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Cancer Genomics & Proteomics

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https://www.readbyqxmd.com/read/29275365/2-methoxyestradiol-affects-mitochondrial-biogenesis-pathway-and-succinate-dehydrogenase-complex-flavoprotein-subunit-a-in-osteosarcoma-cancer-cells
#1
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
https://www.readbyqxmd.com/read/29275364/genetic-variations-in-the-3-untranslated-regions-of-genes-involved-in-the-cell-cycle-and-apoptosis-pathways-affect-bladder-cancer-risk
#2
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
https://www.readbyqxmd.com/read/29275363/consistent-involvement-of-chromosome-13-in-angiolipoma
#3
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
https://www.readbyqxmd.com/read/29275362/regulation-of-%C3%AE-catenin-phosphorylation-by-pr55%C3%AE-in-adenoid-cystic-carcinoma
#4
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
https://www.readbyqxmd.com/read/29275361/applications-of-support-vector-machine-svm-learning-in-cancer-genomics
#5
REVIEW
Shujun Huang, Nianguang Cai, Pedro Penzuti Pacheco, Shavira Narandes, 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
https://www.readbyqxmd.com/read/29275360/the-role-of-micro-rnas-in-breast-cancer-metastasis-preclinical-validation-and-potential-therapeutic-targets
#6
REVIEW
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
https://www.readbyqxmd.com/read/29275359/potential-microrna-related-targets-for-therapeutic-intervention-with-ovarian-cancer-metastasis
#7
REVIEW
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
https://www.readbyqxmd.com/read/29109100/high-resolution-proteomic-analysis-of-the-cervical-cancer-cell-lines-secretome-documents-deregulation-of-multiple-proteases
#8
REVIEW
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
https://www.readbyqxmd.com/read/29109099/targeted-gene-sequencing-of-gallbladder-carcinoma-identifies-high-impact-somatic-and-rare-germline-mutations
#9
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
https://www.readbyqxmd.com/read/29109098/2-methoxyestradiol-reverses-the-pro-carcinogenic-effect-of-l-lactate-in-osteosarcoma-143b-cells
#10
REVIEW
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
https://www.readbyqxmd.com/read/29109097/role-of-melt-curve-analysis-in-interpretation-of-nutrigenomics-microrna-expression-data
#11
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
https://www.readbyqxmd.com/read/29109096/dhplc-elution-patterns-of-vdr-pcr-products-can-predict-prostate-cancer-susceptibility-in-african-american-men
#12
REVIEW
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
https://www.readbyqxmd.com/read/29109095/the-association-of-flap-endonuclease-1-genotypes-with-the-susceptibility-of-endometriosis
#13
REVIEW
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
https://www.readbyqxmd.com/read/29109094/cyp3a4-gene-is-a-novel-biomarker-for-predicting-a-poor-prognosis-in-hepatocellular-carcinoma
#14
REVIEW
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
https://www.readbyqxmd.com/read/29109093/dek-nup214-fusion-identified-by-rna-sequencing-of-an-acute-myeloid-leukemia-with-t-9-12-q34-q15
#15
REVIEW
Ioannis Panagopoulos, Ludmila Gorunova, Synne Torkildsen, Geir E Tjønnfjord, Francesca Micci, Sverre Heim
BACKGROUND/AIM: Given the diagnostic, prognostic, biologic, and even therapeutic impact of leukemia-associated translocations and fusion genes, it is important to detect cryptic genomic rearrangements that may exist in hematological malignancies. CASE REPORT: RNA-sequencing was performed on an acute myeloid leukemia case with the bone marrow karyotype 45,X,-Y,t(9;12) (q34;q15)[16]. RESULTS: The DEK-NUP214 and PRRC2B-DEK fusion genes were found...
November 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29109092/screening-for-multiple-autoantibodies-in-plasma-of-patients-with-breast-cancer
#16
REVIEW
Lauren Bassaro, Stephen J Russell, Elzbieta Pastwa, Stella A Somiari, Richard I Somiari
BACKGROUND/AIM: Autoantibodies have potential as circulating biomarkers for early cancer detection. This study aimed to screen for known autoantibodies in human plasma using an Autoantibody Profiling System (APS) and quantify the levels in plasma of donors with/without breast cancer. MATERIALS AND METHODS: Plasma from nine female donors diagnosed with breast cancer (test group) and nine matched donors with no personal history of cancer (reference group) were screened with an APS containing probes for 30 autoantibodies...
November 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29109091/transcriptomic-profiling-of-mda-mb-231-cells-exposed-to-boswellia-serrata-and-3-o-acetyl-b-boswellic-acid-er-upr-mediated-programmed-cell-death
#17
REVIEW
Elizabeth A Mazzio, Charles A Lewis, Karam F A Soliman
BACKGROUND/AIM: Triple-negative breast cancer (TNBC) is characterized by the absence of hormone receptors (estrogen, progesterone and human epidermal growth factor receptor-2) and a relatively poor prognosis due to inefficacy of hormone receptor-based chemotherapies. It is imperative that we continue to explore natural products with potential to impede growth and metastasis of TNBC. In this study, we screened over 1,000 natural products for capacity to induce cell death in TNBC (MDA-MB -231) cells...
November 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29109090/impact-of-mediterranean-diet-on-cancer-focused-literature-review
#18
REVIEW
Yoram Barak, Dana Fridman
BACKGROUND: Cancer is a major public health problem worldwide, and the number of incident cases increases every year expected to reach 17.1 million a year by 2020. There is evidence that people who adhere to the Mediterranean Diet (MediD) have lower incidence of cancer. However, cancers' location and culture studies seem to affect the MediD impact. We aimed to review these discrepant findings. MATERIALS AND METHODS: A critical review from a focused literature search was conducted...
November 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28871006/post-transcriptional-regulation-of-mmp16-and-timp2-expression-via-mir-382-mir-410-and-mir-200b-in-endometrial-cancer
#19
Beata Rak, Dawid Mehlich, Filip Garbicz, Zofia Domosud, Wiktor Paskal, Janina M Marczewska, Paweł K Włodarski
BACKGROUND/AIM: The post-transcriptional regulation of matrix metalloproteinases (MMPs) via microRNAs (miRNAs) has been recently described in numerous human malignancies. However, the exact mechanisms of miRNA-mediated MMPs deregulation in endometrial cancer (EC) remain unclear. Herein, we aimed to analyze the expression of MMP2, MMP16 and TIMP2 and identify miRNAs that modulate their expression. MATERIALS AND METHODS: Protein expression was assessed by immunohistochemistry in formalin-fixed paraffin-embedded EC samples...
September 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28871005/evaluation-of-podoplanin-expression-in-hepatocellular-carcinoma-using-rnascope-and-immunohistochemistry-a-preliminary-report
#20
Andreea Cioca, Anca Maria Cimpean, Raluca Amalia Ceausu, Valeria Tarlui, Alina Toma, Irina Marin, Marius Raica
BACKGROUND: Podoplanin (PDPN), a mucin-type transmembrane glycoprotein, is expressed in a variety of human cancer types, and contributes to tumor progression. Our goal was to evaluate PDPN expression in hepatocellular carcinoma (HCC) using both immunohistochemistry (IHC) and RNAscope in situ hybridization. MATERIALS AND METHODS: Twenty patients with HCC who underwent partial hepatectomy with curative intent were retrospectively analyzed. RESULTS: IHC gave positive results in 11 cases, while RNAscope assay for PDPN detected amplification in 16 cases...
September 2017: Cancer Genomics & Proteomics
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