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https://www.readbyqxmd.com/read/28930564/expression-and-role-of-long-non-coding-rna-h19-in-carcinogenesis
#1
Hisashi Yoshimura, Yoko Matsuda, Masami Yamamoto, Shinji Kamiya, Toshiyuki Ishiwata
With the recent advent of whole genome and transcriptome sequencing technologies, long non-coding RNAs have been brought into the spotlight in molecular biology. H19 was one of the first reported long non-coding RNAs; its expression is high in embryonic organs and absent or greatly reduced in most adult tissues. Accumulating evidence suggests that H19 plays crucial roles in embryogenesis. However, its levels are increased in different cancers, including breast, hepato-gastrointestinal, urological, respiratory, and brain tumors...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28927585/whole-genome-and-transcriptome-sequencing-of-prostate-cancer-identify-new-genetic-alterations-driving-disease-progression
#2
Shancheng Ren, Gong-Hong Wei, Dongbing Liu, Liguo Wang, Yong Hou, Shida Zhu, Lihua Peng, Qin Zhang, Yanbing Cheng, Hong Su, Xiuqing Zhou, Jibin Zhang, Fuqiang Li, Hancheng Zheng, Zhikun Zhao, Changjun Yin, Zengquan He, Xin Gao, Haiyen E Zhau, Chia-Yi Chu, Jason Boyang Wu, Colin Collins, Stanislav V Volik, Robert Bell, Jiaoti Huang, Kui Wu, Danfeng Xu, Dingwei Ye, Yongwei Yu, Lianhui Zhu, Meng Qiao, Hang-Mao Lee, Yuehong Yang, Yasheng Zhu, Xiaolei Shi, Rui Chen, Yang Wang, Weidong Xu, Yanqiong Cheng, Chuanliang Xu, Xu Gao, Tie Zhou, Bo Yang, Jianguo Hou, Li Liu, Zhensheng Zhang, Yao Zhu, Chao Qin, Pengfei Shao, Jun Pang, Leland W K Chung, Jianfeng Xu, Chin-Lee Wu, Weide Zhong, Xun Xu, Yingrui Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Jun Wang, Haojie Huang, Yinghao Sun
BACKGROUND: Global disparities in prostate cancer (PCa) incidence highlight the urgent need to identify genomic abnormalities in prostate tumors in different ethnic populations including Asian men. OBJECTIVE: To systematically explore the genomic complexity and define disease-driven genetic alterations in PCa. DESIGN, SETTING, AND PARTICIPANTS: The study sequenced whole-genome and transcriptome of tumor-benign paired tissues from 65 treatment-naive Chinese PCa patients...
September 15, 2017: European Urology
https://www.readbyqxmd.com/read/28926134/early-genetic-aberrations-in-patients-with-sporadic-colorectal-cancer
#3
Brooke R Druliner, Xiaoyang Ruan, Hugues Sicotte, Daniel O'Brien, Hongfang Liu, Jean-Pierre A Kocher, Lisa Boardman
Chromosome instability (CIN) is widely observed in both sporadic and hereditary colorectal cancer (CRC). Defects in APC and WNT signaling are primarily associated with CIN in hereditary CRC, but the genetic causes for CIN in sporadic CRC remain elusive. Using high-density SNP array and exome data from The Cancer Genome Atlas, we characterized loss of heterozygosity (LOH) and copy number variation (CNV) in the peripheral blood, normal colon and corresponding tumor tissue in 15 CRC patients with proficient mismatch repair (MMR) and 24 CRC patients with deficient MMR...
September 19, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28924022/pan-genomic-analyses-identify-key-helicobacter-pylori-pathogenic-loci-modified-by-carcinogenic-host-microenvironments
#4
Jennifer M Noto, Abha Chopra, John T Loh, Judith Romero-Gallo, M Blanca Piazuelo, Mark Watson, Shay Leary, Amber C Beckett, Keith T Wilson, Timothy L Cover, Simon Mallal, Dawn A Israel, Richard M Peek
OBJECTIVE: Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease...
