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Cancer Genomics & Proteomics

Jinming Song, Lynn Moscinski, Hailing Zhang, Xiaohui Zhang, Mohammad Hussaini
BACKGROUND: Mutations in splicing factor 3b subunit 1 (SF3B1) have been reported to be associated with a favorable prognosis, while the prognostic impact of tet methylcytosine dioxygenase 2 (TET2) mutations is still controversial. The clinical significance of combined SF3B1 and TET2 mutation is even more uncertain. In this study, the clinical consequences of concurrent double SF3B1/TET2 mutation were compared with isolated SF3B1 or TET2 mutation. MATERIALS AND METHODS: The demographics, diagnosis, cytogenetic abnormalities, and overall survival time of 130 patients with isolated SF3B1 (n=48) or TET2 mutation (n=54), or double SF3B1/TET2 mutation (n=28) were compared by next-generation sequencing...
January 2019: Cancer Genomics & Proteomics
Hengchao Li, Yishen Mao, Yueting Xiong, Huan Huan Zhao, Fenglin Shen, Xing Gao, Pengyuan Yang, Xiaohui Liu, Deliang Fu
BACKGROUND/AIM: Pancreatic cancer (PC) is currently the fourth leading cause of cancer-related mortality worldwide. Peripheral blood mononuclear cells (PBMCs) is a subpopulation of accessible and functional immune cells. Comparative analysis of the proteome of PBMCs can help us elucidate the mechanism of disease and find potential biomarkers for diagnosis. MATERIALS AND METHODS: PBMCs were collected from healthy individuals, patients with benign diseases, and pancreatic cancer...
January 2019: Cancer Genomics & Proteomics
Ryota Fujii, Eiji Osaka, Kentaro Sato, Yasuaki Tokuhashi
BACKGROUND/AIM: miRNA-1(miR-1) is down-regulated in various cancer cells including osteosarcoma cells. This study was conducted to analyze the function of miR-1 in osteosarcoma cells. MATERIALS AND METHODS: miR-1 expression in osteosarcoma cells was evaluated by qRT-PCR. Cell proliferation was evaluated after transfecting miR-1 by WST8 assay and FACS analysis, both in vitro and in vivo. RESULTS: Overexpression of miR-1 suppressed cell proliferation and induced cell-cycle arrest in the G0 -G1 phase by increasing p21 levels via a p53-independent pathway...
January 2019: Cancer Genomics & Proteomics
Steven Lehrer, Peter H Rheinstein
BACKGROUND/AIM: In a previous study we analyzed poliomyelitis incidence in US states, before the introduction of the polio vaccine. We noted an inverse correlation between polio incidence in US states, between 1937 and 1951, and colorectal cancer incidence (2005-2009). To further elucidate the role that poliovirus could play in colorectal cancer, the full human genome for poliovirus sequences was analyzed using the UCSC Genome Browser. MATERIALS AND METHODS: BLAT, the Blast-Like Alignment Tool of the UCSC Genome Browser, was used to compare the poliovirus genome to the human genome...
January 2019: Cancer Genomics & Proteomics
Vikramjit K Zhawar, Raj P Kandpal, Raghbir S Athwal
BACKGROUND: The aberrant regulation of growth and proliferation is a key feature of carcinoma cells. In order to use molecular strategies to correct these defects toward therapeutic purposes, it is important to characterize the entire spectrum of causative molecules. MATERIALS AND METHODS: By using gene transfer technique, SKOV3 ovarian carcinoma cells were transduced with an expression construct of glutamate receptor 6 (glutamate ionotropic receptor kainate type subunit 2, GRIK2) in retroviral vector PQCXIP...
