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Cancer biomarker

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https://www.readbyqxmd.com/read/28227169/biomarker-discovery-based-on-bbha-and-adaboostm1-on-microarray-data-for-cancer-classification
#1
Elnaz Pashaei, Mustafa Ozen, Nizamettin Aydin, Elnaz Pashaei, Mustafa Ozen, Nizamettin Aydin, Nizamettin Aydin, Elnaz Pashaei, Mustafa Ozen
In this paper, a new approach based on Binary Black Hole Algorithm (BBHA) and Adaptive Boosting version Ml (AdaboostM1) is proposed for finding genes that can classify the group of cancers correctly. In this approach, BBHA is used to perform gene selection and AdaboostM1 with 10-fold cross validation is adopted as the classifier. Also, to find the relation between the biomarkers for biological point of view, decision tree algorithm (C4.5) is utilized. The proposed approach is tested on three benchmark microarrays...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225893/lncrna-snhg12-promotes-cell-growth-and-inhibits-cell-apoptosis-in-colorectal-cancer-cells
#2
J Z Wang, C L Xu, H Wu, S J Shen
Several long non-coding RNA (lncRNA) might be correlated with the prognosis of colorectal cancer (CRC) and serve as a diagnostic and prognostic biomarker. However, the exact expression pattern of small nucleolar RNA host gene 12 (SNHG12) in colorectal cancer and its clinical significance remains unclear. The level of SNHG12 was detected by qRT-PCR in CRC tissues and CRC cells. MTT assay and colony formation assay were performed to examine the cell proliferation of CRC cells transfected with pcDNA-SNHG12 or si-SNHG12...
February 20, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28225065/a-comprehensive-analysis-of-metabolomics-and-transcriptomics-in-cervical-cancer
#3
Kai Yang, Bairong Xia, Wenjie Wang, Jinlong Cheng, Mingzhu Yin, Hongyu Xie, Junnan Li, Libing Ma, Chunyan Yang, Ang Li, Xin Fan, Harman S Dhillon, Yan Hou, Ge Lou, Kang Li
Cervical cancer (CC) still remains a common and deadly malignancy among females in developing countries. More accurate and reliable diagnostic methods/biomarkers should be discovered. In this study, we performed a comprehensive analysis of metabolomics (285 samples) and transcriptomics (52 samples) on the potential diagnostic implication and metabolic characteristic description in cervical cancer. Sixty-two metabolites were different between CC and normal controls (NOR), in which 5 metabolites (bilirubin, LysoPC(17:0), n-oleoyl threonine, 12-hydroxydodecanoic acid and tetracosahexaenoic acid) were selected as candidate biomarkers for CC...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225015/identification-of-protein-biomarkers-and-signaling-pathways-associated-with-prostate-cancer-radioresistance-using-label-free-lc-ms-ms-proteomic-approach
#4
Lei Chang, Jie Ni, Julia Beretov, Valerie C Wasinger, Jingli Hao, Joseph Bucci, David Malouf, David Gillatt, Peter H Graham, Yong Li
Identifying biomarkers and signaling pathways are important for the management of prostate cancer (CaP) radioresistance. In this study, we identified differential proteins and signaling pathways from parental CaP cell lines and CaP radioresistant (RR) sublines using a label-free LC-MS/MS proteomics approach. A total of 309 signaling pathway proteins were identified to be significantly altered between CaP and CaP-RR cells (p ≤ 0.05, fold differences >1.5, ≥80% power). Among these proteins, nineteen are common among three paired CaP cell lines and associated with metastasis, progression and radioresistance...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224267/selection-of-dna-aptamers-for-extra-cellular-domain-of-human-epidermal-growth-factor-receptor-2-to-detect-her2-positive-carcinomas
#5
A Sett, B B Borthakur, U Bora
BACKGROUND: Human epidermal growth factor receptor 2 (Her2, an orphan receptor of ErbB family) is considered as an important biomarker as it plays a key role in the development and progression of aggressive types of breast, ovarian, stomach and gastric cancer. In the present study, we developed novel DNA aptamers against the extra-cellular domain (ECD) of Her2 protein for detection of Her2-positive carcinomas. METHODS: We cloned and expressed Her2-ECD protein in E...
