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https://www.readbyqxmd.com/read/28550387/correlation-of-c-met-expression-with-pd-l1-expression-in-metastatic-clear-cell-renal-cell-carcinoma-treated-by-sunitinib-first-line-therapy
#1
Solène-Florence Kammerer-Jacquet, Sarah Medane, Karim Bensalah, Jean-Christophe Bernhard, Mokrane Yacoub, Frantz Dupuis, Alain Ravaud, Grégory Verhoest, Romain Mathieu, Benoit Peyronnet, Angélique Brunot, Brigitte Laguerre, Alexandra Lespagnol, Jean Mosser, Frédéric Dugay, Marc-Antoine Belaud-Rotureau, Nathalie Rioux-Leclercq
BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is highly metastatic. Cabozantinib, an anti-angiogenic tyrosine kinase inhibitor that targets c-MET, provided interesting results in metastatic ccRCC treatment. OBJECTIVE: To understand better the role of c-MET in ccRCC, we assessed its status in a population of patients with metastatic ccRCC. PATIENTS AND METHODS: For this purpose, tumor samples were analyzed for c-MET expression by immunohistochemistry (IHC), for c-MET copy number alterations by fluorescence in situ hybridization (FISH), and for c-MET mutations by next generation sequencing (NGS) in a retrospective cohort of 90 primary ccRCC of patients with metastases treated by first-line sunitinib...
May 26, 2017: Targeted Oncology
https://www.readbyqxmd.com/read/28550183/somatic-mutation-spectrum-in-monoclonal-gammopathy-of-undetermined-significance-indicates-a-less-complex-genomic-landscape-compared-to-multiple-myeloma
#2
Aneta Mikulasova, Christopher P Wardell, Alexander Murison, Eileen M Boyle, Graham H Jackson, Jan Smetana, Zuzana Kufova, Ludek Pour, Viera Sandecka, Martina Almasi, Pavla Vsianska, Evzen Gregora, Petr Kuglik, Roman Hajek, Faith E Davies, Gareth J Morgan, Brian A Walker
Monoclonal gammopathy of undetermined significance (MGUS) is a premalignant precursor of multiple myeloma with a 1% risk of progression per year. Although targeted analyses have shown the presence of specific genetic abnormalities such as IGH translocations, RB1 deletion, 1q gain, hyperdiploidy or RAS genes mutations, little is known about the molecular mechanism of malignant transformation. We have performed whole exome sequencing together with CGH+SNP array analysis in 33 flow-cytometry separated abnormal plasma cell samples from MGUS patients to describe somatic gene mutations and chromosome changes at the genome-wide level...
May 26, 2017: Haematologica
https://www.readbyqxmd.com/read/28549942/tissue-specific-expression-profile-of-some-immune-related-genes-in-labeo-rohita-to-edwardsiella-tarda-infection
#3
Sajal Kole, Deepika Anand, Rupam Sharma, Gayatri Tripathi, Makesh M, Rajendran Kv, Megha Kadam Bedekar
Rohu (Labeo rohita), an Indian Major Carp (IMC) is an economically important aquaculture species in India. Inspite of the technological advances, infectious diseases caused by viruses, bacteria and parasites have been a major limiting factor in the development and profitability of fish farms. At present, information regarding the immune status of the Indian major carps is limited. This lack of knowledge is a major impediment for establishment of effective preventive measures against broad spectrum of infectious agents...
May 23, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28548965/inhibition-of-colorectal-cancer-genomic-copy-number-alterations-and-chromosomal-fragile-site-tumor-suppressor-fhit-and-wwox-deletions-by-dna-mismatch-repair
#4
Sohail Jahid, Jian Sun, Ozkan Gelincik, Pedro Blecua, Winfried Edelmann, Raju Kucherlapati, Kathy Zhou, Maria Jasin, Zeynep H Gümüş, Steven M Lipkin
Homologous recombination (HR) enables precise DNA repair after DNA double strand breaks (DSBs) using identical sequence templates, whereas homeologous recombination (HeR) uses only partially homologous sequences. Homeologous recombination introduces mutations through gene conversion and genomic deletions through single-strand annealing (SSA). DNA mismatch repair (MMR) inhibits HeR, but the roles of mammalian MMR MutL homologues (MLH1, PMS2 and MLH3) proteins in HeR suppression are poorly characterized. Here, we demonstrate that mouse embryonic fibroblasts (MEFs) carrying Mlh1, Pms2, and Mlh3 mutations have higher HeR rates, by using 7,863 uniquely mapping paired direct repeat sequences (DRs) in the mouse genome as endogenous gene conversion and SSA reporters...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28548214/the-performance-of-malbac-and-mda-methods-in-the-identification-of-concurrent-mutations-and-aneuploidy-screening-to-diagnose-beta-thalassaemia-disorders-at-the-single-and-multiple-cell-levels
#5
WeiQiang Liu, HuiMin Zhang, Dan Hu, SiJia Lu, XiaoFang Sun
AIM: To select an optimal whole-genome amplification (WGA) method to improve the efficiency of the preimplantation genetic diagnosis and screening (PGD/PGS) of beta-thalassaemia disorders. METHODS: Fifty-seven fibroblast samples with defined beta-thalassaemia variations and forty-eight single-blastomere samples were amplified from single-, two-, and five-cell samples by multiple annealing and looping-based amplification cycles (MALBAC) and the multiple displacement amplification (MDA) method...
