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  1. 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Immunohistochemical expression of H3.3 G34W in 100 giant cell tumors of bone and its diagnostic mimics, including its value in resolving uncommon diagnostic scenarios: A single institutional study at a tertiary cancer referral center, India.

    Rekhi, Bharat / Dave, Vinayak / Butle, Ashwin / Dharavath, Bhasker / Khetale, Sonali / Redhu, Archana K / Singh, Rudransh / Dutt, Amit

    Indian journal of pathology & microbiology

    2024  

    Abstract: Background: There can be a diagnostic challenge in differentiating giant cell tumor of bone (GCTB) from its mimics. Lately, histone H3F3A (Histone 3.3) G34W has been identified as a promising immunohistochemical marker.: Aims: This study was aimed at ...

    Abstract Background: There can be a diagnostic challenge in differentiating giant cell tumor of bone (GCTB) from its mimics. Lately, histone H3F3A (Histone 3.3) G34W has been identified as a promising immunohistochemical marker.
    Aims: This study was aimed at evaluating H3.3 G34W immunostaining in 100 GCTBs, including its value in resolving diagnostic dilemmas.
    Materials and methods: Immunohistochemical staining for H3.3 G34W was graded in terms of staining intensity (1+ to 3+) and the percentage of tumor cells showing crisp nuclear staining.
    Results: One hundred GCTBs occurred in 58 males and 42 females (M: F ratio = 1.3), of 7-66 years age (average = 31.3, median = 28), commonly in distal femur (26), followed by proximal tibia (17), distal radius (12), proximal humerus (7), metacarpals (7), sacrum (6), proximal fibula (6), and relatively unusual sites (19), including a single multicentric case. Out of 92 GCTBs, wherein H3.3 G34W immunostaining worked, 81 (88.1%) showed positive staining in the mononuclear cells, including tumors with fibrous histiocytoma-like areas, sparing osteoclast-like giant cells, with 3+ staining intensity in 65/81 (80%) tumors. All 7/7 (100%) malignant GCTBs showed positive staining, including the pleomorphic/sarcomatous cells. All 7/7 (100%) metastatic GCTBs showed positive immunostaining. Seven out of 10 post-denosumab treated GCTBs showed positive H3.3 G34W immunostaining in the residual mononuclear cells. None of the other 37 "giant cell-rich" lesions displayed H3.3 G34W immunostaining. Four of 9 GCTBs tested for H3.3 G34W mutation showed positive results.
    Conclusions: The diagnostic sensitivity and specificity of H3.3 G34W for GCTB were 88.1% and 100%, respectively. This constitutes one of the first reports from our country, further validating the diagnostic value of H3.3 G34W in differentiating GCTB, including metastatic and malignant forms from its mimics, including small biopsy samples. Its value in various diagnostic dilemmas is presented and utility in identifying residual tumor cells in post-denosumab treated GCTBs is worth exploring.
    Language English
    Publishing date 2024-02-12
    Publishing country India
    Document type Journal Article
    ZDB-ID 197621-7
    ISSN 0974-5130 ; 0377-4929
    ISSN (online) 0974-5130
    ISSN 0377-4929
    DOI 10.4103/ijpm.ijpm_886_23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome.

    Desai, Sanket / Rashmi, Sonal / Rane, Aishwarya / Dharavath, Bhasker / Sawant, Aniket / Dutt, Amit

    Briefings in bioinformatics

    2021  Volume 22, Issue 2, Page(s) 1065–1075

    Abstract: The analysis of the SARS-CoV-2 genome datasets has significantly advanced our understanding of the biology and genomic adaptability of the virus. However, the plurality of advanced sequencing datasets-such as short and long reads-presents a formidable ... ...

