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Mutational load

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https://www.readbyqxmd.com/read/28926605/assessment-of-common-somatic-mutations-of-egfr-kras-braf-nras-in-pulmonary-non-small-cell-carcinoma-using-iplex%C3%A2-hs-a-new-highly-sensitive-assay-for-the-massarray%C3%A2-system
#1
Bobbie C Sutton, Ryan T Birse, Kevin Maggert, Tammy Ray, Jessica Hobbs, Amobi Ezenekwe, Jason Kazmierczak, Michael Mosko, Joan Kish, Andrew Bullock, Zonggao Shi, M Sharon Stack, Darryl Irwin
Increased early detection and personalized therapy for lung cancer have coincided with greater use of minimally invasive sampling techniques such as endobronchial ultrasound-guided biopsy (EBUS), endoscopic ultrasound-guided biopsy (EUS), and navigational biopsy, as well as thin needle core biopsies. As many lung cancer patients have late stage disease and other comorbidities that make open surgical procedures hazardous, the least invasive biopsy technique with the highest potential specimen yield is now the preferred first diagnostic study...
2017: PloS One
https://www.readbyqxmd.com/read/28926145/a-crispr-reimagining-new-twists-and-turns-of-crispr-beyond-the-genome-engineering-revolution
#2
Robert J Plummer, Yi Guo, Ying Peng
Despite its explosive applications in genome engineering, CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) has been developed into a versatile tool beyond its well-known nuclease function. In this prospect article, we summarize a few exciting "off-label" applications of CRISPR including manipulating DNA sequences, visualizing chromosomal loci in living cells, and modulating transcription and chromatin structures. These novel applications will likely elevate CRISPR tools into yet another level of sophistication and diversity, leading to many more exciting cell biological discoveries...
September 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28925530/the-role-of-a-cytoplasmic-loop-of-mota-in-load-dependent-assembly-and-disassembly-dynamics-of-the-mota-b-stator-complex-in-the-bacterial-flagellar-motor
#3
Seyedeh Noorolhoda Shajari Pourjaberi, Naoya Terahara, Keiichi Namba, Tohru Minamino
The proton-driven flagellar motor of Salmonella enterica can accommodate a dozen MotA/B stators in a load-dependent manner. The C-terminal periplasmic domain of MotB acts as a structural switch to regulate the number of active stators in the motor in response to load change. The cytoplasmic loop termed MotAC is responsible for the interaction with a rotor protein, FliG. Here, to test if MotAC is responsble for stator assembly around the rotor in a load-dependent manner, we analyzed the effect of MotAC mutations, M76V, L78W, Y83C, Y83H, I126F, R131L, A145E and E155K, on motor performance over a wide range of external load...
September 19, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28920005/the-frequency-of-neoantigens-per-somatic-mutation-rather-than-overall-mutational-load-or-number-of-predicted-neoantigens-per-se-is-a-prognostic-factor-in-ovarian-clear-cell-carcinoma
#4
Hirokazu Matsushita, Kosei Hasegawa, Katsutoshi Oda, Shogo Yamamoto, Akira Nishijima, Yuichi Imai, Kayo Asada, Yuji Ikeda, Takahiro Karasaki, Keiichi Fujiwara, Hiroyuki Aburatani, Kazuhiro Kakimi
Neoantigens derived from tumor-specific somatic mutations are excellent targets for anti-tumor immune responses. In ovarian clear cell carcinoma (OCCC), checkpoint blockade yields durable responses in a subset of patients. To approach the question of why only some patients respond, we first investigated neoantigen loads and immune signatures using exome sequencing and expression array data for 74 OCCC patients treated conventionally. Neither the number of missense mutations nor total predicted neoantigens assessed in the tumor correlated with clinical outcomes...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28917978/sen1500-a-novel-oral-amyloid-%C3%AE-aggregation-inhibitor-attenuates-brain-pathology-in-a-mouse-model-of-alzheimer-s-disease
#5
D Brunner, S Flunkert, J Neddens, S Duller, D I C Scopes, J M Treherne, B Hutter-Paier
INTRODUCTION: Amyloid-β (Aβ) aggregation is thought to be a major pathogenic event underlying the neuropathology of Alzheimer's disease (AD). The development of new drugs inhibiting the Aβ aggregation process is, therefore, important. SEN1500, an orally bioavailable and CNS-penetrant Aβ aggregation inhibitor, has previously been shown to reduce spatial learning and memory deficits in an APP transgenic mouse model. To verify that the pharmacological properties of SEN1500 are not unique to this model, we investigated brain Aβ pathology, neuroinflammation, as well as memory in a different mouse model of AD expressing the human amyloid precursor protein with Swedish and London mutations (APPSL)...
