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Cancer Genomics & Proteomics

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https://www.readbyqxmd.com/read/28647702/comparative-mirna-expression-profile-analysis-of-squamous-cell-carcinoma-and-peritumoral-mucosa-from-the-meso-and-hypopharynx
#1
Eva Orosz, Katalin Gombos, Tamas Riedling, Priscilla Afiakurue, Istvan Kiss, Jozsef Pytel, Imre Gerlinger, Istvan Szanyi
BACKGROUND/AIM: The role of microRNAs (miRNA) in carcinogenesis is related to their genome-regulatory function. The aim of the present study was to identify and compare miRNA expression signatures of meso- and hypopharynx squamous cell cancers in consideration of the cancer field hypothesis. PATIENTS AND METHODS: Thirteen snap-frozen biopsy series of tumors and peritumoral tissues from the meso- and hypopharynx were analyzed regarding their miRNA expression with quantitative real-time polymerase chain reaction (qRT-PCR)...
July 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28647701/aberrant-methylation-of-t-cadherin-can-be-a-diagnostic-biomarker-for-colorectal-cancer
#2
Bo-Shi Duan, Long-Fei Xie, Yue Wang
BACKGROUND/AIM: T-cadherin is a tumor suppressor gene, its predictive value in colorectal cancer (CRC) still remains controversial. In this study, we aimed to evaluate the association between T-cadherin promoter methylation and CRC by performing a meta-analysis. MATERIALS AND METHODS: The relevant literature was searched using the PubMed, Cochrane Library, Web of Science and Google Scholar databases for articles published until December 2016. The effect sizes were estimated by measuring an odds ratio (OR) with a 95% confidence interval (CI)...
July 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28647700/molecular-proteomic-characterization-of-a-pediatric-medulloblastoma-xenograft
#3
George T Tsangaris, Konstantinos Dimas, Angeliki Malamou, Angeliki Katsafadou, Chrissa Papathanasiou, Dimitrios J Stravopodis, Constantinos E Vorgias, Maria Gazouli, Athanasios K Anagnostopoulos
BACKGROUND/AIM: Medulloblastoma (MBL), an archetypal primitive neuroectodermal tumor of the cerebellum, is the most common pediatric central nervous system malignancy representing approximately 20% of all childhood brain tumors. Herein, we report on a new xenotransplantable tumor cell line, derived from a 6-year-old female patient with cerebellar medulloblastoma, and the completele proteome molecular characterization of subsequent tumors from MBL xenotrasplanted mice. MATERIALS AND METHODS: Tumors were grown in nude mice as subcutaneous xenografts (MBLX) composed of small round cells with hyperchromatic nuclei and scant cytoplasm...
July 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28647699/proteomic-analysis-of-normal-and-cancer-cervical-cell-lines-reveals-deregulation-of-cytoskeleton-associated-proteins
#4
Kalliopi I Pappa, Vasiliki Lygirou, Georgia Kontostathi, Jerome Zoidakis, Manousos Makridakis, Konstantinos Vougas, George Daskalakis, Alexander Polyzos, Nicholas P Anagnou
BACKGROUND: Both HPV-positive and -negative cervical cancers are primarily associated with features of cell cycle and cytoskeletal disruption; however, the actual biological processes affected remain elusive. To this end, we systematically characterized the intracellular proteomic profiles of four distinct and informative cervical cell lines. MATERIALS AND METHODS: Cell extracts from a normal cervical (HCK1T) and three cervical cancer cell lines, one HPV-negative (C33A), and two HPV-positive, SiHa (HPV16+) and HeLa (HPV18+), were analyzed by 2-dimensional electrophoresis and differentially expressed proteins were identified by MALDI-TOF mass spectrometry, while differential expression was confirmed by western blot analysis...
July 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28647698/increased-expression-of-follistatin-in-breast-cancer-reduces-invasiveness-and-clinically-correlates-with-better-survival
#5
Catherine Zabkiewicz, Jeyna Resaul, Rachel Hargest, Wen Guo Jiang, Lin Ye
BACKGROUND/AIM: Activin and its antagonist follistatin (FST) have been implicated in several solid tumours. This study investigated the role of FST in breast cancer. MATERIALS AND METHODS: FST expression was examined using reverse transcription polymerase chain reaction (RT-PCR), real-time quantitative polymerase chain reaction (qPCR) and immunohistochemistry in a cohort of breast cancer samples. Expression was correlated to pathological and prognostic parameters in our patient cohort...
July 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28647697/analysis-of-k-ras-interactions-by-biotin-ligase-tagging
#6
Christopher Ritchie, Andrew Mack, Logan Harper, Ayna Alfadhli, Philip J S Stork, Xiaolin Nan, Eric Barklis
BACKGROUND: Mutations of the human K-Ras 4B (K-Ras) G protein are associated with a significant proportion of all human cancers. Despite this fact, a comprehensive analysis of K-Ras interactions is lacking. Our investigations focus on characterization of the K-Ras interaction network. MATERIALS AND METHODS: We employed a biotin ligase-tagging approach, in which tagged K-Ras proteins biotinylate neighbor proteins in a proximity-dependent fashion, and proteins are identified via mass spectrometry (MS) sequencing...
July 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28647696/cytokeratin-18-associated-histone-3-modulation-in-hepatocellular-carcinoma-a-mini-review
#7
REVIEW
Yen-Chang Clark Lai, Chiung-Chi Cheng, Yih-Shyong Lai, Yi-Hsiang Liu
Unstable cytokeratins are associated with tumor transformation in the development of human hepatocellular carcinoma. We previously demonstrated that the cytokeratin 18 was modulated and that a histone H3-specific modification occured, among members of the histone family, during the development of human hepatocellular carcinoma. Evidence suggested that the modification of histone H3 was highly correlated with the modulation of cytokeratin 18 and probably plays an important role in tumorigenesis of hepatocytes...
July 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28647695/the-warburg-effect-and-mass-spectrometry-based-proteomic-analysis
#8
REVIEW
Weidong Zhou, Lance A Liotta, Emanuel F Petricoin
Compared to normal cells, cancer cells have a unique metabolism by performing lactic acid fermentation in the presence of oxygen, also known as the Warburg effect. Researchers have proposed several hypotheses to elucidate the phenomenon, but the mechanism is still an enigma. In this review, we discuss three typical models, such as "damaged mitochondria", "adaptation to hypoxia", and "cell proliferation requirement", as well as contributions from mass spectrometry analysis toward our understanding of the Warburg effect...
July 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446534/proteomics-analysis-of-tissue-samples-reveals-changes-in-mitochondrial-protein-levels-in-parathyroid-hyperplasia-over-adenoma
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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