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Genes, Chromosomes & Cancer

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https://www.readbyqxmd.com/read/28316110/proteasome-ubiquitin-receptor-psmd4-is-an-amplification-target-in-breast-cancer-and-may-predict-sensitivity-to-parpi
#1
Marlena S Fejzo, Lee Anderson, Hsiao-Wang Chen, Enrique Guandique, Ondrej Kalous, Dylan Conklin, Dennis J Slamon
Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in DNA repair under investigation as a chemotherapeutic target. Current randomized phase 3 trials of PARPi in metastatic breast cancer are limited to patients with documented BRCA1/2 mutations and no biomarker of PARPi beyond BRCA status is available. In an effort to identify novel biomarkers for PARP inihibition, we created a cell line (HCC1187/TALRES) resistant to the PARP1 inhibitor talazoparib. Herein we show by array-CGH that HCC1187/TALRES has a selective loss of the proteasome ubiquitin receptor PSMD4 amplicon resulting in significant down-regulation of PSMD4...
March 18, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28295846/the-enigmatic-oncogene-and-tumor-suppressor-like-properties-of-rad54b-insights-into-genome-instability-and-cancer
#2
REVIEW
Erin N McAndrew, Kirk J McManus
One of the major challenges to the cell is to ensure genome stability, which can be compromised through endogenous errors or exogenous DNA damaging agents, such as ionizing radiation or common chemotherapeutic agents. To maintain genome stability the cell has a multifaceted line of defense, including cell cycle checkpoints and DNA damage repair pathways. RAD54B is involved in many of these pathways and thus exhibits a role in maintaining and repairing genome stability following DNA damage. RAD54B is involved in cell cycle regulation after DNA damage and participates in homologous recombinational repair, which ensures the precise repair of the most deleterious DNA lesions, double-stranded breaks...
March 13, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28295819/variants-in-bak1-spry4-and-gab2-are-associated-with-pediatric-germ-cell-tumors-a-report-from-the-children-s-oncology-group
#3
Erin L Marcotte, Nathan Pankratz, James F Amatruda, A Lindsay Frazier, Mark Krailo, Stella Davies, Jacqueline R Starr, C Lau Ching, Michelle Roesler, Erica Langer, Caroline Hallstrom, Anthony J Hooten, Jenny N Poynter
Germ cell tumors (GCT) are a rare form of childhood cancer that originate from the primordial germ cell. Recent genome-wide association studies (GWAS) have identified susceptibility alleles for adult testicular GCT (TGCT). We test whether these SNPs are associated with GCT in pediatric and adolescent populations. This case-parent triad study includes individuals with GCT diagnosed between ages 0-19. We evaluated 26 SNPs from GWAS of adult TGCT and estimated main effects for pediatric GCT within complete trios (N=366) using the transmission disequilibrium test...
March 13, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28281307/integrated-expression-analysis-identifies-transcription-networks-in-mouse-and-human-gastric-neoplasia
#4
Zheng Chen, Mohammed Soutto, Bushra Rahman, Muhammad W Fazili, DunFa Peng, Maria Blanca Piazuelo, Heidi Chen, M Kay Washington, Yu Shyr, Wael El-Rifai
Gastric cancer is a leading cause of cancer-related deaths worldwide. The Tff1 knockout (KO) mouse model develops gastric lesions that include low-grade dysplasia (LGD), high-grade dysplasia (HGD), and adenocarcinomas. In this study, we used Affymetrix microarrays gene expression platforms for analysis of molecular signatures in the mouse stomach (Tff1-KO (LGD) and Tff1 wild-type (normal)) and human gastric cancer tissues and their adjacent normal tissue samples. Combined integrated bioinformatics analysis of mouse and human datasets indicated that 172 genes were consistently deregulated in both human gastric cancer samples and Tff1-KO LGD lesions (P<0...
