobe. The study also identified proteins POU1F1 (pituitary-specific positive transcription factor 1), POMC (pro-opiomelanocortin), PCOLCE2 (procollagen C-endopeptidase enhancer 2), and NPTX2 (neuronal pentraxin-2) as pituitary-enriched proteins and was validated for their lobe specificity using parallel reaction monitoring. In addition, three uPE1 proteins, namely THEM6 (mesenchymal stem cell protein DSCD75), FSD1L (coiled-coil domain-containing protein 10), and METTL26 (methyltransferase-like 26), were identified using the NeXtProt database, and depicted tumor markers S100 proteins having high expression in the posterior lobe. In summary, the study documents the first matched anterior and posterior pituitary proteome map acting as a reference control for a better understanding of functional and nonfunctional pituitary adenomas and extrapolating the aim of the Human Proteome Project towards the investigation of the proteome of life.
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Affiliation(s)
- Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deepatarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Shamira Sibal
- Lokmanya Tilak Municipal Medical College, Mumbai, India
| | | | - Abhidha Shah
- Department of Neurosurgery at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Anita Mahadevan
- Human Brain Bank, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Atul Goel
- Department of Neurosurgery at King Edward Memorial Hospital and Seth G. S. Medical College, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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Arya B, Donofrio MT, Freud LR, Hornberger LK, Moon-Grady AJ, Morris SA, Pinto N, Simpson LL, Cuneo BF, Divanovic A, Jaeggi E, Peyvandi S, Puchalski MD, Rychik J, Schidlow DN, Srivastava S, Tacy TA, Tworetzky W, Walsh MJ. Implications of United States Supreme Court's ruling on Dobbs vs Jackson Women's Health Organization: perspective of physicians caring for critically ill fetuses and newborns. Ultrasound Obstet Gynecol 2022; 60:812-813. [PMID: 36353858 DOI: 10.1002/uog.26107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- B Arya
- Seattle Children's Hospital and the University of Washington School of Medicine, Seattle, WA, USA
| | - M T Donofrio
- Children's National Hospital and George Washington School of Medicine, Washington, DC, USA
| | - L R Freud
- The Hospital for Sick Children and the University of Toronto, Toronto, Canada
| | | | - A J Moon-Grady
- University of California at San Francisco, San Francisco, CA, USA
| | - S A Morris
- Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - N Pinto
- Seattle Children's Hospital and the University of Washington School of Medicine, Seattle, WA, USA
| | - L L Simpson
- Columbia University Irving Medical School, New York, NY, USA
| | - B F Cuneo
- Children's Hospital of Colorado, Aurora, CO, USA
| | - A Divanovic
- Cincinnati Children's Hospital and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - E Jaeggi
- The Hospital for Sick Children and the University of Toronto, Toronto, Canada
| | - S Peyvandi
- University of California at San Francisco, San Francisco, CA, USA
| | - M D Puchalski
- Johns Hopkins All Children's Hospital, St Petersburg, FL, USA
| | - J Rychik
- The Children's Hospital of Philadelphia and Perelman, School of Medicine at University of Pennsylvania, Philadelphia, PA, USA
| | - D N Schidlow
- Boston Children's Hospital and Harvard School of Medicine, Boston, MA, USA
| | | | - T A Tacy
- Lucile Packard Children's Hospital at Stanford University, Palo Alto, CA, USA
| | - W Tworetzky
- Boston Children's Hospital and Harvard School of Medicine, Boston, MA, USA
| | - M J Walsh
- Atrium Health Wake Forest Baptist, Winston-Salem, NC, USA
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Rajoria S, Nissa MU, Suvarna K, Khatri H, Srivastava S. Multiomics Data Analysis Workflow to Assess Severity in Longitudinal Plasma Samples of COVID-19 Patients. Data Brief 2022; 46:108765. [PMCID: PMC9678393 DOI: 10.1016/j.dib.2022.108765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/31/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
Elucidation of molecular markers related to the mounted immune response is crucial for the understanding of disease pathogenesis. In this article, we present the mass-spectrometry-based metabolomic and proteomic data of blood plasma of COVID-19 patients collected at two-time points, which showed a transition from non-severe to severe conditions during these time points. Metabolites were extracted and subjected to mass spectrometric analysis using the Q-Exactive mass spectrometer. For proteomic analysis, depleted plasma samples were tryptic digested and subjected to mass spectrometry analysis. The expression of a few significant targeted proteins was also validated by employing the targeted proteomic approach of multiple reaction monitoring (MRM). Integrative pathway analysis was performed with the significant proteins to obtain biological insights into disease severity. For discussion and more information on the dataset creation, please refer to the related full-length article [1].
