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https://www.readbyqxmd.com/read/28088513/an-immunogram-for-the-cancer-immunity-cycle-towards-personalized-immunotherapy-of-lung-cancer
#1
Takahiro Karasaki, Kazuhiro Nagayama, Hideki Kuwano, Jun-Ichi Nitadori, Masaaki Sato, Masaki Anraku, Akihiro Hosoi, Hirokazu Matsushita, Yasuyuki Morishita, Kosuke Kashiwabara, Masaki Takazawa, Osamu Ohara, Kazuhiro Kakimi, Jun Nakajima
INTRODUCTION: The interaction of immune cells and cancer cells shapes the immunosuppressive tumor microenvironment. For successful cancer immunotherapy, comprehensive knowledge of anti-tumor immunity as a dynamic spacio-temporal process is required for each individual patient. To this end, we developed an immunogram for the cancer-immunity cycle using next-generation sequencing. METHODS: Whole-exome sequencing and RNA-Seq was performed in 20 non-small cell lung cancer patients (12 adenocarcinoma, 7 squamous cell carcinoma, and 1 large cell neuroendocrine carcinoma)...
January 11, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28087716/the-piggybac-transposon-derived-genes-tpb1-and-tpb6-mediate-essential-transposon-like-excision-during-the-developmental-rearrangement-of-key-genes-in-tetrahymena-thermophila
#2
Chao-Yin Cheng, Janet M Young, Chih-Yi Gabriela Lin, Ju-Lan Chao, Harmit S Malik, Meng-Chao Yao
Ciliated protozoans perform extreme forms of programmed somatic DNA rearrangement during development. The model ciliate Tetrahymena thermophila removes 34% of its germline micronuclear genome from somatic macronuclei by excising thousands of internal eliminated sequences (IESs), a process that shares features with transposon excision. Indeed, piggyBac transposon-derived genes are necessary for genome-wide IES excision in both Tetrahymena (TPB2 [Tetrahymena piggyBac-like 2] and LIA5) and Paramecium tetraurelia (PiggyMac)...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087643/tumor-brca1-reversion-mutation-arising-during-neoadjuvant-platinum-based-chemotherapy-in-triple-negative-breast-cancer-is-associated-with-therapy-resistance
#3
Anosheh Afghahi, Kirsten M Timms, Shaveta Vinayak, Kristin C Jensen, Allison W Kurian, Robert W Carlson, Pei-Jen Chang, Elizabeth A Schackmann, Anne-Renee Hartman, James M Ford, Melinda L Telli
BACKGROUND: In germline BRCA1 or BRCA2 (BRCA1/2) mutation carriers, restoration of tumor BRCA1/2 function by a secondary mutation is recognized as a mechanism of resistance to platinum and PARP inhibitors, primarily in ovarian cancer. We evaluated this mechanism of resistance in newly diagnosed BRCA1/2-mutant breast cancer patients with poor response to neoadjuvant platinum-based therapy. METHODS: PrECOG 0105 was a phase II neoadjuvant study of gemcitabine, carboplatin and iniparib in patients with stage I-IIIA triple-negative or BRCA1/2 mutation-associated breast cancer (n=80)...
January 13, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28087534/mechanisms-of-horizontal-cell-to-cell-transfer-of-wolbachia-spp-in-drosophila-melanogaster
#4
Pamela M White, Jose E Pietri, Alain Debec, Shelbi Russell, Bhavin Patel, William Sullivan
: Wolbachia is an intracellular endosymbiont present in most arthropod and filarial nematode species. Transmission between hosts is primarily vertical, taking place exclusively through the female germline, though horizontal transmission has also been documented. Several studies indicate that Wolbachia is capable of transfer between somatic and germline cells during nematode development and in adult flies. However, the mechanisms underlying horizontal cell-to-cell transfer remain largely unexplored...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28086752/single-genome-retrieval-of-context-dependent-variability-in-mutation-rates-for-human-germline
#5
Aleksandr B Sahakyan, Shankar Balasubramanian
BACKGROUND: Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. RESULTS: The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081536/wt1-haploinsufficiency-supports-milder-renal-manifestation-in-two-patients-with-denys-drash-syndrome
#6
Mara S Guaragna, Juliana G Ribeiro de Andrade, Bárbara de Freitas Carli, Vera M S Belangero, Andréa T Maciel-Guerra, Gil Guerra-Júnior, Maricilda P de Mello
Denys-Drash syndrome (DDS) is characterized by nephropathy, genital abnormalities, and predisposition to Wilms' tumor. DDS patients usually present heterozygous de novo germline WT1 mutations. The WT1 gene comprises 10 exons encoding the N-terminal transactivation and the C-terminal DNA-binding regions. Two unrelated patients with genital ambiguity and Wilms' tumor were analyzed by sequencing of the WT1 gene, and 3 mutations in exon 1 were identified of which 2 are novel. Patient 1 carried a c.555delC mutation that causes a frameshift and a premature stop codon...
