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Article ; Online: Influence of pathogens on host genome and epigenome in development of head and neck cancer.

Desai, Sanket

Cancer reports (Hoboken, N.J.)

2023 Volume 6, Issue 11, Page(s) e1846

Abstract: Background: Head and neck cancer (HNSCC) is a heterogeneous group of cancers, affecting multiple regions such as oral cavity, pharynx, larynx, and nasal region, each showing a distinct molecular profile. HNSCC accounts for more than 6 million cases ... ...

Abstract	Background: Head and neck cancer (HNSCC) is a heterogeneous group of cancers, affecting multiple regions such as oral cavity, pharynx, larynx, and nasal region, each showing a distinct molecular profile. HNSCC accounts for more than 6 million cases worldwide, soaring mainly in the developing countries. Recent findings: The aetiology of HNSCC is complex and multifactorial, involving both genetic and environmental factors. The critical role of microbiome, which includes bacteria, viruses, and fungi, is under spotlight due to the recent reports on their contribution in the development and progression of HNSCC. This review focuses on the effect of opportunistic pathogens on the host genome and epigenome, which contributes to the disease progression. Drawing parallels from the host-pathogen interactions observed in other tumour types arising from the epithelial tissue such as colorectal cancer, the review also calls attention to the potential explorations of the role of pathogens in HNSCC biology and discusses the clinical implications of microbiome research in detection and treatment of HNSCC. Conclusion: Our understanding of the genomic effects of the microbes on the disease progression and the mechanistic insights of the host-pathogen interaction will pave way to novel treatment and preventive approaches in HNSCC.
MeSH term(s)	Humans ; Squamous Cell Carcinoma of Head and Neck/genetics ; Epigenome ; Head and Neck Neoplasms/genetics ; Disease Progression
Language	English
Publishing date	2023-06-15
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2573-8348
ISSN (online)	2573-8348
DOI	10.1002/cnr2.1846
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The "Trick" Knot-A Modified Technique of the Removable "Shoelace" Knot for Temporary Ligation of the Uterine Artery at Its Origin.

Desai, Pranay / Pisat, Sanket / Desai, Saroj

Journal of minimally invasive gynecology

2022 Volume 29, Issue 12, Page(s) 1291

Abstract: Study objective: To demonstrate the "trick" knot, a technique of temporary ligation of the uterine artery at origin, a modification of the previously published "shoelace" knot.: Design: A video demonstration.: Setting: A private hospital.: ... ...

Abstract	Study objective: To demonstrate the "trick" knot, a technique of temporary ligation of the uterine artery at origin, a modification of the previously published "shoelace" knot. Design: A video demonstration. Setting: A private hospital. Intervention: Bilateral uterine arteries at origin are exposed after dissection of the peritoneum over the triangle formed by the round ligament, the infundibulopelvic ligament, and the pelvic sidewall [Video 1]. A 60-cm long free polyglactin absorbable suture with preformed knots at each end is introduced around the skeletonized uterine artery. Using a single throw, the "trick" knot is made by pulling out a loop of thread. The end is cut short, and the same suture is used to similarly ligate the other uterine artery. Each knot thus formed has a free end and a knotted end. Laparoscopic myomectomy is performed. On completion of the procedure, the knot is released by pulling the free end, restoring the blood supply to the uterus. Conclusion: Bilateral uterine artery ligation, although an effective method to curb bleeding during a laparoscopic myomectomy, when performed permanently, may lead to undesirable outcomes in women who wish to preserve fertility [1-3]. Methods for temporary ligation of the uterine artery at origin, such the removable vascular clips, are thus regarded justifiable [4]. In contrast to the removable "shoelace" knot, which uses a loop to make a throw, the technique of performing the "trick" knot mimics the steps of forming a regular intracorporeal knot [5]. This makes the latter technically easier and hence faster to perform, while still being as economic and reproducible as the former.
Language	English
Publishing date	2022-09-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2186934-0
ISSN	1553-4669 ; 1553-4650
ISSN (online)	1553-4669
ISSN	1553-4650
DOI	10.1016/j.jmig.2022.09.012
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Zs.A 4205: Show issues

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Article ; Online: Singleton mutations in large-scale cancer genome studies: uncovering the tail of cancer genome.

