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https://www.readbyqxmd.com/read/28223310/overexpression-of-vitamin-d-receptor-mrna-correlates-with-poor-prognosis-in-ptc
#1
June Young Choi, Jin Wook Yi, Joon-Hyop Lee, Ra-Yeong Song, Hyeong Won Yu, Hyungju Kwon, Young Jun Chai, Su-Jin Kim, Kyu Eun Lee
The purpose of this study was to assess the relationship between vitamin D receptor (VDR) mRNA expression and prognosis in papillary thyroid cancer. RNA sequencing and somatic mutation data from TCGA (the Cancer Genome Atlas) were analyzed. VDR mRNA expression was compared to clinicopathologic variables by linear regression. Tree-based classification was applied to find VDR cutoff and patients were split into low and high VDR group. Logistic regression, Kaplan-Meier analysis, differentially expressed gene (DEG) test, and pathway analysis were performed to assess differences between groups...
February 21, 2017: Endocrine Connections
https://www.readbyqxmd.com/read/28222777/identification-of-somatic-and-germ-line-dicer1-mutations-in-pleuropulmonary-blastoma-cystic-nephroma-and-rhabdomyosarcoma-tumors-within-a-dicer1-syndrome-pedigree
#2
Lorena Fernández-Martínez, José Antonio Villegas, Íñigo Santamaría, Ana S Pitiot, Marta G Alvarado, Soledad Fernández, Héctor Torres, Ángeles Paredes, Pilar Blay, Milagros Balbín
BACKGROUND: DICER1 syndrome is a pediatric cancer predisposition condition causing a variety of tumor types in children and young adults. In this report we studied a family with two relatives presenting a variety of neoplastic conditions at childhood. METHODS: Germ-line mutation screening of the complete coding region of the DICER1 gene in genomic DNA from the proband was performed. The presence of somatic DICER1 mutation and further alterations in driver genes was investigated in genomic DNA obtained from available tumor samples...
February 21, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28221868/somatic-brca1-2-recovery-as-a-resistance-mechanism-after-exceptional-response-to-poly-adp-ribose-polymerase-inhibition
#3
Stephanie Lheureux, Jeff P Bruce, Julia V Burnier, Katherine Karakasis, Patricia A Shaw, Blaise A Clarke, S Y Cindy Yang, Rene Quevedo, Tiantian Li, Mark Dowar, Valerie Bowering, Trevor J Pugh, Amit M Oza
Purpose Durable and long-term responses to the poly (ADP-ribose) polymerase inhibitor olaparib are observed in patients without BRCA1/2 mutations. However, beyond BRCA1/2 mutations, there are no approved biomarkers for olaparib in high-grade serous ovarian cancer (HGSOC). To determine mechanisms of durable response and resistance to olaparib therapy, we performed an analysis of HGSOC tumors from three patients without germline BRCA1/2 mutations who experienced exceptional responses to olaparib. Patients and Methods We performed integrated exome, low-pass genome, and RNA sequence analysis of tumors at diagnosis and upon relapse from patients with platinum-sensitive HGSOC recurrence who were treated > 5 years with olaparib therapy as a single agent...
February 21, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28220769/a-connexin30-mutation-rescues-hearing-and-reveals-roles-for-gap-junctions-in-cochlear-amplification-and-micromechanics
#4
Victoria A Lukashkina, Snezana Levic, Andrei N Lukashkin, Nicola Strenzke, Ian J Russell
Accelerated age-related hearing loss disrupts high-frequency hearing in inbred CD-1 mice. The p.Ala88Val (A88V) mutation in the gene coding for the gap-junction protein connexin30 (Cx30) protects the cochlear basal turn of adult CD-1Cx30(A88V/A88V) mice from degeneration and rescues hearing. Here we report that the passive compliance of the cochlear partition and active frequency tuning of the basilar membrane are enhanced in the cochleae of CD-1Cx30(A88V/A88V) compared to CBA/J mice with sensitive high-frequency hearing, suggesting that gap junctions contribute to passive cochlear mechanics and energy distribution in the active cochlea...
February 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28220485/epidemiology-of-basal-cell-carcinoma-scholarly-review
#5
REVIEW
J A C Verkouteren, K H R Ramdas, M Wakkee, T Nijsten
Basal cell carcinoma (BCC) is the most common cancer in white-skinned individuals with increasing incidence rates worldwide. Patients with BCC place a large burden on healthcare systems, because of the high incidence and the increased risk of synchronous and metachronous BCCs and other ultraviolet radiation (UVR) related skin cancers (i.e. field cancerization). As a result, the disability-adjusted life years and healthcare costs have risen significantly in recent decades. BCC is a complex disease, in which the interplay between UVR, phenotype (UVR-sensitive) and genotype (somatic mutations and germline mutations/polymorphisms) fulfils a key role in the aetiopathogenesis...