September 18, 2017: Gut
https://www.readbyqxmd.com/read/28923495/crispr-cas9-engineering-of-adult-mouse-liver-demonstrates-that-the-dnajb1-prkaca-gene-fusion-is-sufficient-to-induce-tumors-resembling-fibrolamellar-hepatocellular-carcinoma
#5
Lars H Engelholm, Anjum Riaz, Denise Serra, Frederik Dagnæs-Hansen, Jens V Johansen, Eric Santoni-Rugiu, Steen H Hansen, Francesco Niola, Morten Frödin
BACKGROUND & AIMS: Fibrolamellar hepatocellular carcinoma (FL-HCC) is a primary liver cancer that predominantly affects young adults with no underlying liver disease. A somatic, 400 Kb deletion on chromosome 19 that fuses part of the DnaJ heat shock protein family (Hsp40) member B1 gene (DNAJB1) to the protein kinase cAMP-activated catalytic subunit alpha gene (PRKACA) has been repeatedly identified in patients with FL-HCC. However, the DNAJB1-PRKACA gene fusion has not been shown to induce liver tumorigenesis...
September 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28915574/comparative-study-of-whole-genome-amplification-and-next-generation-sequencing-performance-of-single-cancer-cells
#6
Anna Babayan, Malik Alawi, Michael Gormley, Volkmar Müller, Harriet Wikman, Ryan P McMullin, Denis A Smirnov, Weimin Li, Maria Geffken, Klaus Pantel, Simon A Joosse
BACKGROUND: Whole genome amplification (WGA) is required for single cell genotyping. Effectiveness of currently available WGA technologies in combination with next generation sequencing (NGS) and material preservation is still elusive. RESULTS: In respect to the accuracy of SNP/mutation, indel, and copy number aberrations (CNA) calling, the HiSeq2000 platform outperformed IonProton in all aspects. Furthermore, more accurate SNP/mutation and indel calling was demonstrated using single tumor cells obtained from EDTA-collected blood in respect to CellSave-preserved blood, whereas CNA analysis in our study was not detectably affected by fixation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28912133/use-of-crispr-modified-human-stem-cell-organoids-to-study-the-origin-of-mutational-signatures-in-cancer
#7
Jarno Drost, Ruben van Boxtel, Francis Blokzijl, Tomohiro Mizutani, Nobuo Sasaki, Valentina Sasselli, Joep de Ligt, Sam Behjati, Judith E Grolleman, Tom van Wezel, Serena Nik-Zainal, Roland P Kuiper, Edwin Cuppen, Hans Clevers
Mutational processes underlie cancer initiation and progression. Signatures of these processes in cancer genomes may explain cancer etiology, and hold diagnostic and prognostic value. Here, we develop a strategy that can be used to explore the origin of cancer-associated mutational signatures. We used CRISPR/Cas9 technology to delete key DNA repair genes in human colon organoids, followed by delayed sub-cloning and whole-genome sequencing. We found that mutation accumulation in organoids deficient in the mismatch repair gene MLH1 is driven by replication errors and accurately models the mutation profiles observed in mismatch repair-deficient colorectal cancers...
September 14, 2017: Science
https://www.readbyqxmd.com/read/28911083/multiregion-whole-exome-sequencing-of-matched-primary-and-metastatic-tumors-revealed-genomic-heterogeneity-and-suggested-polyclonal-seeding-in-colorectal-cancer-metastasis
#8
Q Wei, Z Ye, X Zhong, L Li, C Wang, R E Myers, J P Palazzo, D Fortuna, A Yan, S A Waldman, X Chen, J A Posey, A Basu-Mallick, B H Jiang, L Hou, J Shu, Y Sun, J Xing, B Li, H Yang
Background: Distant metastasis accounts for 90% of deaths from colorectal cancer (CRC). Genomic heterogeneity has been reported in various solid malignancies, but remains largely under-explored in metastatic CRC tumors, especially in primary to metastatic tumor evolution. Patients and methods: We conducted high-depth whole-exome sequencing in multiple regions of matched primary and metastatic CRC tumors. Using a total of 28 tumor, normal, and lymph node tissues, we analyzed inter- and intra-individual heterogeneity, inferred the tumor subclonal architectures, and depicted the subclonal evolutionary routes from primary to metastatic tumors...