Desai, Sanket / Ahmad, Suhail / Bawaskar, Bhargavi / Rashmi, Sonal / Mishra, Rohit / Lakhwani, Deepika / Dutt, Amit

NAR cancer

2024 Volume 6, Issue 1, Page(s) zcae010

Abstract: Singleton or low-frequency driver mutations are challenging to identify. We present a domain driver mutation estimator (DOME) to identify rare candidate driver mutations. DOME analyzes positions analogous to known statistical hotspots and resistant ... ...

Abstract	Singleton or low-frequency driver mutations are challenging to identify. We present a domain driver mutation estimator (DOME) to identify rare candidate driver mutations. DOME analyzes positions analogous to known statistical hotspots and resistant mutations in combination with their functional and biochemical residue context as determined by protein structures and somatic mutation propensity within conserved PFAM domains, integrating the CADD scoring scheme. Benchmarked against seven other tools, DOME exhibited superior or comparable accuracy compared to all evaluated tools in the prediction of functional cancer drivers, with the exception of one tool. DOME identified a unique set of 32 917 high-confidence predicted driver mutations from the analysis of whole proteome missense variants within domain boundaries across 1331 genes, including 1192 noncancer gene census genes, emphasizing its unique place in cancer genome analysis. Additionally, analysis of 8799 TCGA (The Cancer Genome Atlas) and in-house tumor samples revealed 847 potential driver mutations, with mutations in tyrosine kinase members forming the dominant burden, underscoring its higher significance in cancer. Overall, DOME complements current approaches for identifying novel, low-frequency drivers and resistant mutations in personalized therapy.
Language	English
Publishing date	2024-03-12
Publishing country	England
Document type	Journal Article
ISSN	2632-8674
ISSN (online)	2632-8674
DOI	10.1093/narcan/zcae010
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Article ; Online: Diagnostic Biomarkers and Therapeutic Targets of Alternative Lengthening of Telomeres-Positive Cancers.

Singh, Manrose / MacKenzie, Danny / Desai, Sanket / Batista, Noelle / Zhang, Dong

Genetic testing and molecular biomarkers

2023 Volume 27, Issue 4, Page(s) 123–125

MeSH term(s)	Humans ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/therapy ; Telomere/genetics ; Telomere/metabolism ; Biomarkers ; Telomerase/genetics ; Telomerase/metabolism
Chemical Substances	Biomarkers ; Telomerase (EC 2.7.7.49)
Language	English
Publishing date	2023-04-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2486664-7
ISSN	1945-0257 ; 1945-0265
ISSN (online)	1945-0257
ISSN	1945-0265
DOI	10.1089/gtmb.2023.29069.mas
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Zs.A 5195: Show issues

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Article ; Online: Corrigendum to "Same-Day Discharge After Outpatient PCI in a VA Hospital: Shared Decision Making and the VA MISSION Act" [Cardiovasc Revasc Med (2020) 1369-1373].

Gokhale, Sanket / Desai, Binnie / Twing, Aamir / Dickens, Helena / Shroff, Adhir

Cardiovascular revascularization medicine : including molecular interventions

2021 Volume 37, Page(s) 158

Language	English
Publishing date	2021-10-07
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2212113-4
ISSN	1878-0938 ; 1553-8389
ISSN (online)	1878-0938
ISSN	1553-8389
DOI	10.1016/j.carrev.2021.09.014
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Article: Recurrent UBE3C-LRP5 translocations in head and neck cancer with therapeutic implications.