January 2019: Cancer Genomics & Proteomics
Paula Alejandra Sacca, Osvaldo Néstor Mazza, Carlos Scorticati, Gonzalo Vitagliano, Gabriel Casas, Juan Carlos Calvo
BACKGROUND/AIM: Periprostatic adipose tissue (PPAT) directs tumour behaviour. Microenvironment secretome provides information related to its biology. This study was performed to identify secreted proteins by PPAT, from both prostate cancer and benign prostate hyperplasia (BPH) patients. PATIENTS AND METHODS: Liquid chromatography-mass spectrometry-based proteomic analysis was performed in PPAT-conditioned media (CM) from patients with prostate cancer (CMs-T) (stage T3: CM-T3, stage T2: CM-T2) or benign disease (CM-BPH)...
January 2019: Cancer Genomics & Proteomics
Kuniaki Sato, Atsushi Niida, Takaaki Masuda, Dai Shimizu, Taro Tobo, Yousuke Kuroda, Hidetoshi Eguchi, Takashi Nakagawa, Yutaka Suzuki, Koshi Mimori
BACKGROUND: Intratumoral heterogeneity (ITH) is a major cause underlying therapeutic difficulty of cancer. Although an understanding of ITH is critically important in order to develop novel therapeutic strategies, experimental models that enable the examination of ITH in a time series are lacking. MATERIALS AND METHODS: We developed an experimental approach based on patient-derived xenograft (PDX) mice and a multiregional sequencing approach (MRA). The multiple regions of primary colorectal cancer (CRC) and serially transplanted PDX tumors were analyzed via whole-exome sequencing and bioinformatic analyses...
January 2019: Cancer Genomics & Proteomics
Ulrich H Weidle, Alexandra Epp, Fabian Birzele, Ulrich Brinkmann
The mortality of patients with hormone-resistant prostate cancer can be ascribed to a large degree to metastasis to distant organs, predominantly to the bones. In this review, we discuss the contribution of micro-RNAs (miRs) to the metastatic process of prostate cancer. The criteria for selection of miRs for this review were the availability of preclinical in vivo metastasis-related data in conjunction with prognostic clinical data. Depending on their function in the metastatic process, the corresponding miRs are up- or down-regulated in prostate cancer tissues when compared to matching normal tissues...
January 2019: Cancer Genomics & Proteomics
Jong Hyuk Yoon, Dayea Kim, Jaeyoon Kim, Hyeongjoo Lee, Jaewang Ghim, Byung Jun Kang, Parkyong Song, Pann-Ghill Suh, Sung Ho Ryu, Taehoon G Lee
BACKGROUND: There are limitations to current colorectal cancer (CRC)-specific diagnostic methods and therapies. Tumorigenesis proceeds because of interaction between cancer cells and various surrounding cells; discovering new molecular mediators through studies of the CRC secretome is a promising approach for the development of CRC diagnostics and therapies. MATERIALS AND METHODS: A comparative secretomic analysis was performed using primary and metastatic human isogenic CRC cells...
November 2018: Cancer Genomics & Proteomics
Kittirat Saharat, Kriengsak Lirdprapamongkol, Daranee Chokchaichamnankit, Chantragan Srisomsap, Jisnuson Svasti, N Monique Paricharttanakul
BACKGROUND/AIM: Resistance to anoikis is a pre-requisite step in metastasis, a major cause of death in patients with cancer, including thyroid cancer. Impairing anoikis resistance is a possible strategy for therapy of metastatic cancer. We, therefore, we aimed to investigate the key players of anoikis resistance. MATERIALS AND METHODS: Papillary-type (BCPAP), follicular-type (FTC133), and anaplastic-type (ARO) thyroid carcinoma cells, cultured in poly(2-hydroxyethyl methacrylate)-coated plates to mimic circulating cells, were used as model systems in this study...
