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Cancer Genomics & Proteomics

Dimitrios Moris, Ioannis Ntanasis-Stathopoulos, Diamantis I Tsilimigras, Mohamad A Adam, Chifu Jeffrey Yang, David Harpole, Stamatios Theocharis
Primary lung neuroendocrine tumors (NETs) consist of typical and atypical carcinoids, large-cell neuroendocrine carcinomas and small-cell lung carcinomas. NETs are highly heterogeneous in histological characteristics, clinical presentation and natural history. While there are morphological and immunohistochemical criteria to establish diagnosis, there is a lack of universal consensus for prognostic factors or therapeutic targets for personalized treatment of the disease. Thus, identifying potential markers of neuroendocrine differentiation and prognostic factors remains of high importance...
March 2018: Cancer Genomics & Proteomics
Patcharawalai Whongsiri, Chaowat Pimratana, Udomsak Wijitsettakul, Depicha Jindatip, Anapat Sanpavat, Wolfgang A Schulz, Michèle J Hoffmann, Wolfgang Goering, Chanchai Boonla
BACKGROUND/AIM: Reactivation of long interspersed nuclear element-1 (LINE-1) and oxidative stress are suggested to have oncogenic potential to drive tumorigenesis and cancer progression. We previously demonstrated that reactive oxygen species (ROS) caused hypomethylation of LINE-1 elements in bladder cancer cells. In this study, we investigated the expression of LINE-1-encoded protein (ORF1p) and oxidative stress marker 4-hydroxynonenal (4-HNE) in human bladder cancer tissues, as well as induction of ORF1p expression by ROS in bladder cancer cell lines...
March 2018: Cancer Genomics & Proteomics
Dimitrios Tsoumas, Sofia Nikou, Efstathia Giannopoulou, Spyridon Champeris Tsaniras, Chaido Sirinian, Ioannis Maroulis, Stavros Taraviras, Vassiliki Zolota, Haralabos P Kalofonos, Vasiliki Bravou
BACKGROUND/AIM: Epithelial-mesenchymal transition (EMT) and cancer stem cells (CSC) are critically implicated in cancer metastasis and chemoresistance. Herein, we investigated integrin-linked kinase (ILK)'s role in human colon cancer (CRC) progression and chemoresistance in relation to EMT and CSC markers. PATIENTS AND METHODS: Expression of ILK, EMT and CSC markers were evaluated by immunohistochemistry in 149 CRC samples. We also generated colon cancer cells resistant to 5-FU and oxaliplatin and studied the effect of ILK inhibition on drug response by MTT assay and on EMT and CSC markers' expression...
March 2018: Cancer Genomics & Proteomics
Mohammad Omar Hussaini, Abu-Sayeef Mirza, Rami Komrokji, Jeffrey Lancet, Eric Padron, Jinming Song
BACKGROUND/AIM: Acute myeloid leukemia (AML) represents a heterogeneous disease with varying morphologic, immunophenotypic, and genetic features, along with varying patient outcomes. The genomic tractability of AML makes it amenable for targeted next-generation sequencing (NGS) testing clinically. MATERIALS AND METHODS: One hundred eights-seven unique patients with a diagnosis of acute myeloid leukemia between May 2011 and Oct 2014 and with mutational analysis by NGS were included in this study...
March 2018: Cancer Genomics & Proteomics
Christian Lopez, Mohammad Abuel-Haija, Luis Pena, Domenico Coppola
BACKGROUND: Cowden syndrome (CS) is a rare autosomal-dominant inherited disorder characterized by multiple hamartomas. While the hamartomas are benign, patients with CS have increased risk of osteosarcoma and of breast, thyroid, endometrial, soft-tissue and colonic neoplasms. Germline mutations of phosphatase and tensin homolog (PTEN) are implicated in CS and in the development of osteosarcoma. We report a patient with CS who presented with osteosarcoma, ganglioneuromatosis and a benign breast mass...
