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Article
Open AccessMethionine-producing tumor micro(be) environment fuels growth of solid tumors
Recent studies have uncovered the near-ubiquitous presence of microbes in solid tumors of diverse origins. Previous literature has shown the impact of specific bacterial species on the progression of cancer. W...
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Article
Plasma membrane V-ATPase controls oncogenic RAS-induced macropinocytosis
Oncogenic activation of RAS is associated with the acquisition of a unique set of metabolic dependencies that contribute to tumour cell fitness. Cells that express oncogenic RAS are able to internalize and deg...
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Article
Pre-neoplastic pancreas cells enter a partially mesenchymal state following transient TGF-β exposure
Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease and a major health problem in the United States. While the cytokine TGF-β has been implicated in PDAC development, it can exert both pro-tumorigenic ...
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Article
Open AccessDecreased microbiome diversity in the HIV small airway epithelium
Persons living with human immunodeficiency virus (PLWH) face an increased burden of chronic obstructive pulmonary disease (COPD). Repeated pulmonary infections, antibiotic exposures, and immunosuppression may ...
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Article
Open AccessDecreased telomere length in the small airway epithelium suggests accelerated aging in the lungs of persons living with human immunodeficiency virus (HIV)
Human immunodeficiency virus (HIV) infection is associated with an increased risk of chronic obstructive pulmonary disease (COPD) independent of cigarette smoke exposure. Previous studies have demonstrated tha...
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Article
Open AccessThe bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus
Chronic Obstructive Pulmonary Disease (COPD) is an important comorbidity in patients living with human immunodeficiency virus (HIV). Previous bacterial microbiome studies have shown increased abundance of spec...
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Article
Open AccessEmerging roles of T helper 17 and regulatory T cells in lung cancer progression and metastasis
Lung cancer is a leading cause of cancer-related deaths worldwide. Lung cancer risk factors, including smoking and exposure to environmental carcinogens, have been linked to chronic inflammation. An integral f...
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Article
Open AccessUnique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology
Human PIWI-interacting RNAs (piRNAs) are known to be expressed in germline cells, functionally silencing LINEs and SINEs. Their expression patterns in somatic tissues are largely uncharted. We analyzed 6,260 h...
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Article
Open AccessSmoking status impacts microRNA mediated prognosis and lung adenocarcinoma biology
Cigarette smoke is associated with the majority of lung cancers: however, 25% of lung cancer patients are non-smokers, and half of all newly diagnosed lung cancer patients are former smokers. Lung tumors exhib...
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Article
Open AccessFrequent concerted genetic mechanisms disrupt multiple components of the NRF2 inhibitor KEAP1/CUL3/RBX1 E3-ubiquitin ligase complex in thyroid cancer
Reactive oxygen species contribute to normal thyroid function. The NRF2 oxidative response pathway is frequently and constitutively activated in multiple tumor types, including papillary thyroid carcinoma (PTC...
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Article
Open AccessAn integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer
Genomics has substantially changed our approach to cancer research. Gene expression profiling, for example, has been utilized to delineate subtypes of cancer, and facilitated derivation of predictive and progn...
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Protocol
Copy Number Variations in the Human Genome and Strategies for Analysis
The structure and sequence of the genome is immensely variable in the human population. Segmental copy number variants (CNVs) contribute to the extensive phenotypic diversity among humans and have been shown t...
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Protocol
Methylation Analysis by DNA Immunoprecipitation (MeDIP)
Alteration in epigenetic regulation of gene expression is a common event in human cancer and developmental disease. CpG island hypermethylation and consequent gene silencing is observed for many genes involved...
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Article
Open AccessSIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes
High throughput microarray technologies have afforded the investigation of genomes, epigenomes, and transcriptomes at unprecedented resolution. However, software packages to handle, analyze, and visualize data...
