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Cancer Genomics & Proteomics

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https://www.readbyqxmd.com/read/28446534/proteomics-analysis-of-tissue-samples-reveals-changes-in-mitochondrial-protein-levels-in-parathyroid-hyperplasia-over-adenoma
#1
Gurler Akpinar, Murat Kasap, Nuh Zafer Canturk, Mehin Zulfigarova, Eylül Ece Islek, Sertac Ata Guler, Turgay Simsek, Zeynep Canturk
BACKGROUND/AIM: To unveil the pathophysiology of primary hyperparathyroidism, molecular details of parathyroid hyperplasia and adenoma have to be revealed. Such details will provide the tools necessary for differentiation of these two look-alike diseases. Therefore, in the present study, a comparative proteomic study using postoperative tissue samples from the parathyroid adenoma and parathyroid hyperplasia patients was performed. MATERIALS AND METHODS: Protein extracts were prepared from tissue samples (n=8 per group)...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446533/prognostic-evaluation-of-epidermal-growth-factor-receptor-egfr-genotype-and-phenotype-parameters-in-triple-negative-breast-cancers
#2
Sofia Levva, Vassiliki Kotoula, Ioannis Kostopoulos, Kyriaki Manousou, Christos Papadimitriou, Kyriaki Papadopoulou, Sotiris Lakis, Kyriakos Koukoulias, Vasilios Karavasilis, George Pentheroudakis, Eufemia Balassi, Flora Zagouri, Ioannis G Kaklamanos, Dimitrios Pectasides, Evangelia Razis, Gerasimos Aravantinos, Pavlos Papakostas, Dimitrios Bafaloukos, Grigorios Rallis, Helen Gogas, George Fountzilas
BACKGROUND: Epidermal growth factor receptor (EGFR) aberrations have been implicated in the pathogenesis of triple-negative breast cancer (TNBC) but their impact on prognosis and, therefore, druggability, remain controversial. Herein, we studied EGFR aberrations at different molecular levels and assessed their prognostic impact in patients with operable TNBC treated with adjuvant anthracycline-based chemotherapy. MATERIALS AND METHODS: We evaluated the prognostic impact of EGFR gene status by fluorescent in situ hybridization (FISH), EGFR coding mutations by Sanger and next-generation sequencing, relative EGFR messenger RNA (mRNA) levels by qPCR (upper quartile) and EGFR and p53 protein expression by immunohistochemistry (IHC), in 352 centrally-assessed tumors from an equal number of TNBC patients...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446532/next-generation-sequencing-ngs-analysis-on-single-circulating-tumor-cells-ctcs-with-no-need-of-whole-genome-amplification-wga
#3
Raffaele Palmirotta, Domenica Lovero, Erica Silvestris, Claudia Felici, Davide Quaresmini, Paola Cafforio, Franco Silvestris
BACKGROUND: Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS)...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446531/mining-exosomal-genes-for-pancreatic-cancer-targets
#4
Amy Makler, Ramaswamy Narayanan
BACKGROUND: Exosomes, cell-derived vesicles encompassing lipids, DNA, proteins coding genes and noncoding RNAs (ncRNAs) are present in diverse body fluids. They offer novel biomarker and drug therapy potential for diverse diseases, including cancer. MATERIALS AND METHODS: Using gene ontology, exosomal genes database and GeneCards metadata analysis tools, a database of cancer-associated protein coding genes and ncRNAs (n=2,777) was established. Variant analysis, expression profiling and pathway mapping were used to identify putative pancreatic cancer exosomal gene candidates...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446530/long-non-coding-rnas-and-their-role-in-metastasis
#5
REVIEW
Ulrich H Weidle, Fabian Birzele, Gwen Kollmorgen, Rüdiger Rüger
The perception of long non-coding RNAs as chunk RNA and transcriptional noise has been steadily replaced by their role as validated targets for a diverse set of physiological processes in the past few years. However, for the vast majority of lncRNAs their precise mode of action and physiological function remain to be uncovered. A large body of evidence has revealed their essential role in all stages of cancirogenesis and metastasis. In this review we focus on the role of lncRNAs in metastasis. We grouped selected lncRNAs into three categories based on in vitro and in vivo mode of action-related studies and clinical relevance for metastasis...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28387653/overexpression-of-microrna-196b-accelerates-invasiveness-of-cancer-cells-in-recurrent-epithelial-ovarian-cancer-through-regulation-of-homeobox-a9
#6
Gun Oh Chong, Hyo-Sung Jeon, Hyung Soo Han, Ji Woong Son, Yoon Hee Lee, Dae Gy Hong, Hong Jun Park, Yoon Soon Lee, Young Lae Cho
BACKGROUND/AIM: Although microRNAs (miRNAs) are known to influence messenger RNA post-transcriptional control and contribute to human tumorigenesis, little is known about the differences in miRNA expression between primary and recurrent epithelial ovarian cancer (EOC). The purpose of this study was to assess the differential miRNA expression between primary and recurrent EOC and to investigate whether miR-196b could regulate the expression of the Homeobox A9 (HOXA9) gene, and thus affect the invasiveness of cancer cells in recurrent EOC...