September 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28904067/whole-genome-sequencing-reveals-breast-cancers-with-mismatch-repair-deficiency
#9
Helen Davies, Sandro Morganella, Colin A Purdie, Se Jin Jang, Elin Borgen, Hege Russnes, Dominik Glodzik, Xueqing Zou, Alain Viari, Andrea L Richardson, Anne-Lise Børresen-Dale, Alastair Thompson, Jorunn E Eyfjord, Gu Kong, Michael R Stratton, Serena Nik-Zainal
Mismatch repair (MMR)-deficient cancers have been discovered to be highly responsive to immune therapies such as PD-1 checkpoint blockade, making their definition in patients, where they may be relatively rare, paramount for treatment decisions. In this study, we utilized patterns of mutagenesis known as mutational signatures, which are imprints of the mutagenic processes associated with MMR deficiency, to identify MMR-deficient breast tumors from a whole-genome sequencing dataset comprising a cohort of 640 patients...
September 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28894165/evolution-analysis-of-heterogeneous-non-small-cell-lung-carcinoma-by-ultra-deep-sequencing-of-the-mitochondrial-genome
#10
Wafa Amer, Csaba Toth, Erik Vassella, Jeannine Meinrath, Ulrike Koitzsch, Anne Arens, Jia Huang, Hannah Eischeid, Alexander Adam, Reinhard Buettner, Andreas Scheel, Stephan C Schaefer, Margarete Odenthal
Accurate assessment of tumour heterogeneity is an important issue that influences prognosis and therapeutic decision in molecular pathology. Due to the shortage of protective histones and a limited DNA repair capacity, the mitochondrial (mt)-genome undergoes high variability during tumour development. Therefore, screening of mt-genome represents a useful molecular tool for assessing precise cell lineages and tracking tumour history. Here, we describe a highly specific and robust multiplex PCR-based ultra-deep sequencing technology for analysis of the whole mt-genome (wmt-seq) on low quality-DNA from formalin-fixed paraffin-embedded tissues...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28892047/a-system-for-detecting-high-impact-low-frequency-mutations-in-primary-tumors-and-metastases
#11
M Anjanappa, Y Hao, E R Simpson, P Bhat-Nakshatri, J B Nelson, S A Tersey, R G Mirmira, A A Cohen-Gadol, M R Saadatzadeh, L Li, F Fang, K P Nephew, K D Miller, Y Liu, H Nakshatri
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis...
September 11, 2017: Oncogene
https://www.readbyqxmd.com/read/28891274/breast-cancer-risk-and-germline-genomic-profiling-of-women-with-neurofibromatosis-type-1-who-developed-breast-cancer
#12
Xia Wang, Jamie K Teer, Renee N Tousignant, Albert M Levin, David Boulware, Dhananjay A Chitale, Brandon M Shaw, Zhihua Chen, Yonghong Zhang, Jaishri O Blakeley, Maria T Acosta, Ludwine M Messiaen, Bruce R Korf, Michael A Tainsky
NF1 mutations predispose to neurofibromatosis type1 (NF1) and women with NF1 have a moderately elevated risk for breast cancer, especially under age 50. Germline genomic analysis may better define the risk so screening and prevention can be applied to the individuals who benefit the most. Survey conducted in several neurofibromatosis clinics in the United States has demonstrated a 17.2% lifetime risk of breast cancer in women affected with NF1. Cumulated risk to age 50 is estimated to be 9.27%. For genomic profiling, fourteen women with NF1 and a history of breast cancer were recruited and underwent whole exon sequencing (WES), targeted genomic DNA based and RNA based analysis of the NF1 gene...
