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https://www.readbyqxmd.com/read/29145449/estimation-of-the-proteomic-cancer-co-expression-sub-networks-by-using-association-estimators
#1
Cihat Erdoğan, Zeyneb Kurt, Banu Diri
In this study, the association estimators, which have significant influences on the gene network inference methods and used for determining the molecular interactions, were examined within the co-expression network inference concept. By using the proteomic data from five different cancer types, the hub genes/proteins within the disease-associated gene-gene/protein-protein interaction sub networks were identified. Proteomic data from various cancer types is collected from The Cancer Proteome Atlas (TCPA). Correlation and mutual information (MI) based nine association estimators that are commonly used in the literature, were compared in this study...
2017: PloS One
https://www.readbyqxmd.com/read/29145283/the-relationship-between-rassf1a-promoter-methylation-and-thyroid-carcinoma-a-meta-analysis-of-14-articles-and-a-bioinformatics-of-2-databases-prisma
#2
Heng Niu, Jingyu Yang, Kunxian Yang, Yingze Huang
BACKGROUND: DNA promoter methylation can suppresses gene expression and shows an important role in the biological functions of Ras association domain family 1A (RASSF1A). Many studies have performed to elucidate the role of RASSF1A promoter methylation in thyroid carcinoma, while the results were conflicting and heterogeneous. Here, we analyzed the data of databases to determine the relationship between RASSF1A promoter methylation and thyroid carcinoma. METHODS: We used the data from 14 cancer-normal studies and Gene Expression Omnibus (GEO) database to analyze RASSF1A promoter methylation in thyroid carcinoma susceptibility...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29145245/case-reports-about-an-overlooked-cause-of-neck-pain-calcific-tendinitis-of-the-longus-colli-case-reports
#3
Yeong-Jin Kim, Jae-Young Park, Ki-Young Choi, Bong-Ju Moon, Jung-Kil Lee
STUDY DESIGN: Case description. OBJECTIVE: Acute calcific tendinitis of the longus colli muscle is a rare clinical entity that causes severe neck pain. This entity is not well recognized due to its nonspecific presentation such as acute neck pain, neck stiffness, and odynophagia. The importance of this disease with a review of the literature is presented. SUMMARY OF BACKGROUND DATA: Acute calcific tendinitis of the longus colli muscle is an inflammatory condition caused by deposition of calcium hydroxyapatite in the superior oblique tendon fibers of the longus colli muscle...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29144233/a-high-resolution-mrna-expression-time-course-of-embryonic-development-in-zebrafish
#4
Richard J White, John E Collins, Ian M Sealy, Neha Wali, Christopher M Dooley, Zsofia Digby, Derek L Stemple, Daniel N Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J Enright, Elisabeth M Busch-Nentwich
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3' end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation...
November 16, 2017: ELife
https://www.readbyqxmd.com/read/29143717/white-matter-abnormalities-in-22q11-2-deletion-syndrome-patients-showing-cognitive-decline
#5
Jasper Olivier Nuninga, Marc Marijn Bohlken, Sanne Koops, Ania M Fiksinski, René C W Mandl, Elemi J Breetvelt, Sasja N Duijff, René S Kahn, Iris E C Sommer, Jacob A S Vorstman
BACKGROUND: Decline in cognitive functioning precedes the first psychotic episode in the course of schizophrenia and is considered a hallmark symptom of the disorder. Given the low incidence of schizophrenia, it remains a challenge to investigate whether cognitive decline coincides with disease-related changes in brain structure, such as white matter abnormalities. The 22q11.2 deletion syndrome (22q11DS) is an appealing model in this context, as 25% of patients develop psychosis. Furthermore, we recently showed that cognitive decline also precedes the onset of psychosis in individuals with 22q11DS...
November 16, 2017: Psychological Medicine
https://www.readbyqxmd.com/read/29143637/impact-of-malaria-interventions-on-child-mortality-in-endemic-african-settings-comparison-and-alignment-between-list-and-spectrum-malaria-model
#6
Eline Korenromp, Matthew Hamilton, Rachel Sanders, Guy Mahiané, Olivier J T Briët, Thomas Smith, William Winfrey, Neff Walker, John Stover
BACKGROUND: In malaria-endemic countries, malaria prevention and treatment are critical for child health. In the context of intervention scale-up and rapid changes in endemicity, projections of intervention impact and optimized program scale-up strategies need to take into account the consequent dynamics of transmission and immunity. METHODS: The new Spectrum-Malaria program planning tool was used to project health impacts of Insecticide-Treated mosquito Nets (ITNs) and effective management of uncomplicated malaria cases (CMU), among other interventions, on malaria infection prevalence, case incidence and mortality in children 0-4 years, 5-14 years of age and adults...