May 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28548128/genomic-profiling-of-breast-secretory-carcinomas-reveals-distinct-genetics-from-other-breast-cancers-and-similarity-to-mammary-analog-secretory-carcinomas
#6
Gregor Krings, Nancy M Joseph, Gregory R Bean, David Solomon, Courtney Onodera, Eric Talevich, Iwei Yeh, James P Grenert, Elizabeth Hosfield, Emily D Crawford, Richard C Jordan, Annemieke van Zante, Charles Zaloudek, Sandra J Shin, Yunn-Yi Chen
Secretory carcinomas of the breast are rare tumors with distinct histologic features, recurrent t(12;15)(p13;q25) translocation resulting in ETV6-NTRK3 gene fusion and indolent clinical behavior. Mammary analog secretory carcinomas arising in other sites are histopathologically similar to the breast tumors and also harbor ETV6-NTRK3 fusions. Breast secretory carcinomas are often triple (estrogen and progesterone receptor, HER2) negative with a basal-like immunophenotype. However, genomic studies are lacking, and whether these tumors share genetic features with other basal and/or triple negative breast cancers is unknown...
May 26, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28548125/next-generation-sequencing-based-molecular-characterization-of-primary-urinary-bladder-adenocarcinoma
#7
Somak Roy, Dinesh Pradhan, Wayne L Ernst, Stephanie Mercurio, Yana Najjar, Rahul Parikh, Anil V Parwani, Reetesh K Pai, Rajiv Dhir, Marina N Nikiforova
Primary bladder adenocarcinoma is a rare and aggressive tumor with poor clinical outcomes and no standard of care therapy. Molecular biology of this tumor is unknown due to the lack of comprehensive molecular profiling studies. The study aimed to identify genomic alterations of clinical and therapeutic significance using next-generation sequencing and compare genomic profile of primary bladder adenocarcinoma with that of high-grade urothelial carcinoma and colorectal adenocarcinoma. A cohort of 15 well-characterized primary bladder adenocarcinoma was subjected to targeted next-generation sequencing for the identification of mutations and copy-number changes in 51 cancer-related genes...
May 26, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28548104/genomic-analysis-of-oesophageal-squamous-cell-carcinoma-identifies-alcohol-drinking-related-mutation-signature-and-genomic-alterations
#8
Jiang Chang, Wenle Tan, Zhiqiang Ling, Ruibin Xi, Mingming Shao, Mengjie Chen, Yingying Luo, Yanjie Zhao, Yun Liu, Xiancong Huang, Yuchao Xia, Jinlin Hu, Joel S Parker, David Marron, Qionghua Cui, Linna Peng, Jiahui Chu, Hongmin Li, Zhongli Du, Yaling Han, Wen Tan, Zhihua Liu, Qimin Zhan, Yun Li, Weimin Mao, Chen Wu, Dongxin Lin
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28547520/small-scale-intraspecific-patterns-of-adaptive-immunogenetic-polymorphisms-and-neutral-variation-in-lake-superior-lake-trout
#9
Shauna M Baillie, Riley R Hemstock, Andrew M Muir, Charles C Krueger, Paul Bentzen
Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species' evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake...
May 25, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28546826/ipf-lasso-integrative-l1-penalized-regression-with-penalty-factors-for-prediction-based-on-multi-omics-data
#10
Anne-Laure Boulesteix, Riccardo De Bin, Xiaoyu Jiang, Mathias Fuchs
As modern biotechnologies advance, it has become increasingly frequent that different modalities of high-dimensional molecular data (termed "omics" data in this paper), such as gene expression, methylation, and copy number, are collected from the same patient cohort to predict the clinical outcome. While prediction based on omics data has been widely studied in the last fifteen years, little has been done in the statistical literature on the integration of multiple omics modalities to select a subset of variables for prediction, which is a critical task in personalized medicine...
