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Article ; Online: Community detection in Epstein-Barr virus associated carcinomas and role of tyrosine kinase in etiological mechanisms for oncogenesis.

Chatterjee, S / Sanjeev, B S

2023 Volume 180, Page(s) 106115

Abstract: ... of the virus in causing infectious mononucleosis (IM) affecting B-cells and epithelial cells and ...

Abstract	Background: Epstein-Barr virus (EBV) affects more than 90% of global population. The role of the virus in causing infectious mononucleosis (IM) affecting B-cells and epithelial cells and in the development of EBV associated cancers is well documented. Investigating the associated interactions can pave way for the discovery of novel therapeutic targets for EBV associated lymphoproliferative (Burkitt's Lymphoma and Hodgkin's Lymphoma) and non-lymphoproliferative diseases (Gastric cancer and Nasopharyngeal cancer). Methods: Based on the DisGeNET (v7.0) data set, we constructed a disease-gene network to identify genes that are involved in various carcinomas, viz. Gastric cancer (GC), Nasopharyngeal cancer (NPC), Hodgkin's lymphoma (HL) and Burkitt's lymphoma (BL). We identified communities in the disease-gene network and performed functional enrichment using over-representation analysis to detect significant biological processes/pathways and the interactions between them. Result: We identified the modular communities to explore the relation of this common causative pathogen (EBV) with different carcinomas such as GC, NPC, HL and BL. Through network analysis we identified the top 10 genes linked with EBV associated carcinomas as CASP10, BRAF, NFKBIA, IFNA2, GSTP1, CSF3, GATA3, UBR5, AXIN2 and POLE. Further, the tyrosine-protein kinase (ABL1) gene was significantly over-represented in 3 out of 9 critical biological processes, viz. in regulatory pathways in cancer, the TP53 network and the Imatinib and chronic myeloid leukemia biological processes. Consequently, the EBV pathogen appears to target critical pathways involved in cellular growth arrest/apoptosis. We make our case for BCR-ABL1 tyrosine-kinase inhibitors (TKI) for further clinical investigations in the inhibition of BCR-mediated EBV activation in carcinomas for better prognostic and therapeutic outcomes.
MeSH term(s)	Humans ; Herpesvirus 4, Human/genetics ; Burkitt Lymphoma/genetics ; Burkitt Lymphoma/complications ; Epstein-Barr Virus Infections/genetics ; Epstein-Barr Virus Infections/complications ; Hodgkin Disease/complications ; Stomach Neoplasms/complications ; Nasopharyngeal Neoplasms/genetics ; Nasopharyngeal Neoplasms/complications ; Protein-Tyrosine Kinases ; Carcinoma ; Carcinogenesis/genetics ; Tyrosine
Chemical Substances	Protein-Tyrosine Kinases (EC 2.7.10.1) ; Tyrosine (42HK56048U)
Language	English
Publishing date	2023-05-01
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2023.106115
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Article ; Online: Over-representation analysis of angiogenic factors in immunosuppressive mechanisms in neoplasms and neurological conditions during COVID-19.

Chatterjee, S / Sanjeev, B S

Microbial pathogenesis

2023 Volume 185, Page(s) 106386

Abstract: Background: Recent studies emphasized the necessity to identify key (human) biological processes and pathways targeted by the Coronaviridae family of viruses, especially Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronavirus Disease ( ... ...