November 7, 2017: BMC Public Health
https://www.readbyqxmd.com/read/29142336/multi-atlas-based-ct-synthesis-from-conventional-mri-with-patch-based-refinement-for-mri-based-radiotherapy-planning
#7
Junghoon Lee, Aaron Carass, Amod Jog, Can Zhao, Jerry L Prince
Accurate CT synthesis, sometimes called electron density estimation, from MRI is crucial for successful MRI-based radiotherapy planning and dose computation. Existing CT synthesis methods are able to synthesize normal tissues but are unable to accurately synthesize abnormal tissues (i.e., tumor), thus providing a suboptimal solution. We propose a multi-atlas-based hybrid synthesis approach that combines multi-atlas registration and patch-based synthesis to accurately synthesize both normal and abnormal tissues...
February 2017: Proceedings of SPIE
https://www.readbyqxmd.com/read/29142225/comparative-genomic-analysis-of-esophageal-squamous-cell-carcinoma-between-asian-and-caucasian-patient-populations
#8
Jiaying Deng, Hu Chen, Daizhan Zhou, Junhua Zhang, Yun Chen, Qi Liu, Dashan Ai, Hanting Zhu, Li Chu, Wenjia Ren, Xiaofei Zhang, Yi Xia, Menghong Sun, Huiwen Zhang, Jun Li, Xinxin Peng, Liang Li, Leng Han, Hui Lin, Xiujun Cai, Jiaqing Xiang, Shufeng Chen, Yihua Sun, Yawei Zhang, Jie Zhang, Haiquan Chen, Shijian Zhang, Yi Zhao, Yun Liu, Han Liang, Kuaile Zhao
Esophageal squamous cell carcinoma is a major histological type of esophageal cancer, with distinct incidence and survival patterns among races. Although previous studies have characterized somatic mutations in this disease, a rigorous comparison between different patient populations has not been conducted. Here we sequence the samples of 316 Chinese patients, combine them with those from The Cancer Genome Atlas, and perform a comparative analysis between Asian and Caucasian patients. We find that mutated CSMD3 is associated with better prognosis in Asian patients...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142158/computed-tomography-magnetic-resonance-imaging-and-a-novel-surgical-approach-of-atlanto-axial-instability-with-incongruence-in-dogs
#9
Mario Dolera, Luca Malfassi, Simone Pavesi, Sara Finesso, Giovanni Mazza, Silvia Marcarini, Massimo Sala, Nancy Carrara, Cristina Bianchi, Jennifer M Gambino
Atlanto-axial (AA) instability due to ligament insufficiency is a common cause of cervical spinal cord compression in toy breeds. However, in some dogs a difference in size between the atlas and the axis leads to joint incongruence that exacerbates AA subluxation and makes surgical treatment challenging. Twelve dogs with AA instability with incongruence were enrolled in a single institution prospective observational study. Computed tomography (CT) and magnetic resonance imaging (MRI) of the AA joint were compared to a retrospectively reviewed control group...
November 15, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/29141981/impact-of-tumor-purity-on-immune-gene-expression-and-clustering-analyses-across-multiple-cancer-types
#10
Je-Keun Rhee, Yu Chae Jung, Kyu Ryung Kim, Jinseon Yoo, Jeeyoon Kim, Yong-Jae Lee, Yoon Ho Ko, Han Hong Lee, Byoung Chul Cho, Tae-Min Kim
Surgical archives of tumor specimens are often impure. The presence of RNA transcripts from nontumor cells, such as immune and stromal cells, can impede analyses of cancer expression profiles. To systematically analyze the impact of tumor purity, the gene expression profiles and tumor purities were obtained for 7794 tumor specimens across 21 tumor types (available in the Cancer Genome Atlas consortium). First, we observed that genes with roles in immunity and oxidative phosphorylation were significantly inversely correlated and correlated with the tumor purity, respectively...