February 20, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/28218421/frameshift-mutational-target-gene-analysis-identifies-similarities-and-differences-in-constitutional-mismatch-repair-deficiency-and-lynch-syndrome
#6
Claudia Maletzki, Maja Huehns, Ingrid Bauer, Tim Ripperger, Maureen M Mork, Eduardo Vilar, Sabine Klöcking, Heike Zettl, Friedrich Prall, Michael Linnebacher
Mismatch-repair deficient (MMR-D) malignancies include Lynch Syndrome (LS), which is secondary to germline mutations in one of the MMR genes, and the rare childhood-form of constitutional mismatch repair-deficiency (CMMR-D); caused by bi-allelic MMR gene mutations. A hallmark of LS-associated cancers is microsatellite instability (MSI), characterized by coding frameshift mutations (cFSM) in target genes. By contrast, tumors arising in CMMR-D patients are thought to display a somatic mutation pattern differing from LS...
February 20, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28216139/investigation-of-braf-mutation-analysis-with-different-technical-platforms-in-metastatic-melanoma
#7
Ebru Sener, Pinar Yildirim, Ayca Tan, Ozay Gokoz, Gaye Guler Tezel
In metastatic melanoma, the detection of somatic mutations in the BRAF gene is crucial regarding patient selection for targeted therapy. Several screening methods have been developed to identify BRAF gene mutations. In this study, our objective was to evaluate the detection of the BRAF V600 mutations using two molecular methods, real-time polymerase chain (real-time PCR) assay and pyrosequencing, and immunohistochemistry (IHC), and to compare the results of these different technical platforms. This study included 98 patients diagnosed with metastatic melanoma at the Hacettepe University, Department of Pathology between 2002 and 2014...
January 21, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28215707/hsp90-shapes-the-consequences-of-human-genetic-variation
#8
Georgios I Karras, Song Yi, Nidhi Sahni, Máté Fischer, Jenny Xie, Marc Vidal, Alan D D'Andrea, Luke Whitesell, Susan Lindquist
HSP90 acts as a protein-folding buffer that shapes the manifestations of genetic variation in model organisms. Whether HSP90 influences the consequences of mutations in humans, potentially modifying the clinical course of genetic diseases, remains unknown. By mining data for >1,500 disease-causing mutants, we found a strong correlation between reduced phenotypic severity and a dominant (HSP90 ≥ HSP70) increase in mutant engagement by HSP90. Examining the cancer predisposition syndrome Fanconi anemia in depth revealed that mutant FANCA proteins engaged predominantly by HSP70 had severely compromised function...
February 16, 2017: Cell
https://www.readbyqxmd.com/read/28215400/somatic-mutations-in-tsc1-and-tsc2-cause-focal-cortical-dysplasia
#9
Jae Seok Lim, Ramu Gopalappa, Se Hoon Kim, Suresh Ramakrishna, Minji Lee, Woo-Il Kim, Junho Kim, Sang Min Park, Junehawk Lee, Jung-Hwa Oh, Heung Dong Kim, Chang-Hwan Park, Joon Soo Lee, Sangwoo Kim, Dong Seok Kim, Jung Min Han, Hoon-Chul Kang, Hyongbum Henry Kim, Jeong Ho Lee
Focal cortical dysplasia (FCD) is a major cause of the sporadic form of intractable focal epilepsies that require surgical treatment. It has recently been reported that brain somatic mutations in MTOR account for 15%-25% of FCD type II (FCDII), characterized by cortical dyslamination and dysmorphic neurons. However, the genetic etiologies of FCDII-affected individuals who lack the MTOR mutation remain unclear. Here, we performed deep hybrid capture and amplicon sequencing (read depth of 100×-20,012×) of five important mTOR pathway genes-PIK3CA, PIK3R2, AKT3, TSC1, and TSC2-by using paired brain and saliva samples from 40 FCDII individuals negative for MTOR mutations...
February 12, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28215280/molecular-mechanisms-of-somatic-hypermutation-and-class-switch-recombination
#10
S P Methot, J M Di Noia
In order to promote an efficient humoral immune response, germinal center B cells modify both the antigen recognition and effector domains by programmed genetic alterations of their antibody genes. To do so, B cells use the enzyme activation-induced deaminase (AID), which transforms deoxycytidine into deoxyuridine at the immunoglobulin genes, triggering mutagenic DNA repair. Data accumulated during the past decade have significantly advanced our understanding of how AID activity is regulated and preferentially targeted to the immunoglobulin genes...