January 13, 2017: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/28081303/the-novel-fusion-transcript-nr5a2-klhl29ft-is-generated-by-an-insertion-at-the-klhl29-locus
#7
Zhenguo Sun, Xiquan Ke, Steven L Salzberg, Daehwan Kim, Valentin Antonescu, Yulan Cheng, Binbin Huang, Jee Hoon Song, John M Abraham, Sariat Ibrahim, Hui Tian, Stephen J Meltzer
BACKGROUND: Novel fusion transcripts (FTs) caused by chromosomal rearrangement are common factors in the development of cancers. In the current study, the authors used massively parallel RNA sequencing to identify new FTs in colon cancers. METHODS: RNA sequencing (RNA-Seq) and TopHat-Fusion were used to identify new FTs in colon cancers. The authors then investigated whether the novel FT nuclear receptor subfamily 5, group A, member 2 (NR5A2)-Kelch-like family member 29 FT (KLHL29FT) was transcribed from a genomic chromosomal rearrangement...
January 12, 2017: Cancer
https://www.readbyqxmd.com/read/28076423/unique-features-of-germline-variation-in-five-egyptian-familial-breast-cancer-families-revealed-by-exome-sequencing
#8
Yeong C Kim, Amr S Soliman, Jian Cui, Mohamed Ramadan, Ahmed Hablas, Mohamed Abouelhoda, Nehal Hussien, Ola Ahmed, Abdel-Rahman Nabawy Zekri, Ibrahim A Seifeldin, San Ming Wang
Genetic predisposition increases the risk of familial breast cancer. Recent studies indicate that genetic predisposition for familial breast cancer can be ethnic-specific. However, current knowledge of genetic predisposition for the disease is predominantly derived from Western populations. Using this existing information as the sole reference to judge the predisposition in non-Western populations is not adequate and can potentially lead to misdiagnosis. Efforts are required to collect genetic predisposition from non-Western populations...
2017: PloS One
https://www.readbyqxmd.com/read/28074573/structural-functional-and-clinical-characterization-of-a-novel-ptpn11-mutation-cluster-underlying-noonan-syndrome
#9
Luca Pannone, Gianfranco Bocchinfuso, Elisabetta Flex, Cesare Rossi, Giuseppina Baldassarre, Christina Lissewski, Francesca Pantaleoni, Federica Consoli, Francesca Lepri, Monia Magliozzi, Massimiliano Anselmi, Giovanni Sorge, Kadri Karaer, Goran Cuturilo, Alessandro Sartorio, Sigrid Tinschert, Maria Accadia, Maria C Digilio, Giuseppe Zampino, Alessandro De Luca, Hélène Cavé, Martin Zenker, Bruce D Gelb, Bruno Dallapiccola, Lorenzo Stella, Giovanni B Ferrero, Simone Martinelli, Marco Tartaglia
Germline mutations in PTPN11, the gene encoding the Src-homology 2 (SH2) domain-containing protein tyrosine phosphatase (SHP2), cause Noonan syndrome (NS), a relatively common, clinically variable, multisystem disorder. Here, we report on the identification of five different PTPN11 missense changes affecting residues Leu(261) , Leu(262) and Arg(265) in 16 unrelated individuals with clinical diagnosis of NS or with features suggestive for this disorder, specifying a novel disease-causing mutation cluster. Expression of the mutant proteins in HEK293T cells documented their activating role on MAPK signaling...
January 10, 2017: Human Mutation
https://www.readbyqxmd.com/read/28074523/familial-gastrointestinal-stromal-tumors-lentigines-and-caf%C3%A3-au-lait-macules-associated-with-germline-c-kit-mutation-treated-with-imatinib
#10
Divya Gupta, Laxmisha Chandrashekar, Lidia Larizza, Elisa A Colombo, Laura Fontana, Cristina Gervasini, Devinder M Thappa, Medha Rajappa, Kalai Selvi Rajendiran, Gubbi Shamanna Sreenath, Vikram Kate
BACKGROUND: Familial lentiginosis syndromes are characterized by a wide array of manifestations resulting from activation of molecular pathways which control growth, proliferation, and differentiation of a broad range of tissues. Familial gastrointestinal stromal tumors (GISTs) are often accompanied by additional features like hyperpigmentation, mastocytosis, and dysphagia. They have been described with mutations in c-kit (most commonly), platelet-derived growth factor receptor A, neurofibromatosis-1, and succinate dehydrogenase genes...