2017: Computational and Mathematical Methods in Medicine
https://www.readbyqxmd.com/read/28546779/emerging-treatment-options-for-the-management-of-hodgkin-s-lymphoma-clinical-utility-of-nivolumab
#11
REVIEW
David A Bond, Lapo Alinari
Classical Hodgkin's lymphoma (cHL) is a B-cell malignancy comprised of pathologic Reed Sternberg cells with a surrounding immune-tolerant inflammatory milieu. RS cells evade immune recognition in part through programmed death ligand 1 (PD-L1) overexpression, which is genetically programmed through copy number alterations, polysomy, and amplification of the 9p24.1 locus encoding PD-L1. By engaging with PD-1+ T-cells, PD-L1 delivers a potent immune suppressive signal promoting immunologic escape of the tumor cell...
2017: Journal of Blood Medicine
https://www.readbyqxmd.com/read/28546418/single-cell-dna-sequencing-reveals-a-late-dissemination-model-in-metastatic-colorectal-cancer
#12
Marco L Leung, Alexander Davis, Ruli Gao, Anna Casasent, Yong Wang, Emi Sei, Eduardo Sanchez, Dipen Maru, Scott Kopetz, Nicholas E Navin
Metastasis is a complex biological process that has been difficult to delineate in human colorectal (CRC) cancer patients. A major obstacle in understanding metastatic lineages is the extensive intratumor heterogeneity at the primary and metastatic tumor sites. To address this problem, we developed a highly-multiplexed single cell DNA sequencing approach to trace the metastatic lineages of two CRC patients with matched liver metastases. Single cell copy number or mutational profiling was performed, in addition to bulk exome and targeted deep-sequencing...
May 25, 2017: Genome Research
https://www.readbyqxmd.com/read/28546026/the-crustin-like-peptide-plays-opposite-role-in-shrimp-immune-response-to-vibrio-alginolyticus-and-white-spot-syndrome-virus-wssv-infection
#13
Baozhen Sun, Zhi Wang, Fei Zhu
Crustin is an antimicrobial peptide (AMP) that plays a key role in innate immunity of crustaceans. In this study, we cloned the entire 660 bp crustin-like sequence with a 507 bp open reading frame encoding a 168 amino acid from Marsupenaeus japonicus. The crustin-like gene was primarily expressed in gills and over-expressed in shrimp hemocytes after challenge with WSSV or Vibrio alginolyticus. After knockdown crustin-like gene using specific double-stranded RNA (CRU-dsRNA), IMD, Rab7, L-lectin, mitogen-activated protein kinase, p53, prophenoloxidase and Rho were down-regulated and nitric oxide synthase, myosin and tumor necrosis factor-α were up-regulated in hemocytes at 24 h post dsRNA treatment...
May 22, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28545960/vaccination-with-multimeric-recombinant-vp28-induces-high-protection-against-white-spot-syndrome-virus-in-shrimp
#14
Suparat Taengchaiyaphum, Hideki Nakayama, Jiraporn Srisala, Ratny Khiev, Diva January Aldama-Cano, Siripong Thitamadee, Kallaya Sritunyalucksana
To improve the efficacy of WSSV protection, multimeric (tetrameric) recombinant VP28 (4XrVP28) was produced and tested in comparison with those of monomeric VP28 (1XrVP28). In vitro binding of either 1XrVP28 or 4XrVP28 to shrimp hemocyte surface was evident as early as 10 min after protein inoculation. Similar results were obtained in vivo when shrimp were injected with recombinant proteins that the proteins bound to the hemocyte surface could be detected since 5 min after injection. Comparison of the WSSV protection efficiencies of 1XrVP28 or 4XrVP28 were performed by injection the purified 1XrVP28 or 4XrVP28 (22...
