keyword
MENU ▼
Read by QxMD icon Read
search

Cancer genome

keyword
https://www.readbyqxmd.com/read/29779155/prioritising-risk-factors-for-type-2-diabetes-causal-inference-through-genetic-approaches
#1
REVIEW
Laura B L Wittemans, Luca A Lotta, Claudia Langenberg
PURPOSE OF THE REVIEW: Causality has been demonstrated for few of the many putative risk factors for type 2 diabetes (T2D) emerging from observational epidemiology. Genetic approaches are increasingly being used to infer causality, and in this review, we discuss how genetic discoveries have shaped our understanding of the causal role of factors associated with T2D. RECENT FINDINGS: Genetic discoveries have led to the identification of novel potential aetiological factors of T2D, including the protective role of peripheral fat storage capacity and specific metabolic pathways, such as the branched-chain amino acid breakdown...
May 19, 2018: Current Diabetes Reports
https://www.readbyqxmd.com/read/29779017/-xpg-rs17655-g-c-polymorphism-associated-with-cancer-risk-evidence-from-60-studies
#2
Jie Zhao, Shanshan Chen, Haixia Zhou, Ting Zhang, Yang Liu, Jing He, Jinhong Zhu, Jichen Ruan
Xeroderma pigmentosum group G (XPG), a key component in nucleotide excision repair pathway, functions to cut DNA lesions during DNA repair. Genetic variations that alter DNA repair gene expression or function may decrease DNA repair ability and impair genome integrity, thereby predisposing to cancer. The association between XPG rs17655 G>C polymorphism and cancer risk has been investigated extensively, but the results remain contradictory. To get a more accurate conclusion, we performed a comprehensive meta-analysis of 60 case-control studies, involving 27,098 cancer cases and 30,535 healthy controls...
May 20, 2018: Aging
https://www.readbyqxmd.com/read/29778876/genome-sequence-analysis-of-a-novel-bacillus-thuringiensis-strain-blb406-active-against-aedes-aegypti-larvae-a-novel-potential-bioinsecticide
#3
Raida Zribi Zghal, Kais Ghedira, Jihen Elleuch, Marwa Kharrat, Slim Tounsi
BLB406 is a novel isolate of Bacillus thuringiensis with a larvicidal activity against Aedes aegypti larvae. It displays original plasmidic and crystal protein patterns. The present work reported molecular and bioinformatic analyses for the genome sequence of BLB406 using MiSeq Illumina next-generation sequencing technology. The reads were assembled by Velvet tool. Using RAST program and PGAAP the genome of BLB406 strain was shown to contain 6297 genes corresponding to 5924 protein coding sequences. The BLB406 genome investigation with BtToxin_scanner program shows that this strain has an original and different combination of toxins compared to the published ones: five cry genes (cry11, cry22, cry2, cry60, cry64) and two distinct vegetative insecticidal vip4 genes...
May 17, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29778836/interrogation-of-mammalian-protein-complex-structure-function-and-membership-using-genome-scale-fitness-screens
#4
Joshua Pan, Robin M Meyers, Brittany C Michel, Nazar Mashtalir, Ann E Sizemore, Jonathan N Wells, Seth H Cassel, Francisca Vazquez, Barbara A Weir, William C Hahn, Joseph A Marsh, Aviad Tsherniak, Cigall Kadoch
Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex...
May 14, 2018: Cell Systems
https://www.readbyqxmd.com/read/29778426/germline-cytoskeletal-and-extra-cellular-matrix-related-single-nucleotide-variations-associated-with-distinct-cancer-survival-rates
#5
Shayan Falasiri, Tasnif Rahman, Yaping N Tu, Timothy J Fawcett, George Blanck
BACKGROUND: Human mutagenesis has a large stochastic component. Thus, large coding regions, especially cytoskeletal and extra-cellular matrix protein (CECMP) coding regions are particularly vulnerable to mutations. Recent results have verified a high level of somatic mutations in the CECMP coding regions in the cancer genome atlas (TCGA), and a relatively common occurrence of germline, deleterious mutations in the TCGA breast cancer dataset. METHODS: The objective of this study was to determine the correlations of CECMP coding region, germline nucleotide variations with both overall survival (OS) and disease-free survival (DFS)...