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Rastogi M, Gandhi A, Khurana R, Poojari A, Srivastava S, Srivastava A, Bharati A, Mishra S, Chauhan A. Prospective Evaluation of Role of Hybrid Approach Brachytherapy with MRI Only at First Fraction Followed by CT Based IGBT in Subsequent Sessions in Cervical Cancer Patients. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Banerjee A, Ray A, Barpanda A, Dash A, Gupta I, Nissa MU, Zhu H, Shah A, Duttagupta SP, Goel A, Srivastava S. Evaluation of autoantibody signatures in pituitary adenoma patients using human proteome arrays. Proteomics Clin Appl 2022; 16:e2100111. [PMID: 35939377 DOI: 10.1002/prca.202100111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/08/2022] [Accepted: 08/03/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE To identify the specific diagnostic biomarkers related to pituitary adenomas (PAs), we performed serological antibody profiles for three types of PAs, namely Acromegaly, Cushing's and Nonfunctional Pituitary Adenomas (NFPAs), using the human proteome (HuProt) microarray. This is the first study describing the serum autoantibody profile of PAs. EXPERIMENTAL DESIGN We performed serological autoantibody profiling of four healthy controls, four Acromegaly, three Cushing's and three NFPAs patient samples to obtain their autoantibody profiles, which were used for studying expression, interaction and altered biological pathways. Further, significant autoantibodies of PAs were compared with data available for glioma, meningioma and AAgAtlas for their specificity. RESULTS Autoantibody profile of PAs led to the identification of differentially expressed significant proteins such as AKNAD1 (AT-Hook Transcription Factor [AKNA] Domain Containing 1), NINJ1 (Nerve injury-induced protein 1), L3HYPDH (Trans-3-hydroxy-L-proline dehydratase), RHOG (Rho-related GTP-binding protein) and PTP4A1 (Protein Tyrosine Phosphatase Type IVA 1) in Acromegaly. Protein ABR (Active breakpoint cluster region-related protein), ST6GALNAC6 (ST6 N-acetylgalactosaminide alpha-2, 6-sialyltransferase 6), NOL3 (Nucleolar protein 3), ANXA8 (Annexin A8) and POLR2H (RNA polymerase II, I and III subunit H) showed an antigenic response in Cushing's patient's serum samples. Protein dipeptidyl peptidase 3 (DPP3) and reticulon-4 (RTN4) exhibited a very high antigenic response in NFPA patients. These proteins hold promise as potential autoantibody biomarkers in PAs.
