Significance of bacterial and viral genotypes as a risk factor in driving cancer (Review)

Jangam, Diwash; Butzmann, Alexandra; Sridhar, Kaushik; Deresinski, Stanley C.; Banaei, Niaz; Ohgami, Robert S.

doi:10.3892/mco.2020.2043

Cited by 3 publications

(1 citation statement)

References 43 publications

(57 reference statements)

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“…We extracted DNA from formalin fixed and paraffin embedded (FFPE) tissue using the DNA Storm Kit (Cell Data Science, CA, USA). For our DNA libraries, we developed a customized SureSelect XT HS (Agilent Technologies, CA, USA) Heme Malignancies Evaluation and Infectious Detection panel (HeME-ID), which includes 354 genes that are important for lympho- or leukemogenesis in addition to 13 viruses and bacteria associated with hematolymphoid diseases ( 9 , 10 ). 100 base-pair paired-end targeted deep sequencing was performed at an average coverage depth of 1500-fold on a high-throughput sequencing platform (HiSeq4000).…”

Section: Methodsmentioning

confidence: 99%

Mutations in JAK/STAT and NOTCH1 Genes Are Enriched in Post-Transplant Lymphoproliferative Disorders

et al. 2022

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Post-transplant lymphoproliferative disorders (PTLD) are diseases occurring in immunocompromised patients after hematopoietic stem cell transplantation (HCT) or solid organ transplantation (SOT). Although PTLD occurs rarely, it may be associated with poor outcomes. In most cases, PTLD is driven by Epstein-Barr virus (EBV) infection. Few studies have investigated the mutational landscape and gene expression profile of PTLD. In our study, we performed targeted deep sequencing and RNA-sequencing (RNA-Seq) on 16 cases of florid follicular hyperplasia (FFH) type PTLD and 15 cases of other PTLD types that include: ten monomorphic (M-PTLD), three polymorphic (P-PTLD), and two classic Hodgkin lymphoma type PTLDs (CHL-PTLD). Our study identified recurrent mutations in JAK3 in five of 15 PTLD cases and one of 16 FFH-PTLD cases, as well as 16 other genes that were mutated in M-PTLD, P-PTLD, CHL-PTLD and FFH-PTLD. Digital image analysis demonstrated significant differences in single cell area, major axis, and diameter when comparing cases of M-PTLD and P-PTLD to FFH-PTLD. No morphometric relationship was identified with regards to a specific genetic mutation. Our findings suggest that immune regulatory pathways play an essential role in PTLD, with the JAK/STAT pathway affected in many PTLDs.

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Section: Methodsmentioning

confidence: 99%

Mutations in JAK/STAT and NOTCH1 Genes Are Enriched in Post-Transplant Lymphoproliferative Disorders

et al. 2022

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A Case of EBV-Negative Aggressive NK-cell Leukemia: Use of Next-Generation Sequencing in Demystifying a Diagnostic Dilemma and Guiding Clinical Care

Kennedy

Ruíz-Cordero

Jangam

et al. 2021

Clinical Lymphoma Myeloma and Leukemia

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Assessing four-dimensional CT stress maps derived from patient-specific biomechanical models of the lung with pulmonary function test data in lung cancer patients

Shiinoki

Fujimoto

Kawazoe

et al. 2023

The British Journal of Radiology

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Objectives: This study aims to retrospectively compare the stress map of the lung with pulmonary function test (PFT) results in lung cancer patients and to evaluate the potential of the stress map as an imaging biomarker for chronic obstructive pulmonary disease (COPD). Methods: Twenty-five lung cancer patients with pre-treatment 4D-CT and PFT data were retrospectively analysed. PFT metrics were used to diagnose obstructive lung disease. For each patient, forced expiratory volume in 1 s (FEV1 % predicted) and the ratio of FEV1 and forced vital capacity (FEV1/FVC) were recorded. Four-dimensional CT and biomechanical model-deformable image registration (BM-DIR) were used to obtain the lung stress map. The relationship between the mean of the total lung stress and PFT data was evaluated, and the COPD classification grade was also evaluated. Results: The mean values of the total lung stress and FEV1 % predicted showed a significant strong correlation [R = 0.833, (p < 0.001)]. The mean values and FEV1/FVC showed a significant strong correlation [R = 0.805, (p < 0.001)]. For the total lung stress, the area under the curve and the optimal cut-off value were 0.94 and 510.8 Pa for the classification of normal or abnormal lung function, respectively. Conclusions: This study has demonstrated the potential of lung stress maps based on BM-DIR to accurately assess lung function by comparing them with PFT data. Advances in knowledge: The derivation of stress map directly from 4D-CT is novel method. The BM-DIR-based lung stress map can provide an accurate assessment of lung function.

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Significance of bacterial and viral genotypes as a risk factor in driving cancer (Review)

Cited by 3 publications

References 43 publications

Mutations in JAK/STAT and NOTCH1 Genes Are Enriched in Post-Transplant Lymphoproliferative Disorders

Mutations in JAK/STAT and NOTCH1 Genes Are Enriched in Post-Transplant Lymphoproliferative Disorders

A Case of EBV-Negative Aggressive NK-cell Leukemia: Use of Next-Generation Sequencing in Demystifying a Diagnostic Dilemma and Guiding Clinical Care

Assessing four-dimensional CT stress maps derived from patient-specific biomechanical models of the lung with pulmonary function test data in lung cancer patients

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