Abstract	Background: Recent studies emphasized the necessity to identify key (human) biological processes and pathways targeted by the Coronaviridae family of viruses, especially Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronavirus Disease (COVID-19) caused up to 33-55 % death rates in COVID-19 patients with malignant neoplasms and Alzheimer's disease. Given this scenario, we identified biological processes and pathways involved in various diseases which are most likely affected by COVID-19. Methods: The COVID-19 DisGeNET data set (v4.0) contains the associations between various diseases and human genes known to interact with viruses from Coronaviridae family and were obtained from the IntAct Coronavirus data set annotated with DisGeNET data. We constructed the disease-gene network to identify genes that are involved in various comorbid diseased states. Communities from the disease-gene network were identified using Louvain method and functional enrichment through over-representation analysis methodology was used to discover significant biological processes and pathways shared between COVID-19 and other diseases. Result: The COVID-19 DisGeNET data set (v4.0) comprised of 828 human genes and 10,473 diseases (including various phenotypes) that together constituted nodes in the disease-gene network. Each of the 70,210 edges connects a human gene with an associated disease. The top 10 genes linked to most number of diseases were VEGFA, BCL2, CTNNB1, ALB, COX2, AGT, HLA-A, HMOX1, FGF2 and COMT. The most vulnerable group of patients thus discovered had comorbid conditions such as carcinomas, malignant neoplasms and Alzheimer's disease. Finally, we identified 15 potentially useful biological processes and pathways for improved therapies. Vascular endothelial growth factor (VEGF) is the key mediator of angiogenesis in cancer. It is widely distributed in the brain and plays a crucial role in brain inflammation regulating the level of angiopoietins. With a degree of 1899, VEGFA was associated with maximum number of diseases in the disease-gene network. Previous studies have indicated that increased levels of VEGFA in the blood results in dyspnea, Pulmonary Edema (PE), Acute Lung Injury (ALI) and Acute Respiratory Distress Syndrome (ARDS). In case of COVID-19 patients with neoplasms and other neurological symptoms, our results indicate VEGFA as a therapeutic target for inflammation suppression. As VEGFs are known to disproportionately affect cancer patients, improving endothelial permeability and vasodilation with anti-VEGF therapy could lead to suppression of inflammation and also improve oxygenation. As an outcome of our study, we make case for clinical investigations towards anti-VEGF therapies for such comorbid conditions affected by COVID-19 for better therapeutic outcomes.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Vascular Endothelial Growth Factor A/genetics ; Vascular Endothelial Growth Factor A/metabolism ; Alzheimer Disease/genetics ; Inflammation ; Neoplasms/genetics ; Immunosuppressive Agents
Chemical Substances	Vascular Endothelial Growth Factor A ; Immunosuppressive Agents
Language	English
Publishing date	2023-10-19
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2023.106386
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Article ; Online: MD simulations indicate Omicron P132H of SARS-CoV-2 M

Bhat, Zahoor Ahmad / Khan, Mohd Muzammil / Rehman, Ayyub / Iqbal, Jawed / Sanjeev, B S / Madhumalar, Arumugam

International journal of biological macromolecules

2024 Volume 262, Issue Pt 2, Page(s) 130077

Abstract: The SARS-CoV-2 main protease ... ...

Abstract	The SARS-CoV-2 main protease M
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Catalytic Domain ; COVID-19 ; Molecular Dynamics Simulation ; Protease Inhibitors/chemistry ; Molecular Docking Simulation
Chemical Substances	Protease Inhibitors
Language	English
Publishing date	2024-02-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.130077
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Book ; Online: Network strategies to study Epstein-Barr virus associated carcinomas and potential etiological mechanisms for oncogenesis

Chatterjee, S. / Sanjeev, B. S.

2022

Abstract: ... in causing infectious mononucleosis (IM) affecting B-cells and epithelial cells and the development of EBV ...