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Affiliation(s)
- Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Arka Ray
- Centre for Research in Nanotechnology & Science (CRNTS), Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ankita Dash
- Miranda House, University of Delhi, University Enclave, New Delhi, Delhi, India
| | - Ishika Gupta
- Department of Biotechnology Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences/High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abhidha Shah
- Department of Neurosurgery at King Edward Memorial Hospital and Seth G. S. Medical College, Parel, Mumbai, India
| | - Siddhartha P Duttagupta
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Atul Goel
- Department of Neurosurgery at King Edward Memorial Hospital and Seth G. S. Medical College, Parel, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Nissa MU, Banerjee A, Goswami M, Srivastava S. Comprehensive Data and Workflow for Mapping Global Proteome and Post-Translational Modifications in Indian Major Carp, Labeo rohita. Data Brief 2022; 45:108746. [DOI: 10.1016/j.dib.2022.108746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 11/15/2022] Open
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Biswas D, Kumari N, Lachén-Montes M, Dutta S, Agrawal I, Samanta D, Shenoy SV, Halder A, Fernández-Irigoyen J, Padhye AR, Santamaría E, Srivastava S. Deep Phosphoproteome Landscape of Interhemispheric Functionality of Neuroanatomical Regions of the Human Brain. J Proteome Res 2022; 22:1043-1055. [PMID: 36317652 DOI: 10.1021/acs.jproteome.2c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Post-translational modifications (PTMs) are one of the compulsive and predominant biological processes that regulate the diverse molecular mechanism, modulate the onset of disease, and are the reason behind the functional diversity of proteins. Despite the widespread research findings in neuroproteomics, one of the key drawbacks has been the lack of proteome-level knowledge of hemispheric lateralization. We have investigated the proteome level expression in different neuroanatomical regions under the Human Brain Proteome Project (HBPP) and developed the global interhemispheric brain proteome map (Brainprot) earlier. Furthermore, this study has extended to decipher the phosphoproteome map of human brain interhemispheric regions through high-resolution mass spectrometry. The phosphoproteomics examination of 12 unique interhemispheric neurological brain regions using Orbitrap fusion liquid chromatography with tandem mass spectrometry provided comprehensive coverage of 996 phosphoproteins, 2010 phosphopeptides, and 3567 phosphosites. Moreover, interhemispheric phosphoproteome profiling has been categorized according to synaptic ontologies and interhemispheric expression to understand the functionality. Finally, we have integrated the phosphosites data under the PhosphoMap section in the Inter-Hemispheric Brain Proteome Map Portal (https://www.brainprot.org/) for the advancement and support of the ongoing neuroproteomics research worldwide. Data is available via ProteomeXchange with the identifier PXD031188.
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Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Neha Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sampurna Dutta
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Ishita Agrawal
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi221005, India
| | - Debabrata Samanta
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal721302, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Advait Rahul Padhye
- Department of Computer Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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Nissa MU, Pinto N, Varshnay A, Goswami M, Srivastava S. Ecological Monitoring and Omics: A Comprehensive Comparison of Workflows for Mass Spectrometry-Based Quantitative Proteomics of Fish ( Labeo rohita) Liver Tissue. OMICS 2022; 26:489-503. [PMID: 36036978 DOI: 10.1089/omi.2022.0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Introduction: The liver is highly sensitive to the environmental factors. Liver tissue, particularly from fish, is often used as a biological target in ecological monitoring, disease research, and stress response studies. Labeo rohita (rohu) is a fish with a significant role in the global aquaculture economy. Methods: Bottom-up proteomics relies on efficient sample preparation for performing mass spectrometric analysis of the liver tissue. Optimization of protein solubilization and digestion strategies is the key step to obtain reliable data for a successful proteomics experiment. Because the goal of extraction is to acquire the optimum protein quality and yield, the first step should be to choose an appropriate extraction method based on the type of sample. Solubilization buffers containing sodium dodecyl sulfate (SDS) or urea, and digestion methods such as filter-aided sample preparation (FASP), suspension trap (S-Trap) and in-solution are often used in proteomics but are in need of comparative evaluation with an eye to protocol optimization. Experiment: We applied two different solubilization buffers (one containing SDS, and other containing urea) and three digestion methods (FASP, S-Trap, and in-solution) to the proteomic analysis of the fish (L. rohita) liver tissue. Label-free quantification analysis was performed to analyze the similarities and differences in the results with each method. Gene ontology-based functional analysis was performed for the identified proteome across the experimental conditions to overview their protein classes, molecular functions, and biological processes. Results: SDS lysis followed by S-Trap digestion outperformed the other combinations of lysis and digestion in terms of higher protein coverage, consistency in the results and repeatability. Filter-based methods provided comparatively better results than in-solution digestion. Discussion: This protocol presents new insights on ways to optimize discovery and targeted proteomic analyses of liver tissue using the fish L. rohita as a case study. Other tissues can also be evaluated in the future drawing from the results in this study. This would help the scientific community with hypothesis-driven studies on topics ranging from basic biology to applied aquaculture research and ecological monitoring. This is particularly relevant in the current era of ecological crises and environmental pollution, where advances and optimization in research protocols can contribute to in-depth studies of ecosystems and planetary health.