February 21, 2017: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/28224081/rna-seq-analysis-of-human-cell-lines-established-from-normal-and-neoplastic-esophageal-squamous-epithelium
#6
Ichiro Akagi, Osamu Ishibashi
Esophageal cancer (EC) is the eighth most common cancer globally in 2012 and predominantly occurs in the man (Enzinger and Mayer, 2003; Conteduca et al., 2012). EC is classified mainly into two types, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma, accounting for 60-70% and 20-30% of all EC cases, respectively. In a previous statistical study it was reported that the numbers of new EC cases and EC-related deaths worldwide in 2008 were estimated to be 482,300 and 406,800, respectively (Jemal et al...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28224023/evaluation-of-liver-cirrhosis-and-hepatocellular-carcinoma-using-protein-protein-interaction-networks
#7
Mohammad Javad Ehsani Ardakani, Akram Safaei, Afsaneh Arefi Oskouie, Hesam Haghparast, Mehrdad Haghazali, Hamid Mohaghegh Shalmani, Hassan Peyvandi, Nosratollah Naderi, Mohammad Reza Zali
AIM: In the current study, we analysised only the articles that investigate serum proteome profile of cirrhosis patients or HCC patients versus healthy controls. BACKGROUND: Increased understanding of cancer biology has enabled identification of molecular events that lead to the discovery of numerous potential biomarkers in diseases. Protein-protein interaction networks is one of aspect that could elevate the understanding level of molecular events and protein connections that lead to the identification of genes and proteins associated with diseases...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28223550/nadh-autofluorescence-a-new-metabolic-biomarker-for-cancer-stem-cells-identification-of-vitamin-c-and-cape-as-natural-products-targeting-stemness
#8
Gloria Bonuccelli, Ernestina Marianna De Francesco, Rianne de Boer, Herbert B Tanowitz, Michael P Lisanti
Here, we assembled a broad molecular "tool-kit" to interrogate the role of metabolic heterogeneity in the propagation of cancer stem-like cells (CSCs). First, we subjected MCF7 cells to "metabolic fractionation" by flow cytometry, using fluorescent mitochondrial probes to detect PCG1α activity, as well ROS and hydrogen-peroxide (H2O2) production; NADH levels were also monitored by auto-fluorescence. Then, the various cell populations were functionally assessed for "stem cell activity", using the mammosphere assay (3D-spheroids)...
February 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28223429/cancer-mortality-in-hispanic-ethnic-groups
#9
Paulo S Pinheiro, Karen E Callahan, Rebecca L Siegel, Hongbin Jin, Cyllene R Morris, Edward J Trapido, Scarlett Lin Gomez
Background: Cancer is the leading cause of death among Hispanics. The burden of cancer mortality within Hispanic groups has not been well quantified.Methods: Cancer mortality rates for 2008-2012 in Florida were computed on the basis of race, ethnicity, and birthplace, specifically focusing on major Hispanic groups-Mexicans, Puerto Ricans, Cubans, Central Americans, South Americans, and Dominicans. Age-adjusted mortality rate ratios derived from negative binomial regression were used to compare Hispanics, aggregated and by group, to nonHispanic whites (NHW)...
February 21, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28223415/science-signaling-podcast-for-21-february-2017-pentraxin-3-in-basal-like-breast-cancer
#10
Antoine E Karnoub, Annalisa M VanHook
This Podcast features an interview with Antoine Karnoub, senior author of a Research Article that appears in the 21 February 2017 issue of Science Signaling, about how pentraxin-3 (PTX3) links increased phosphoinositide 3-kinase (PI3K) signaling to stem cell properties in basal-like breast cancer (BLBC). BLBC is an aggressive type of breast cancer in which the tumor cells exhibit increased PI3K signaling and have stem cell-like properties. Thomas et al found that aberrant PI3K signaling in BLBCs stimulated the expression of PTX3, which encodes a protein that functions in innate immunity...
February 21, 2017: Science Signaling
https://www.readbyqxmd.com/read/28223411/pentraxin-3-is-a-pi3k-signaling-target-that-promotes-stem-cell-like-traits-in-basal-like-breast-cancers
#11
Clémence Thomas, Whitney Henry, Benjamin G Cuiffo, Anthony Y Collmann, Elisabetta Marangoni, Vanessa Benhamo, Manoj K Bhasin, Cheng Fan, Laetitia Fuhrmann, Albert S Baldwin, Charles Perou, Anne Vincent-Salomon, Alex Toker, Antoine E Karnoub
Basal-like breast cancers (BLBCs) exhibit hyperactivation of the phosphoinositide 3-kinase (PI3K) signaling pathway because of the frequent mutational activation of the PIK3CA catalytic subunit and the genetic loss of its negative regulators PTEN (phosphatase and tensin homolog) and INPP4B (inositol polyphosphate-4-phosphatase type II). However, PI3K inhibitors have had limited clinical efficacy in BLBC management because of compensatory amplification of PI3K downstream signaling loops. Therefore, identification of critical PI3K mediators is paramount to the development of effective BLBC therapeutics...