February 2017: International Journal of Dermatology
https://www.readbyqxmd.com/read/28074003/dna-polymerase-beta-germline-variant-confers-cellular-response-to-cisplatin-therapy
#11
Antonia A Nemec, Laura Abriola, Jane S Merkel, Elisa deStanchina, Michelle DeVeaux, Daniel Zelterman, Peter M Glazer, Joann B Sweasy
: Resistance to cancer chemotherapies leads to deadly consequences, yet current research focuses only on the roles of somatically acquired mutations in this resistance. The mutational status of the germline is also likely to play a role in the way cells respond to chemotherapy. The carrier status for the POLB rs3136797 germline mutation encoding P242R DNA polymerase beta (Pol β) is associated with poor prognosis for lung cancer, specifically in response to treatment with cisplatin. Here, it is revealed that the P242R mutation is sufficient to promote resistance to cisplatin in human cells and in mouse xenografts...
January 10, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28073152/characterizing-pharmacogenomic-guided-medication-use-with-a-clinical-data-repository
#12
Patrick C Mathias, Nathaniel Hendrix, Wei-Jhih Wang, Katelyn Keyloun, Maher Khelifi, Peter Tarczy-Hornoch, Beth Devine
The extent to which pharmacogenomic-guided medication use has been adopted in various health systems is unclear. To assess the uptake of pharmacogenomic-guided medication use, we determined its frequency across our health system, which does not have a structured testing program. Using a multi-site clinical data repository, we identified adult patients' first prescribed medications between January 2011 and December 2013 and investigated the frequency of germline and somatic pharmacogenomic testing, by PharmGKB level of FDA label information...
January 10, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28072956/-clinical-and-immunological-analysis-of-the-patient-with-autoimmunity-due-to-germline-stat3-gain-of-function-mutation
#13
Y Ding, Y Zhang, Y P Wang, H Y Zhao, X M Chen, X H Xue, X M Bai, Y F An, Z Y Zhang, X M Tang, X D Zhao
Objective: To investigate the clinical and immunological laboratory features and gene mutation in a female patient who carried a germline gain-of-function mutation in STAT3. Method: A patient with lymphadenopathy and pancytopenia, visited the Department of Rheumatology and Immunology of Children's Hospital of Chongqing Medical University in May 2016. The clinical and laboratory characteristics, results of immunophenotyping and exome sequencing were analyzed retrospectively and related literature was reviewed...
January 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28072954/-clinical-and-immunological-analysis-of-patients-with-activated-phosphoinositide-3-kinase-%C3%AE-syndrome-resulting-from-pik3cd-mutation
#14
W J Tang, W Wang, Y Luo, Y P Wang, L Li, Y F An, L J Gou, M S Ma, T Y He, J Yang, X D Zhao, H M Song
Objective: To explore the clinical and immunological features, gene mutations, treatment and prognosis in patients with activated phosphoinositide 3-kinase δ syndrome (APDS) caused by PIK3CD gene heterozygous germline mutation. Method: The data of clinical, immunological phenotype, treatment, and prognosis of 15 patients with APDS, who visited Children's Hospital of Chongqing Medical University, Peking Union Medical College Hospital, and Shenzhen Children's Hospital from June 2014 to November 2016, were collected and analyzed...
January 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28072736/von-hippel-lindau-disease-involving-pancreas-and-biliary-system-a-rare-case-report
#15
Xu-Ting Zhi, Qi-Yu Bo, Feng Zhao, Dong Sun, Tao Li
RATIONALE: Von Hippel-Lindau (VHL) disease is a rare inherited, autosomal-dominant syndrome caused by heterozygous germline mutations in the VHL gene. VHL patients are prone to develop benign and malignant tumors and cysts in multiple organ systems involving kidneys, pancreas and central nervous system (CNS). The varied and complex clinical manifestations and radiological findings of VHL are of interest. PATIENT CONCERNS: We report a 38-year-old woman with a ten-year history of VHL disease involving both pancreas and biliary system...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28072465/splicing-regulation-and-dysregulation-of-cholinergic-genes-expressed-at-the-neuromuscular-junction
#16
REVIEW
Kinji Ohno, Mohammad Alinoor Rahman, Mohammad Nazim, Farhana Nasrin, Yingni Lin, Jun-Ichi Takeda, Akio Masuda
We humans have evolved by acquiring diversity of alternative RNA metabolisms including alternative means of splicing and transcribing non-coding genes, and not by acquiring new coding genes. Tissue-specific and developmental stage-specific alternative RNA splicing is achieved by tightly regulated spatiotemporal regulation of expressions and activations of RNA-binding proteins that recognize their cognate splicing cis-elements on nascent RNA transcripts. Genes expressed at the neuromuscular junction (NMJ) are also alternatively spliced...