May 22, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28545447/filamentous-ascomycete-genomes-provide-insights-into-copia-retrotransposon-diversity-in-fungi
#15
Tifenn Donnart, Mathieu Piednoël, Dominique Higuet, Éric Bonnivard
BACKGROUND: The relative scarcity of Copia retrotransposons has been recently characterized in metazoans in comparison with the other superfamilies of LTR elements. Furthermore, Copia retrotransposons have often a particular dynamics that results in a highly predominant single clade of elements within a large host taxon, such as the GalEa-like retrotransposons in crustaceans. Taking advantage of the skyrocketing amount of genomic data available for fungi, we carried out the first large-scale comparative genomic analysis of the Copia clades in filamentous ascomycetes...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28545122/spot-a-novel-and-streamlined-microarray-platform-for-observing-cellular-trna-levels
#16
Simon Grelet, Ariel McShane, Eveline Hok, Jensen Tomberlin, Philip H Howe, Renaud Geslain
Recent studies have placed transfer RNA (tRNA), a housekeeping molecule, in the heart of fundamental cellular processes such as embryonic development and tumor progression. Such discoveries were contingent on the concomitant development of methods able to deliver high-quality tRNA profiles. The present study describes the proof of concept obtained in Escherichia coli (E. coli) for an original tRNA analysis platform named SPOt (Streamlined Platform for Observing tRNA). This approach comprises three steps. First, E...
2017: PloS One
https://www.readbyqxmd.com/read/28544881/mammalian-systems-biotechnology-reveals-global-cellular-adaptations-in-a-recombinant-cho-cell-line
#17
Faraaz Noor Khan Yusufi, Meiyappan Lakshmanan, Ying Swan Ho, Bernard Liat Wen Loo, Pramila Ariyaratne, Yuansheng Yang, Say Kong Ng, Tessa Rui Min Tan, Hock Chuan Yeo, Hsueh Lee Lim, Sze Wai Ng, Ai Ping Hiu, Chung Ping Chow, Corrine Wan, Shuwen Chen, Gavin Teo, Gao Song, Ju Xin Chin, Xiaoan Ruan, Ken Wing Kin Sung, Wei-Shou Hu, Miranda Gek Sim Yap, Muriel Bardor, Niranjan Nagarajan, Dong-Yup Lee
Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544703/high-ubiquitin-specific-protease-44-expression-induces-dna-aneuploidy-and-provides-independent-prognostic-information-in-gastric-cancer
#18
Sho Nishimura, Eiji Oki, Koji Ando, Makoto Iimori, Yu Nakaji, Yuichiro Nakashima, Hiroshi Saeki, Yoshinao Oda, Yoshihiko Maehara
Chromosomal instability (CIN), characterized by aneuploidy, is a major molecular subtype of gastric cancer. The deubiquitinase USP44 is an important regulator of APC activation in the spindle checkpoint and leads to proper chromosome separation to prevent aneuploidy. Aberrant expression of USP44 leads CIN in cells; however, the correlation between USP44 and DNA aneuploidy in gastric cancer is largely unknown. We analyzed USP44 expression in 207 patients with gastric cancer by immunohistochemistry and found that the proportion of USP44 expression was higher in gastric cancer tumors (mean, 39...
May 23, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28544321/assessment-of-mode-of-delivery-and-predictors-of-emergency-caesarean-section-among-women-living-with-hiv-in-a-matched-pair-setting-with-women-from-the-general-population-in-denmark-2002-2014
#19
M Ørbaek, K Thorsteinsson, M Helleberg, E Moseholm, T L Katzenstein, M Storgaard, I S Johansen, G Pedersen, N Weis, A-M Lebech
OBJECTIVES: We aimed to assess mode of delivery and predictors of emergency caesarean section (EmCS) in women living with HIV (WLWH) in a matched-pair setting with women from the general population (WGP) in Denmark. Further, we analysed birth plan in WLWH. METHODS: All WLWH giving birth to live-born children from 2002 to 2014 were included in the study. Data were retrieved from medical records and national registries. WLWH were matched 1:5 by age, birth year, parity and ethnicity to WGP...
May 24, 2017: HIV Medicine
https://www.readbyqxmd.com/read/28544224/quantification-of-specific-t-and-b-cells-immunological-markers-in-children-with-chronic-and-transient-itp
#20
Sarina Levy-Mendelovich, Atar Lev, Shraga Aviner, Nurit Rosenberg, Caim Kaplinsky, Nechama Sharon, Hagit Miskin, Aviya Dvir, Gili Kenet, Irit Eisen Schushan, Raz Somech
BACKGROUND: Immune thrombocytopenic purpura (ITP) is characterized by a transient (nonchronic) or permanent (chronic) decline in the number of platelets. Predicting the course of ITP, at the time of diagnosis, is of importance. Here we studied at diagnosis, clinical and immunological parameters in order to distinguish between different courses. The latter included the measure of new B and T cells using quantification of kappa-deleting recombination excision circles (KRECs) and T-cell receptor excision circles (TRECs), respectively...
May 22, 2017: Pediatric Blood & Cancer
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