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Affiliation(s)
- Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Nevil Pinto
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Mumbai, Maharashtra, India
| | | | - Mukunda Goswami
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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Mukherjee A, Ghosh S, Biswas D, Rao A, Shetty P, Epari S, Moiyadi A, Srivastava S. Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples. OMICS 2022; 26:512-520. [PMID: 36036964 DOI: 10.1089/omi.2022.0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Clinical proteomics is a rapidly emerging frontier in laboratory medicine. High-throughput proteomic investigations of biopsy tissues provide mechanistic insights into complex human diseases. For large-scale proteomics, formalin-fixed and paraffin-embedded (FFPE) tissue samples offer a viable alternative to fresh-frozen (FF) tissues that have restricted availability. In this context, meningioma is one of the most common primary brain tumors where innovation in diagnostics and therapeutic targets can benefit from clinical proteomics. We present here an integrated workflow for quantitative proteomics and biomarker validation of meningioma FFPE tissues. Applying label-free quantitative (LFQ) proteomics, we reproducibly (Pearson's correlation: 0.84-0.91) obtained an in-depth proteome coverage (nearly 4000 proteins per sample) from 120 min gradient of single unfractionated mass spectrometry run. Furthermore, building upon LFQ data and literature curated set of meningioma-associated proteins, we validated VIM, AHNAK, and CLU from FFPE tissues using selected reaction monitoring (SRM) assay and compared its performance with FF tissues. This study illustrates how knowledge from label-free proteomics can be integrated for selecting peptides for targeted validation and suggests that FFPE tissues are comparable to FF tissues for SRM assays. This quantitative clinical proteomics workflow is scalable for large-scale clinical diagnostics studies in the future, for example, utilizing the global repository of FFPE tissues in meningioma and possibly in other cancers.
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Affiliation(s)
- Arijit Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Susmita Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Aishwarya Rao
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | | | | | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Banerjee A, Halder A, Jadhav P, Bankar R, Pattarkine J, Hole A, Shah A, Goel A, Murali Krishna C, Srivastava S. Metabolomics Profiling of Pituitary Adenomas by Raman Spectroscopy, Attenuated Total Reflection-Fourier Transform Infrared Spectroscopy, and Mass Spectrometry of Serum Samples. Anal Chem 2022; 94:11898-11907. [PMID: 35980087 DOI: 10.1021/acs.analchem.2c02487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To date, no studies are available in which pituitary adenomas (PAs) have been studied using techniques like confocal Raman spectroscopy, attenuated total reflection-Fourier transform infrared (FT-IR), and liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the same serum samples. To understand the metabolomics fingerprint, Raman spectra of 16 acromegaly, 19 Cushing's, and 33 nonfunctional PA (NFPA) and ATR-FTIR spectral acquisition of 16 acromegaly, 18 Cushing's, and 22 NFPA patient's serum samples were acquired. Next, Principal component-based linear discriminant analysis (PC-LDA) models were developed, Raman spectral analysis classified acromegaly with an accuracy of 79.17%, sensitivity of 75%, and specificity of 81.25%, Cushing's with an accuracy of 66.67%, sensitivity of 100%, and specificity of 52.63%, and NFPA with an accuracy of 73.17%, sensitivity of 75%, and specificity of 72.73%. ATR-FTIR spectral analysis classified acromegaly with an accuracy of 95.83%, sensitivity of 100%, and specificity of 93.75%, Cushing's with an accuracy of 65.38%, sensitivity of 87.5%, and specificity of 55.56%, and NFPA with an accuracy of 70%, sensitivity of 87.5%, and specificity of 43.75%. In either of the cases, healthy individual cohorts were clearly segregated from the disease cohort, which identified differential regulated regions of nucleic acids, lipids, amides, phosphates, and polysaccharide/C-C residue α helix regions. Furthermore, LC-MS/MS-based analysis of sera samples resulted in the identification of various sphingosine, lipids, acylcarnitines, amino acids, ethanolamine, choline, and their derivatives that differentially regulated in each tumor cohort. We believe cues obtained from the study may be used to generate the metabolite-based test to diagnose PAs from serum in addition to conventional techniques and also to understand disease biology for better disease management, point of care, and improving quality of life in PA patients.