November 15, 2017: Cancer Immunology Research
https://www.readbyqxmd.com/read/29141854/a-p53-deficiency-gene-signature-predicts-recurrence-risk-of-patients-with-early-stage-lung-adenocarcinoma
#11
Yanding Zhao, Frederick S Varn, Guoshuai Cai, Feifei Xiao, Christopher I Amos, Chao Cheng
BACKGROUND: Lung cancer is associated with the highest mortality rate of all cancer types, and the most common histological subtype of lung cancer is adenocarcinoma. In order to apply more effective therapeutic treatment, molecular markers that are able to predict the recurrence risk of patients with adenocarcinoma are critically needed. Mutations in TP53 tumor suppressor gene have been found in approximately 50% of lung adenocarcinoma cases, but the presence of a TP53 mutation does not always associate with increased mortality...
November 15, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/29141226/a-pan-cancer-analysis-of-the-expression-and-clinical-relevance-of-small-nucleolar-rnas-in-human-cancer
#12
Jing Gong, Yajuan Li, Chun-Jie Liu, Yu Xiang, Chunlai Li, Youqiong Ye, Zhao Zhang, David H Hawke, Peter K Park, Lixia Diao, John A Putkey, Liuqing Yang, An-Yuan Guo, Chunru Lin, Leng Han
Increasing evidence has demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in >10,000 samples across 31 cancer types from The Cancer Genome Atlas. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29140994/copy-number-gains-at-chr3p25-and-chr11p11-are-associated-with-lymph-node-involvement-and-survival-in-muscle-invasive-bladder-tumors
#13
Karla J Lindquist, Thomas Sanford, Terence W Friedlander, Pamela L Paris, Sima P Porten
Patients with muscle-invasive bladder cancer (MIBC) have poorer prognoses if cancer has metastasized to the lymph nodes. Genomic markers of lymph node involvement (LNI) would be useful for treatment planning, especially if measured at the biopsy stage, but large-scale studies of tumor tissue at any stage are needed to discover robust markers of LNI. We performed a genome-wide query of copy number alterations (CNA) in 237 MIBC surgical tumor specimens from patients in The Cancer Genome Atlas who had radical cystectomy and lymphadenectomy without neoadjuvant treatment...
2017: PloS One
https://www.readbyqxmd.com/read/29138825/utility-of-mir%C3%A2-133a%C3%A2-3p-as-a-diagnostic-indicator-for-hepatocellular-carcinoma-an-investigation-combined-with-geo-tcga-meta%C3%A2-analysis-and-bioinformatics
#14
Hai-Wei Liang, Xia Yang, Dong-Yue Wen, Li Gao, Xiang-Yu Zhang, Zhi-Hua Ye, Jie Luo, Zu-Yun Li, Yun He, Yu-Yan Pang, Gang Chen
Increasing evidence has demonstrated that microRNA (miR)‑133a‑3p is an important regulator of hepatocellular carcinoma (HCC). In the present study, the diagnostic role of miR‑133a‑3p in HCC, and the potential functional pathways, were both explored based on publicly available data. Eligible microarray datasets were collected from NCBI Gene Expression Omnibus (GEO) database and ArrayExpress database. The data related to HCC and matched adjacent normal tissues were also downloaded from The Cancer Genome Atlas (TCGA)...