March 9, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28236351/genomic-array-as-compared-to-karyotyping-in-myelodysplastic-syndromes-in-a-prospective-clinical-trial
#5
Marian J Stevens-Kroef, Daniel Olde Weghuis, Najat ElIdrissi-Zaynoun, Bert van der Reijden, Eline M P Cremers, Canan Alhan, Theresia M Westers, Heleen A Visser-Wisselaar, Dana A Chitu, Sonia M Cunha, Edo Vellenga, Saskia K Klein, Pierre Wijermans, Georgine E de Greef, M R Schaafsma, Petra Muus, Gert J Ossenkoppele, Arjan A van de Loosdrecht, Joop H Jansen
Karyotyping is considered as the gold standard in the genetic subclassification of myelodysplastic syndrome (MDS). Oligo/SNP-based genomic array profiling is a high-resolution tool that also enables genome wide analysis. We compared karyotyping with oligo/SNP-based array profiling in 104 MDS patients from the HOVON-89 study. Oligo/SNP-array identified all cytogenetically defined genomic lesions, except for subclones in two cases and balanced translocations in three cases. On the other hand oligo/SNP-based genomic array profiling had a higher success rate, showing 55 abnormal cases, while an abnormal karyotype was found in only 35 patients...
February 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28233365/etv-transcriptional-upregulation-is-more-reliable-than-rna-sequencing-algorithms-and-fish-in-diagnosing-round-cell-sarcomas-with-cic-gene-rearrangements
#6
Yu-Chien Kao, Yun-Shao Sung, Chun-Liang Chen, Lei Zhang, Brendan C Dickson, David Swanson, Sumathi Vaiyapuri, Farida Latif, Abdullah Alholle, Shih-Chiang Huang, Jason L Hornick, Cristina R Antonescu
CIC rearrangements have been reported in two-thirds of EWSR1-negative small blue round cell tumors (SBRCTs). However, a number of SBRCTs remain unclassified despite exhaustive analysis. We collected 14 SBRCTs lacking driver genetic events by RNA sequencing (RNAseq) analysis. Unsupervised hierarchical clustering was performed using samples from our RNAseq database, including 13 SBRCTs with non-CIC genetic abnormalities and 2 CIC-rearranged angiosarcomas among others. Remarkably, all 14 study cases showed high mRNA levels of ETV1/4/5, and by unsupervised clustering most grouped into a distinct cluster, separate from other tumors...
February 24, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28233357/promotion-of-invasion-by-mutant-ras-is-dependent-on-activation-of-the-wasf3-metastasis-promoter-gene
#7
Yong Teng, Lambert Ngoka, John K Cowell
Metastasis represents an end stage in the evolution of cancer progression and has been related to specific genetic pathways. Overexpression of mutant RAS in particular appears to promote invasion and metastasis, although exactly how this occurs has not been well characterized. We have previously shown that activation of the WASF3 protein regulates actin cytoskeleton dynamics that promote invasion. In this report we investigated how WASF3 overexpression interacts with mutant RAS to increased invasion and metastasis...
February 24, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28196408/somatic-mutations-in-murine-models-of-leukemia-and-lymphoma-disease-specificity-and-clinical-relevance
#8
Liat Goldberg, Sheryl M Gough, Fan Lee, Christine Dang, Robert L Walker, Yeulin J Zhu, Sven Bilke, Marbin Pineda, Masahiro Onozawa, Yang Jo Chung, Paul S Meltzer, Peter D Aplan
Malignant transformation is a multistep process that is dictated by acquisition of multiple genomic aberrations that provide growth and survival advantage. During the post genomic era, high throughput genomic sequencing has advanced exponentially, leading to identification of countless cancer associated mutations with potential for targeted therapy. Mouse models of cancer serve as excellent tools to examine the functionality of gene mutations and their contribution to the malignant process. However, it remains unclear whether the genetic events that occur during transformation are similar in mice and humans...