September 13, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28917639/protein-oxidation-involved-in-cys-tyr-post-translational-modification
#6
Susan E Hromada, Adam M Hilbrands, Elysa M Wolf, Jackson L Ross, Taylor R Hegg, Andrew G Roth, Matthew T Hollowell, Carolyn E Anderson, David E Benson
Some post-translationally modified tyrosines can perform reversible redox chemistry similar to metal cofactors. The most studied of these tyrosine modifications is the intramolecular thioether-crosslinked 3'-(S-cysteinyl)-tyrosine (Cys-Tyr) in galactose oxidase. This Cu-mediated tyrosine modification in galactose oxidase involves direct electron transfer (inner-sphere) to the coordinated tyrosine. Mammalian cysteine dioxygenase enzymes also contain a Cys-Tyr that is formed, presumably, through outer-sphere electron transfer from a non-heme iron center ~6Å away from the parent residues...
September 14, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28917518/genome-stability-of-programmed-stem-cell-products
#7
REVIEW
Ulrich Martin
Inherited and acquired genomic abnormalities are known to cause genetic diseases and contribute to cancer formation. Recent studies demonstrated a substantial mutational load in mouse and human embryonic and induced pluripotent stem cells (ESCs and iPSCs). Single nucleotide variants, copy number variations, and larger chromosomal abnormalities may influence the differentiation capacity of pluripotent stem cells and the functionality of their derivatives in disease modelling and drug screening, and are considered a serious risk for cellular therapies based on ESC or iPSC derivatives...
September 13, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/28914798/genome-instability-and-%C3%AE-h2ax
#8
REVIEW
Anastasios Georgoulis, Constantinos E Vorgias, George P Chrousos, Emmy P Rogakou
γH2AX has emerged in the last 20 years as a central player in the DDR (DNA damage response), with specificity for DSBs (double-strand breaks). Upon the generation of DSBs, γ-phosphorylation extends along megabase-long domains in chromatin, both sides of the damage. The significance of this mechanism is of great importance; it depicts a biological amplification mechanism where one DSB induces the γ-phosphorylation of thousands of H2AX molecules along megabaselong domains of chromatin, that are adjusted to the sites of DSBs...
September 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28912673/improving-the-delivery-of-sod1-antisense-oligonucleotides-to-motor-neurons-using-calcium-phosphate-lipid-nanoparticles
#9
Liyu Chen, Clare Watson, Marco Morsch, Nicholas J Cole, Roger S Chung, Darren N Saunders, Justin J Yerbury, Kara L Vine
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease affecting the upper and lower motor neurons in the motor cortex and spinal cord. Abnormal accumulation of mutant superoxide dismutase I (SOD1) in motor neurons is a pathological hallmark of some forms of the disease. We have shown that the orderly progression of the disease may be explained by misfolded SOD1 cell-to-cell propagation, which is reliant upon its active endogenous synthesis. Reducing the levels of SOD1 is therefore a promising therapeutic approach...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28912405/-exploring-the-possibility-of-new-biomarkers-of-immune-checkpoint-inhibitors-for-non-small-cell-lung-cancer-nsclc
#10
Yuki Owada, Takuya Inoue, Yuzuru Watanabe, Mitsuro Fukuhara, Takumi Yamaura, Satoshi Muto, Yuki Matsumura, Takeo Hasegawa, Daisuke Tanaka, Ryo Kanno, Emi Ito, Hideaki Nanamiya, Junichi Imai, Takao Isogai, Shinya Watanabe, Hiroyuki Suzuki
Mutation burden in a tumor, presumably involving neo-antigens in the tumor tissue, is also thought to be one of the better predictors for the efficacy of immune checkpoint inhibitors. However, it is difficult to analyze the mutation burden routinely in the clinic. Here, we describe more convenient factors that can be used as surrogate markers of mutation burden. Ninety-four patients with NSCLC who underwent resection in our institution were recruited for this study. Mutation burden and major gene alterations were analyzed by using next generation sequencing...