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Affiliation(s)
- Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Priyanka Jadhav
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC). Sector-22, Kharghar, Navi Mumbai 410210, India
| | - Renuka Bankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Janhavi Pattarkine
- Department of Biotechnology, Dr. D.Y. Patil Arts, Commerce and Science College, Pimpri, Pune 411018, India
| | - Arti Hole
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC). Sector-22, Kharghar, Navi Mumbai 410210, India
| | - Abhidha Shah
- Department of Neurosurgery, King Edward Memorial Hospital and Seth G. S. Medical College, Dr E Borges Road, Acharya Donde Marg, Parel, Opposite Tata & Wadia Hospital, Mumbai 400012, India
| | - Atul Goel
- Department of Neurosurgery, King Edward Memorial Hospital and Seth G. S. Medical College, Dr E Borges Road, Acharya Donde Marg, Parel, Opposite Tata & Wadia Hospital, Mumbai 400012, India
| | - C Murali Krishna
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC). Sector-22, Kharghar, Navi Mumbai 410210, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Akkerman OW, Duarte R, Tiberi S, Schaaf HS, Lange C, Alffenaar JWC, Denholm J, Carvalho ACC, Bolhuis MS, Borisov S, Bruchfeld J, Cabibbe AM, Caminero JA, Carvalho I, Chakaya J, Centis R, Dalcomo MP, D Ambrosio L, Dedicoat M, Dheda K, Dooley KE, Furin J, García-García JM, van Hest NAH, de Jong BC, Kurhasani X, Märtson AG, Mpagama S, Torrico MM, Nunes E, Ong CWM, Palmero DJ, Ruslami R, Saktiawati AMI, Semuto C, Silva DR, Singla R, Solovic I, Srivastava S, de Steenwinkel JEM, Story A, Sturkenboom MGG, Tadolini M, Udwadia ZF, Verhage AR, Zellweger JP, Migliori GB. Clinical standards for drug-susceptible pulmonary TB. Int J Tuberc Lung Dis 2022; 26:592-604. [PMID: 35768923 PMCID: PMC9272737 DOI: 10.5588/ijtld.22.0228] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND: The aim of these clinical standards is to provide guidance on 'best practice´ for diagnosis, treatment and management of drug-susceptible pulmonary TB (PTB).METHODS: A panel of 54 global experts in the field of TB care, public health, microbiology, and pharmacology were identified; 46 participated in a Delphi process. A 5-point Likert scale was used to score draft standards. The final document represents the broad consensus and was approved by all 46 participants.RESULTS: Seven clinical standards were defined: Standard 1, all patients (adult or child) who have symptoms and signs compatible with PTB should undergo investigations to reach a diagnosis; Standard 2, adequate bacteriological tests should be conducted to exclude drug-resistant TB; Standard 3, an appropriate regimen recommended by WHO and national guidelines for the treatment of PTB should be identified; Standard 4, health education and counselling should be provided for each patient starting treatment; Standard 5, treatment monitoring should be conducted to assess adherence, follow patient progress, identify and manage adverse events, and detect development of resistance; Standard 6, a recommended series of patient examinations should be performed at the end of treatment; Standard 7, necessary public health actions should be conducted for each patient. We also identified priorities for future research into PTB.CONCLUSION: These consensus-based clinical standards will help to improve patient care by guiding clinicians and programme managers in planning and implementation of locally appropriate measures for optimal person-centred treatment for PTB.