    Abstract The analysis of the SARS-CoV-2 genome datasets has significantly advanced our understanding of the biology and genomic adaptability of the virus. However, the plurality of advanced sequencing datasets-such as short and long reads-presents a formidable computational challenge to uniformly perform quantitative, variant or phylogenetic analysis, thus limiting its application in public health laboratories engaged in studying epidemic outbreaks. We present a computational tool, Infectious Pathogen Detector (IPD), to perform integrated analysis of diverse genomic datasets, with a customized analytical module for the SARS-CoV-2 virus. The IPD pipeline quantitates individual occurrences of 1060 pathogens and performs mutation and phylogenetic analysis from heterogeneous sequencing datasets. Using IPD, we demonstrate a varying burden (5.055-999655.7 fragments per million) of SARS-CoV-2 transcripts across 1500 short- and long-read sequencing SARS-CoV-2 datasets and identify 4634 SARS-CoV-2 variants (~3.05 variants per sample), including 449 novel variants, across the genome with distinct hotspot mutations in the ORF1ab and S genes along with their phylogenetic relationships establishing the utility of IPD in tracing the genome isolates from the genomic data (as accessed on 11 June 2020). The IPD predicts the occurrence and dynamics of variability among infectious pathogens-with a potential for direct utility in the COVID-19 pandemic and beyond to help automate the sequencing-based pathogen analysis and in responding to public health threats, efficaciously. A graphical user interface (GUI)-enabled desktop application is freely available for download for the academic users at http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html and for web-based processing at http://ipd.actrec.gov.in/ipdweb/ to generate an automated report without any prior computational know-how.
    MeSH term(s) Computational Biology ; Genome, Viral ; Humans ; Mutation Rate ; SARS-CoV-2/genetics
    Language English
    Publishing date 2021-01-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbaa437
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Role of miR-944/MMP10/AXL- axis in lymph node metastasis in tongue cancer.

    Dharavath, Bhasker / Butle, Ashwin / Pal, Ankita / Desai, Sanket / Upadhyay, Pawan / Rane, Aishwarya / Khandelwal, Risha / Manavalan, Sujith / Thorat, Rahul / Sonawane, Kavita / Vaish, Richa / Gera, Poonam / Bal, Munita / D'Cruz, Anil K / Nair, Sudhir / Dutt, Amit

    Communications biology

    2023  Volume 6, Issue 1, Page(s) 57

    Abstract: Occult lymph-node metastasis is a crucial predictor of tongue cancer mortality, with an unmet need to understand the underlying mechanism. Our immunohistochemical and real-time PCR analysis of 208 tongue tumors show overexpression of Matrix ... ...

    Abstract Occult lymph-node metastasis is a crucial predictor of tongue cancer mortality, with an unmet need to understand the underlying mechanism. Our immunohistochemical and real-time PCR analysis of 208 tongue tumors show overexpression of Matrix Metalloproteinase, MMP10, in 86% of node-positive tongue tumors (n = 79; p < 0.00001). Additionally, global profiling for non-coding RNAs associated with node-positive tumors reveals that of the 11 significantly de-regulated miRNAs, miR-944 negatively regulates MMP10 by targeting its 3'-UTR. We demonstrate that proliferation, migration, and invasion of tongue cancer cells are suppressed by MMP10 knockdown or miR-944 overexpression. Further, we show that depletion of MMP10 prevents nodal metastases using an orthotopic tongue cancer mice model. In contrast, overexpression of MMP10 leads to opposite effects upregulating epithelial-mesenchymal-transition, mediated by a tyrosine kinase gene, AXL, to promote nodal and distant metastasis in vivo. Strikingly, AXL expression is essential and sufficient to mediate the functional consequence of MMP10 overexpression. Consistent with our findings, TCGA-HNSC data suggests overexpression of MMP10 or AXL positively correlates with poor survival of the patients. In conclusion, our results establish that the miR-944/MMP10/AXL- axis underlies lymph node metastases with potential therapeutic intervention and prediction of nodal metastases in tongue cancer patients.
    MeSH term(s) Animals ; Mice ; Lymphatic Metastasis ; Matrix Metalloproteinase 10/genetics ; MicroRNAs/genetics ; Tongue Neoplasms/genetics ; Tongue Neoplasms/pathology ; Axl Receptor Tyrosine Kinase/genetics
    Chemical Substances Matrix Metalloproteinase 10 (EC 3.4.24.22) ; MicroRNAs ; AXL receptor tyrosine kinase, mouse ; Axl Receptor Tyrosine Kinase
    Language English
    Publishing date 2023-01-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-023-04437-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Fusobacterium nucleatum

