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Target sequencing

Ina A Eilertsen, Anita Sveen, Jonas M Strømme, Rolf I Skotheim, Arild Nesbakken, Ragnhild A Lothe
KRAS mutation is a well-known marker for poor response to targeted treatment and patient prognosis in microsatellite stable (MSS) colorectal cancer (CRC). However, variation in clinical outcomes among patients wild-type for KRAS underlines that this is not a homogeneous population. Here, we evaluated the prognostic impact of KRAS alternative splicing in relation to mutation status in a single-hospital series of primary MSS CRCs (N = 258). Using splicing-sensitive microarrays and RNA sequencing, the relative expression of KRAS-4A versus KRAS-4B transcript variants was confirmed to be down-regulated in CRC compared to normal colonic mucosa (N = 41; P ≤ 0...
August 19, 2018: International Journal of Cancer. Journal International du Cancer
Ovidiu Paun, Koen J F Verhoeven, Christina L Richards
I. II. III. IV. V. VI. SUMMARY: Investigating the features and implications of epigenetic mechanisms across the breadth of organisms and ecosystems is important for understanding the ecological relevance of epigenetics. Several cost-effective reduced representation bisulfite sequencing approaches (RRBS) have been recently developed and applied to different organisms that lack a well annotated reference genome. These new approaches improve the assessment of epigenetic diversity in ecological settings and may provide functional insights...
August 19, 2018: New Phytologist
Ziyu Dai, Kyle R Pomraning, Shuang Deng, Beth A Hofstad, Ellen A Panisko, Diana Rodriguez, Mark G Butcher, David E Culley, Jon K Magnuson
The objective of this study was to disrupt the non-homologous end-joining (NHEJ) pathway gene (Lsku70Δ) and evaluate the effects of selected gene deletions related to glycogen synthesis (LsGSY1) and lipid degradation (LsMFE1, LsPEX10, and LsTGL4) on lipid production in the oleaginous yeast Lipomyces starkeyi. Disruption of the NHEJ pathway to reduce the rate of non-homologous recombination is a common approach used to overcome low-efficiency targeted deletion or insertion in various organisms. Here, the homologue of the LsKU70 gene was identified and disrupted in L...
August 18, 2018: Current Genetics
Zhi Wang, Weizhou Xu, Jiyue Kang, Min Li, Jin Huang, Qingbo Ke, Ho Soo Kim, Bingcheng Xu, Sang-Soo Kwak
The multifunctional Orange (Or) protein plays crucial roles in carotenoid homeostasis, photosynthesis stabilization, and antioxidant activity in plants under various abiotic stress conditions. The Or gene has been cloned in several crops but not in alfalfa (Medicago sativa L.). Alfalfa is widely cultivated across the world; however, its cultivation is largely limited by various abiotic stresses, including drought. In this study, we isolated the Or gene from alfalfa (MsOr) cv. Xinjiang Daye. The amino acid sequence of the deduced MsOr protein revealed that the protein contained two trans-membrane domains and a DnaJ cysteine-rich zinc finger domain, and showed a high level of similarity with the Or protein of other plants species...
August 14, 2018: Plant Physiology and Biochemistry: PPB
Smadar Laufer-Geva, Anna Belilovski Rozenblum, Tal Twito, Roxana Grinberg, Addie Dvir, Lior Soussan-Gutman, Maya Ilouze, Laila C Roisman, Elizabeth Dudnik, Alona Zer, Ofer Rotem, Richard B Lanman, Nir Peled
INTRODUCTION: Next-generation sequencing (NGS) of cell-free circulating tumor DNA (cfDNA) enables non-invasive genomic analysis of non-small cell lung cancer (NSCLC) patients. Although plasma-detected genomic alterations (GAs) have been shown to predict targeted therapy response, evidence of durability of response is lacking or limited to small cohorts as is the impact of cfDNA NGS results on clinical decisions. METHODS: This retrospective study of stage IIIB/IV NSCLC patients between the years 2014-2017 in Israel utilized cfDNA NGS (Guardant360) to identify targetable GAs...