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Affiliation(s)
- O W Akkerman
- TB Center Beatrixoord, University Medical Center Groningen, University of Groningen, Haren, the Netherlands, Department of Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - R Duarte
- Centro Hospitalar de Vila Nova de Gaia/Espinho; Instituto de Ciencias Biomédicas de Abel Saalazar, Universidade do Porto, Instituto de Saúde Publica da Universidade do Porto, Unidade de Investigação Clínica, ARS Norte, Porto, Portugal
| | - S Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Division of Infection, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - H S Schaaf
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - C Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany, German Center for Infection Research (DZIF) Clinical Tuberculosis Unit, Borstel, Germany, Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany, The Global Tuberculosis Program, Texas Children´s Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - J W C Alffenaar
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia, School of Pharmacy, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia
| | - J Denholm
- Victorian Tuberculosis Program, Melbourne Health, Department of Infectious diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - A C C Carvalho
- Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - M S Bolhuis
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - S Borisov
- Moscow Research and Clinical Center for Tuberculosis Control, Moscow, Russia
| | - J Bruchfeld
- Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Solna, Stockholm, Sweden, Department of Infectious Disease, Karolinska University Hospital, Stockholm, Sweden
| | - A M Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - J A Caminero
- Department of Pneumology, University General Hospital of Gran Canaria "Dr Negrin", Las Palmas, Spain, ALOSA (Active Learning over Sanitary Aspects) TB Academy, Spain
| | - I Carvalho
- Pediatric Department, Vila Nova de Gaia Outpatient Tuberculosis Centre, Vila Nova de Gaia Hospital Centre, Vila Nova de Gaia, Portugal
| | - J Chakaya
- Department of Medicine, Therapeutics and Dermatology, Kenyatta University, Nairobi, Kenya, Department of Clinical Sciences. Liverpool School of Tropical Medicine, Liverpool, UK
| | - R Centis
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
| | - M P Dalcomo
- Reference Center Helio Fraga, FIOCRUZ, Brazil
| | - L D Ambrosio
- Public Health Consulting Group, Lugano, Switzerland
| | - M Dedicoat
- Department of Infectious Diseases, Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - K Dheda
- Centre for Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Cape Town, South Africa, South African Medical Research Council Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - K E Dooley
- Center for Tuberculosis Research, Johns Hopkins, Baltimore, MD
| | - J Furin
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | | | - N A H van Hest
- Department of Pulmonary Diseases and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands, Municipal Public Health Service Groningen, Groningen, The Netherlands
| | - B C de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - X Kurhasani
- UBT-Higher Education Institution Prishtina, Kosovo
| | - A G Märtson
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - S Mpagama
- Kilimanjaro Christian Medical University College, Moshi, United Republic of Tanzani, Kibong´oto Infectious Diseases Hospital, Sanya Juu, Siha, Kilimanjaro, United Republic of Tanzania
| | - M Munoz Torrico
- Clínica de Tuberculosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, México City, Mexico
| | - E Nunes
- Department of Pulmonology of Central Hospital of Maputo, Maputo, Mozambique, Faculty of Medicine of Eduardo Mondlane University, Maputo, Mozambique
| | - C W M Ong
- Infectious Disease Translational Research Programme, Department of Medicine, National University of Singapore, Yong Loo Lin School of Medicine, Singapore, National University of Singapore Institute for Health Innovation & Technology (iHealthtech), Singapore, Division of Infectious Diseases, Department of Medicine, National University Hospital, Singapore
| | - D J Palmero
- Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - R Ruslami
- Department of Biomedical Science, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia, Research Center for Care and Control of Infectious Disease (RC3iD), Universitas Padjadjaran, Bandung, Indonesia
| | - A M I Saktiawati
- Department of Internal Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia, Center for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - C Semuto
- Research, Innovation and Data Science Division, Rwanda Biomedical Center, Kigali, Rwanda
| | - D R Silva
- Instituto Vaccarezza, Hospital Muñiz, Buenos Aires, Argentina
| | - R Singla
- National Institute of Tuberculosis & Respiratory Diseases, New Delhi, India
| | - I Solovic
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Faculty of Health, Catholic University, Ružomberok, Vyšné Hágy, Slovakia
| | - S Srivastava
- Department of Pulmonary Immunology, University of Texas Health Science Centre at Tyler, Tyler, TX, USA
| | - J E M de Steenwinkel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - A Story
- Institute of Epidemiology and Healthcare, University College London, London, UK, Find and Treat, University College Hospitals NHS Foundation Trust, London, UK
