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https://www.readbyqxmd.com/read/29334376/positively-selected-enhancer-elements-endow-osteosarcoma-cells-with-metastatic-competence
#1
James J Morrow, Ian Bayles, Alister P W Funnell, Tyler E Miller, Alina Saiakhova, Michael M Lizardo, Cynthia F Bartels, Maaike Y Kapteijn, Stevephen Hung, Arnulfo Mendoza, Gursimran Dhillon, Daniel R Chee, Jay T Myers, Frederick Allen, Marco Gambarotti, Alberto Righi, Analisa DiFeo, Brian P Rubin, Alex Y Huang, Paul S Meltzer, Lee J Helman, Piero Picci, Henri Versteeg, John Stamatoyannopolus, Chand Khanna, Peter C Scacheri
Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in enhancer activity between primary and metastatic human tumors and between near isogenic pairs of highly lung metastatic and nonmetastatic osteosarcoma cell lines. We term these regions metastatic variant enhancer loci (Met-VELs)...
January 15, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29334356/p53-suppresses-mutagenic-rad52-and-pol%C3%AE-pathways-by-orchestrating-dna-replication-restart-homeostasis
#2
Sunetra Roy, Karl-Heinz Tomaszowski, Jessica W Luzwick, Soyoung Park, Jun Li, Maureen Murphy, Katharina Schlacher
Classically, p53 tumor suppressor acts in transcription, apoptosis, and cell cycle arrest. Yet, replication-mediated genomic instability is integral to oncogenesis, and p53 mutations promote tumor progression and drug-resistance. By delineating human and murine separation-of-function p53 alleles, we find that p53 null and gain-of-function (GOF) mutations exhibit defects in restart of stalled or damaged DNA replication forks driving genomic instability genetically separable from transcription activation. By assaying protein-DNA fork interactions in single cells, we unveil a p53-MLL3-enabled recruitment of MRE11 DNA replication restart nuclease...
January 15, 2018: ELife
https://www.readbyqxmd.com/read/29331262/can-interrogation-of-tumour-characteristics-lead-us-to-safely-omit-adjuvant-radiotherapy-in-patients-with-early-breast-cancer
#3
I S Bhattacharya, A M Kirby, J M Bliss, C E Coles
Adjuvant radiotherapy after breast-conserving surgery has been an important component of the standard of care for early breast cancer. Improvements in breast cancer care have resulted in a substantial reduction in local relapse rates over recent decades. Although the proportional benefits of adjuvant radiotherapy are similar for different prognostic risk groups of patients, the absolute benefits depend on the risk of relapse and therefore vary considerably between prognostic groups. Radiotherapy is not without risk and for some patients at very low risk of relapse the risks of radiotherapy may outweigh the benefit, leading to potential overtreatment...
January 10, 2018: Clinical Oncology: a Journal of the Royal College of Radiologists
https://www.readbyqxmd.com/read/29331171/the-genotypic-and-phenotypic-spectrum-of-mto1-deficiency
#4
James J O'Byrne, Maja Tarailo-Graovac, Aisha Ghani, Michael Champion, Charu Deshpande, Ali Dursun, Riza K Ozgul, Peter Freisinger, Ian Garber, Tobias B Haack, Rita Horvath, Ivo Barić, Ralf A Husain, Leo A J Kluijtmans, Urania Kotzaeridou, Andrew A Morris, Colin J Ross, Saikat Santra, Jan Smeitink, Mark Tarnopolsky, Saskia B Wortmann, Johannes A Mayr, Michaela Brunner-Krainz, Holger Prokisch, Wyeth W Wasserman, Ron A Wevers, Udo F Engelke, Richard J Rodenburg, Teck Wah Ting, Robert McFarland, Robert W Taylor, Ramona Salvarinova, Clara D M van Karnebeek
BACKGROUND: Mitochondrial diseases, a group of multi-systemic disorders often characterized by tissue-specific phenotypes, are usually progressive and fatal disorders resulting from defects in oxidative phosphorylation. MTO1 (Mitochondrial tRNA Translation Optimization 1), an evolutionarily conserved protein expressed in high-energy demand tissues has been linked to human early-onset combined oxidative phosphorylation deficiency associated with hypertrophic cardiomyopathy, often referred to as combined oxidative phosphorylation deficiency-10 (COXPD10)...