November 14, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29138577/identification-and-validation-of-potential-prognostic-gene-biomarkers-for-predicting-survival-in-patients-with-acute-myeloid-leukemia
#15
Rui Huang, Xiwen Liao, Qiaochuan Li
Background: Molecular analysis is a promising source of clinically useful prognostic biomarkers. The aim of this investigation was to identify prognostic biomarkers for patients with acute myeloid leukemia (AML) by using the gene expression profile dataset from public database. Methods: The gene expression profile dataset and corresponding overall survival (OS) information of three cohorts of AML patients from GSE12417 and The Cancer Genome Atlas AML project (TCGA-LAML) were included in the present study...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29137433/upregulation-of-homeobox-gene-is-correlated-with-poor-survival-outcomes-in-cervical-cancer
#16
Kyung Jin Eoh, Hee Jung Kim, Jung-Yun Lee, Eun Ji Nam, Sunghoon Kim, Sang Wun Kim, Young Tae Kim
HOX family members encode transcription factors crucial for embryogenesis and may be associated with carcinogenesis. Here, we evaluated the expression of 39 HOX genes in cervical cancer by using clinicopathological information and gene expression data of 308 patients from The Cancer Genome Atlas (TCGA) database. Correlations between mRNA expression of HOX family members and clinicopathological variables were explored. Seventy-three (23.7%) patients died during the follow-up period (median, 22.0 months). Overall mortality was significantly associated with advanced FIGO stage, lymph node metastasis, lymphovascular invasion, and increased HOXA1, HOXA5, HOXA6, and HOXC11 mRNA expression...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137369/lrh-1-expression-patterns-in-breast-cancer-tissues-are-associated-with-tumour-aggressiveness
#17
Jia-Min B Pang, Ramyar Molania, Ashwini Chand, Kevin Knower, Elena A Takano, David J Byrne, Thomas Mikeska, Ewan K A Millar, Cheok Soon Lee, Sandra A O'Toole, Colin Clyne, Kylie L Gorringe, Alexander Dobrovic, Stephen B Fox
The significance and regulation of liver receptor homologue 1 (LRH-1, NR5A2), a tumour-promoting transcription factor in breast cancer cell lines, is unknown in clinical breast cancers. This study aims to determine LRH-1/NR5A2 expression in breast cancers and relationship with DNA methylation and tumour characteristics. In The Cancer Genome Atlas breast cancer cohort NR5A2 expression was positively associated with intragenic CpG island methylation (1.4-fold expression for fully methylated versus not fully methylated, p=0...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137326/overexpression-of-carbonic-anhydrase-ix-induces-cell-motility-by-activating-matrix-metalloproteinase-9-in-human-oral-squamous-cell-carcinoma-cells
#18
Jia-Sin Yang, Chiao-Wen Lin, Yi-Hsien Hsieh, Ming-Hsien Chien, Chun-Yi Chuang, Shun-Fa Yang
Oral cancer is a solid malignant tumor that is prone to occur following hypoxia. There are no clear studies showing a link between hypoxia and oral carcinogenesis. Carbonic anhydrase IX (CAIX), which is a hypoxia-induced transmembrane protein, is highly expressed in various types of human cancer. However, the effects of CAIX on the metastasis of human oral cancer cells and the underlying molecular mechanisms have not been clarified. In this study, we observed that CAIX overexpression increased the migratory and invasive abilities of SCC-9 and SAS cells...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137231/an-oral-keratinocyte-life-cycle-model-identifies-novel-host-genome-regulation-by-human-papillomavirus-16-relevant-to-hpv-positive-head-and-neck-cancer
#19
Michael R Evans, Claire D James, Oonagh Loughran, Tara J Nulton, Xu Wang, Molly L Bristol, Brad Windle, Iain M Morgan
Many aspects of the HPV life cycle have been characterized in cervical cell lines (W12, CIN612) and in HPV immortalized primary foreskin keratinocytes. There is now an epidemic of HPV positive oropharyngeal cancers (HPV16 is responsible for 80-90% of these); therefore increased understanding of the HPV16 life cycle in oral keratinocytes is a priority. To date there have been limited reports characterizing the HPV16 life cycle in oral keratinocytes. Using TERT immortalized "normal" oral keratinocytes (NOKs) we generated clonal cell lines maintaining the HPV16 genome as an episome, NOKs+HPV16...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137177/comprehensive-profiling-of-lincrnas-in-lung-adenocarcinoma-of-never-smokers-reveals-their-roles-in-cancer-development-and-prognosis
#20
Ying Li, Zheng Wang, Asha Nair, Wei Song, Ping Yang, Xiaoju Zhang, Zhifu Sun
Long intergenic non-coding RNA (lincRNA) is a family of gene transcripts, the functions of which are largely unknown. Although cigarette smoking is the main cause for lung cancer, lung cancer in non-smokers is a separate entity and its underlying cause is little known. Growing evidence suggests lincRNAs play a significant role in cancer development and progression; however, such data is lacking for lung cancer in non-smokers, or those who have never smoked. This study conducted comprehensive profiling of lincRNAs from RNA sequencing (RNA-seq) data of non-smoker patients with lung adenocarcinoma...
November 13, 2017: Genes
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