Browsing by Author "Bose, Pinaki"

Now showing 1 - 9 of 9
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    Bax expression measured by AQUAnalysis is an independent prognostic marker in oral squamous cell carcinoma
    (BioMed Central, 2012-08-01) Dort, Joseph C; Bose, Pinaki; Klimowicz, Alexander C; Kornaga, Elizabeth; Petrillo, Stephanie K; Matthews,T Wayne; Chandarana, Shamir; Magliocco, Anthony M; Brockton, Nigel T; Medicine
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    Development, Validation, and Implementation of Cytologically Indeterminate Thyroid Nodule Molecular Testing
    (2024-04-17) Stewardson, Paul; Eszlinger, Markus; Paschke, Ralf; Demetrick, Douglas J.; Bose, Pinaki; Morris, Donald; Wiseman, Sam M.
    Introduction: Genetic testing is increasingly used to diagnose or rule out thyroid cancer in indeterminate fine-needle aspirations. The research in this dissertation aimed to locally develop and validate a novel molecular test (ThyroSPEC), explore ancillary risk stratification, and measure the impacts of introducing molecular testing at the population level including for therapy selection. Methods: Comprehensive clinical data were collected prospectively for the first 615 consecutive patients with indeterminate thyroid nodules (ITNs) in a centralized healthcare system following implementation of ThyroSPEC. Accuracy of molecular testing and the impact of the introduction of molecular testing were calculated. A 16-miRNA panel was developed and validated in 127 air-dried smear indeterminate thyroid FNAC specimens and 157 liquid thyroid FNAC specimens. In a separate study on therapy selection, 86 high risk thyroid cancer patients were retrospectively identified and screened for NTRK fusions and RET fusions/mutations with molecular tests including ThyroSPEC. Results: A locally developed, low-cost molecular test achieved an NPV of 76-91% and a PPV of 46-65% in ITNs using only residual biopsy material. Following implementation of molecular testing, diagnostic yield increased 14% (p=0.2442) and repeat FNAs decreased by 24% (p=0.05). A miRNA expression classifier achieved sensitivity of 100% and specificity of 83% in the air-dried smear sample type as an adjunct to ThyroSPEC. However, miRNA expression was indistinguishable between benign and malignant tumors in local liquid cytology specimens. Molecular testing of advanced thyroid cancer patients resulted in the detection of NTRK or RET fusions in up to 40% of systematically defined patient subsets. Conclusion: Introduction of molecular testing offers clinical benefits, even in a low resection rate setting, and directly influences surgical decision-making. ThyroSPEC improved preoperative risk stratification of indeterminate thyroid nodules but requires further stratification for negative test results and intermediate risk mutations. This research also presented a novel miRNA expression classifier that could be used to incrementally risk stratify indeterminate air-dried smear FNAC and suggests that methanol-based preservation of thyroid liquid FNAC may hinder use of miRNA expression levels for molecular diagnostics. Our findings also indicate that ThyroSPEC may be suitable to detect NTRK and RET fusions in advanced thyroid cancers.