    Desai, Sanket / Dharavath, Bhasker / Manavalan, Sujith / Rane, Aishwarya / Redhu, Archana Kumari / Sunder, Roma / Butle, Ashwin / Mishra, Rohit / Joshi, Asim / Togar, Trupti / Apte, Shruti / Bala, Pratyusha / Chandrani, Pratik / Chopra, Supriya / Bashyam, Murali Dharan / Banerjee, Anirban / Prabhash, Kumar / Nair, Sudhir / Dutt, Amit

    NAR cancer

    2022  Volume 4, Issue 1, Page(s) zcac006

    Abstract: Persistent pathogen infection is a known cause of malignancy, although with sparse systematic evaluation across tumor types. We present a comprehensive landscape of 1060 infectious pathogens across 239 whole exomes and 1168 transcriptomes of breast, lung, ...

    Abstract Persistent pathogen infection is a known cause of malignancy, although with sparse systematic evaluation across tumor types. We present a comprehensive landscape of 1060 infectious pathogens across 239 whole exomes and 1168 transcriptomes of breast, lung, gallbladder, cervical, colorectal, and head and neck tumors. We identify known cancer-associated pathogens consistent with the literature. In addition, we identify a significant prevalence of
    Language English
    Publishing date 2022-03-04
    Publishing country England
    Document type Journal Article
    ISSN 2632-8674
    ISSN (online) 2632-8674
    DOI 10.1093/narcan/zcac006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2.

    Dharavath, Bhasker / Yadav, Neelima / Desai, Sanket / Sunder, Roma / Mishra, Rohit / Ketkar, Madhura / Bhanshe, Prasanna / Gupta, Anurodh / Redhu, Archana Kumari / Patkar, Nikhil / Dutt, Shilpee / Gupta, Sudeep / Dutt, Amit

    Heliyon

    2020  Volume 6, Issue 7, Page(s) e04405

    Abstract: Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically ...

    Abstract Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts-based on experiments performed by spiking total human RNA with
    Keywords covid19
    Language English
    Publishing date 2020-07-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e04405
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Cloning, localization and differential expression of Neuropeptide-Y during early brain development and gonadal recrudescence in the catfish, Clarias gariepinus.

    Sudhakumari, Cheni-Chery / Anitha, Arumugam / Murugananthkumar, Raju / Tiwari, Dinesh Kumar / Bhasker, Dharavath / Senthilkumaran, Balasubramanian / Dutta-Gupta, Aparna

    General and comparative endocrinology

    2017  Volume 251, Page(s) 54–65

    Abstract: Neuropeptide-Y (NPY) has diverse physiological functions which are extensively studied in vertebrates. However, regulatory role of NPY in relation to brain ontogeny and recrudescence with reference to reproduction is less understood in fish. Present ... ...

    Abstract Neuropeptide-Y (NPY) has diverse physiological functions which are extensively studied in vertebrates. However, regulatory role of NPY in relation to brain ontogeny and recrudescence with reference to reproduction is less understood in fish. Present report for the first time evaluated the significance of NPY by transient esiRNA silencing and also analyzed its expression during brain development and gonadal recrudescence in the catfish, Clarias gariepinus. As a first step, full-length cDNA of NPY was cloned from adult catfish brain, which shared high homology with its counterparts from other teleosts upon phylogenetic analysis. Tissue distribution revealed dominant expression of NPY in brain and testis. NPY expression increased during brain development wherein the levels were higher in 100 and 150days post hatch females than the respective age-matched males. Seasonal cycle analysis showed high expression of NPY in brain during pre-spawning phase in comparison with other reproductive phases. Localization studies exhibited the presence of NPY, abundantly, in the regions of preoptic area, hypothalamus and pituitary. Transient silencing of NPY-esiRNA directly into the brain significantly decreased NPY expression in both the male and female brain of catfish which further resulted in significant decrease of transcripts of tryptophan hydroxylase 2, catfish gonadotropin-releasing hormone (cfGnRH), tyrosine hydroxylase and 3β-hydroxysteroid dehydrogenase in brain and luteinizing hormone-β/gonadotropin-II (lh-β/GTH-II) in pituitary exhibiting its influence on gonadal axis. In addition, significant decrease of several ovary-related transcripts was observed in NPY-esiRNA silenced female catfish, indicating the plausible role of NPY in ovary through cfGnRH-GTH axis.
    Language English
    Publishing date 2017-09-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1851-x
    ISSN 1095-6840 ; 0016-6480
    ISSN (online) 1095-6840
    ISSN 0016-6480
    DOI 10.1016/j.ygcen.2017.03.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2