March 2018: Cancer Genomics & Proteomics
Eigil Kjeldsen, Christine J F Nielsen, Amit Roy, Cinzia Tesauro, Ann-Katrine Jakobsen, Magnus Stougaard, Birgitta R Knudsen
Acquisition of resistance to topoisomerase I (TOP1)-targeting camptothecin (CPT) derivatives is a major clinical problem. Little is known about the underlying chromosomal and genomic mechanisms. We characterized the CPT-K5 cell line expressing mutant CPT-resistant TOP1 and its parental T-cell derived acute lymphoblastic leukemia CPT-sensitive RPMI-8402 cell line by karyotyping and molecular genetic methods, including subtractive oligo-based array comparative genomic hybridization (soaCGH) analysis. Karyotyping revealed that CPT-K5 cells had acquired additional structural aberrations and a reduced modal chromosomal number compared to RPMI-8402...
March 2018: Cancer Genomics & Proteomics
Magdalena Gorska-Ponikowska, Alicja Kuban-Jankowska, Stephan A Eisler, Ugo Perricone, Giosuè Lo Bosco, Giampaolo Barone, Stephan Nussberger
BACKGROUND/AIM: Dysregulation of mitochondrial pathways is implicated in several diseases, including cancer. Notably, mitochondrial respiration and mitochondrial biogenesis are favored in some invasive cancer cells, such as osteosarcoma. Hence, the aim of the current work was to investigate the effects of 2-methoxyestradiol (2-ME), a potent anticancer agent, on the mitochondrial biogenesis of osteosarcoma cells. MATERIALS AND METHODS: Highly metastatic osteosarcoma 143B cells were treated with 2-ME separately or in combination with L-lactate, or with the solvent (non-treated control cells)...
January 2018: Cancer Genomics & Proteomics
Qiang Zhang, Wenying Wang, Weidong Xu, Mulong Du`, Gaoxiang Ma, Hanting Liu, Haiyan Chu, N A Tong, Meilin Wang, Jianfeng Shao, Zhengdong Zhang, Lin Yuan, Jing Qian
BACKGROUND: Key genes related to cell cycle and apoptosis pathways play critical roles in bladder cancer. Single nucleotide polymorphisms (SNPs) in the 3'-untranslated regions (3'-UTR) of genes may impact microRNA (miRNA)-messenger RNA (mRNA) binding capacity and alter gene expression to contribute to the susceptibility of cancers. However, an association of genetic variations in cell cycle and apoptosis pathways with bladder cancer risk, has not been reported. MATERIALS AND METHODS: We selected SNPs in the 3'-UTR of cell cycle and apoptosis pathways genes and genotyped them with a case-control study consisting of 578 bladder cancer patients and 1,006 cancer-free subjects...
January 2018: Cancer Genomics & Proteomics
Ioannis Panagopoulos, Ludmila Gorunova, Kristin Andersen, Ingvild Lobmaier, Bodil Bjerkehagen, Sverre Heim
BACKGROUND/AIM: Angiolipoma is a rare benign soft tissue tumor composed of mature adipocytes and blood vessels. Genetic information on angiolipomas is scarce. With the single exception of one tumor which carried a t(X;2)(p22;p12), all angiolipomas hitherto investigated cytogenetically had normal karyotypes. MATERIALS AND METHODS: G-banding chromosome analysis was performed on three short-term cultured angiolipomas. Fluorescence in situ hybridization (FISH) analysis using a commercially available RB1 deletion probe was also done...