January 2018: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29330334/detection-of-heterozygous-mutation-in-hook-microtubule-tethering-protein-1-in-three-patients-with-decapitated-and-decaudated-spermatozoa-syndrome
#5
Huixing Chen, Yong Zhu, Zijue Zhu, Erlei Zhi, Keming Lu, Xiaobo Wang, Feng Liu, Zheng Li, Weiliang Xia
BACKGROUND: The mechanism of intramanchette transport is crucial to the transformation of sperm tail and the nuclear condensation during spermiogenesis. Although few dysfunctional proteins could result in abnormal junction between the head and tail of spermatozoon, little is known about the genetic cues in this process. OBJECTIVE: Based on patients with severe decapitated and decaudated spermatozoa (DDS) syndrome, the study aimed to validate whether new mutation exists on their Hook microtubule-tethering protein 1 (HOOK1) genes and follow their results of assisted reproduction treatment (ART)...
January 12, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29330025/the-role-of-extracellular-and-intracellular-nicotinamide-phosphoribosyl-transferase-in-cancer-diagnostic-and-therapeutic-perspectives-and-challenges
#6
REVIEW
Maria Dalamaga, Gerasimos Socrates Christodoulatos, Christos S Mantzoros
Nicotinamide phosphoribosyl-transferase (Nampt) or pre-B cell colony-enhancing factor or visfatin represents a pleiotropic molecule acting as an enzyme, a cytokine and a growth factor. Intracellular Nampt plays an important role in cellular bioenergetics and metabolism, particularly NAD biosynthesis. NAD biosynthesis is critical in DNA repair, oncogenic signal transduction, transcription, genomic integrity and apoptosis. Although its insulin-mimetic function remains a controversial issue, extracellular Nampt presents proliferative, anti-apoptotic, pro-inflammatory, pro-angiogenic and metastatic properties...
January 9, 2018: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/29329368/discovering-personalized-driver-mutation-profiles-of-single-samples-in-cancer-by-network-control-strategy
#7
Wei-Feng Guo, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qian-Qian Shi, Lei Zhang, Ying Tang, Tao Zeng, Luonan Chen
Motivation: It is a challenging task to discover personalized driver genes that provide crucial information on disease risk and drug sensitivity for individual patients. However, few methods have been proposed to identify the personalized-sample driver genes from the cancer omics data due to the lack of samples for each individual. To circumvent this problem, here we present a novel single-sample controller strategy (SCS) to identify personalized driver mutation profiles from network controllability perspective...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29329300/symmetric-dimeric-bisbenzimidazoles-dbp-n-reduce-methylation-of-rarb-and-pten-while-significantly-increase-methylation-of-rrna-genes-in-mcf-7-cancer-cells
#8
Svetlana V Kostyuk, Margarita A Kvasha, Daria A Khrabrova, Olga V Kirsanova, Elizaveta S Ershova, Elena M Malinovskaya, Natalia N Veiko, Alexander A Ivanov, Vasiliy S Koval, Alexei L Zhuze, Vadim H Tashlitsky, Pavel E Umriukhin, Sergey I Kutsev, Elizaveta S Gromova
BACKGROUND: Hypermethylation is observed in the promoter regions of suppressor genes in the tumor cancer cells. Reactivation of these genes by demethylation of their promoters is a prospective strategy of the anticancer therapy. Previous experiments have shown that symmetric dimeric bisbenzimidazoles DBP(n) are able to block DNA methyltransferase activities. It was also found that DBP(n) produces a moderate effect on the activation of total gene expression in HeLa-TI population containing epigenetically repressed avian sarcoma genome...
2018: PloS One
https://www.readbyqxmd.com/read/29329208/advances-in-molecular-profiling-and-categorisation-of-pancreatic-adenocarcinoma-and-the-implications-for-therapy
#9
REVIEW
Rille Pihlak, Jamie M J Weaver, Juan W Valle, Mairéad G McNamara
Pancreatic ductal adenocarcinoma (PDAC) continues to be a disease with poor outcomes and short-lived treatment responses. New information is emerging from genome sequencing identifying potential subgroups based on somatic and germline mutations. A variety of different mutations and mutational signatures have been identified; the driver mutation in around 93% of PDAC is KRAS, with other recorded alterations being SMAD4 and CDKN2A. Mutations in the deoxyribonucleic acid (DNA) damage repair pathway have also been investigated in PDAC and multiple clinical trials are ongoing with DNA-damaging agents...