September 10, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28886384/hpv16-e7-genetic-conservation-is-critical-to-carcinogenesis
#13
Lisa Mirabello, Meredith Yeager, Kai Yu, Gary M Clifford, Yanzi Xiao, Bin Zhu, Michael Cullen, Joseph F Boland, Nicolas Wentzensen, Chase W Nelson, Tina Raine-Bennett, Zigui Chen, Sara Bass, Lei Song, Qi Yang, Mia Steinberg, Laurie Burdett, Michael Dean, David Roberson, Jason Mitchell, Thomas Lorey, Silvia Franceschi, Philip E Castle, Joan Walker, Rosemary Zuna, Aimée R Kreimer, Daniel C Beachler, Allan Hildesheim, Paula Gonzalez, Carolina Porras, Robert D Burk, Mark Schiffman
Although most cervical human papillomavirus type 16 (HPV16) infections become undetectable within 1-2 years, persistent HPV16 causes half of all cervical cancers. We used a novel HPV whole-genome sequencing technique to evaluate an exceptionally large collection of 5,570 HPV16-infected case-control samples to determine whether viral genetic variation influences risk of cervical precancer and cancer. We observed thousands of unique HPV16 genomes; very few women shared the identical HPV16 sequence, which should stimulate a careful re-evaluation of the clinical implications of HPV mutation rates, transmission, clearance, and persistence...
September 7, 2017: Cell
https://www.readbyqxmd.com/read/28881617/germline-whole-exome-sequencing-and-large-scale-replication-identifies-fancm-as-a-likely-high-grade-serous-ovarian-cancer-susceptibility-gene
#14
Ed Dicks, Honglin Song, Susan J Ramus, Elke Van Oudenhove, Jonathan P Tyrer, Maria P Intermaggio, Siddhartha Kar, Patricia Harrington, David D Bowtell, Aocs Study Group, Mine S Cicek, Julie M Cunningham, Brooke L Fridley, Jennifer Alsop, Mercedes Jimenez-Linan, Anna Piskorz, Teodora Goranova, Emma Kent, Nadeem Siddiqui, James Paul, Robin Crawford, Samantha Poblete, Shashi Lele, Lara Sucheston-Campbell, Kirsten B Moysich, Weiva Sieh, Valerie McGuire, Jenny Lester, Kunle Odunsi, Alice S Whittemore, Natalia Bogdanova, Matthias Dürst, Peter Hillemanns, Beth Y Karlan, Aleksandra Gentry-Maharaj, Usha Menon, Marc Tischkowitz, Douglas Levine, James D Brenton, Thilo Dörk, Ellen L Goode, Simon A Gayther, D P Paul Pharoah
We analyzed whole exome sequencing data in germline DNA from 412 high grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas Project and identified 5,517 genes harboring a predicted deleterious germline coding mutation in at least one HGSOC case. Gene-set enrichment analysis showed enrichment for genes involved in DNA repair (p = 1.8×10(-3)). Twelve DNA repair genes - APEX1, APLF, ATX, EME1, FANCL, FANCM, MAD2L2, PARP2, PARP3, POLN, RAD54L and SMUG1 - were prioritized for targeted sequencing in up to 3,107 HGSOC cases, 1,491 cases of other epithelial ovarian cancer (EOC) subtypes and 3,368 unaffected controls of European origin...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28881577/a-comprehensively-characterized-cell-line-panel-highly-representative-of-clinical-ovarian-high-grade-serous-carcinomas
#15
Kelsie L Thu, Mahboubeh Papari-Zareei, Victor Stastny, Kai Song, Michael Peyton, Victor D Martinez, Yu-An Zhang, Isabel B Castro, Marileila Varella-Garcia, Hanquan Liang, Chao Xing, Ralf Kittler, Sara Milchgrub, Diego H Castrillon, Heather L Davidson, C Patrick Reynolds, Wan L Lam, Jayanthi Lea, Adi F Gazdar
Recent literature suggests that most widely used ovarian cancer (OVCA) cell models do not recapitulate the molecular features of clinical tumors. To address this limitation, we generated 18 cell lines and 3 corresponding patient-derived xenografts predominantly from high-grade serous carcinoma (HGSOC) peritoneal effusions. Comprehensive genomic characterization and comparison of each model to its parental tumor demonstrated a high degree of molecular similarity. Our characterization included whole exome-sequencing and copy number profiling for cell lines, xenografts, and matched non-malignant tissues, and DNA methylation, gene expression, and spectral karyotyping for a subset of specimens...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28877932/detection-and-genomic-characterization-of-a-mammary-like-adenocarcinoma
#16
Jasleen K Grewal, Peter Eirew, Martin Jones, Kenrry Chiu, Basile Tessier-Cloutier, Anthony N Karnezis, Aly Karsan, Andy Mungall, Chen Zhou, Stephen Yip, Anna V Tinker, Janessa Laskin, Marco Marra, Steven J M Jones
Whole-genome and transcriptome sequencing were performed to identify potential therapeutic strategies in the absence of viable treatment options for a patient initially diagnosed with vulvar adenocarcinoma. Genomic events were prioritized by comparison against variant distributions in the TCGA pan-cancer dataset, and complemented with detailed transcriptome sequencing and copy number analysis. These findings were considered against published scientific literature in order to evaluate the functional effects of potentially relevant genomic events...