August 16, 2018: Journal of Thoracic Oncology
Eunhyang Park, Soyeon Ahn, Hyojin Kim, Soo Young Park, Jisun Lim, Hyun Jung Kwon, Yeon Bi Han, Choon-Taek Lee, Sukki Cho, Jin-Haeng Chung
INTRODUCTION: Lung adenocarcinoma (ADC) and synchronous ground-glass/lepidic (GG/L) nodules are considered a distinct disease entity in multiple synchronous lung cancers. Few studies have performed next-generation sequencing (NGS) analysis on these synchronous sequential lesions, and genetic alterations of GG/L nodules must be further investigated. METHODS: We performed targeted sequencing in ADC with synchronous atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), or minimally invasive adenocarcinoma (MIA) from 16 patients...
August 16, 2018: Journal of Thoracic Oncology
Jaclyn F Hechtman, Ghassan K Abou Alfa, Zsofia K Stadler, Diana L Mandelker, Michael H A Roehrl, Ahmet Zehir, Efsevia Vakiani, Sumit Middha, David S Klimstra, Jinru Shia
Mutations of Hepatocyte-Nuclear-Factor-1-Homeobox-A gene and loss of Liver-Fatty-Acid-Binding-Protein are well documented in hepatocellular adenoma. However, the role of Hepatocyte-Nuclear-Factor-1-Homeobox-A mutations in hepatocellular carcinoma remains to be determined. In this study, all hepatocellular neoplasms evaluated by our institutional Memorial Sloan Kettering-Integrated Mutational Profiling of Actionable Clinical Targets assay or the Cancer Genome Atlas sequencing, and cases reported in the literature, were queried for Hepatocyte-Nuclear-Factor-1-Homeobox-A mutations...
August 16, 2018: Human Pathology
Xiong Liu, Chun Li, Rengdong Zhang, Wenjun Xiao, Xia Niu, Xiajun Ye, Zijia Li, Yuxian Guo, Junyu Tan, Yaochen Li
It is well known that epithelial-mesenchymal transition (EMT) can confer cancer cells with invasive and migratory capabilities associated with distant metastasis. As a key upstream factor in the Hippo pathway, Kibra (wwc1 gene) has been shown to suppress EMT in breast cancer cells, and we have found that its expression is reduced or lost completely in both human breast cancer cell lines and clinical tissue samples, particularly in triple negative breast cancer (TNBC). Unfortunately, the molecular mechanisms underlying this progression-associated event remain to be elucidated...
August 16, 2018: Cellular Signalling
Connor R Fitzpatrick, Patricia Lu-Irving, Julia Copeland, David S Guttman, Pauline W Wang, David A Baltrus, Katrina M Dlugosch, Marc T J Johnson
BACKGROUND: The ability to efficiently characterize microbial communities from host individuals can be limited by co-amplification of host organellar sequences (mitochondrial and/or plastid), which share a common ancestor and thus sequence similarity with extant bacterial lineages. One promising approach is the use of sequence-specific peptide nucleic acid (PNA) clamps, which bind to, and block amplification of, host-derived DNA. Universal PNA clamps have been proposed to block host plant-derived mitochondrial (mPNA) and plastid (pPNA) sequences at the V4 16S rRNA locus, but their efficacy across a wide range of host plant species has not been experimentally tested...
August 18, 2018: Microbiome
Balabhadrapatruni V S K Chakravarthi, Maria Del Carmen Rodriguez Pena, Sumit Agarwal, Darshan S Chandrashekar, Sai Akshaya Hodigere Balasubramanya, Fayez J Jabboure, Andres Matoso, Trinity J Bivalacqua, Katayoon Rezaei, Alcides Chaux, William E Grizzle, Guru Sonpavde, Jennifer Gordetsky, George J Netto, Sooryanarayana Varambally
Genomic and transcriptome sequencing of bladder cancer (BLCA) has identified multiple molecular alterations during cancer progression. Many of these identified genetic and epigenetic changes play a role in the progression of this disease. Studies have identified molecular subtypes in muscle-invasive bladder cancer (MIBC) with different sensitivities to frontline therapy suggesting the heterogeneity in these tumors and the importance of molecular characterization of MIBC to provide effective treatment. Specifically, it has become increasingly evident, as demonstrated by The Cancer Genome Atlas project, that metabolic enzymes are commonly dysregulated in BLCA...