January 12, 2018: Cancers
https://www.readbyqxmd.com/read/29329112/master-protocols-in-lung-cancer-experience-from-lung-master-protocol
#10
Vincent K Lam, Vassiliki Papadimitrakopoulou
PURPOSE OF REVIEW: Contemporary advances in the understanding of the molecular and immunologic basis of metastatic lung cancer have firmly changed its treatment paradigm to a personalized, biomarker-driven approach. However, the majority of lung-cancer patients [especially lung squamous cell carcinoma (LUSC)] still do not have effective targeted therapeutic options. Master protocols, such as Lung-MAP, represent an innovative clinical trial approach designed to accelerate evaluation of novel biomarker-driven therapies...
January 10, 2018: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29328507/genetics-of-immune-mediated-inflammatory-diseases
#11
REVIEW
Trixy David, Stephanie Ling, Anne Barton
Immune-mediated inflammatory diseases (IMIDs) are characterised by dysregulation of the normal immune response, which leads to inflammation. Together, they account for a high disease burden in the population, given that they are usually chronic conditions with associated co-morbidities. Examples include systemic lupus erythematosus, rheumatoid arthritis, Crohn's disease and type 1 diabetes. Since the advent of genome-wide association studies, evidence of considerable genetic overlap in the loci predisposing to a wide range of IMIDs has emerged...
January 12, 2018: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/29328368/identification-of-significant-biomarkers-and-pathways-associated-with-gastric-carcinogenesis-by-whole-genome-wide-expression-profiling-analysis
#12
Hong-Jun Fei, Song-Chang Chen, Jun-Yu Zhang, Shu-Yuan Li, Lan-Lan Zhang, Yi-Yao Chen, Chun-Xin Chang, Chen-Ming Xu
The incidence of gastric cancer (GC) is extremely high in East Asia. GC is also one of the most common and lethal forms of cancer from a global perspective. However, to date, we have not been able to determine one or several genes as biomarkers in the diagnosis of GC and have also been unable to identify the genes which are important in the therapy of GC. In this study, we analyzed all genome-wide expression profiling arrays uploaded onto the Gene Expression Omnibus (GEO) database to filtrate the differentially expressed genes (DEGs) between normal stomach tissues and GC tissues...
January 11, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29327716/genomic-heterogeneity-of-alk-fusion-breakpoints-in-non-small-cell-lung-cancer
#13
Jason N Rosenbaum, Ryan Bloom, Jason T Forys, Jeff Hiken, Jon R Armstrong, Julie Branson, Samantha McNulty, Priya D Velu, Kymberlie Pepin, Haley Abel, Catherine E Cottrell, John D Pfeifer, Shashikant Kulkarni, Ramaswamy Govindan, Eric Q Konnick, Christina M Lockwood, Eric J Duncavage
In lung adenocarcinoma, canonical EML4-ALK inversion results in a fusion protein with a constitutively active ALK kinase domain. Evidence of ALK rearrangement occurs in a minority (2-7%) of lung adenocarcinoma, and only ~60% of these patients will respond to targeted ALK inhibition by drugs such as crizotinib and ceritinib. Clinically, targeted anti-ALK therapy is often initiated based on evidence of an ALK genomic rearrangement detected by fluorescence in situ hybridization (FISH) of interphase cells in formalin-fixed, paraffin-embedded tissue sections...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29326307/mycophenolate-mofetil-in-combination-with-steroids-for-treatment-of-c3-glomerulopathy-a-case-series
#14
Rupali S Avasare, Pietro A Canetta, Andrew S Bomback, Maddalena Marasa, Yasar Caliskan, Yasemin Ozluk, Yifu Li, Ali G Gharavi, Gerald B Appel
BACKGROUND AND OBJECTIVES: C3 glomerulopathy is a form of complement-mediated GN. Immunosuppressive therapy may be beneficial in the treatment of C3 glomerulopathy. Mycophenolate mofetil is an attractive treatment option given its role in the treatment of other complement-mediated diseases and the results of the Spanish Group for the Study of Glomerular Diseases C3 Study. Here, we study the outcomes of patients with C3 glomerulopathy treated with steroids and mycophenolate mofetil. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: We conducted a retrospective chart review of patients in the C3 glomerulopathy registry at Columbia University and identified patients treated with mycophenolate mofetil for at least 3 months and follow-up for at least 1 year...
January 11, 2018: Clinical Journal of the American Society of Nephrology: CJASN
https://www.readbyqxmd.com/read/29326244/gene-therapy-comes-of-age
#15
REVIEW
Cynthia E Dunbar, Katherine A High, J Keith Joung, Donald B Kohn, Keiya Ozawa, Michel Sadelain
After almost 30 years of promise tempered by setbacks, gene therapies are rapidly becoming a critical component of the therapeutic armamentarium for a variety of inherited and acquired human diseases. Gene therapies for inherited immune disorders, hemophilia, eye and neurodegenerative disorders, and lymphoid cancers recently progressed to approved drug status in the United States and Europe, or are anticipated to receive approval in the near future. In this Review, we discuss milestones in the development of gene therapies, focusing on direct in vivo administration of viral vectors and adoptive transfer of genetically engineered T cells or hematopoietic stem cells...