February 14, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28196407/comprehensive-genomic-and-phenotypic-characterization-of-germline-fh-deletion-in-hereditary-leiomyomatosis-and-renal-cell-carcinoma-hlrcc
#9
Cathy D Vocke, Christopher J Ricketts, Maria J Merino, Ramaprasad Srinivasan, Adam R Metwalli, Lindsay A Middelton, James Peterson, Youfeng Yang, W Marston Linehan
Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a familial cancer syndrome associated with the development of cutaneous and uterine leiomyomas, and an aggressive form of type 2 papillary kidney cancer. HLRCC is characterized by germline mutation of the FH gene. This study evaluated the prevalence and clinical phenotype of FH deletions in HLRCC patients. Patients with phenotypic manifestations consistent with HLRCC who lacked detectable germline FH intragenic mutations were investigated for FH deletion...
February 14, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28177558/tmem16a-ano1-suppression-improves-response-to-antibody-mediated-targeted-therapy-of-egfr-and-her2-erbb2
#10
Sucheta Kulkarni, Anke Bill, Neal R Godse, Nayel I Khan, Jason I Kass, Kevin Steehler, Carolyn Kemp, Kara Davis, Carol A Bertrand, Avani R Vyas, Douglas E Holt, Jennifer R Grandis, L Alex Gaither, Umamaheswar Duvvuri
TMEM16A, a Ca(2+) -activated Cl(-) channel, contributes to tumor growth in breast cancer and head and neck squamous cell carcinoma (HNSCC). Here, we investigated whether TMEM16A influences the response to EGFR/HER family-targeting biological therapies. Inhibition of TMEM16A Cl(-) channel activity in breast cancer cells with HER2 amplification induced a loss of viability. Cells resistant to trastuzumab, a monoclonal antibody targeting HER2, showed an increase in TMEM16A expression and heightened sensitivity to Cl(-) channel inhibition...
February 8, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28165652/candidate-susceptibility-variants-for-esophageal-squamous-cell-carcinoma
#11
Iikki Donner, Riku Katainen, Tomas Tanskanen, Eevi Kaasinen, Mervi Aavikko, Kristian Ovaska, Miia Artama, Eero Pukkala, Lauri A Aaltonen
Esophageal cancer is common worldwide, and often fatal. The major histological subtype is esophageal squamous cell carcinoma (ESCC). ESCC shows familial aggregation and high heritability. Mutations in RHBDF2 cause tylosis, a very rare disorder characterized by high life-time risk of ESCC, but no other well-established predisposition genes have been identified. To identify candidate susceptibility variants for ESCC we utilized the Population Information System and the Finnish cancer registry to find study materials by clustering ESCC patients by family name at birth and municipality at birth...
February 6, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28165644/hif1a-gene-polymorphisms-and-human-diseases-graphical-review-of-97-association-studies
#12
REVIEW
I Gladek, J Ferdin, S Horvat, G A Calin, T Kunej
Hypoxia-inducible factors (HIFs) belong to a family of transcription factors (TF) responsive to a low O2 availability, which is often a characteristic feature of solid tumors. The alpha subunit of the HIF heterodimer is O2 -sensitive, and once stabilized in hypoxia, it functions as a master regulator of various genes involved in hypoxia pathway. Changes in the HIF1A (hypoxia inducible factor 1, alpha subunit) nucleotide sequence or expression has been shown to be associated with development of several diseases...
February 6, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28052524/cross-species-analysis-of-the-canine-and-human-bladder-cancer-transcriptome-and-exome
#13
Stephen A Ramsey, Tanjin Xu, Cheri Goodall, Adelaide C Rhodes, Amita Kashyap, Jun He, Shay Bracha
We investigated the correspondence between transcriptome and exome alterations in canine bladder cancer and the correspondence between these alterations and cancer-driving genes and transcriptional alterations in human bladder cancer. We profiled canine bladder tumors using mRNA-seq and exome-seq in order to investigate the similarity of transcriptional alterations in bladder cancer, in humans and canines, at the levels of gene functions, pathways, and cytogenetic regions. We found that the transcriptomes of canine and human bladder cancer are remarkably similar at the functional and pathway levels...