August 14, 2018: Neoplasia: An International Journal for Oncology Research
Shi Yang, Dominick A Leone, Asok Biswas, April Deng, Drazen Jukic, Rajendra Singh, Uma Sundram, Meera Mahalingam
Despite the efficacy of BRAF-targeted and PD-L1-related immune therapies in tackling metastatic melanoma, a significant number of patients exhibit resistance. Given this, the objective of the current study was to ascertain concordance of somatic mutations in BRAF/ NRAS/TERT and, immunohistochemical PD-L1 and CD8 in matched primary cutaneous and metastatic melanoma. A total of 43 archival paired samples with sufficient material for genetic and immunohistochemical analyses met criteria for inclusion in the study...
August 15, 2018: Human Pathology
Robert H Press, Chao Zhang, Richard J Cassidy, Matthew J Ferris, Jim Zhong, Conor E Steuer, Rathi N Pillai, Taofeek K Owonikoko, Shannon Kahn, Suresh S Ramalingam, Pretesh R Patel, Walter J Curran, Hui-Kuo G Shu, Gabriel L Sica, Kristin A Higgins
BACKGROUND: Treatment for advanced lung adenocarcinoma (AC) has become increasingly personalized based on molecular results. However, for patients with AC brain metastases (BMs), intracranial outcomes based on molecular subtype and the frequency of molecular aberrations are less well defined. This study sought to report targeted next-generation sequencing results and investigate molecularly based outcomes for patients with AC-BMs treated with radiotherapy. METHODS: The records of 132 patients with AC-BMs treated at Emory University from September 2008 to August 2016 with successful next-generation sequencing were reviewed...
August 18, 2018: Cancer
Niti Kumari, Aman Kumar, Babu Ram Thapa, Manish Modi, Arnab Pal, Rajendra Prasad
Wilson disease (WD), a copper metabolism disorder, occurs due to the presence of mutations in the gene encoding ATP7B, a protein that primarily facilitates hepatic copper excretion. A better understanding of spectrum and functional significance of ATP7B variants is critical to formulating targeted and personalized therapies. Henceforth, we screened and sequenced 21 exons of ATP7B gene from 50 WD patients and 60 healthy subjects. We identified 28 variants comprising, seven novels in 20% alleles, while eight variations affecting 23% alleles were first time reported in Indian cohort...
August 18, 2018: Human Mutation
Antonella Minutolo, Marina Potestà, Angelo Gismondi, Stefano Pirrò, Marco Cirilli, Fabiano Gattabria, Andrea Galgani, Libera Sessa, Maurizio Mattei, Antonella Canini, Rosario Muleo, Vittorio Colizzi, Carla Montesano
Functional foods include compounds with nutritional and health properties. The human diet could play a stronger role in cancer prevention. Only a few studies have described the presence of plant small RNA, in humans who were fed with plant foods, which demonstrated the ability of these molecules to modulate consumer's genes and evidenced the existence of a plant-animal regulation. Through in silico prediction, Olea europaea small RNAs (sRs), which had been previously reported as miRNAs, were identified, each with functional homology to hsa-miR34a...
August 17, 2018: Scientific Reports
Margherita Cacaci, Caroline Giraud, Loic Leger, Riccardo Torelli, Cecilia Martini, Brunella Posteraro, Valentina Palmieri, Maurizio Sanguinetti, Francesca Bugli, Axel Hartke
Enterococcus faecium is an important health care-associated pathogen that is difficult to treat due to the high level of antibiotic resistance of clinical isolates. The identification of new potential therapeutic targets or vaccination strategies is therefore urgently needed. In this regard, we carried out a transcriptomic analysis of the E. faecium vancomycin-resistant strain AUS0004, comparing the gene expression of bacteria grown under laboratory conditions and bacteria isolated from an infection site. This analysis highlighted more than 360 genes potentially induced under infection conditions...