September 2017: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/28912396/-immune-checkpoint-inhibitors-for-lung-cancer-with-egfr-mutation
#11
Hidetoshi Hayashi, Tetsuya Mitsudomi
Recent clinical evidence that anti-PD-1/PD-L1 antibody therapy is superior to cytotoxic chemotherapy for patients with non-small cell lung cancer(NSCLC)that expresses PD-L1 has lead to a paradigm shift in treatment strategies for those patients. However, efficacy of anti-PD-1/PD-L1 antibodies for patients with NSCLC harboring EGFR mutation is generally poor. This lack ofresponse is at least partially attributed to suppression oftumor infiltrating lymphocytes caused by EGFR pathway activation or to low non-synonymous mutation load in NSCLC with EGFR mutation...
September 2017: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/28911086/large-scale-prospective-screening-of-egfr-mutations-in-the-blood-of-advanced-nsclc-patients-to-guide-treatment-decisions
#12
C Mayo-de-Las-Casas, N Jordana-Ariza, M Garzón-Ibañez, A Balada-Bel, J Bertrán-Alamillo, S Viteri-Ramírez, N Reguart, M A Muñoz-Quintana, P Lianes-Barragan, C Camps, E Jantús, J Remon-Massip, S Calabuig, D Aguiar, M L Gil, N Viñolas, A K Santos-Rodríguez, M Majem, B García-Peláez, S Villatoro, A Pérez-Rosado, J C Monasterio, E Ovalle, M J Catalán, R Campos, D Morales-Espinosa, A Martínez-Bueno, M González-Cao, X González, I Moya-Horno, A E Sosa, N Karachaliou, R Rosell, M A Molina-Vila
Background: In a significant percentage of advanced non-small-cell lung cancer (NSCLC) patients, tumor tissue is unavailable or insufficient for genetic analyses. We prospectively analyzed if circulating-free DNA (cfDNA) purified from blood can be used as a surrogate in this setting to select patients for treatment with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). Patients and methods: Blood samples were collected in 119 hospitals from 1138 advanced NSCLC patients at presentation (n = 1033) or at progression to EGFR-TKIs (n = 105) with no biopsy or insufficient tumor tissue...
September 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28906532/the-aetiology-of-cardiovascular-disease-a-role-for-mitochondrial-dna
#13
REVIEW
Marianne Venter, Francois H van der Westhuizen, Joanna L Elson
Cardiovascular disease (CVD) is a world-wide cause of mortality in humans and its incidence is on the rise in Africa. In this review, we discuss the putative role of mitochondrial dysfunction in the aetiology of CVD and consequently identify mitochondrial DNA (mtDNA) variation as a viable genetic risk factor to be considered. We then describe the contribution and pitfalls of several current approaches used when investigating mtDNA in relation to complex disease. We also propose an alternative approach, the adjusted mutational load hypothesis, which would have greater statistical power with cohorts of moderate size, and is less likely to be affected by population stratification...
August 25, 2017: Cardiovascular Journal of Africa
https://www.readbyqxmd.com/read/28899102/community-based-antiretroviral-treatment-in-rural-zimbabwe
#14
Benjamin Chimukangara, Justen Manasa, Rebecca Mitchell, Georgina Nyabadza, David Katzenstein, Collen Masimirembwa
INTRODUCTION: Treatment of HIV has reduced HIV/AIDS-related mortality. Sustaining >90% virologic suppression in sub-Saharan Africa requires decentralized care and prevention services to rural communities. In Zimbabwe, the number of people receiving ART has increased rapidly. However, access to treatment monitoring tools such as viral load and drug resistance testing is limited. We assessed virologic treatment outcomes among ART recipients in Nyamutora, a rural community receiving bimonthly ART and prevention services...
September 13, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28898438/collagen-xi-mutation-lowers-susceptibility-to-load-induced-cartilage-damage-in-mice
#15
Derek T Holyoak, Miguel Otero, Naa Shidaa Armar, Sophia N Ziemian, Ariana Otto, Devinne Cullinane, Timothy M Wright, Steven R Goldring, Mary B Goldring, Marjolein C H van der Meulen
Interactions among risk factors for osteoarthritis (OA) are not well understood. We investigated the combined impact of two prevalent risk factors: mechanical loading and genetically abnormal cartilage tissue properties. We used cyclic tibial compression to simulate mechanical loading in the cho/+ (Col11a1 haploinsufficient) mouse, which has abnormal collagen fibrils in cartilage due to a point mutation in the Col11a1 gene. We hypothesized that the mutant collagen would not alter phenotypic bone properties and that cho/+ mice, which develop early onset OA, would develop enhanced load-induced cartilage damage compared to their littermates...