May 17, 2018: Gene
https://www.readbyqxmd.com/read/29777908/breast-cancer-in-the-gcc-countries-a-focus-on-brca1-2-and-non-brca1-2-genes
#6
REVIEW
Sumaya Rahman, Hatem Zayed
The GCC is an economic alliance of six Arab countries, including Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, and United Arab Emirates (UAE). The rate of endogamous marriage among the GCC countries is approaching 100%, with very high consanguineous marriage rates. Although breast cancer is on the rise in the GCC countries, there are dearth of studies reporting on the genetic epidemiology of breast cancer. In this study, we investigated the frequency of BRCA1/2 and non-BRCA1/2 mutations in breast cancer patients in the GCC countries...
May 16, 2018: Gene
https://www.readbyqxmd.com/read/29777785/psmd2-regulates-breast-cancer-cell-proliferation-and-cell-cycle-progression-by-modulating-p21-and-p27-proteasomal-degradation
#7
Yunhai Li, Jing Huang, Beilei Zeng, Dejuan Yang, Jiazheng Sun, Xuedong Yin, Mengqi Lu, Zhu Qiu, Weiyan Peng, Tingxiu Xiang, Hongzhong Li, Guosheng Ren
Alterations in the ubiquitin-proteasome system (UPS) and UPS-associated proteins have been implicated in the development of many human malignancies. In this study, we investigated the expression profiles of 797 UPS-related genes using HiSeq data from The Cancer Genome Atlas and identified that PSMD2 was markedly upregulated in breast cancer. High PSMD2 expression was significantly correlated with poor prognosis. Gene set enrichment analysis revealed that transcriptome signatures involving proliferation, cell cycle, and apoptosis were critically enriched in specimens with elevated PSMD2...
May 16, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29777112/micrornas-as-potential-therapeutics-to-enhance-chemosensitivity-in-advanced-prostate-cancer
#8
Hui-Ming Lin, Iva Nikolic, Jessica Yang, Lesley Castillo, Niantao Deng, Chia-Ling Chan, Nicole K Yeung, Eoin Dodson, Benjamin Elsworth, Calan Spielman, Brian Y Lee, Zoe Boyer, Kaylene J Simpson, Roger J Daly, Lisa G Horvath, Alexander Swarbrick
Docetaxel and cabazitaxel are taxane chemotherapy treatments for metastatic castration-resistant prostate cancer (CRPC). However, therapeutic resistance remains a major issue. MicroRNAs are short non-coding RNAs that can silence multiple genes, regulating several signalling pathways simultaneously. Therefore, synthetic microRNAs may have therapeutic potential in CRPC by regulating genes involved in taxane response and minimise compensatory mechanisms that cause taxane resistance. To identify microRNAs that can improve the efficacy of taxanes in CRPC, we performed a genome-wide screen of 1280 microRNAs in the CRPC cell lines PC3 and DU145 in combination with docetaxel or cabazitaxel treatment...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29777108/factor-xiiia-expressing-inflammatory-monocytes-promote-lung-squamous-cancer-through-fibrin-cross-linking
#9
Alessandro Porrello, Patrick L Leslie, Emily B Harrison, Balachandra K Gorentla, Sravya Kattula, Subrata K Ghosh, Salma H Azam, Alisha Holtzhausen, Yvonne L Chao, Michele C Hayward, Trent A Waugh, Sanggyu Bae, Virginia Godfrey, Scott H Randell, Cecilia Oderup, Liza Makowski, Jared Weiss, Matthew D Wilkerson, D Neil Hayes, H Shelton Earp, Albert S Baldwin, Alisa S Wolberg, Chad V Pecot
Lung cancer is the leading cause of cancer-related deaths worldwide, and lung squamous carcinomas (LUSC) represent about 30% of cases. Molecular aberrations in lung adenocarcinomas have allowed for effective targeted treatments, but corresponding therapeutic advances in LUSC have not materialized. However, immune checkpoint inhibitors in sub-populations of LUSC patients have led to exciting responses. Using computational analyses of The Cancer Genome Atlas, we identified a subset of LUSC tumors characterized by dense infiltration of inflammatory monocytes (IMs) and poor survival...