January 2018: Cancer Genomics & Proteomics
Kana Ishibashi, Kotaro Ishii, Goro Sugiyama, Y U Kamata, Azusa Suzuki, Wataru Kumamaru, Yukiko Ohyama, Hiroyuki Nakano, Tamotsu Kiyoshima, Tomoki Sumida, Tomohiro Yamada, Yoshihide Mori
BACKGROUND/AIM: Adenoid cystic carcinoma (AdCC) is a rare cancer of the salivary gland with high risk of recurrence and metastasis. Wnt signalling is critical for determining tumor grade in AdCC, as it regulates invasion and migration. β-catenin dephosphorylation plays an important role in the Wnt pathway, but its underlying molecular mechanism remains unclear. MATERIALS AND METHODS: Because the regulatory subunits of protein phosphatase 2A (PP2A) drive Wnt signalling via target molecules, including β-catenin, we used qRT-PCR and immunoblot analysis to investigate the expression of these subunits in an AdCC cell line (ACCS) and a more aggressive subline (ACCS-M)...
January 2018: Cancer Genomics & Proteomics
Shujun Huang, Nianguang Cai, Pedro Penzuti Pacheco, Shavira Narrandes, Yang Wang, Wayne Xu
Machine learning with maximization (support) of separating margin (vector), called support vector machine (SVM) learning, is a powerful classification tool that has been used for cancer genomic classification or subtyping. Today, as advancements in high-throughput technologies lead to production of large amounts of genomic and epigenomic data, the classification feature of SVMs is expanding its use in cancer genomics, leading to the discovery of new biomarkers, new drug targets, and a better understanding of cancer driver genes...
January 2018: Cancer Genomics & Proteomics
Ulrich H Weidle, Steffen Dickopf, Corinna Hintermair, Gwendlyn Kollmorgen, Fabian Birzele, Ulrich Brinkmann
Despite the approval of several molecular therapies in the last years, breast cancer-associated death ranks as the second highest in women. This is due to metastatic disease, which represents a challenge for treatment. A better understanding of the molecular mechanisms of metastasis is, therefore, of paramount importance. In this review we summarize the role of micro RNAs (miRs) involved in metastasis of breast cancer. We present an overview on metastasis-promoting, -suppressing and context-dependent miRs with both activities...
January 2018: Cancer Genomics & Proteomics
Ulrich H Weidle, Fabian Birzele, Gwen Kollmorgen, Adam Nopora
Treatment of disseminated epithelial ovarian cancer (EOC) is an unmet medical need. Therefore, the identification along with preclinical and clinical validation of new targets is an issue of high importance. In this review we focus on microRNAs that mediate metastasis of EOC. We summarize up-regulated metastasis-promoting and down-regulated metastasis-suppressing microRNAs. We focus on preclinical in vitro and in vivo functions as well as their metastasis-related clinical correlations. Finally, we outline modalities for therapeutic intervention and critical issues of microRNA-based therapeutics in the context of metastatic EOC...
January 2018: Cancer Genomics & Proteomics
Kalliopi I Pappa, Georgia Kontostathi, Manousos Makridakis, Vasiliki Lygirou, Jerome Zoidakis, George Daskalakis, Nicholas P Anagnou
BACKGROUND: Oncogenic infection by HPV, eventually leads to cervical carcinogenesis, associated by deregulation of specific pathways and protein expression at the intracellular and secretome level. Thus, secretome analysis can elucidate the biological mechanisms contributing to cervical cancer. In the present study we systematically analyzed its constitution in four cervical cell lines employing a highly sensitive proteomic technology coupled with bioinformatics analysis. MATERIALS AND METHODS: LC/MS-MS proteomics and bioinformatics analysis were performed in the secretome of four informative cervical cell lines SiHa (HPV16(+)), HeLa (HPV18(+)), C33A (HPV(-)) and HCK1T (normal)...
November 2017: Cancer Genomics & Proteomics
Saurabh Yadav, Navonil DE Sarkar, Niraj Kumari, Narendra Krishnani, Ashok Kumar, Balraj Mittal
BACKGROUND: Gallbladder carcinoma (GBC) is a subtype of biliary tract malignancy with poor prognosis and high fatality rate. The present study was designed to uncover somatic and rare germline mutations in GBC to reveal the disease biology and understand the clinical importance of mutation profile in terms of prognostics and actionability. MATERIALS AND METHODS: We performed ultra-deep sequencing across 409 cancer-related genes in 11 GBC patients of North-Indian descent...