Abstract	Diseased conditions are a consequence of some abnormality that are associated with clinical conditions in numerous cells and tissues affecting various organs. The common role of EBV (Epstein-Barr virus) in causing infectious mononucleosis (IM) affecting B-cells and epithelial cells and the development of EBV-associated cancers has been an area of active research. Investigating such significant interactions may help discover new therapeutic targets for certain EBV-associated lymphoproliferative (Burkitt's Lymphoma and Hodgkin's Lymphoma) and non-lymphoproliferative diseases (Gastric cancer and Nasopharyngeal cancer). Based on the DisGeNET (v7.0) data set, we constructed a disease-gene network bipartite graph to identify genes that are involved in various carcinomas namely, gastric cancer (GC), nasopharyngeal cancer (NPC), Hodgkin's lymphoma (HL) and Burkitt's lymphoma (BL). Using the community detection algorithm (Louvain method), we identified communities followed by functional enrichment using over-representation analysis methodology. In this study, we identified the modular communities to explore the relation of this common causative pathogen (EBV) with different carcinomas such as GC, NPC, HL and BL. We could identify the top 10 genes as CASP10, BRAF, NFKBIA, IFNA2, GSTP1, CSF3, GATA3, UBR5, AXIN2 and POLE based on their degree of distribution. Further over-representation analysis showed that the ABL1 gene was significantly over-represented in 3 out of 9 critical biological processes. As a result, we can infer that the EBV pathogen is selective in targeting critical pathways to bring about cellular growth arrest/apoptosis and interfering with vital biological processes, including the TP53 network of genes that leads to further proliferation of damage to vital cellular activities. Comment: 12 pages, 5 figures
Keywords	Quantitative Biology - Molecular Networks ; Quantitative Biology - Subcellular Processes
Subject code	610
Publishing date	2022-07-31
Publishing country	us
Document type	Book ; Online
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Book ; Online: Network-based community detection of comorbidities and their association with SARS-CoV-2 virus during COVID-19 pathogenesis

Chatterjee, S. / Sanjeev, B. S.

2022

Abstract: Recent studies emphasized the necessity to identify key (human) biological processes and pathways targeted by the Coronaviridae family of viruses, especially SARS-CoV-2. COVID-19 caused up to 33-55\% death rates in COVID-19 patients with malignant ... ...

Abstract	Recent studies emphasized the necessity to identify key (human) biological processes and pathways targeted by the Coronaviridae family of viruses, especially SARS-CoV-2. COVID-19 caused up to 33-55\% death rates in COVID-19 patients with malignant neoplasms and Alzheimer's disease. Given this scenario, we identified biological processes and pathways which are most likely affected by COVID-19. The associations between various diseases and human genes known to interact with viruses from Coronaviridae family were obtained from the IntAct COVID-19 data set annotated with DisGeNET data. We constructed the disease-gene network to identify genes that are involved in various comorbid diseased states. Communities from the disease-gene network through Louvain method were identified and functional enrichment through over-representation analysis methodology was used to discover significant biological processes and pathways shared between COVID-19 and other diseases. The IntAct COVID-19 data set comprised of 828 human genes and 10,473 diseases that together constituted nodes in the disease-gene network. Each of the 70,210 edges connects a human gene with an associated disease. The top 10 genes linked to most number of diseases were VEGFA, BCL2, CTNNB1, ALB, COX2, AGT, HLA-A, HMOX1, FGT2 and COMT. The most vulnerable group of patients thus discovered had comorbid conditions such as carcinomas, malignant neoplasms and Alzheimer's disease. Finally, we identified 37 potentially useful biological processes and pathways for improved therapies.
Keywords	Quantitative Biology - Molecular Networks ; Quantitative Biology - Subcellular Processes
Subject code	610
Publishing date	2022-05-31
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mapping antigens of membranous nephropathy: almost there.

Sethi, Sanjeev / Madden, Benjamin

Kidney international

2023 Volume 103, Issue 3, Page(s) 469–472

Abstract: Membranous nephropathy (MN) is characterized by subepithelial accumulation of immune complexes along the glomerular basement membranes. The immune complexes compromise IgG and the corresponding target antigen. Recent advances have led to the discovery of ...