May 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29776993/tumor-immune-evasion-arises-through-loss-of-tnf-sensitivity
#10
Conor J Kearney, Stephin J Vervoort, Simon J Hogg, Kelly M Ramsbottom, Andrew J Freeman, Najoua Lalaoui, Lizzy Pijpers, Jessica Michie, Kristin K Brown, Deborah A Knight, Vivien Sutton, Paul A Beavis, Ilia Voskoboinik, Phil K Darcy, John Silke, Joseph A Trapani, Ricky W Johnstone, Jane Oliaro
Immunotherapy has revolutionized outcomes for cancer patients, but the mechanisms of resistance remain poorly defined. We used a series of whole-genome clustered regularly interspaced short palindromic repeat (CRISPR)-based screens performed in vitro and in vivo to identify mechanisms of tumor immune evasion from cytotoxic lymphocytes [CD8+ T cells and natural killer (NK) cells]. Deletion of key genes within the tumor necrosis factor (TNF) signaling, interferon-γ (IFN-γ) signaling, and antigen presentation pathways provided protection of tumor cells from CD8+ T cell-mediated killing and blunted antitumor immune responses in vivo...
May 18, 2018: Science Immunology
https://www.readbyqxmd.com/read/29776954/role-of-elevated-phip-copy-number-as-a-prognostic-and-progression-marker-for-cutaneous-melanoma
#11
Vladimir Bezrookove, Mehdi Nosrati, James R Miller, David de Semir, Altaf A Dar, Elham Vosoughi, Edith Vaquero, Antje Sucker, Alexander J Lazar, Jeffrey E Gershenwald, Michael A Davies, Dirk Schadendorf, Mohammed Kashani-Sabet
PURPOSE: Previous studies have indicated an important role for pleckstrin homology domain-interacting protein (PHIP) as a marker and mediator of melanoma metastasis. Here we aimed to confirm the role of PHIP copy number in successive stages of melanoma progression. EXPERIMENTAL DESIGN: PHIP copy number was examined using fluorescence in situ hybridization (FISH) in three independent cohorts by recording the percentage of cells harboring > 3 copies of PHIP...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29776953/the-landscape-of-actionable-genomic-alterations-in-cell-free-circulating-tumor-dna-from-21-807-advanced-cancer-patients
#12
Oliver A Zill, Kimberly C Banks, Stephen R Fairclough, Stefanie Mortimer, James V Vowles, Reza Mokhtari, David R Gandara, Philip C Mack, Justin I Odegaard, Rebecca J Nagy, Arthur M Baca, Helmy Eltoukhy, Darya I Chudova, Richard B Lanman, AmirAli Talasaz
PURPOSE: Cell-free DNA (cfDNA) sequencing provides a non-invasive method for obtaining actionable genomic information to guide personalized cancer treatment, but the presence of multiple alterations in circulation related to treatment and tumor heterogeneity complicate the interpretation of the observed variants. Experimental Design: We describe the somatic mutation landscape of 70 cancer genes from cfDNA deep-sequencing analysis of 21,807 patients with treated, late-stage cancers across >50 cancer types...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29776650/signaling-pathway-deregulation-and-molecular-alterations-across-pediatric-medulloblastomas
#13
REVIEW
B Lhermitte, A F Blandin, A Coca, E Guerin, A Durand, N Entz-Werlé
Medulloblastomas (MBs) account for 15% of brain tumors in children under the age of 15. To date, the overall 5-year survival rate for all children is only around 60%. Recent advances in cancer genomics have led to a fundamental change in medulloblastoma classification and is evolving along with the genomic discoveries, allowing to regularly reclassify this disease. The previous molecular classification defined 4 groups (WNT-activated MB, SHH-activated MB and the groups 3 and 4 characterized partially by NMYC and MYC driven MBs)...
May 15, 2018: Neuro-Chirurgie
https://www.readbyqxmd.com/read/29776638/breast-carcinoma-updates-in-molecular-profiling-2018
#14
REVIEW
Sudeshna Bandyopadhyay, Martin H Bluth, Rouba Ali-Fehmi
The most significant contribution of molecular subtyping of breast carcinomas has been the identification of estrogen-positive and estrogen-negative tumor subtypes. Knowledge of genetic alterations in these tumors will help clinicians identify novel therapeutic targets. Understanding the progression pathways involved in the transition of in situ carcinoma to invasive carcinoma might lead to efficient risk stratification in these patients. The Cancer Genome Analysis Network has collected genomic and epigenomic data to provide comprehensive information regarding carcinogenesis and pathway interactions...
