scholarly journals Review On Feature Selection Techniques And The Impact Of Svm For Cancer Classification Using Gene Expression Profile

2011 ◽  
Vol 2 (3) ◽  
pp. 16-27 ◽  
Author(s):  
Victo Sudha George ◽  
Cyril Raj
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Cancer Classification ◽  
The Impact ◽  
Feature Selection Techniques

scholarly journals TFEB is a master regulator of tumor-associated macrophages in breast cancer

2020 ◽  
Vol 8 (1) ◽  
pp. e000543 ◽  
Author(s):  
Yong Li ◽  
Johnie Hodge ◽  
Qing Liu ◽  
Junfeng Wang ◽  
Yuzhen Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Tumor Growth ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Breast Tumor ◽  
Tumor Development ◽  
Tumor Associated Macrophages ◽  
And Function ◽  
The Impact

BackgroundTumor-associated macrophages (TAMs) play key roles in the development of many malignant solid tumors including breast cancer. They are educated in the tumor microenvironment (TME) to promote tumor growth, metastasis, and therapy resistance. However, the phenotype of TAMs is elusive and how to regulate them for therapeutic purpose remains unclear; therefore, TAM-targeting therapies have not yet achieved clinical success. The purposes of this study were to examine the role of transcription factor EB (TFEB) in regulating TAM gene expression and function and to determine if TFEB activation can halt breast tumor development.MethodsMicroarrays were used to analyze the gene expression profile of macrophages (MΦs) in the context of breast cancer and to examine the impact of TFEB overexpression. Cell culture studies were performed to define the mechanisms by which TFEB affects MΦ gene expression and function. Mouse studies were carried out to investigate the impact of MΦ TFEB deficiency or activation on breast tumor growth. Human cancer genome data were analyzed to reveal the prognostic value of TFEB and its regulated genes.ResultsTAM-mimic MΦs display a unique gene expression profile, including significant reduction in TFEB expression. TFEB overexpression favorably modulates TAM gene expression through multiple signaling pathways. Specifically, TFEB upregulates suppressor of cytokine signaling 3 (SOCS3) and peroxisome proliferator-activated receptor γ (PPARγ) expression and autophagy/lysosome activities, inhibits NLRP3 (NLR Family Pyrin Domain Containing 3) inflammasome and hypoxia-inducible factor (HIF)-1α mediated hypoxia response, and thereby suppresses an array of effector molecules in TAMs including arginase 1, interleukin (IL)-10, IL-1β, IL-6 and prostaglandin E2. MΦ-specific TFEB deficiency promotes, while activation of TFEB using the natural disaccharide trehalose halts, breast tumor development by modulating TAMs. Analysis of human patient genome database reveals that expression levels of TFEB, SOCS3 and PPARγ are positive prognostic markers, while HIF-1α is a negative prognostic marker of breast cancer.ConclusionsOur study identifies TFEB as a master regulator of TAMs in breast cancer. TFEB controls TAM gene expression and function through multiple autophagy/lysosome-dependent and independent pathways. Therefore, pharmacological activation of TFEB would be a promising therapeutic approach to improve the efficacy of existing treatment including immune therapies for breast cancer by favorably modulating TAM function and the TME.

scholarly journals Prognostic Significance of Expression of a Single MicroRNA,miR-181a, in Cytogenetically Normal Acute Myeloid Leukemia: A Cancer and Leukemia Group B Study

2010 ◽  
Vol 28 (36) ◽  
pp. 5257-5264 ◽  
Author(s):  
Sebastian Schwind ◽  
Kati Maharry ◽  
Michael D. Radmacher ◽  
Krzysztof Mrózek ◽  
Kelsi B. Holland ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Myeloid Leukemia ◽  
Prognostic Significance ◽  
Comprehensive Cancer Center ◽  
Wild Type ◽  
The Impact ◽  
Acute Myeloid

PurposeTo evaluate the prognostic significance of expression levels of a single microRNA, miR-181a, in the context of established molecular markers in cytogenetically normal acute myeloid leukemia (CN-AML), and to gain insight into the leukemogenic role of miR-181a.Patients and MethodsmiR-181a expression was measured in pretreatment marrow using Ohio State University Comprehensive Cancer Center version 3.0 arrays in 187 younger (< 60 years) adults with CN-AML. Presence of other molecular prognosticators was assessed centrally. A gene-expression profile associated with miR-181a expression was derived using microarrays and evaluated by Gene-Ontology analysis.ResultsHigher miR-181a expression associated with a higher complete remission (CR) rate (P = .04), longer overall survival (OS; P = .01) and a trend for longer disease-free survival (DFS; P = .09). The impact of miR-181a was most striking in poor molecular risk patients with FLT3-internal tandem duplication (FLT3-ITD) and/or NPM1 wild-type, where higher miR-181a expression associated with a higher CR rate (P = .009), and longer DFS (P < .001) and OS (P < .001). In multivariable analyses, higher miR-181a expression was significantly associated with better outcome, both in the whole patient cohort and in patients with FLT3-ITD and/or NPM1 wild-type. These results were also validated in an independent set of older (≥ 60 years) patients with CN-AML. A miR-181a-associated gene-expression profile was characterized by enrichment of genes usually involved in innate immunity.ConclusionTo our knowledge, we provide the first evidence that the expression of a single microRNA, miR-181a, is associated with clinical outcome of patients with CN-AML and may refine their molecular risk classification. Targeted treatments that increase endogenous levels of miR-181a might represent novel therapeutic strategies.