November 2017: Cancer Genomics & Proteomics
Magdalena Gorska-Ponikowska, Alicja Kuban-Jankowska, Agnieszka Daca, Stephan Nussberger
BACKGROUND/AIM: According to the reverse Warburg effect, tumor cells may metabolize lactate as an energy source and shuttle L-lactate to neighboring cancer cells, adjacent stroma, and vascular endothelial cells, thus inducing metabolic reprogramming. An increased tumor L-lactate level strictly correlates with increased metastasis, tumor recurrence and a poor outcome. A potent anticancer agent that may act on L-lactate activated cells is 2-metoxyestradiol. Thus, the aim of the study was to evaluate whether a potent anticancer agent, 2-methoxyestradiol, is able to reverse L-lactate-induced metabolic reprogramming in osteosarcoma 143B cells...
November 2017: Cancer Genomics & Proteomics
Farid E Ahmed, Mostafa M Gouda, Laila A Hussein, Nancy C Ahmed, Paul W Vos, Mahmoud A Mohammad
This article illustrates the importance of melt curve analysis (MCA) in interpretation of mild nutrogenomic micro(mi)RNA expression data, by measuring the magnitude of the expression of key miRNA molecules in stool of healthy human adults as molecular markers, following the intake of Pomegranate juice (PGJ), functional fermented sobya (FS), rich in potential probiotic lactobacilli, or their combination. Total small RNA was isolated from stool of 25 volunteers before and following a three-week dietary intervention trial...
November 2017: Cancer Genomics & Proteomics
Robert L Copeland, Desta Beyene, Victor Apprey, Mohammad R Daremipouran, Tammey J Naab, Olakunle O Kassim, Yasmine M Kanaan
BACKGROUND/AIM: Denaturing high-performance liquid chromatography (DHPLC) is a technique that is used to detect mutations. The aim of the present study was to determine whether DHPLC elution patterns of vitamin D receptor (VDR) gene PCR products can serve as indicators of susceptibility to prostate cancer (PCa) risk. MATERIALS AND METHODS: DNA samples of PCa cases and controls were screened for mutations and/or polymorphisms in coding exons of VDR gene using DHPLC analysis...
November 2017: Cancer Genomics & Proteomics
An-Kuo Chou, Ming-Yi Shen, Fang-Yu Chen, Chieh-Lun Hsiao, Liang-Chun Shih, Wen-Shin Chang, Chia-Wen Tsai, Tsung-Ho Ying, Ming-Hsien Wu, Chung-Yu Huang, DA-Tian Bau
BACKGROUND/AIM: Flap endonuclease 1 (FEN1), a protein with multiple functions in genome stability maintenance, is important in cancer prevention. The two functional germline variants of FEN1, rs174538 and rs4246215, regarding cancer susceptibility have been reported in lung, breast, liver, esophageal, gastric, colorectal cancer, glioma and leukemia, but not endometriosis. In this study, we firstly aimed at evaluating the contribution of FEN1 genotypes to endometriosis risk in a representative Taiwan population...
November 2017: Cancer Genomics & Proteomics
Ryo Ashida, Yukiyasu Okamura, Keiichi Ohshima, Yuko Kakuda, Katsuhiko Uesaka, Teiichi Sugiura, Takaaki Ito, Yusuke Yamamoto, Takashi Sugino, Kenichi Urakami, Masatoshi Kusuhara, Ken Yamaguchi
BACKGROUND/AIM: Project HOPE (High-tech Omics-based Patient Evaluation) began in 2014 using integrated gene expression profiling (GEP) of cancer tissues as well as diathesis of each patient who underwent operation at our Institution. The aim of this study was to identify novel genes displaying altered gene expression related to the survival and early recurrence after hepatectomy for hepatocellular carcinoma (HCC) using the results of integrated GEP analysis. MATERIALS AND METHODS: The present study included 92 patients...
November 2017: Cancer Genomics & Proteomics
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