June 2018: Clinics in Laboratory Medicine
https://www.readbyqxmd.com/read/29776351/a-computational-study-of-hedgehog-signalling-involved-in-basal-cell-carcinoma-reveals-the-potential-and-limitation-of-combination-therapy
#15
Antoine Buetti-Dinh, Rebecca Jensen, Ran Friedman
BACKGROUND: The smoothened (SMO) receptor is an essential component of the Sonic hedgehog (SHH) signalling, which is associated with the development of skin basal cell carcinoma (BCC). SMO inhibitors are indicated for BCC patients when surgical treatment or radiation therapy are not possible. Unfortunately, SMO inhibitors are not always well tolerated due to severe side effects, and their therapeutical success is limited by resistance mutations. METHODS: We investigated how common are resistance-causing mutations in two genomic databases which are not linked to BCC or other cancers, namely 1000 Genomes and ExAC...
May 18, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29776329/convaq-a-web-tool-for-copy-number-variation-based-association-studies
#16
Simon Jonas Larsen, Luisa Matos do Canto, Silvia Regina Rogatto, Jan Baumbach
BACKGROUND: Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. RESULTS: We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29775779/metabolomics-in-breast-cancer-a-decade-in-review
#17
REVIEW
Amelia McCartney, Alessia Vignoli, Laura Biganzoli, Richard Love, Leonardo Tenori, Claudio Luchinat, Angelo Di Leo
Breast cancer (BC) is a heterogeneous disease which has been characterised and stratified by many platforms such as clinicopathological risk factors, genomic assays, computer generated models, and various "-omic" technologies. Genomic, proteomic and transcriptomic analysis in breast cancer research is well established, and metabolomics, which can be considered a downstream manifestation of the former disciplines, is of growing interest. The past decade has seen significant progress made within the field of clinical metabolomic BC research, with several groups demonstrating results with significant promise in the setting of BC screening and biological characterisation, as well as future potential for prognostic metabolomic biomarkers...
May 3, 2018: Cancer Treatment Reviews
https://www.readbyqxmd.com/read/29775688/gyneco-oncological-genomics-and-emerging-biomarkers-for-cancer-treatment-with-immune-checkpoint-inhibitors
#18
REVIEW
Giuseppe Curigliano
In gynecological cancers tumor infiltrating lymphocytes and upregulation of immune-related gene signatures have been associated with a better prognosis. Knowledge of tumor immunogenicity and associated gene signatures suggests that the tumor immune landscape is a key determinant to define patient prognosis and potentially to predict response to immune-checkpoint inhibitors. The aim of this review is to give an overview of immune gene signatures across gynecology histological cancer types, defining their prognostic and potential predictive role...
May 15, 2018: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/29775610/monocarboxylate-transporters-in-breast-cancer-and-adipose-tissue-are-novel-biomarkers-and-potential-therapeutic-targets
#19
Zhiyu Li, Qi Wu, Si Sun, Juan Wu, Juanjuan Li, Yimin Zhang, Changhua Wang, Jingping Yuan, Shengrong Sun
Monocarboxylate transporters (MCTs) are transmembrane proteins that control the lactate metabolism and associated with poor prognosis in solid tumors including breast cancer (BC). This study aimed to evaluate the clinical and prognostic value of MCTs used by immunohistochemistry and quantum dots-based fluorescent imaging technique in BC and surrounding stroma with emphasis on the interaction between tumour and stroma. Moreover, the data from The Cancer Genome Atlas (TCGA) was analyzed to evaluate the association between MCTs mRNA expression and prognosis of breast cancer patients...
May 15, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29774870/radiomics-in-gliomas-a-promising-assistance-for-glioma-clinical-research
#20
Yueshuang Leng, Xiaoyi Wang, Weihua Liao, Ya Cao
Gliomas are the most common brain primary tumors worldwide, which is the earliest sequenced cancer gene in the Cancer Genome Atlas (TCGA) project. The World Health Organization Classification Update of Central Nervous System (CNS) Tumors 2016 highlights that glioma is the first tumor classified based on both of the molecular markers and histology. Radiomics is an extraction approach for high-throughput data which collects the quantitative image information appearing. Combined imaging data with genomics and proteomics, radiomics show promising prediction for cancer diagnosis, treatment, and prognosis...
April 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
keyword
keyword
15712
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"