November 2018: Cancer Genomics & Proteomics
Christos Christodoulou, Georgios Oikonomopoulos, Georgia Angeliki Koliou, Ioannis Kostopoulos, Vassiliki Kotoula, Mattheos Bobos, George Pentheroudakis, George Lazaridis, Maria Skondra, Sofia Chrisafi, Angelos Koutras, Dimitrios Bafaloukos, Evangelia Razis, Kyriaki Papadopoulou, Pavlos Papakostas, Haralambos P Kalofonos, Dimitrios Pectasides, Pantelis Skarlos, Konstantine T Kalogeras, George Fountzilas
BACKGROUND: Trastuzumab is a monoclonal antibody against HER2-positive breast cancer. Despite improving the natural history of the disease, there is a number of patients who are resistant to it, whereas all patients will eventually develop resistance and disease will progress. Inconsistent preclinical data show that the IGF-R pathway may contribute to either de novo or acquired resistance to trastuzumab. MATERIALS AND METHODS: In total, 227 trastuzumab-treated metastatic breast cancer patients were evaluated for IGF-1, IGF-1R, GLP-1R, Akt1, Akt2 Akt3 mRNA expression, and IGF-1Rα, IGF-1Rβ, IGF-2R protein expression...
November 2018: Cancer Genomics & Proteomics
Chun-Ming Yen, Chia-Wen Tsai, Wen-Shin Chang, Yi-Chin Yang, Yi-Wen Hung, Hsu-Tung Lee, Chiung-Chyi Shen, Meei-Ling Sheu, Ju-Yu Wang, Chi-Li Gong, Wen-Yu Cheng, DA-Tian Bau
AIM: Arsenic trioxide (As2 O3 ), known as pi-shuang and the most toxic compound in traditional Chinese medicine, has been used as an antitumor agent for thousands of years. Resveratrol (3,5,4'-trihydroxy-trans-stilbene) is a natural phenol that has significant anti-bacterial, anti-fungaI and antiaging activities. Our study aimed to examine the combined anticancer effects of As2 O3 and resveratrol against human neuroblastoma SK-N-SH cells, and elucidate the underlying intracellular signaling...
November 2018: Cancer Genomics & Proteomics
Ritika Gera, Leon Mokbel, Wen G Jiang, Kefah Mokbel
BACKGROUND: Cyclin-dependent kinase 2-associated protein 1 (CDK2AP1) interacts with CDK2AP2, modulates the actions of transforming growth factor-B1, cyclin-dependent kinase 2 and retinoblastoma protein, and closely interacts with micro-RNA21 and micro-RNA25. Our objective was to determine if CDK2AP1 mRNA expression levels were consistent with tumour-suppressive functions in breast cancer. MATERIALS AND METHODS: A total of 134 samples were analysed. CDK2AP1 mRNA levels were measured using quantitative polymerase chain reaction (RT-PCR) and normalised against glyceraldehyde 3-phosphate dehydrogenase mRNA...
November 2018: Cancer Genomics & Proteomics
Lene E Johannessen, Petter Brandal, Tor Åge Myklebust, Sverre Heim, Francesca Micci, Ioannis Panagopoulos
BACKGROUND: Although methylation of the O6 -methylguanine-DNA methyltransferase (MGMT) gene promoter predicts response to temozolomide in patients with glioblastoma, no consensus exists as to which assay is best for its detection. MATERIALS AND METHODS: Methylation of MGMT promoter was examined by methylation-specific polymerase chain reaction (MSP), quantitative real-time MSP, methylation-sensitive high-resolution melting analysis, and two commercial pyrosequencing (PSQ) kits...
November 2018: Cancer Genomics & Proteomics
Ourania Romanidou, Vassiliki Kotoula, George Fountzilas
Isocitrate dehydrogenases 1 and 2 (IDH1/2) are enzymes that play a major role in the Krebs cycle. Mutations in these enzymes are found in the majority of lower gliomas and secondary glioblastomas, but also in myeloid malignancies and other cancers. IDH1 and IDH2 mutations are restricted to specific arginine residues in the active site of the enzymes and are gain-of-function, i.e. they confer a neomorphic enzyme activity resulting in the accumulation of D-2-hydroxyglutarate (2-HG). 2-HG is an oncometabolite causing profound metabolic dysregulation which, among others, results in methylator phenotypes and in defects in homologous recombination repair...