Dharavath, Bhasker / Butle, Ashwin / Chaudhary, Akshita / Pal, Ankita / Desai, Sanket / Chowdhury, Aniket / Thorat, Rahul / Upadhyay, Pawan / Nair, Sudhir / Dutt, Amit

NPJ precision oncology

2024 Volume 8, Issue 1, Page(s) 63

Abstract: Head and neck cancer is a major cause of morbidity and mortality worldwide. The identification of genetic alterations in head and neck cancer may improve diagnosis and treatment outcomes. In this study, we report the identification and functional ... ...

Abstract	Head and neck cancer is a major cause of morbidity and mortality worldwide. The identification of genetic alterations in head and neck cancer may improve diagnosis and treatment outcomes. In this study, we report the identification and functional characterization of UBE3C-LRP5 translocation in head and neck cancer. Our whole transcriptome sequencing and RT-PCR analysis of 151 head and neck cancer tumor samples identified the LRP5-UBE3C and UBE3C-LRP5 fusion transcripts in 5.3% of patients of Indian origin (n = 151), and UBE3C-LRP5 fusion transcripts in 1.2% of TCGA-HNSC patients (n = 502). Further, whole genome sequencing identified the breakpoint of UBE3C-LRP5 translocation. We demonstrate that UBE3C-LRP5 fusion is activating in vitro and in vivo, and promotes the proliferation, migration, and invasion of head and neck cancer cells. In contrast, depletion of UBE3C-LRP5 fusion suppresses the clonogenic, migratory, and invasive potential of the cells. The UBE3C-LRP5 fusion activates the Wnt/β-catenin signaling by promoting nuclear accumulation of β-catenin, leading to upregulation of Wnt/β-catenin target genes, MYC, CCND1, TCF4, and LEF1. Consistently, treatment with the FDA-approved drug, pyrvinium pamoate, significantly reduced the transforming ability of cells expressing the fusion protein and improved survival in mice bearing tumors of fusion-overexpressing cells. Interestingly, fusion-expressing cells upon knockdown of CTNNB1, or LEF1 show reduced proliferation, clonogenic abilities, and reduced sensitivity to pyrvinium pamoate. Overall, our study suggests that the UBE3C-LRP5 fusion is a promising therapeutic target for head and neck cancer and that pyrvinium pamoate may be a potential drug candidate for treating head and neck cancer harboring this translocation.
Language	English
Publishing date	2024-03-04
Publishing country	England
Document type	Journal Article
ISSN	2397-768X
ISSN	2397-768X
DOI	10.1038/s41698-024-00555-4
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Article ; Online: Intravascular Microaxial Left Ventricular Assist Device vs Intra-aortic Balloon Pump for Cardiogenic Shock-Reply.

Dhruva, Sanket S / Mortazavi, Bobak J / Desai, Nihar R

JAMA

2020 Volume 324, Issue 3, Page(s) 303–304

MeSH term(s)	Heart-Assist Devices ; Humans ; Intra-Aortic Balloon Pumping ; Myocardial Infarction ; Shock, Cardiogenic
Language	English
Publishing date	2020-07-21
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	2958-0
ISSN	1538-3598 ; 0254-9077 ; 0002-9955 ; 0098-7484
ISSN (online)	1538-3598
ISSN	0254-9077 ; 0002-9955 ; 0098-7484
DOI	10.1001/jama.2020.7560
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Article ; Online: Trends in Spending and Claims for P2Y12 Inhibitors by Medicare and Medicaid From 2015 to 2020.

Essa, Mohammed / Ross, Joseph S / Dhruva, Sanket S / Desai, Nihar R / Yeh, Robert W / Faridi, Kamil F

Journal of the American Heart Association

2023 Volume 12, Issue 8, Page(s) e028869

MeSH term(s)	Aged ; Humans ; United States ; Medicaid ; Medicare ; Platelet Aggregation Inhibitors ; Clopidogrel ; Prasugrel Hydrochloride ; Purinergic P2Y Receptor Antagonists ; Acute Coronary Syndrome ; Percutaneous Coronary Intervention ; Treatment Outcome
Chemical Substances	Platelet Aggregation Inhibitors ; Clopidogrel (A74586SNO7) ; Prasugrel Hydrochloride (G89JQ59I13) ; Purinergic P2Y Receptor Antagonists
Language	English
Publishing date	2023-04-12
Publishing country	England
Document type	Letter ; Research Support, N.I.H., Extramural
ZDB-ID	2653953-6
ISSN	2047-9980 ; 2047-9980
ISSN (online)	2047-9980
ISSN	2047-9980
DOI	10.1161/JAHA.122.028869
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Article ; Online: IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome.