January 12, 2018: Science
https://www.readbyqxmd.com/read/29325989/proteomic-analysis-reveals-the-important-roles-of-alpha-5-collagen-and-atp5%C3%AE-during-skin-ulceration-syndrome-progression-of-sea-cucumber-apostichopus-japonicus
#16
Zelong Zhao, Jingwei Jiang, Yongjia Pan, Hongjuan Sun, Xiaoyan Guan, Shan Gao, Zhong Chen, Ying Dong, Zunchun Zhou
Apostichopus japonicus is one of the most important aquaculture species in China. Skin ulceration syndrome (SUS) of sea cucumber is a common and serious disease affected the development of A. japonicus culture industry. To better understand the response mechanisms of A. japonicus during SUS progression, the protein variations in the body wall of A. japonicus at different stages of SUS were investigated by a comparative proteomic approach based on isobaric tags for relative and absolute quantification. A total of 1449 proteins were identified from the samples at different SUS stages...
January 8, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29325609/the-cag-polyglutamine-repeat-diseases-a-clinical-molecular-genetic-and-pathophysiologic-nosology
#17
Colleen A Stoyas, Albert R La Spada
Throughout the genome, unstable tandem nucleotide repeats can expand to cause a variety of neurologic disorders. Expansion of a CAG triplet repeat within a coding exon gives rise to an elongated polyglutamine (polyQ) tract in the resultant protein product, and accounts for a unique category of neurodegenerative disorders, known as the CAG-polyglutamine repeat diseases. The nine members of the CAG-polyglutamine disease family include spinal and bulbar muscular atrophy (SBMA), Huntington disease, dentatorubral pallidoluysian atrophy, and six spinocerebellar ataxias (SCA 1, 2, 3, 6, 7, and 17)...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325072/sensitive-and-specific-post-call-filtering-of-genetic-variants-in-xenograft-and-primary-tumors
#18
Brian K Mannakee, Uthra Balaji, Agnieszka K Witkiewicz, Ryan N Gutenkunst, Erik S Knudsen
Motivation: Tumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination can generate many spurious calls when sequencing patient-derived xenografts (PDXs). Paralogous genome sequences can also generate spurious calls when sequencing any tumor. We developed a BLAST-based algorithm, MAPEX, to identify and filter out spurious calls from both these sources. Results: When calling variants from xenografts, MAPEX has similar sensitivity and specificity to more complex algorithms...
January 8, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29325035/amplicon-based-next-generation-sequencing-of-plasma-cell-free-dna-for-detection-of-driver-and-resistance-mutations-in-advanced-non-small-cell-lung-cancer
#19
N Guibert, Y Hu, N Feeney, Y Kuang, V Plagnol, G Jones, K Howarth, J F Beeler, C P Paweletz, G R Oxnard
Background: Genomic analysis of plasma cell-free DNA is transforming lung cancer care, however available assays are limited by cost, turnaround time, and imperfect accuracy. Here we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC). Methods: Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1 and other rare genotypes) were collected while on therapy and analyzed, blinded to tumor genotype...
January 9, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29324842/effect-of-analytical-treatment-interruption-and-reinitiation-of-antiretroviral-therapy-on-hiv-reservoirs-and-immunologic-parameters-in-infected-individuals
#20
Katherine E Clarridge, Jana Blazkova, Kevin Einkauf, Mary Petrone, Eric W Refsland, J Shawn Justement, Victoria Shi, Erin D Huiting, Catherine A Seamon, Guinevere Q Lee, Xu G Yu, Susan Moir, Michael C Sneller, Mathias Lichterfeld, Tae-Wook Chun
Therapeutic strategies aimed at achieving antiretroviral therapy (ART)-free HIV remission in infected individuals are under active investigation. Considering the vast majority of HIV-infected individuals experience plasma viral rebound upon cessation of therapy, clinical trials evaluating the efficacy of curative strategies would likely require inclusion of ART interruption. However, it is unclear what impact short-term analytical treatment interruption (ATI) and subsequent reinitiation of ART have on immunologic and virologic parameters of HIV-infected individuals...
January 2018: PLoS Pathogens
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