| | - M G G Sturkenboom
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - M Tadolini
- Infectious Diseases Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy, Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Z F Udwadia
- P. D. Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - A R Verhage
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - J P Zellweger
- TB Competence Center, Swiss Lung Association, Berne, Switzerland
| | - G B Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
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Alffenaar JWC, Stocker SL, Forsman LD, Garcia-Prats A, Heysell SK, Aarnoutse RE, Akkerman OW, Aleksa A, van Altena R, de Oñata WA, Bhavani PK, Van't Boveneind-Vrubleuskaya N, Carvalho ACC, Centis R, Chakaya JM, Cirillo DM, Cho JG, D Ambrosio L, Dalcolmo MP, Denti P, Dheda K, Fox GJ, Hesseling AC, Kim HY, Köser CU, Marais BJ, Margineanu I, Märtson AG, Torrico MM, Nataprawira HM, Ong CWM, Otto-Knapp R, Peloquin CA, Silva DR, Ruslami R, Santoso P, Savic RM, Singla R, Svensson EM, Skrahina A, van Soolingen D, Srivastava S, Tadolini M, Tiberi S, Thomas TA, Udwadia ZF, Vu DH, Zhang W, Mpagama SG, Schön T, Migliori GB. Clinical standards for the dosing and management of TB drugs. Int J Tuberc Lung Dis 2022; 26:483-499. [PMID: 35650702 PMCID: PMC9165737 DOI: 10.5588/ijtld.22.0188] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND: Optimal drug dosing is important to ensure adequate response to treatment, prevent development of drug resistance and reduce drug toxicity. The aim of these clinical standards is to provide guidance on 'best practice´ for dosing and management of TB drugs.METHODS: A panel of 57 global experts in the fields of microbiology, pharmacology and TB care were identified; 51 participated in a Delphi process. A 5-point Likert scale was used to score draft standards. The final document represents the broad consensus and was approved by all participants.RESULTS: Six clinical standards were defined: Standard 1, defining the most appropriate initial dose for TB treatment; Standard 2, identifying patients who may be at risk of sub-optimal drug exposure; Standard 3, identifying patients at risk of developing drug-related toxicity and how best to manage this risk; Standard 4, identifying patients who can benefit from therapeutic drug monitoring (TDM); Standard 5, highlighting education and counselling that should be provided to people initiating TB treatment; and Standard 6, providing essential education for healthcare professionals. In addition, consensus research priorities were identified.CONCLUSION: This is the first consensus-based Clinical Standards for the dosing and management of TB drugs to guide clinicians and programme managers in planning and implementation of locally appropriate measures for optimal person-centred treatment to improve patient care.
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Affiliation(s)
- J W C Alffenaar
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia, School of Pharmacy, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia
| | - S L Stocker
- School of Pharmacy, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia, Department of Clinical Pharmacology and Toxicology, St Vincent´s Hospital, Sydney, NSW, Australia, St Vincent´s Clinical Campus, University of NSW, Kensington, NSW, Australia
| | - L Davies Forsman
- Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Solna, Sweden, Department of Infectious Diseases Karolinska University Hospital, Solna, Sweden
| | - A Garcia-Prats
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa, Department of Pediatrics, University of Wisconsin, Madison, WI
| | - S K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - R E Aarnoutse
- Department of Pharmacy, Radboud Institute for Health Sciences & Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - O W Akkerman
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases and Tuberculosis, Groningen, The Netherlands, University of Groningen, University Medical Center Groningen, Tuberculosis Center Beatrixoord, Haren, The Netherlands
| | - A Aleksa
- Educational Institution "Grodno State Medical University", Grodno, Belarus
| | - R van Altena
- Asian Harm Reduction Network (AHRN) and Medical Action Myanmar (MAM) in Yangon, Myanmar
| | - W Arrazola de Oñata
- Belgian Scientific Institute for Public Health (Belgian Lung and Tuberculosis Association), Brussels, Belgium
| | - P K Bhavani
- Indian Council of Medical Research-National Institute for Research in Tuberculosis-International Center for Excellence in Research, Chennai, India
| | - N Van't Boveneind-Vrubleuskaya
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands, Department of Public Health TB Control, Metropolitan Public Health Services, The Hague, The Netherlands
| | - A C C Carvalho
- Laboratório de Inovações em Terapias, Ensino e Bioprodutos (LITEB), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - R Centis
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Tradate, Italy
| | - J M Chakaya
- Department of Medicine, Therapeutics and Dermatology, Kenyatta University, Nairobi, Kenya, Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - D M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - J G Cho
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia, Parramatta Chest Clinic, Parramatta, NSW, Australia
| | - L D Ambrosio
- Public Health Consulting Group, Lugano, Switzerland