January 3, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28124441/confirmation-of-mutation-landscape-of-nf1-associated-malignant-peripheral-nerve-sheath-tumors
#14
Pierre Sohier, Armelle Luscan, Angharad Lloyd, Kevin Ashelford, Ingrid Laurendeau, Audrey Briand-Suleau, Dominique Vidaud, Nicolas Ortonne, Eric Pasmant, Meena Upadhyaya
The commonest tumors associated with neurofibromatosis type 1 (NF1) are benign peripheral nerve sheath tumors, called neurofibromas. Malignant transformation of neurofibromas into aggressive MPNSTs may occur with a poor patient prognosis. A cooperative role of SUZ12 or EED inactivation, along with NF1, TP53, and CDKN2A loss-of-function, has been proposed to drive progression to MPNSTs. An exome sequencing analysis of eight MPNSTs, one plexiform neurofibroma, and seven cutaneous neurofibromas was undertaken...
May 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28124401/brca1-alterations-with-additional-defects-in-dna-damage-response-genes-may-confer-chemoresistance-to-brca-like-breast-cancers-treated-with-neoadjuvant-chemotherapy
#15
Mamoru Takada, Shigenori Nagai, Masayuki Haruta, Ryuichi P Sugino, Katsunori Tozuka, Hiroyuki Takei, Fumie Ohkubo, Kenichi Inoue, Masafumi Kurosumi, Masaru Miyazaki, Aiko Sato-Otsubo, Yusuke Sato, Seishi Ogawa, Yasuhiko Kaneko
The BRCA-like phenotype is a feature that some sporadic breast cancers share with those occurring in BRCA1 or BRCA2 mutation carriers. As tumors with the phenotype have defects in the DNA damage response pathway, which may increase sensitivity to drugs such as DNA cross-linking agents and PARP inhibitors, a method to identify this phenotype is important. The prediction of chemoresistance, which frequently develops in these tumors, is also crucial for improving therapy. We examined genomic aberrations and BRCA1 promoter methylation in tumors of 73 breast cancer (20 HR-/HER2- and 53 HR+/HER2-) patients, who received neoadjuvant chemotherapy with anthracycline, cyclophosphamide, and taxane, using SNP array CGH and quantitative PCR...
May 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28124395/alterations-of-type-ii-classical-cadherin-cadherin-10-cdh10-is-associated-with-pancreatic-ductal-adenocarcinomas
#16
Natini Jinawath, Meng-Shin Shiao, Alexis Norris, Kathleen Murphy, Alison P Klein, Raluca Yonescu, Christine Iacobuzio-Donahue, Alan Meeker, Artit Jinawath, Charles J Yeo, James R Eshleman, Ralph H Hruban, Jonathan R Brody, Constance A Griffin, Shuko Harada
Pancreatic ductal adenocarcinoma (PDAC), either sporadic or familial, has a dismal prognosis and finding candidate genes involved in development of the cancer is crucial for the patient care. First, we identified two patients with germline alterations in or adjacent to CDH10 by chromosome studies and sequencing analyses in 41 familial pancreatic cancer (FPC) cases. One patient had a balanced translocation between chromosome 5 and 20. The breakpoint on chromosome band 5p14.2 was āˆ¼810 Kb upstream of CDH10, while that on chromosome arm 20p was in the pericentromeric region which might result in inactivation of one copy of the gene leading to reduced expression of CDH10...