March 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28387652/pediatric-ependymoma-a-proteomics-perspective
#7
George Th Tsangaris, Chrissa Papathanasiou, Panagiotis G Adamopoulos, Andreas Scorilas, Constantinos E Vorgias, Neofytos Prodromou, Foteini Tzortzatou Stathopoulou, Dimitrios J Stravopodis, Athanasios K Anagnostopoulos
BACKGROUND/AIM: Proteomics based on high-resolution mass spectrometry (MS) is the tool of choice for the analysis of protein presence, modifications and interactions, with increasing emphasis on the examination of tumor tissues. Application of MS-based proteomics offers a detailed picture of tumor tissue characteristics, facilitating the appreciation of different tumor entities, whilst providing reliable and fast results for therapeutic marker targeting and prognostic factor assessment...
March 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28387651/the-contribution-of-matrix-metalloproteinase-1-genotypes-to-hepatocellular-carcinoma-susceptibility-in-taiwan
#8
Yi-Liang Lai, Chi-Li Gong, Chun-Kai Fu, Te-Cheng Yueh, Chia-Wen Tsai, Wen-Shin Chang, Chieh-Lun Hsiao, Shiou-Ting Yen, Hsin-Ting Li, Long-Bin Jeng, Shou-Cheng Wang, DA-Tian Bau
BACKGROUND/AIM: Metalloproteinases (MMPs) are a family of proteases which have been shown to be overexpressed in various types of cancers. However, the contribution of MMP1 genotype to hepatocellular carcinoma (HCC) has not been well studied. This study aimed to evaluate the contribution of MMP1 promoter 1607 genotype to the risk of HCC in Taiwan, where HCC incidence is relatively high in the world. MATERIALS AND METHODS: In this case-control study, MMP1 genotype and its interaction with consumption of cigarettes and alcohol in determining HCC risk was investigated among 298 HCC patients and 889 age- and gender-matched healthy controls...
March 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28387650/a-proteomic-analysis-of-the-malignant-mesothelioma-secretome-using-itraq
#9
Jenette Creaney, Ian M Dick, Justine S Leon, Bruce W S Robinson
Backgound/Aim: Malignant mesothelioma (MM) is an aggressive and fatal pleural cancer. The cell secretome offers information allowing insight into the pathogenesis of MM while offering the possibility to identify potential therapeutic targets and biomarkers. In the present study the secretome protein profile of MM cell lines was compared to normal mesothelial cells. MATERIALS AND METHODS: Six MM cell lines were compared against three primary mesothelial cell culture preparations using iTRAQ® mass spectrometry...
March 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28387649/monochromosomal-hybrids-and-chromosome-transfer-a-functional-approach-for-gene-identification
#10
REVIEW
Raj P Kandpal, Arbans K Sandhu, Gurpreet Kaur, Gursurinder P Kaur, Raghbir S Athwal
Functional complementation of cellular defects has been a valuable approach for localizing causative genes to specific chromosomes. The complementation strategy was followed by positional cloning and characterization of genes for their biological relevance. We herein describe strategies used for the construction of monochromosomal hybrids and their applications for cloning and characterization of genes related to cell growth, cell senescence and DNA repair. We have cloned RNaseT2, GluR6 (glutamate ionotropic receptor kainate type subunit 2-GRIK2) and protein tyrosine phosphatase, receptor type K (PTPRK) genes using these strategies...