February 21, 2017: Science Signaling
https://www.readbyqxmd.com/read/28223274/long-term-responders-on-olaparib-maintenance-in-high-grade-serous-ovarian-cancer-clinical-and-molecular-characterization
#12
Stephanie Lheureux, Zhongwu Lai, Brian A Dougherty, Sarah Runswick, Darren Hodgson, Kirsten M Timms, Jerry S Lanchbury, Stanley B Kaye, Charlie Gourley, David D L Bowtell, Elise C Kohn, Clare L Scott, Ursula A Matulonis, Tony Panzarella, Katherine Karakasis, Julia V Burnier, Blake Gilks, Mark J O'Connor, Jane D Robertson, Jonathan Ledermann, J Carl Barrett, Tony W Ho, Amit M Oza
PURPOSE: Maintenance therapy with olaparib has improved progression-free survival in women with high-grade serous ovarian cancer (HGSOC), particularly those harboring BRCA1/2 mutations. The objective of this study was to characterize long-term (LT) versus short-term (ST) responders to olaparib. EXPERIMENTAL DESIGN: A comparative molecular analysis of Study 19 (NCT00753545), a randomized Phase II trial assessing olaparib maintenance after response to platinum-based chemotherapy in HGSOC, was conducted...
February 21, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28223273/pd-l1-studies-across-tumor-types-its-differential-expression-and-predictive-value-in-patients-treated-with-immune-checkpoint-inhibitors
#13
Harriet M Kluger, Christopher R Zito, Gabriela Turcu, Marina Baine, Hongyi Zhang, Adebowale Adeniran, Mario Sznol, David L Rimm, Yuval Kluger, Lieping Chen, Justine V Cohen, Lucia B Jilaveanu
PURPOSE: With recent approval of inhibitors of PD-1 in melanoma, non-small cell lung cancer (NSCLC) and renal cell carcinoma (RCC), extensive efforts are underway to develop biomarkers predictive of response. PD-L1 expression has been most widely studied, and is more predictive in NSCLC than RCC or melanoma. We therefore studied differences in expression patterns across tumor types. EXPERIMENTAL DESIGN: We employed tissue microarrays with tumors from NSCLC, RCC or melanoma and a panel of cell lines to study differences between tumor types...
February 21, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28223233/unravelling-the-pharmacologic-opportunities-and-future-directions-for-targeted-therapies-in-gastro-intestinal-cancers-part-1-gi-carcinomas
#14
REVIEW
Cindy Neuzillet, Benoît Rousseau, Hemant Kocher, Philippe Bourget, Christophe Tournigand
Until the 1990s, cytotoxic chemotherapy has been the cornerstone of medical therapy for gastrointestinal (GI) cancers. Better understanding of the molecular biology of cancer cell has led to the therapeutic revolution of targeted therapies, i.e. monoclonal antibodies or small molecule inhibitors directed against proteins that are specifically overexpressed or mutated in cancer cells. These agents being more specific to cancer cells were expected to be less toxic than cytotoxic agents. Targeted agents have provided clinical benefit in many GI cancer types...
February 13, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28223232/the-versatility-and-paradox-of-gdf-11
#15
REVIEW
A Jamaiyar, W Wan, D M Janota, M K Enrick, W M Chilian, L Yin
In addition to its roles in embryonic development, Growth and Differentiation Factor 11 (GDF 11) has recently drawn much interest about its roles in other processes, such as aging. GDF 11 has been shown to play pivotal roles in the rescue of the proliferative and regenerative capabilities of skeletal muscle, neural stem cells and cardiomyocytes. We would be remiss not to point that some controversy exists regarding the role of GDF 11 in biological processes and whether it will serve as a therapeutic agent. The latest studies have shown that the level of circulating GDF 11 correlates with the outcomes of patients with cardiovascular diseases, cancer and uremia...
February 13, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28223169/igf1-igf1r-stat3-signaling-inducible-ifitm2-promotes-gastric-cancer-growth-and-metastasis
#16
Li Xu, Rui Zhou, Lezhong Yuan, Shiqing Wang, Xiaoyin Li, Huanrong Ma, Minyu Zhou, Changqie Pan, Jingwen Zhang, Na Huang, Min Shi, Jianping Bin, Yulin Liao, Wangjun Liao
Interferon-induced transmembrane proteins (IFITMs) are expressed in some types of cancer. However, their precise roles in tumor progression remain unclear. The present study investigated the function of IFITM2 in gastric cancer (GC) progression. A retrospective analysis of a public database and 167 GC patients revealed that IFITM2 expression was upregulated in gastric tumor samples, which was positively correlated with disease progression, more frequent postoperative recurrence, and higher mortality rate. IFITM2 knockdown decreased GC cell proliferation, migration, invasion, and epithelial-to-mesenchymal transition in vitro...