May 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28063196/asxl2-mutations-are-frequently-found-in-pediatric-aml-patients-with-t-8-21-runx1-runx1t1-and-associated-with-a-better-prognosis
#17
Genki Yamato, Norio Shiba, Kenichi Yoshida, Yuichi Shiraishi, Yusuke Hara, Kentaro Ohki, Jun Okubo, Haruna Okuno, Kenichi Chiba, Hiroko Tanaka, Akitoshi Kinoshita, Hiroshi Moritake, Nobutaka Kiyokawa, Daisuke Tomizawa, Myoung-Ja Park, Manabu Sotomatsu, Takashi Taga, Souichi Adachi, Akio Tawa, Keizo Horibe, Hirokazu Arakawa, Satoru Miyano, Seishi Ogawa, Yasuhide Hayashi
ASXL2 is an epigenetic regulator involved in polycomb repressive complex regulation or recruitment. Clinical features of pediatric acute myeloid leukemia (AML) patients with ASXL2 mutations remain unclear. Thus, we investigated frequencies of ASXL1 and ASXL2 mutations, clinical features of patients with these mutations, correlations of these mutations with other genetic alterations including BCOR/BCORL1 and cohesin complex component genes, and prognostic impact of these mutations in 369 pediatric patients with de novo AML (0-17 years)...
May 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28063190/prognostic-impact-of-specific-molecular-profiles-in-pediatric-acute-megakaryoblastic-leukemia-in-non-down-syndrome
#18
Yusuke Hara, Norio Shiba, Kentaro Ohki, Ken Tabuchi, Genki Yamato, Myoung-Ja Park, Daisuke Tomizawa, Akitoshi Kinoshita, Akira Shimada, Hirokazu Arakawa, Akiko M Saito, Nobutaka Kiyokawa, Akio Tawa, Keizo Horibe, Takashi Taga, Souichi Adachi, Tomohiko Taki, Yasuhide Hayashi
Pediatric acute megakaryoblastic leukemia in non-Down syndrome (AMKL) is a unique subtype of acute myeloid leukemia (AML). Novel CBFA2T3-GLIS2 and NUP98-KDM5A fusions recurrently found in AMKL were recently reported as poor prognostic factors. However, their detailed clinical and molecular characteristics in patients treated with recent improved therapies remain uncertain. We analyzed molecular features of 44 AMKL patients treated on two recent Japanese AML protocols, the AML99 and AML-05 trials. We identified CBFA2T3-GLIS2, NUP98-KDM5A, RBM15-MKL1, and KMT2A rearrangements in 12 (27%), 4 (9%), 2 (5%), and 3 (7%) patients, respectively...
May 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28063177/comparable-clinical-outcomes-in-patients-with-her2-mutant-and-egfr-mutant-lung-adenocarcinomas
#19
Chien-Hung Gow, Hou-Tai Chang, Chor-Kuan Lim, Chao-Yu Liu, Jin-Shing Chen, Jin-Yuan Shih
HER2 is a major proliferative driver in lung cancer. HER2 gene aberrations impact the prognosis of lung adenocarcinoma (ADC). A one-step reverse transcription-polymerase chain reaction was performed using RNA samples from 888 Asian lung cancer patients to detect HER2, EGFR, KRAS, ALK, and ROS1 mutations. The demographic data and treatment outcomes of HER2 mutation-positive lung ADC patients were analyzed and compared to those with HER2 mutation-negative tumors. HER2 mutation was identified in 40 (4.5%) lung ADC patients...
May 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28033648/characterisation-of-the-genomic-landscape-of-crlf2-rearranged-acute-lymphoblastic-leukemia
#20
Lisa J Russell, Lisa Jones, Amir Enshaei, Stefano Tonin, Sarra L Ryan, Jeyanthy Eswaran, Sirintra Nakjang, Elli Papaemmanuil, Jose M C Tubio, Adele K Fielding, Ajay Vora, Peter J Campbell, Anthony V Moorman, Christine J Harrison
Deregulated expression of the type I cytokine receptor, CRLF2, is observed in 5-15% of precursor B-cell acute lymphoblastic leukaemia (B-ALL). We aimed to determine the clinical and genetic landscape of those with IGH-CRLF2 or P2RY8-CRLF2 (CRLF2-r) using multiple genomic approaches. Clinical and demographic features of CRLF2-r patients were characteristic of B-ALL. Patients with IGH-CRLF2 were older (14 y vs. 4 y, Pā€‰<ā€‰.001), while the incidence of CRLF2-r among Down syndrome patients was high (50/161, 31%)...
May 2017: Genes, Chromosomes & Cancer
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