September 6, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28875369/-personalized-oncology
#17
REVIEW
C Heining, P Horak, S Gröschel, H Glimm, S Fröhling
CLINICAL ISSUE: Innovative next generation sequencing (NGS) technologies and comprehensive sequencing investigations in large patient cohorts have paved the way for very promising personalized treatment strategies based on the molecular characteristics of individual tumors. STANDARD TREATMENT: Targeted therapies, such as tyrosine kinase inhibitors, antibodies and modern immunotherapeutic approaches are well established as monotherapy and combination therapy for many hematological and oncological malignancies...
September 5, 2017: Der Radiologe
https://www.readbyqxmd.com/read/28870239/evaluating-somatic-tumor-mutation-detection-without-matched-normal-samples
#18
Jamie K Teer, Yonghong Zhang, Lu Chen, Eric A Welsh, W Douglas Cress, Steven A Eschrich, Anders E Berglund
BACKGROUND: Observations of recurrent somatic mutations in tumors have led to identification and definition of signaling and other pathways that are important for cancer progression and therapeutic targeting. As tumor cells contain both an individual's inherited genetic variants and somatic mutations, challenges arise in distinguishing these events in massively parallel sequencing datasets. Typically, both a tumor sample and a "normal" sample from the same individual are sequenced and compared; variants observed only in the tumor are considered to be somatic mutations...
September 4, 2017: Human Genomics
https://www.readbyqxmd.com/read/28867604/characterization-and-genomic-localization-of-a-smad4-processed-pseudogene
#19
Christopher M Watson, Nick Camm, Laura A Crinnion, Agne Antanaviciute, Julian Adlard, Alexander F Markham, Ian M Carr, Ruth Charlton, David T Bonthron
Like many clinical diagnostic laboratories, we undertake routine investigation of cancer-predisposed individuals by high-throughput sequencing of patient DNA that has been target-enriched for genes associated with hereditary cancer. Accurate diagnosis using such reagents requires alertness against rare nonpathogenic variants that may interfere with variant calling. In a cohort of 2042 such cases, we identified five that initially appeared to be carriers of a 95-bp deletion of SMAD4 intron 6. More detailed analysis indicated that these individuals all carried one copy of a SMAD4 processed gene...
August 31, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28866361/targeted-next-generation-sequencing-of-glandular-odontogenic-cyst-a-preliminary-study
#20
Elisa Carvalho de Siqueira, Silvia Ferreira de Sousa, Josiane Alves França, Marina Gonçalves Diniz, Thaís Dos Santos Fontes Pereira, Rennan Garcias Moreira, Pablo Agustin Vargas, Ricardo Santiago Gomez, Carolina Cavalieri Gomes
OBJECTIVE: Glandular odontogenic cyst (GOC) is an uncommon developmental cyst. Its molecular pathogenesis is unclear, and deep sequencing may help identify causative low-frequency variants in tumors. We investigated in GOC mutations in 50 genes commonly altered in human cancers. STUDY DESIGN: Targeted next-generation sequencing was used to interrogate a panel of approximately 2800 mutations in GOC. RESULTS: Six missense single nucleotide variations (SNVs) were reported...
July 26, 2017: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
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