Abstract	Membranous nephropathy (MN) is characterized by subepithelial accumulation of immune complexes along the glomerular basement membranes. The immune complexes compromise IgG and the corresponding target antigen. Recent advances have led to the discovery of novel target MN antigens. In this study, by Caza et al., 7 novel "putative" antigens are proposed. Target antigens can now be identified in approximately 90% of cases of MN. In addition to describing another 10 novel putative antigens, we propose a working algorithm for evaluating the target antigens in MN.
MeSH term(s)	Humans ; Glomerulonephritis, Membranous ; Antigen-Antibody Complex ; Glomerular Basement Membrane
Chemical Substances	Antigen-Antibody Complex
Language	English
Publishing date	2023-02-23
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	120573-0
ISSN	1523-1755 ; 0085-2538
ISSN (online)	1523-1755
ISSN	0085-2538
DOI	10.1016/j.kint.2023.01.003
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Article ; Online: Environmental persistence of Listeria monocytogenes and its implications in dairy processing plants.

Chowdhury, Bhaswati / Anand, Sanjeev

Comprehensive reviews in food science and food safety

2023 Volume 22, Issue 6, Page(s) 4573–4599

Abstract: Listeriosis, an invasive illness with a fatality rate between 20% and 30%, is caused by the ubiquitous bacterium Listeria monocytogenes. Human listeriosis has long been associated with foods. This is because the ubiquitous nature of the bacteria renders ... ...

Abstract	Listeriosis, an invasive illness with a fatality rate between 20% and 30%, is caused by the ubiquitous bacterium Listeria monocytogenes. Human listeriosis has long been associated with foods. This is because the ubiquitous nature of the bacteria renders it a common food contaminant, posing a significant risk to the food processing sector. Although several sophisticated stress coping mechanisms have been identified as significant contributing factors toward the pathogen's persistence, a complete understanding of the mechanisms underlying persistence across various strains remains limited. Moreover, aside from genetic aspects that promote the ability to cope with stress, various environmental factors that exist in food manufacturing plants could also contribute to the persistence of the pathogen. The objective of this review is to provide insight into the challenges faced by the dairy industry because of the pathogens' environmental persistence. Additionally, it also aims to emphasize the diverse adaptation and response mechanisms utilized by L. monocytogenes in food manufacturing plants to evade environmental stressors. The persistence of L. monocytogenes in the food processing environment poses a serious threat to food safety and public health. The emergence of areas with high levels of L. monocytogenes contamination could facilitate Listeria transmission through aerosols, potentially leading to the recontamination of food, particularly from floors and drains, when sanitation is implemented alongside product manufacturing. Hence, to produce safe dairy products and reduce the frequency of outbreaks of listeriosis, it is crucial to understand the factors that contribute to the persistence of this pathogen and to implement efficient control strategies.
MeSH term(s)	Humans ; Listeria monocytogenes ; Food Microbiology ; Food Contamination/analysis ; Listeriosis/epidemiology ; Listeriosis/microbiology ; Listeriosis/prevention & control ; Public Health
Language	English
Publishing date	2023-09-07
Publishing country	United States
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2185829-9
ISSN	1541-4337 ; 1541-4337
ISSN (online)	1541-4337
ISSN	1541-4337
DOI	10.1111/1541-4337.13234
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Article ; Online: Foveal triangular fibrocartilage complex pathology: a potentially under-recognized injury.

Welling, Benjamin / Kakar, Sanjeev

The Journal of hand surgery, European volume

2023 Volume 49, Issue 4, Page(s) 412–419

Abstract: The primary aim of the present study was to present a case series of 24 patients with foveal triangular fibrocartilage complex (TFCC) injuries that were treated with arthroscopically assisted TFCC foveal repair. In total, 19 patients had a stable distal ... ...