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    Identification of Somatic Mutational Patterns with Biological and Clinical Significance in Solid and Hematological Malignancies
    (2024-01-17) McNeil, Reid Evan; Bose, Pinaki; Khan, Faisal; Storek, Jan; Lynch, Tarah
    Cancers use Darwinian evolution to naturally select for advantageous DNA alterations that allow these malignancies to escape normal biological control mechanisms. Advantageous alterations are known as driver mutations that modify cellular phenotype causing cancer cells to proliferate, invade adjacent tissues, and metastasize to other organs. Even across very different types of cancers, DNA alteration events are an underlying commonality. Using DNA alterations as a lens to analyze cancers can potentially identify cross cancer biomarkers implicated in disease development, progression, prognostication, and therapeutic drug targeting and response. In this MSc thesis, we hypothesis that in squamous cell carcinomas a subtype of alteration called DNA amplification events can modulate tumor biology through gene expression, and that point mutations in myeloid malignancies can predict clinical outcomes like disease relapse after bone marrow transplant. Aim one of my thesis investigated DNA amplifications to identify how they modulate mRNA and protein expression in head and neck and lung SCCs. Using genomic, transcriptomic, and proteomics data we identify amplification driven expression programs with biological and clinical significance in SCCs. Aim two of my thesis investigated point mutation profiles of myeloid malignancies using the Illumina TruSight Tumor (TST) Myeloid sequencing panel and machine learning analysis. Mutational landscape analysis of all myeloid samples annotated for DNA mutations of clinical relevance. Machine learning analysis was used point mutation profiles to predict relapse status of patients after transplant. The main research findings indicated that in SCCs, the 3q22-29 and 11q13 DNA amplifications were the top events in HNSCs and LUSCs. Several genes from 3q22-29 (ABCC5, ALG3, FXR1, TFRC, and RFC4) and 11q13 amplified regions (CTTN, FADD, and PPFIA1) were overexpressed on the mRNA and protein level. These genes were majority expressed in tumoral tissue and cancerous cells, and when overexpressed led to worse patient survival. The 3q22-29 amplified samples were negatively correlated with immune related pathways in the tumor microenvironment. Specifically, TRAIL and IFNG signaling levels were lower in 3q22-29 amplified samples, along with lower levels of immune cell infiltration of natural killer and cytotoxic cells. In myeloid malignancies, point mutations of clinical significance were identified, the most common mutations across 545 AML samples were TET2, ASXL1, and DNMT3A. The TET2 gene modulates DNA methylation levels and mutations to this gene trigger malignant transformation of myeloid progenitor cells and development of cancer. Patients with TET2 mutations can be treated with azacitidine in combination with chemotherapies to increase overall patient survival. The machine learning analysis of mutation profiles of myeloid patients who went through a bone marrow transplant were able to predict relapse status of patients from mutations profiles generated at disease diagnosis. The random forest model was the best performing model (AUC = 0.845) to predict relapse status after transplantation. Altogether, this analysis demonstrated the ability and importance DNA alterations have in diseases like cancer.
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    Ing1 protein function in apoptosis and senescence
    (2010) Bose, Pinaki; Riabowol, Karl T.
    ING proteins act as readers and writers of the histone epigenetic code, affecting DNA repair, cellular senescence and apoptosis. My doctoral research focused upon understanding the molecular mechanisms underlying the involvement of ING1 in stress signaling. My work began with elucidating novel interacting partners of ING proteins using a cross-species (yeast, fly, and human) bioinformatics-based approach. We identified 381 proteins in a yeast interactome analysis that interacted with ING and also had human counterparts. I then biochemically confirmed the validity of the screen, showing that ING1 interacts with three proteins involved in stress signaling: p38MAPK, MEKK4 and RAD50. Our bioinformatics screen indicated that ING proteins in yeast interact with several mitochondrial proteins. Given that ING1 and p53 can functionally interact and that p53 has a transcription-independent role in apoptosis in the mitochondria, I asked if ING1 might also function outside the nucleus. We found that ING1 translocates to the mitochondria in primary fibroblasts and in established epithelial cell lines in response to apoptosis-inducing stimuli, independent of cellular p53 status. I also determined that endogenous ING1 specifically interacts with the pro-apoptotic BCL2 machinery in the mitochondria, suggesting a model in which the ING1-BAX interaction promotes mitochondrial membrane permeability, thereby promoting apoptosis. Since cellular aging is widely thought to represent a form of telomere­induced stress, I also investigated if ING1 interacted with the telomeric protein TRF2 that is involved in DNA damage and repair pathways. We found that, indeed, endogenous ING1 protein interacted with TRF2. Interestingly, TRF2 protein levels were also seen to decrease in senescent primary fibroblasts without a concomitant decrease in TRF2 mRNA levels. Further, our data provides evidence for the fact that telomere binding of TRF2 is required for its stability thereby indicating that a decrease in TRF2 levels might affect the induction of senescence caused by telomere attrition. Lastly, I characterized the DNA damage response in young versus senescent fibroblasts in which ING1 levels are altered, using 53BP1 focus formation as a surrogate marker for DNA damage. I found that decreased ability of senescent cells to process DNA damage foci correlates well with the loss of ING1 b during senescence, consistent with a role for ING1 bin DNA repair.