2017: Advances in Immunology
https://www.readbyqxmd.com/read/28214862/differential-clonal-expansion-in-an-invading-cell-population-clonal-advantage-or-dumb-luck
#11
Donald F Newgreen, Dongcheng Zhang, Bevan L Cheeseman, Benjamin J Binder, Kerry A Landman
In neoplastic cell growth, clones and subclones are variable both in size and mutational spectrum. The largest of these clones are believed to represent those cells with mutations that make them the most "fit," in a Darwinian sense, for expansion in their microenvironment. Thus, the degree of quantitative clonal expansion is regarded as being determined by innate qualitative differences between the cells that originate each clone. Here, using a combination of mathematical modelling and clonal labelling experiments applied to the developmental model system of the forming enteric nervous system, we describe how cells which are qualitatively identical may consistently produce clones of dramatically different sizes: most clones are very small while a few clones we term "superstars" contribute most of the cells to the final population...
2017: Cells, Tissues, Organs
https://www.readbyqxmd.com/read/28212566/genetic-characterization-of-polish-ccrcc-patients-somatic-mutation-analysis-of-pbrm1-bap1-and-kdmc5-genomic-snp-array-analysis-in-tumor-biopsy-and-preliminary-results-of-chromosome-aberrations-analysis-in-plasma-cell-free-dna
#12
Katarzyna Kluzek, Malgorzata I Srebniak, Weronika Majer, Agnieszka Ida, Tomasz Milecki, Kinga Huminska, Robert M van der Helm, Adrian Silesian, Tomasz M Wrzesinski, Jacek Wojciechowicz, Berna H Beverloo, Zbigniew Kwias, Hans A R Bluyssen, Joanna Wesoly
BACKGROUND: Mutation analysis and cytogenetic testing in clear cell renal cell carcinoma (ccRCC) is not yet implemented in a routine diagnostics of ccRCC. MATERIAL AND METHODS: We characterized the chromosomal alterations in 83 ccRCC tumors from Polish patients using whole genome SNP genotyping assay. Moreover, the utility of next generation sequencing of cell free DNA (cfDNA) in patients plasma as a potential tool for non-invasive cytogenetic analysis was tested...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28211887/germline-mutations-predisposing-to-diffuse-large-b-cell-lymphoma
#13
REVIEW
O C Leeksma, N F de Miranda, H Veelken
Genetic studies of diffuse large B-cell lymphomas (DLBCLs) in humans have revealed numerous targets of somatic mutations and an increasing number of potentially relevant germline alterations. The latter often affect genes involved in DNA repair and/or immune function. In general, defects in these genes also predispose to other conditions. Knowledge of these mutations can lead to disease-preventing measures in the patient and relatives thereof. Conceivably, these germline mutations will be taken into account in future therapy of the lymphoma...
February 17, 2017: Blood Cancer Journal
https://www.readbyqxmd.com/read/28209900/dna-damage-is-a-pervasive-cause-of-sequencing-errors-directly-confounding-variant-identification
#14
Lixin Chen, Pingfang Liu, Thomas C Evans, Laurence M Ettwiller
Mutations in somatic cells generate a heterogeneous genomic population and may result in serious medical conditions. Although cancer is typically associated with somatic variations, advances in DNA sequencing indicate that cell-specific variants affect a number of phenotypes and pathologies. Here, we show that mutagenic damage accounts for the majority of the erroneous identification of variants with low to moderate (1 to 5%) frequency. More important, we found signatures of damage in most sequencing data sets in widely used resources, including the 1000 Genomes Project and The Cancer Genome Atlas, establishing damage as a pervasive cause of sequencing errors...
February 17, 2017: Science
https://www.readbyqxmd.com/read/28208660/splice-variants-of-the-rtk-family-their-role-in-tumour-progression-and-response-to-targeted-therapy
#15
REVIEW
Cherine Abou-Fayçal, Anne-Sophie Hatat, Sylvie Gazzeri, Beatrice Eymin
Receptor tyrosine kinases (RTKs) belong to a family of transmembrane receptors that display tyrosine kinase activity and trigger the activation of downstream signalling pathways mainly involved in cell proliferation and survival. RTK amplification or somatic mutations leading to their constitutive activation and oncogenic properties have been reported in various tumour types. Numerous RTK-targeted therapies have been developed to counteract this hyperactivation. Alternative splicing of pre-mRNA has recently emerged as an important contributor to cancer development and tumour maintenance...