March 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28031240/combination-of-a-stat3-inhibitor-and-an-mtor-inhibitor-against-a-temozolomide-resistant-glioblastoma-cell-line
#11
Haruo Miyata, Tadashi Ashizawa, Akira Iizuka, Ryota Kondou, Chizu Nonomura, Takashi Sugino, Kenichi Urakami, Akira Asai, Nakamasa Hayashi, Koichi Mitsuya, Yoko Nakasu, Ken Yamaguchi, Yasuto Akiyama
BACKGROUND: Temozolomide-resistant (TMZ-R) glioblastoma is very difficult to treat, and a novel approach to overcome resistance is needed. MATERIALS AND METHODS: The efficacy of a combination treatment of STAT3 inhibitor, STX-0119, with rapamycin was investigated against our established TMZ-resistant U87 cell line. RESULTS: The growth-inhibitory effect of the combination treatment was significant against the TMZ-R U87 cell line (IC50: 78 μM for STX-0119, 30...
January 2, 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28031239/micrornas-142-3p-mir-155-and-mir-203-are-deregulated-in-gastric-malt-lymphomas-compared-to-chronic-gastritis
#12
Concepción Fernández, Beatriz Bellosillo, Mariana Ferraro, Agustín Seoane, Blanca Sánchez-González, Silvia Pairet, Aina Pons, Luis Barranco, María Carmen Vela, Eva Gimeno, Lluís Colomo, Carles Besses, Alfons Navarro, Antonio Salar
BACKGROUND: Over the last years, our knowledge on pathogenesis of gastric MALT lymphoma has greatly improved, but its morphological diagnosis is still hampered by overlapping histological features with advanced chronic gastritis. MicroRNAs are deregulated in lymphomas, but their role and usefulness in gastric MALT lymphoma has not been extensively investigated. MATERIALS AND METHODS: We analyzed the expression of 384 miRNAs using TaqMan microRNA assay in a training series of 10 gastric MALT lymphomas, 3 chronic gastritis and 2 reactive lymph nodes...
January 2, 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28031238/customized-array-comparative-genomic-hybridization-analysis-of-25-phosphatase-encoding-genes-in-colorectal-cancer-tissues
#13
Izabela Laczmanska, Pawel Skiba, Pawel Karpinski, Marek Bebenek, Maria M Sasiadek
BACKGROUND/AIM: Molecular mechanisms of alterations in protein tyrosine phosphatases (PTPs) genes in cancer have been previously described and include chromosomal aberrations, gene mutations, and epigenetic silencing. However, little is known about small intragenic gains and losses that may lead to either changes in expression or enzyme activity and even loss of protein function. MATERIALS AND METHODS: The aim of this study was to investigate 25 phosphatase genes using customized array comparative genomic hybridization in 16 sporadic colorectal cancer tissues...
January 2, 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28031237/expression-profiling-of-a-human-thyroid-cell-line-stably-expressing-the-brafv600e-mutation
#14
Byoung-Ae Kim, Hyeon-Gun Jee, Jin Wook Yi, Su-Jin Kim, Young Jun Chai, June Young Choi, Kyu Eun Lee
BACKGROUND/AIM: The BRAF(V600E) mutation acts as an initiator of cancer development in papillary thyroid carcinoma (PTC). Gene expression changes caused by the BRAF(V600E) mutation may have an important role in thyroid cancer development. MATERIALS AND METHODS: To study genomic alterations caused by the BRAF(V600E) mutation, we made human thyroid cell lines that harbor the wild-type BRAF gene (Nthy/WT) and the V600E mutant-type BRAF gene (Nthy/V600E). RESULTS: Flow cytometry and western blotting showed stable transfection of the BRAF gene...
January 2, 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28031236/proteomics-analysis-of-ovarian-cancer-cell-lines-and-tissues-reveals-drug-resistance-associated-proteins
#15
Isa N Cruz, Helen M Coley, Holger B Kramer, Thumuluru Kavitah Madhuri, Nur A M Safuwan, Ana Rita Angelino, Min Yang
BACKGROUND: Carboplatin and paclitaxel form the cornerstone of chemotherapy for epithelial ovarian cancer, however, drug resistance to these agents continues to present challenges. Despite extensive research, the mechanisms underlying this resistance remain unclear. MATERIALS AND METHODS: A 2D-gel proteomics method was used to analyze protein expression levels of three human ovarian cancer cell lines and five biopsy samples. Representative proteins identified were validated via western immunoblotting...