| | - M P Dalcolmo
- Reference Center Hélio Fraga, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - P Denti
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - K Dheda
- Centre for Lung Infection and Immunity, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Cape Town, South Africa, University of Cape Town Lung Institute & South African MRC Centre for the Study of Antimicrobial Resistance, Cape Town, South Africa, Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - G J Fox
- Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia, Woolcock Institute of Medical Research, Glebe, NSW, Australia
| | - A C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa
| | - H Y Kim
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia, School of Pharmacy, The University of Sydney Faculty of Medicine and Health, Sydney, NSW, Australia, Westmead Hospital, Sydney, NSW, Australia
| | - C U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - B J Marais
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia, Department of Infectious Diseases and Microbiology, The Children´s Hospital at Westmead, Westmead, NSW, Australia
| | - I Margineanu
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - A G Märtson
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - M Munoz Torrico
- Clínica de Tuberculosis, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México, Mexico
| | - H M Nataprawira
- Division of Paediatric Respirology, Department of Child Health, Faculty of Medicine, Universitas Padjadjaran, Hasan Sadikin Hospital, Bandung, Indonesia
| | - C W M Ong
- Infectious Disease Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore, Division of Infectious Diseases, Department of Medicine, National University Hospital, Singapore
| | - R Otto-Knapp
- German Central Committee against Tuberculosis (DZK), Berlin, Germany
| | - C A Peloquin
- Infectious Disease Pharmacokinetics Laboratory, Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA
| | - D R Silva
- Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - R Ruslami
- TB/HIV Research Centre, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia, Department of Biomedical Sciences, Division of Pharmacology and Therapy, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - P Santoso
- Division of Respirology and Critical Care, Department of Internal Medicine, Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin General Hospital, Bandung, Indonesia
| | - R M Savic
- Department of Bioengineering and Therapeutic Sciences, Division of Pulmonary and Critical Care Medicine, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA, USA
| | - R Singla
- Department of TB & Respiratory Diseases, National Institute of TB & Respiratory Diseases, New Delhi, India
| | - E M Svensson
- Department of Pharmacy, Radboud Institute for Health Sciences & Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands, Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - A Skrahina
- The Republican Research and Practical Centre for Pulmonology and TB, Minsk, Belarus
| | - D van Soolingen
- National Institute for Public Health and the Environment, TB Reference Laboratory (RIVM), Bilthoven, The Netherlands
| | - S Srivastava
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - M Tadolini
- Infectious Diseases Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy, Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - S Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - T A Thomas
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Z F Udwadia
- P. D. Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - D H Vu
- National Drug Information and Adverse Drug Reaction Monitoring Centre, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - W Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People´s Republic of China
| | - S G Mpagama
- Kilimanjaro Christian Medical University College, Moshi, United Republic of Tanzania, Kibong´oto Infectious Diseases Hospital, Sanya Juu, Siha, Kilimanjaro, United Republic of Tanzania
| | - T Schön
- Department of Infectious Diseases, Linköping University Hospital, Linköping, Sweden, Institute of Biomedical and Clinical Sciences, Division of Infection and Inflammation, Linköping University, Linköping, Sweden, Department of Infectious Diseases, Kalmar County Hospital, Kalmar, Linköping University, Linköping, Sweden
| | - G B Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Tradate, Italy
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Srivastava A, Rawat P, Kumar M, Nirala V, Singh SP, Prabhu KN, Sundaresan V, Srivastava S. Identification of potential source of quality raw material of Costus speciosus from Western coast of Malabar. JPC-J PLANAR CHROMAT 2022. [DOI: 10.1007/s00764-022-00167-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Srivastava S, Kv A, Jabir A M, Moirangthem Singh N. MO-0304 Dosimetric comparison of ACE algorithm and TG-43 formalism in HDR brachytherapy of carcinoma cervix. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)02336-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Rai S, Srivastava S, Krishnan S, Murlimanju B, Hegde A, Jolly A. Work-Related Musculoskeletal Disorders among Sonologists during the Pre-COVID-19 and Present COVID-19 Era: a Survey and Review of Best Practices. Muscles Ligaments Tendons J 2022. [DOI: 10.32098/mltj.02.2022.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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