    Dharavath, Bhasker / Yadav, Neelima / Desai, Sanket / Sunder, Roma / Mishra, Rohit / Ketkar, Madhura / Bhanshe, Prasanna / Gupta, Anurodh / Redhu, Archana Kumari / Patkar, Nikhil / Dutt, Shilpee / Gupta, Sudeep / Dutt, Amit

    Heliyon. 2020 July, v. 6, no. 7

    2020  

    Abstract: Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically ...

    Abstract Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts—based on experiments performed by spiking total human RNA with in vitro synthesized viral transcripts. The assay was evaluated by performing 184 validations for the SARS-CoV-2 Nucleocapsid gene and human RNase P as an internal control reference gene with dilutions ranging from 1-100 ng for human RNA on a cohort of 26 clinical samples. 5 of 26 patients were confirmed to be infected with SARS-CoV-2, while 21 tested negative, consistent with the standards. The accuracy of the assay was found to be 100% sensitive and 100% specific based on the 26 clinical samples that need to be further verified using a large number of clinical samples. In summary, we present a rapid, easy to implement real-time PCR based assay with automated analysis using a novel COVID qPCR Analyzer tool with graphical user interface (GUI) to analyze the raw qRT-PCR data in an unbiased manner at a cost of under $3 per reaction and turnaround time of less than 2h, to enable in-house SARS-CoV-2 testing across laboratories.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; automation ; early diagnosis ; genes ; humans ; nucleocapsid ; quantitative polymerase chain reaction ; ribonucleases ; user interface
    Language English
    Dates of publication 2020-07
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e04405
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2

    Bhasker Dharavath / Neelima Yadav / Sanket Desai / Roma Sunder / Rohit Mishra / Madhura Ketkar / Prasanna Bhanshe / Anurodh Gupta / Archana Kumari Redhu / Nikhil Patkar / Shilpee Dutt / Sudeep Gupta / Amit Dutt

    Heliyon, Vol 6, Iss 7, Pp e04405- (2020)

    2020  

    Abstract: Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically ...

    Abstract Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts—based on experiments performed by spiking total human RNA with in vitro synthesized viral transcripts. The assay was evaluated by performing 184 validations for the SARS-CoV-2 Nucleocapsid gene and human RNase P as an internal control reference gene with dilutions ranging from 1-100 ng for human RNA on a cohort of 26 clinical samples. 5 of 26 patients were confirmed to be infected with SARS-CoV-2, while 21 tested negative, consistent with the standards. The accuracy of the assay was found to be 100% sensitive and 100% specific based on the 26 clinical samples that need to be further verified using a large number of clinical samples. In summary, we present a rapid, easy to implement real-time PCR based assay with automated analysis using a novel COVID qPCR Analyzer tool with graphical user interface (GUI) to analyze the raw qRT-PCR data in an unbiased manner at a cost of under $3 per reaction and turnaround time of less than 2h, to enable in-house SARS-CoV-2 testing across laboratories.
    Keywords Infectious disease ; Microbial genomics ; Genomics ; Molecular biology ; Virology ; Diagnostics ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99 ; covid19
    Subject code 610
    Language English
    Publishing date 2020-07-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2

    Dharavath, Bhasker / Yadav, Neelima / Desai, Sanket / Sunder, Roma / Mishra, Rohit / Ketkar, Madhura / Bhanshe, Prasanna / Gupta, Anurodh / Redhu, Archana Kumari / Patkar, Nikhil / Dutt, Shilpee / Gupta, Sudeep / Dutt, Amit

    Heliyon

    2020  Volume 6, Issue 7, Page(s) e04405

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e04405
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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