September 12, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28893855/mitigating-mitochondrial-genome-erosion-without-recombination
#16
Arunas L Radzvilavicius, Hanna Kokko, Joshua R Christie
Mitochondria are ATP-producing organelles of bacterial ancestry that played a key role in the origin and early evolution of complex eukaryotic cells. Most modern eukaryotes transmit mitochondrial genes uniparentally, often without recombination among genetically divergent organelles. While this asymmetric inheritance maintains the efficacy of purifying selection at the level of the cell, the absence of recombination could also make the genome susceptible to Muller's ratchet. How mitochondria escape this irreversible defect accumulation is a fundamental unsolved question...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28893561/genotyping-of-single-nucleotide-polymorphism-by-probe-gated-silica-nanoparticles
#17
Meltem Ercan, Veli C Ozalp, Bilge G Tuna
The development of simple, reliable, and rapid approaches for molecular detection of common mutations is important for prevention and early diagnosis of genetic diseases, including Thalessemia. Oligonucleotide-gated mesoporous nanoparticles-based analysis is a new platform for mutation detection that has the advantages of sensitivity, rapidity, accuracy, and convenience. A specific mutation in β-thalassemia, one of the most prevalent inherited diseases in several countries, was used as model disease in this study...
September 8, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28890504/an-alarmingly-high-proportion-of-anti-retroviral-drugs-resistant-hiv-1-infection-among-high-risk-groups-in-central-vietnam-a-sub-study-of-the-national-sentinel-survey
#18
Hung Thai Do, Dong Thanh Nguyen, Lan Anh Thi Nguyen, Duong Huy Do, Huy Xuan Le, Xuan Mai Thi Trinh, Hong Vy Nu Ton, Ikumi Sawada, Noriko Kitamura, Nhat Minh Le, Keisuke Yoshihara, Thu Huong Thi Phan, Chien Trong Bui, Koya Ariyoshi, Lay Myint Yoshida
We investigated the prevalence of HIV drug resistance among high risk groups such as injecting drug user (IDU), female sex worker (FSW) and men having sex with men (MSM) in central Vietnam. We used HIV positive samples from 2012-2013 sentinel surveillance surveys. Study subjects were screened for HIV infection by standardized screening assays and the positive samples were further tested for HIV viral load and drug resistant mutations by in-house assays. Drug resistant mutations (DRMs) were determined using the Stanford University online sequence analysis tool...
September 11, 2017: Japanese Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28888924/mesothelin-specific-immune-responses-predict-survival-of-patients-with-brain-metastasis
#19
Liu Zhenjiang, Martin Rao, Xiaohua Luo, Elisabeth Sandberg, Jiri Bartek, Esther Schoutrop, Anna von Landenberg, Qingda Meng, Davide Valentini, Thomas Poiret, Georges Sinclair, Inti-Harvey Peredo, Ernest Dodoo, Markus Maeurer
BACKGROUND: Patients with advanced malignancies, e.g. lung cancer, ovarian cancer or melanoma, frequently present with brain metastases. Clinical presentation and disease progression of cancer is in part shaped by the interaction of the immune system with malignant cells. Antigen-targeted immune responses have been implicated in the prolonged survival of patients with cancer. This includes the tumor-associated antigen (TAA) mature mesothelin, a 40kDa cell surface-bound antigen that is overexpressed in several malignancies including lung ovarian and pancreatic cancer...
August 30, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28884263/efficient-propagation-of-archetype-jc-polyomavirus-in-cos-7-cells-evaluation-of-rearrangements-within-the-nccr-structural-organization-after-transfection
#20
Carla Prezioso, Daniela Scribano, Anna Bellizzi, Elena Anzivino, Donatella Maria Rodio, Maria Trancassini, Anna Teresa Palamara, Valeria Pietropaolo
John Cunningham virus (JCPyV) is an ubiquitous human pathogen that causes disease in immunocompromised patients. The JCPyV genome is composed of an early region and a late region, which are physically separated by the non-coding control region (NCCR). The DNA sequence of the NCCR distinguishes two forms of JCPyV, the designated archetype and the prototype, which resulted from a rearrangement of the archetype sequence. To date, the cell culture systems for propagating JCPyV archetype have been very limited in their availability and robustness...
September 7, 2017: Archives of Virology
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