January 10, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28072387/embryonic-origin-of-adult-stem-cells-required-for-tissue-homeostasis-and-regeneration
#17
Erin L Davies, Kai Lei, Christopher W Seidel, Amanda E Kroesen, Sean A McKinney, Longhua Guo, Sofia Mc Robb, Eric J Ross, Kirsten Gotting, Alejandro Sánchez Alvarado
Planarian neoblasts are pluripotent, adult somatic stem cells and lineage-primed progenitors required for production and maintenance of all differentiated cell types, including the germline. Neoblasts, originally defined as undifferentiated cells residing in the adult parenchyma, are frequently compared to embryonic stem cells yet their developmental origin remains obscure. We investigated the provenance of neoblasts during S. mediterranea embryogenesis, and report that neoblasts arise from an anarchic, cycling piwi-1+ population wholly responsible for production of all temporary and definitive organs during embryogenesis...
January 10, 2017: ELife
https://www.readbyqxmd.com/read/28071690/generation-of-germline-ablated-male-pigs-by-crispr-cas9-editing-of-the-nanos2-gene
#18
Ki-Eun Park, Amy V Kaucher, Anne Powell, Muhammad Salman Waqas, Shelley E S Sandmaier, Melissa J Oatley, Chi-Hun Park, Ahmed Tibary, David M Donovan, Le Ann Blomberg, Simon G Lillico, C Bruce A Whitelaw, Alan Mileham, Bhanu P Telugu, Jon M Oatley
Genome editing tools have revolutionized the generation of genetically modified animals including livestock. In particular, the domestic pig is a proven model of human physiology and an agriculturally important species. In this study, we utilized the CRISPR/Cas9 system to edit the NANOS2 gene in pig embryos to generate offspring with mono-allelic and bi-allelic mutations. We found that NANOS2 knockout pigs phenocopy knockout mice with male specific germline ablation but other aspects of testicular development are normal...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070481/lung-adenocarcinoma-and-adrenocortical-carcinoma-in-a-patient-with-multiple-endocrine-neoplasia-type-1
#19
Nobumasa Ohara, Masanori Kaneko, Masahiro Ikeda, Fumio Ishizaki, Kazuya Suzuki, Ryo Maruyama, Takeshi Komeyama, Kazuhiro Sato, Kenichi Togashi, Hiroyuki Usuda, Yuto Yamazaki, Hironobu Sasano, Kenzo Kaneko, Kyuzi Kamoi
Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder caused by heterozygous germline mutations in the tumor suppressor gene MEN1, which encodes a nuclear protein, menin. MEN1 is characterized by the combined occurrence of tumors involving the pituitary gland, pancreatic islets, and parathyroid glands. Additionally, patients with MEN1 often exhibit adrenal tumors. Although most MEN1-associated tumors are benign, malignant lesions arising in these endocrine organs have been reported. Additionally, malignant diseases of non-endocrine organs concomitant with MEN1 have also been reported...
2017: Respiratory Medicine Case Reports
https://www.readbyqxmd.com/read/28069055/novel-germline-mutations-in-flcn-gene-identified-in-two-chinese-patients-with-birt-hogg-dub%C3%A3-syndrome
#20
Teng Li, Xianghui Ning, Qun He, Kan Gong
Birt-Hogg-Dubé (BHD) syndrome, a hereditary renal cancer syndrome caused by mutations in the folliculin (FLCN) gene, is characterized by the presence of fibrofolliculomas, pulmonary cysts, spontaneous pneumothorax, and renal cell carcinoma (RCC). Few BHD syndrome cases have been reported in Asian countries, and cutaneous presentations are relatively rare in Asian patients. Asian BHD patients may be misdiagnosed due to their atypical manifestations. Here, we report two Chinese BHD patients with novel FLCN mutations (c...
January 9, 2017: Chinese Journal of Cancer
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