February 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28205231/analysis-of-ctdna-to-predict-prognosis-and-monitor-treatment-responses-in-metastatic-pancreatic-cancer-patients
#16
He Cheng, Chen Liu, Jiahao Jiang, Guopei Luo, Yu Lu, Kaizhou Jin, Meng Guo, Zhenzhen Zhang, Jin Xu, Liang Liu, Quanxing Ni, Xianjun Yu
Cell-free circulating tumor DNA (ctDNA) in plasma has been used as a potential noninvasive biomarker for various tumors. The current study was performed to evaluate the clinical implications of ctDNA detection in patients with metastatic pancreatic cancer. Firstly, we attempted to prospectively screen a panel of 60 genes in cell-free DNA (cfDNA) from ten metastatic pancreatic cancer patients via exome sequencing. Secondly, droplet digital PCR (ddPCR) was used to identify potential mutations in a cohort of 188 patients with metastatic pancreatic cancer...
February 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28203297/therapeutic-approach-to-treating-patients-with-braf-mutant-lung-cancer-latest-evidence-and-clinical-implications
#17
REVIEW
Adrianus J de Langen, Egbert F Smit
Lung adenocarcinoma is known for its high rate of somatic mutations and genomic rearrangements. The identification of epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) rearrangements that sensitize tumors to specific drugs has changed the therapeutic approach and prognosis in these molecularly-defined subgroups. Several other key genetic alterations have been identified, of which BRAF mutations are found in 4% of non-small cell lung cancer (NSCLC) cases. Targeted drugs against BRAF and downstream MEK were recently approved for the treatment of BRAF-positive melanoma and have entered clinical evaluation in NSCLC...
January 2017: Therapeutic Advances in Medical Oncology
https://www.readbyqxmd.com/read/28202529/aberrant-syk-kinase-signaling-is-essential-for-tumorigenesis-induced-by-tsc2-inactivation
#18
Ye Cui, Wendy K Steagall, Anthony Lamattina, Gustavo Pacheco-Rodriguez, Mario Stylianou, Pranav Kidambi, Benjamin Stump, Fernanda Golzarri, Ivan O Rosas, Carmen Priolo, Elizabeth P Henske, Joel Moss, Souheil El-Chemaly
Somatic or germline mutations in the tuberous sclerosis complex (TSC) tumor suppressor genes are associated closely with the pathogenesis of lymphangioleiomyomatosis (LAM), a rare and progressive neoplastic disease that predominantly affects women in their childbearing years. Serum levels of the lymphangiogeneic growth factor VEGF-D are elevated significantly in LAM. However, there are gaps in knowledge regarding VEGF-D dysregulation and its cellular origin in LAM. Here we show that increased expression and activation of the tyrosine kinase Syk in TSC2-deficient cells and pulmonary nodules from LAM patients contributes to tumor growth...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28202519/correlates-of-prenatal-and-early-life-tobacco-smoke-exposure-and-frequency-of-common-gene-deletions-in-childhood-acute-lymphoblastic-leukemia
#19
Adam J de Smith, Maneet Kaur, Semira Gonseth, Alyson A Endicott, Steve Selvin, Luoping Zhang, Ritu Roy, Xiaorong Shao, Helen M Hansen, Alice Y Kang, Kyle M Walsh, Gary V Dahl, Roberta McKean-Cowdin, Catherine Metayer, Joseph L Wiemels
Tobacco smoke exposure has been associated with risk of childhood acute lymphoblastic leukemia (ALL). Understanding the relationship between tobacco exposures and specific mutations may yield etiologic insights. We carried out a case-only analysis to explore whether prenatal and early-life tobacco smoke exposure influences the formation of leukemogenic genomic deletions. Somatic copy-number of 8 genes frequently deleted in ALL (CDKN2A, ETV6, IKZF1, PAX5, RB1, BTG1, PAR1 region, and EBF1) was assessed in 559 pre-treatment tumor samples from the California Childhood Leukemia Study...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28202491/organoid-technologies-meet-genome-engineering
#20
REVIEW
Jing Nie, Eri Hashino
Three-dimensional (3D) stem cell differentiation cultures recently emerged as a novel model system for investigating human embryonic development and disease progression in vitro, complementing existing animal and two-dimensional (2D) cell culture models. Organoids, the 3D self-organizing structures derived from pluripotent or somatic stem cells, can recapitulate many aspects of structural organization and functionality of their in vivo organ counterparts, thus holding great promise for biomedical research and translational applications...
February 15, 2017: EMBO Reports
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