January 2, 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28031235/htp-nutraceutical-screening-for-histone-deacetylase-inhibitors-and-effects-of-hdacis-on-tumor-suppressing-mirnas-by-trichostatin-a-and-grapeseed-vitis-vinifera-in-hela-cells
#16
Elizabeth A Mazzio, Karam F A Soliman
BACKGROUND/AIM: Aggressive tumor malignancies are a consequence of delayed diagnosis, epigenetic/phenotype changes and chemo-radiation resistance. Histone deacetylases (HDACs) are a major epigenetic regulator of transcriptional repression, which are highly overexpressed in advanced malignancy. While original chemotherapy drugs were modeled after phytochemicals elucidated by botanical screenings, HDAC inhibitors (HDACi) such as apicidin, trichostatin A (TSA) and butyrate were discovered as products of fungus and microbes, in particular, gut microbiota...
January 2, 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28031234/the-multiple-roles-of-exosomes-in-metastasis
#17
REVIEW
Ulrich H Weidle, Fabian Birzele, Gwen Kollmorgen, Rüdiger Rüger
Exosomes are important contributors to cell-cell communication and their role as diagnostic markers for cancer and the pathogenesis for cancer is under intensive investigation. Here, we focus on their role in metastasis-related processes. We discuss their impact regarding promotion of invasion and migration of tumor cells, conditioning of lymph nodes, generation of premetastatic niches and organotropism of metastasis. Furthermore, we highlight interactions of exosomes with bone marrow and stromal components such as fibroblasts, endothelial cells, myeloid- and other immune-related cells in the context of metastases...
January 2, 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/27807074/platelet-derived-growth-factor-bb-a-must-have-therapeutic-target-redivivus-in-ovarian-cancer
#18
Anca Maria Cimpean, Ionut Marcel Cobec, Raluca Amalia Ceaușu, Roxana Popescu, Anca Tudor, Marius Raica
BACKGROUND: We aimed to validate PDGF-BB protein expression by RNAscope, a sensitive method for PDGF-BB mRNA evaluation on paraffin embedded (FFPE) specimens of ovarian tumors. MATERIALS AND METHODS: Seventy-five FFPE ovarian cancer biopsies were assessed by immunohistochemistry followed by PDGF-BB mRNA RNAscope validation. RESULTS AND CONCLUSION: Dual PDGF-BB expression in tumor and stromal cells have been observed, being highly suggestive for PDGF-BB mediated stromal-tumor cells reciprocal interaction in ovarian cancer (p=0...
November 2016: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/27807073/archetype-and-rearranged-non-coding-control-regions-in-urothelial-bladder-carcinoma-of-immunocompetent-individuals
#19
Elena Anzivino, Maria Antonella Zingaropoli, Marco Iannetta, Valeria Antonietta Pietropaolo, Alessandra Oliva, Francesco Iori, Antonio Ciardi, Donatella Maria Rodio, Francesca Antonini, Cesare Giovanni Fedele, Alessandra D'Abramo, Claudio Maria Mastroianni, Vincenzo Vullo, Maria Rosa Ciardi
BACKGROUND: Polyomaviruses (PyVs) are potential transforming viruses. Despite their involvement in human tumours still being debated, there is evidence to suggest a role for PyVs in bladder carcinoma (BC). Therefore, a possible association between PyVs and BC was investigated. MATERIALS AND METHODS: Urine, blood and fresh bladder tissue specimens were collected from 29 patients with BC. PyV prevalence, non-coding control region (NCCR) organization and genotypic analysis were assessed...
November 2016: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/27807072/introduction-of-id2-enhances-invasiveness-in-id2-null-oral-squamous-cell-carcinoma-cells-via-the-snail-axis
#20
Y U Kamata, Tomoki Sumida, Yosuke Kobayashi, Akiko Ishikawa, Wataru Kumamaru, Yoshihide Mori
AIM: Inhibitor of DNA-binding (ID) proteins are negative regulators of basic helix-loop-helix transcription factors that generally stimulate cell proliferation and inhibit differentiation. However, the role of ID2 in cancer progression remains ambiguous. Here, we investigated the function of ID2 in ID2-null oral squamous cell carcinoma (OSCC) cells. MATERIALS AND METHODS: We introduced an ID2 cDNA construct into ID2-null OSCC cells and compared them with empty-vector-transfected cells in terms of cell proliferation, invasion, and activity and expression of matrix metalloproteinase (MMP)...
November 2016: Cancer Genomics & Proteomics
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