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    Interspecies data mining to predict novel ING-protein interactions in human
    (BioMed Central, 2008) Gordon, Paul; Soliman, Mohamed A; Bose, Pinaki; Sensen, Christoph W; Riabowol, Karl T.
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    Multi-tyrosine kinase inhibitors in preclinical studies for pediatric CNS AT/RT: Evidence for synergy with Topoisomerase-I inhibition
    (BioMed Central, 2011-12-29) Jayanthan, Aarthi; Bernoux, Delphine; Bose, Pinaki; Riabowol, Karl; Narendran, Aru
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    Polo-like kinase-1 (PLK-1) inhibitors as novel therapeutics in oral squamous cell carcinoma
    (2019-07-22) Sarkar, Subhanwita; Bose, Pinaki; Narendran, Aru; Bonni, Dr. Shirin; Childs, Sarah J.
    Polo-like kinase-1 (PLK-1) belongs to a family of conserved serine/threonine kinases and is an oncogenic protein in many cancers. Therefore, PLK-1 is an attractive therapeutic target and clinical trials are ongoing to test the efficacy of PLK-1 inhibitors in several cancer-types. Oral squamous cell carcinoma (OSCC) is a common head and neck cancer. OSCC is associated with frequent recurrences after initial curative therapy and overall poor prognosis. We analysed RNA sequencing data from The Cancer Genome Atlas (TCGA) and found that PLK-1 mRNA levels are elevated in OSCC compared to normal oral cavity squamous epithelium and high PLK-1 expression in OSCC is associated with worse survival. Based on these results, we tested the efficacy of PLK-1 inhibitors in a panel of ten OSCC cell lines. The PLK-1 inhibitor, volasertib effected cell death at low nanomolar concentrations in most tested OSCC cell lines but not in normal oral keratinocytes. Flowcytometry analysis showed that volasertib induces G2/M arrest in sensitive cell lines. Western blot analysis showed that levels of total PLK-1 and phospho PLK-1 were reduced after volasertib treatment in sensitive cell lines. Volasertib also triggered apoptosis confirmed by the cleavage of PARP and Caspase 3. Cell lines resistant to volasertib did not show any alteration in total PLK-1 and pPLK-1 after volasertib treatment. Post-operative radiotherapy is a common treatment modality in OSCC patients. In two OSCC cell lines that were refractory to volasertib treatment, a combination of volasertib and γ-radiation significantly lowered cell survival compared to volasertib or γ-radiation alone. Combination therapy with γ-radiation and volasertib in resistant cell lines resulted in S-phase arrest. Western blot analysis showed a significant reduction of total PLK-1 and pPLK-1 after combinatorial therapy. Apoptosis was induced in volasertib resistant cells as a result of combination therapy. Taken together, these in vitro studies establish the rationale for further investigation of volasertib efficacy in orthotopic OSCC xenograft models and clinical trials.
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    REAP: A two minute cell fractionation method
    (BioMed Central, 2010-11-10) Suzuki, Keiko; Bose, Pinaki; Leong-Quong, Rebecca Y. Y.; Fujita, Donald J.; Riabowol, Karl T.
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    The Identification of Target Gene to Increase Immunotherapy Response in Patients with Solid Tumors using Experimental and Computational Approaches
    (2023-07) Nasr, Sahar; Wang, Edwin; Mahoney, Douglas; Bathe, Oliver; Bose, Pinaki
    Conventional cancer therapies have limitations which can lead to high recurrence rates and reduced quality of life. Immune checkpoint inhibitors (ICI) have been shown to have more durable responses and fewer side effects. This makes them an alternative treatment for solid tumors like bladder cancer and MSI-high colorectal carcinoma. However, many patients do not respond to ICI or develop resistance due to factors such as the absence of CD8+ T cells in the tumor microenvironment, dysfunctional CD8+ T cells, and impaired tumor-specific memory T cells generation. This study shows that inhibiting Sun1 enhances tumor-infiltrating lymphocyte infiltration, inhibits tumor growth in mice, and improves the response to anti-PD-1 treatment. Although the role of Sun1 in chromatin organization and gene expression regulation is not fully clear, its inhibition can upregulate the immune-related genes within the knockout cell lines. This approach suggests a potential strategy for enhancing ICI effectiveness in cancer treatment.