Abstract	The primary aim of the present study was to present a case series of 24 patients with foveal triangular fibrocartilage complex (TFCC) injuries that were treated with arthroscopically assisted TFCC foveal repair. In total, 19 patients had a stable distal radioulnar joint (DRUJ) and five had an unstable DRUJ. Despite this, all patients were found to have a foveal tear upon DRUJ arthroscopy. Magnetic resonance imaging (MRI) scans detected only eight out of 23 patients with foveal injuries. In addition to their foveal injury, 19 of the 24 patients had additional pathology that required treatment. At a mean follow-up of 18 months, there was a statistically significant improvement in pain, range of motion, grip strength and functional scores. In this study, we demonstrate that having a stable DRUJ upon clinical examination and normal MRI findings does not rule out foveal TFCC injury and a high index of clinical suspicion is needed when managing patients with ulnar sided wrist pain.
MeSH term(s)	Humans ; Triangular Fibrocartilage/injuries ; Wrist Injuries/diagnosis ; Wrist Joint ; Arthroscopy/methods ; Pain ; Joint Instability ; Retrospective Studies
Language	English
Publishing date	2023-10-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2272801-6
ISSN	2043-6289 ; 1753-1934
ISSN (online)	2043-6289
ISSN	1753-1934
DOI	10.1177/17531934231206426
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Article ; Online: Health Care Professional Distress and Mental Health: A Call to the Continuing Professional Development Community.

Turco, Mary G / Sockalingam, Sanjeev / Williams, Betsy

The Journal of continuing education in the health professions

2024

Abstract: Abstract: COVID-19 unleashed a maelstrom of distress on health care professionals. The pandemic contributed to a host of stressors for workers because of the need for rapid acquisition of new knowledge and skills to provide best treatment while ... ...

Abstract	Abstract: COVID-19 unleashed a maelstrom of distress on health care professionals. The pandemic contributed to a host of stressors for workers because of the need for rapid acquisition of new knowledge and skills to provide best treatment while simultaneously dealing with personal safety, limited resources, staffing shortages, and access to care issues. Concurrently, problems with systemic racial inequality and discrimination became more apparent secondary to difficulties with accessing health care for minorities and other marginalized groups. These problems contributed to many health care professionals experiencing severe moral injury and burnout as they struggled to uphold core values and do their jobs professionally. Some left or disengaged. Others died. As continuing professional development leaders focused on all health professionals, we must act deliberately to address health care professionals' distress and mental health. We must incorporate wellness and mental health as organizing principles in all we do. We must adopt a new mental model that recognizes the importance of learners' biopsychosocial functioning and commit to learners' wellness by developing activities that embrace a biopsychosocial point of view. As educators and influencers, we must demonstrate that the Institute for Healthcare Improvement's fourth aim to improve clinician well-being and safety (2014) and fifth aim to address health equity and the social determinants of health (2021) matter. It is crucial that continuing professional development leaders globally use their resources and relationships to accomplish this imperative call for action.
Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	639445-0
ISSN	1554-558X ; 0894-1912
ISSN (online)	1554-558X
ISSN	0894-1912
DOI	10.1097/CEH.0000000000000547
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Article ; Online: Physiological models to study the effect of molecular crowding on multi-drug bound proteins: insights from SARS-CoV-2 main protease.

Sanjeev, B S / Chitara, Dheeraj / Madhumalar, Arumugam

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 24, Page(s) 13564–13580

Abstract: Molecular Dynamics simulations are often used in drug design. However, such simulations do not account for the physiological environment of the receptor; hence overlook its impact on biomolecular interactions. To address this lacuna, we identified three ... ...

Abstract	Molecular Dynamics simulations are often used in drug design. However, such simulations do not account for the physiological environment of the receptor; hence overlook its impact on biomolecular interactions. To address this lacuna, we identified three objectives to pursue - develop models of physiological environment, study a drug-receptor complex in such environments, and identify methods to analyze these complicated simulations. Two novel physiological models were developed and studied. The first, called 'm10', comprises of 10 of the most abundant cytoplasmic metabolites at physiological concentrations. The second, called 'phy', supplements m10 with an additional crowder protein to elicit macromolecular crowding effect. The main protease (M
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Coronavirus 3C Proteases ; Molecular Dynamics Simulation ; Peptide Hydrolases ; Molecular Docking Simulation ; Protease Inhibitors
Chemical Substances	3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Peptide Hydrolases (EC 3.4.-) ; Protease Inhibitors
Language	English
Publishing date	2021-10-26
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1993342
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