Desai, Sanket / Rane, Aishwarya / Joshi, Asim / Dutt, Amit

BMC bioinformatics

2021 Volume 22, Issue 1, Page(s) 247

Abstract: Background: Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SARS-CoV-2 sequence data ... ...

Abstract	Background: Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SARS-CoV-2 sequence data generated at an unprecedented rate. Results: We present an updated version of the SARS-CoV-2 analysis module of our automated computational pipeline, Infectious Pathogen Detector (IPD) 2.0, to perform genomic analysis to understand the variability and dynamics of the virus. It adopts the recent clade nomenclature and demonstrates the clade prediction accuracy of 92.8%. IPD 2.0 also contains a SARS-CoV-2 updater module, allowing automatic upgrading of the variant database using genome sequences from GISAID. As a proof of principle, analyzing 208,911 SARS-CoV-2 genome sequences, we generate an extensive database of 2.58 million sample-wise variants. A comparative account of lineage-specific mutations in the newer SARS-CoV-2 strains emerging in the UK, South Africa and Brazil and data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution. Conclusions: A novel and dynamic feature of the SARS-CoV-2 module of IPD 2.0 makes it a contemporary tool to analyze the diverse and growing genomic strains of the virus and serve as a vital tool to help facilitate rapid genomic surveillance in a population to identify variants involved in breakthrough infections. IPD 2.0 is freely available from http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html and the web-application is available at http://ipd.actrec.gov.in/ipdweb/ .
MeSH term(s)	Brazil ; COVID-19 ; Genome, Viral ; Humans ; Mutation ; Phylogeny ; SARS-CoV-2
Language	English
Publishing date	2021-05-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-021-04172-x
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Article ; Online: IPD 2.0

Sanket Desai / Aishwarya Rane / Asim Joshi / Amit Dutt

BMC Bioinformatics, Vol 22, Iss 1, Pp 1-

To derive insights from an evolving SARS-CoV-2 genome

2021 Volume 9

Abstract: Abstract Background Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SARS-CoV-2 sequence data ...

Abstract	Abstract Background Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SARS-CoV-2 sequence data generated at an unprecedented rate. Results We present an updated version of the SARS-CoV-2 analysis module of our automated computational pipeline, Infectious Pathogen Detector (IPD) 2.0, to perform genomic analysis to understand the variability and dynamics of the virus. It adopts the recent clade nomenclature and demonstrates the clade prediction accuracy of 92.8%. IPD 2.0 also contains a SARS-CoV-2 updater module, allowing automatic upgrading of the variant database using genome sequences from GISAID. As a proof of principle, analyzing 208,911 SARS-CoV-2 genome sequences, we generate an extensive database of 2.58 million sample-wise variants. A comparative account of lineage-specific mutations in the newer SARS-CoV-2 strains emerging in the UK, South Africa and Brazil and data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution. Conclusions A novel and dynamic feature of the SARS-CoV-2 module of IPD 2.0 makes it a contemporary tool to analyze the diverse and growing genomic strains of the virus and serve as a vital tool to help facilitate rapid genomic surveillance in a population to identify variants involved in breakthrough infections. IPD 2.0 is freely available from http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html and the web-application is available at http://ipd.actrec.gov.in/ipdweb/ .
Keywords	SARS-CoV-2 ; Pathogen analysis pipeline ; Phylogenetic clade analysis ; Next-generation sequencing ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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