February 18, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28222762/the-hippo-component-yap-localizes-in-the-nucleus-of-human-papilloma-virus-positive-oropharyngeal-squamous-cell-carcinoma
#17
Faisal Alzahrani, Leanne Clattenburg, Shanmugam Muruganandan, Martin Bullock, Kaitlyn MacIsaac, Michael Wigerius, Blair A Williams, M Elise R Graham, Matthew H Rigby, Jonathan R B Trites, S Mark Taylor, Christopher J Sinal, James P Fawcett, Robert D Hart
BACKGROUND: HPV infection causes cervical cancer, mediated in part by the degradation of Scribble via the HPV E6 oncoprotein. Recently, Scribble has been shown to be an important regulator of the Hippo signaling cascade. Deregulation of the Hippo pathway induces an abnormal cellular transformation, epithelial to mesenchymal transition, which promotes oncogenic progression. Given the recent rise in oropharyngeal HPV squamous cell carcinoma we sought to determine if Hippo signaling components are implicated in oropharyngeal squamous cell carcinoma...
February 22, 2017: Journal of Otolaryngology—Head & Neck Surgery
https://www.readbyqxmd.com/read/28222664/prevalence-and-coexistence-of-kras-braf-pik3ca-nras-tp53-and-apc-mutations-in-indian-colorectal-cancer-patients-next-generation-sequencing-based-cohort-study
#18
Mayank Jauhri, Akanksha Bhatnagar, Satish Gupta, Manasa Bp, Sachin Minhas, Yogender Shokeen, Shyam Aggarwal
Colorectal cancer incidences are on a rise in India. In this study, we have analyzed the mutation frequencies of six potential biomarkers, their coexistence, association with clinicopathological characteristics, and tumor location in Indian colorectal cancer patients. Next-generation sequencing was performed to identify mutations in the six potential biomarker genes using formalin-fixed paraffin-embedded tissue blocks of 112 colorectal cancer patients. The mutation frequency observed in KRAS, BRAF, PIK3CA, NRAS, TP53, and APC was 35...
February 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28222662/foxf2-promoter-methylation-is-associated-with-prognosis-in-esophageal-squamous-cell-carcinoma
#19
Xiaoying Chen, Haochang Hu, Jing Liu, Yong Yang, Guili Liu, Xiuru Ying, Yingmin Chen, Bin Li, Cong Ye, Dongping Wu, Shiwei Duan
Esophageal squamous cell carcinoma is a commonly malignant tumor of digestive tract with poor prognosis. Previous studies suggested that forkhead box F2 ( FOXF2) could be a candidate gene for assessing and predicting the prognosis of human cancers. However, the relationship between FOXF2 promoter methylation and the prognosis of esophageal squamous cell carcinoma remained unclear. Formalin-fixed, paraffin-embedded esophageal squamous cell carcinoma tissues of 135 esophageal squamous cell carcinoma patients were detected for FOXF2 promoter methylation status by methylation-specific polymerase chain reaction approach...
February 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28222223/prostate-cancer-major-changes-in-the-american-joint-committee-on-cancer-eighth-edition-cancer-staging-manual
#20
Mark K Buyyounouski, Peter L Choyke, Jesse K McKenney, Oliver Sartor, Howard M Sandler, Mahul B Amin, Michael W Kattan, Daniel W Lin
Answer questions and earn CME/CNE The eighth edition of the American Joint Committee on Cancer (AJCC) tumor-node-metastasis (TNM) Staging Manual has been updated and improved to ensure the highest degree of clinical relevance and to improve its utility for patient evaluation and clinical research. Major changes include: 1) pathologically organ-confined disease is now considered pT2 and is no longer subclassified by extent of involvement or laterality, 2) tumor grading now includes both the Gleason score (as in the seventh edition criteria) and the grade group (introduced in the eighth edition criteria), 3) prognostic stage group III includes select, organ-confined disease based on prostate-specific antigen and Gleason/grade group status, and 4) 2 statistical prediction models are included in the staging manual...
February 21, 2017: CA: a Cancer Journal for Clinicians
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