scholarly journals Effects of histamine and various histamine receptor antagonists on gene expression profiles of macrophages during compressive strain

2021 ◽  
Author(s):  
Agnes Schröder ◽  
Catharina Petring ◽  
Anna Damanaki ◽  
Jonathan Jantsch ◽  
Peter Proff ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Periodontal Ligament ◽  
Tooth Movement ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Compressive Strain ◽  
Orthodontic Tooth Movement ◽  
The Impact

Abstract Purpose Tissue hormone histamine can accumulate locally within the periodontal ligament via nutrition or may be released during allergic reactions by mast cells, which may have an impact on orthodontic tooth movement. In addition to periodontal ligament fibroblasts, cells of the immune system such as macrophages are exposed to compressive strain. The aim of this study was thus to investigate the impact of histamine on the gene expression profile of macrophages in the context of simulated orthodontic compressive strain. Methods Macrophages were incubated with different histamine concentrations (50, 100, 200 µM) for 24 h and then either left untreated or compressed for another 4 h. To assess the role of different histamine receptors, we performed experiments with antagonists for histamine 1 receptor (cetirizine), histamine 2 receptor (ranitidine) and histamine 4 receptor (JNJ7777120) under control and pressure conditions. We tested for lactate dehydrogenase release and analyzed the expression of genes involved in inflammation and bone remodeling by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Results Histamine elevated gene expression of tumor necrosis factor under control conditions and in combination with pressure application. Increased prostaglandin-endoperoxide synthase‑2 mRNA was observed when histamine was combined with compressive force. Interleukin‑6 gene expression was not affected by histamine treatment. In macrophages, compressive strain increased osteoprotegerin gene expression. Histamine further elevated this effect. Most of the observed histamine effects were blocked by the histamine 1 receptor antagonist cetirizine. Conclusions Histamine has an impact on the gene expression profile of macrophages during compressive strain in vitro, most likely having an impairing effect on orthodontic tooth movement by upregulation of osteoprotegerin expression.

scholarly journals MON-031 A Gene Expression Profile of the Adolescent Breast and the Impact of Obesity

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Dennis Y Akrobetu ◽  
Adam B Burkholder ◽  
Thai-Vu T Ton ◽  
Susan Kim ◽  
Arun Pandiri ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Ethinyl Estradiol ◽  
Breast Development ◽  
Aromatase Activity ◽  
Adult Women ◽  
Extracellular Matrix Components ◽  
The Impact ◽  
Upstream Regulators

Abstract Environmental exposures that occur early in life affect breast development and breast cancer (BC) risk in adulthood. Puberty is one such developmental ‘window of susceptibility’ when estrogen (E) stimulates breast adipocytes and stromal and epithelial cells to proliferate at an exponential rate, making them vulnerable to carcinogens. Excess adiposity during adulthood may increase BC risk through obesity-associated inflammation and/or aromatase activity, which increases local E levels. While obesity during puberty might be expected to also increase future BC risk, epidemiological studies suggest that pediatric obesity may actually be protective. The current studies investigated the gene expression profile of the normal adolescent breast and how early life factors such as obesity may influence these profiles. We performed RNA-seq in 62 histologically-normal breast tissue samples from adolescent girls and young women (mean age 17.8 yrs) who underwent breast reduction surgery. Twenty-nine patients were normal weight (NW; mean BMI 23.2 kg/m2) and 33 were overweight/obese (OB; BMI 31.7). Comparison of our adolescent dataset with published mammary RNAseq datasets from pubertal mice, rats, macaques, and adult women (mean age 38 yrs) revealed relatively poor (~ 30%) overlap with other species, but 88% overlap with adults for the 500 most highly expressed genes in each dataset. The small gene set (n=43) common to all groups was enriched for extracellular matrix components. We used DESeq2 to identify differentially-expressed (DE) genes in NW vs OB samples. To avoid confounding due to differences in the cellular composition of NW and OB samples, we first used CIBERSORT to computationally estimate the adipocyte fraction of each sample and included this estimate as a covariate. We identified 74 up-regulated and 73 down-regulated genes in NW vs. OB (padj &lt; 0.05). We used Ingenuity Pathway Analysis (IPA) to determine whether the DE genes might reflect activation or inhibition of upstream transcriptional regulators in OB samples. IPA identified the cytokines CSF1 and CSF2 and the chemokine receptor CCR2 as the most highly activated upstream regulators, suggesting a signature of increased inflammation in OB samples. While classical E receptor (ER) targets (e.g., PR, AREG) were not DE’d, IPA identified ESR1, 17-α-ethinyl estradiol, genistein, and PR, as well as growth factors/receptors (EGF, IGF-1, HGF, HER3) and kinases (AKT1, ERK) involved in hormone-independent ER activation, as activated upstream regulators in OB samples. These studies represent the first investigation of the human breast transcriptome during late puberty and demonstrate that in adolescents, as in adults, OB is associated with increased inflammation which may augment E action in the breast microenvironment.

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