September 2018: Cancer Genomics & Proteomics
Norihisa Saeki, Akira Saito, Yuki Sugaya, Mitsuhiro Amemiya, Hiroki Sasaki
BACKGROUND/AIM: Overall survival for the high-risk group of neuroblastoma (NB) patients still remains at 40-50%, necessitating the establishment of a curable treatment. LIM domain only 1 (LMO1) gene encoding a transcriptional regulator is an NB-susceptibility gene with a tumor-promoting activity. Previously we conducted chromatin immunoprecipitation and DNA sequencing analyses on NB cell lines and identified 3 protein-coding genes regulated by LMO1. In this study, we extended our analyses to capture microRNA genes directly or indirectly regulated by LMO1...
September 2018: Cancer Genomics & Proteomics
Te-Cheng Yueh, Yi-Wen Hung, Tzu-Ching Shih, Cheng-Nan Wu, Shou-Cheng Wang, Yi-Liang Lai, Shih-Wei Hsu, Ming-Hsien Wu, Chun-Kai Fu, Yun-Chi Wang, Tao-Wei Ke, Wen-Shin Chang, Chia-Wen Tsai, DA-Tian Bau
BACKGROUND/AIM: The genomic role of human mouse double minute 2 (MDM2) in colorectal cancer (CRC) is unclear, therefore, our study aimed to evaluate the contribution of MDM2 genotype to the risk of CRC in Taiwan. MATERIALS AND METHODS: In this case-control study, MDM2 SNP309 T to G (rs2279744) genotypes were determined and their association with CRC risk were investigated among 362 patients with CRC and 362 age- and gender-matched healthy controls in central Taiwan...
September 2018: Cancer Genomics & Proteomics
Josef Maryáš, Jakub Faktor, Lenka Čápková, Petr Müller, Petr Skládal, Pavel Bouchal
BACKGROUND/AIM: Pul-down assay is a popular in vitro method for identification of physical interactors of selected proteins. Here, for the first time, we compared three conventional variants of pull-down assay with the streptavidin-modified surface plasmon resonance (SPR) chips for the detection of PDZ and LIM domain protein 2 (PDLIM2) interaction partners. MATERIALS AND METHODS: PDLIM2 protein-protein interactions were analysed by three variants of pull-down assay on streptavidin beads using LC-MS/MS in "Sequential Window Acquisition of all Theoretical fragment ion spectra (SWATH)" mode and compared with LC-SWATH-MS/MS data from SPR chips...
September 2018: Cancer Genomics & Proteomics
Steven Lehrer, Peter H Rheinstein
BACKGROUND: One aspect of smoking and lung cancer that has not been closely examined, is that regarding genes that may predispose to tobacco dependence. Smoking and mental illness are tightly linked, apparently the result of smokers using cigarettes to self-medicate for mental problems. The gene for solute carrier family 18 member A1 (vesicular monoamine transporter; SLC18A1) is of particular interest in this regard because of its association with schizophrenia, autism and bipolar illness as well as with cancer...
September 2018: Cancer Genomics & Proteomics
Ioannis Panagopoulos, Ludmila Gorunova, Henning Leske, Pitt Niehusmann, Lene E Johannessen, Julie Staurseth, Nina Øino, Torstein R Meling, Sverre Heim, Francesca Micci, Petter Brandal
BACKGROUND: Methylation of the O6 -methylguanine-DNA methyltransferase (MGMT) gene promoter is a well-established predictor of response to the DNA-alkylating agent temozolomide in patients with glioblastoma. MATERIALS AND METHODS: Pyrosequencing analysis was used to determine the MGMT promoter methylation status in 61 meningiomas, to clarify whether it might have a predictive role. RESULTS: Only two tumors (3%) had a mean methylation frequency higher than the cut-off value of 10% for the four CpG sites examined...
September 2018: Cancer Genomics & Proteomics
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