August 17, 2018: Scientific Reports
Jeong Eun Kim, Ji Won Hong, Hannah S Lee, Wankyu Kim, Jisun Lim, Yoon Shin Cho, Ho Jeong Kwon
Ubiquinol cytochrome c reductase binding protein (UQCRB) is known to play crucial roles in the development of various types of diseases. However, the link between UQCRB and microRNAs remains unknown. In the present study, we performed microRNA sequencing of mutant UQCRB-expressing stable cell lines that exhibited pro-oncogenic activities caused by expression of the mutant UQCRB gene. Results showed that hsa-miR-10a-5p was significantly downregulated in the mutant UQCRB-expressing cell lines. Furthermore, mRNA sequencing and gene ontology analysis of differentially expressed genes (DEGs) revealed that the cholesterol biosynthesis pathway might be activation by mutant UQCRB expression...
August 17, 2018: Scientific Reports
Shuolin Li, Sida Liu, Weicheng Chen, Yuan Yuan, Ruoyi Gu, Yangliu Song, Jian Li, Yinyin Cao, Yixiang Lin, Jun Xu, Huijun Wang, Duan Ma, Xiaojing Ma, Wei Sheng, Guoying Huang
Heterotaxy syndrome (HTX) is characterized by left-right (LR) asymmetry disturbances associated with severe heart malformations. However, the exact genetic cause of HTX pathogenesis remains unclear. The aim of this study was to investigate the pathogenic mechanism underlying heterotaxy syndrome. Targeted next-generation sequencing (NGS) was performed for twenty-two candidate genes correlated with LR axis development in sixty-six HTX patients from unrelated families. Variants were filtered from databases and predicted in silico using prediction programs...
August 17, 2018: Scientific Reports
Suzanne E de Bruijn, Sanne K Verbakel, Erik de Vrieze, Hannie Kremer, Frans P M Cremers, Carel B Hoyng, L Ingeborgh van den Born, Susanne Roosing
BACKGROUND: Retinitis pigmentosa (RP) shows substantial genetic heterogeneity. It has been estimated that in approximately 60%-80% of RP cases, the genetic diagnosis can be found using whole exome sequencing (WES). In this study, the purpose was to identify causative variants in individuals with genetically unexplained retinal disease, which included one consanguineous family with two affected siblings and one case with RP. METHODS: To identify the genetic defect, WES was performed in both probands, and clinical analysis was performed...
August 17, 2018: Journal of Medical Genetics
Bea Unterer, Veit Wiesmann, Mekala Gunasekaran, Heinrich Sticht, Clara Tenkerian, Jürgen Behrens, Maria Leone, Felix B Engel, Nathalie Britzen-Laurent, Elisabeth Naschberger, Thomas Wittenberg, Michael Stürzl
Interferon-gamma (IFN‑γ) is a pleiotropic cytokine that exerts important functions in inflammation, infectious diseases and cancer. The large GTPase human guanylate-binding protein 1 (GBP‑1) is among the most strongly IFN‑γ-induced cellular proteins. Previously it has been shown that GBP-1 mediates manifold cellular responses to IFN‑γ including the inhibition of proliferation, spreading, migration, and invasion and through this exerts anti-tumorigenic activity. However, the mechanisms of GBP-1 anti-tumorigenic activities remain poorly understood...
August 17, 2018: Biochemical Journal
Wilbur H Chen, Kathleen M Neuzil, C Rebecca Boyce, Marcela F Pasetti, Mardi K Reymann, Lionel Martellet, Nancy Hosken, F Marc LaForce, Rajeev M Dhere, Sambhaji S Pisal, Amol Chaudhari, Prasad S Kulkarni, Ray Borrow, Helen Findlow, Valerie Brown, Megan L McDonough, Len Dally, Mark R Alderson
BACKGROUND: Invasive meningococcal disease is an important public health problem, especially in sub-Saharan Africa. After introduction of MenAfriVac in 2010, Neisseria meningitidis serogroup A disease has been almost eliminated from the region. However, serogroups C, W, Y, and X continue to cause disease outbreaks. We assessed the NmCV-5 pentavalent meningococcal conjugate vaccine targeting A, C, Y, W, and X serogroups in a first-in-man, phase 1 study. METHODS: We did a single-centre, double-blind, randomised controlled trial at a research clinic in Baltimore (MD, USA)...
August 14, 2018: Lancet Infectious Diseases
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