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Cancer Genomics & Proteomics

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https://www.readbyqxmd.com/read/29695404/establishment-and-characteristics-of-a-novel-mantle-cell-lymphoma-derived-cell-line-and-a-bendamustine-resistant-subline
#1
Tomoko Takimoto-Shimomura, Hisao Nagoshi, Saori Maegawa, Yuto Fujibayashi, Taku Tsukamoto, Yayoi Matsumura-Kimoto, Yoshimi Mizuno, Yoshiaki Chinen, Shinsuke Mizutani, Yuji Shimura, Shigeo Horiike, Masafumi Taniwaki, Tsutomu Kobayashi, Junya Kuroda
BACKGROUND/AIM: Bendamustine hydrochloride (BH) is a key therapeutic agent for mantle cell lymphoma (MCL), while the mechanism underlying BH-resistance has not been verified. MATERIALS AND METHODS: We compared molecular/biological characteristics of a newly-generated MCL-derived cell line KPUM-YY1 and its BH-resistant subline KPUM-YY1R. RESULTS: The growth-inhibitory IC50 for BH was 20 μM in KPUM-YY1 cells, while cell proliferation was not inhibited by up to 60 μM BH in KPUM-YY1R cells...
May 2018: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29695403/the-contribution-of-mmp-7-genotypes-to-colorectal-cancer-susceptibility-in-taiwan
#2
Te-Cheng Yueh, Cheng-Nan Wu, Yi-Wen Hung, Wen-Shin Chang, Chun-Kai Fu, Jen-Sheng Pei, Ming-Hsien Wu, Yi-Liang Lai, Yi-Min Lee, Shiou-Ting Yen, Hsin-Ting Li, Chia-Wen Tsai, DA-Tian Bau
BACKGROUND/AIM: Matrix metalloproteinases (MMPs) play important roles in inflammation and carcinogenesis, but the genotypic role of MMP-7 has never been investigated in colorectal cancer (CRC) among the Taiwanese. Therefore, in this study we aimed to evaluate the contribution of MMP-7 genotypes to the risk of CRC in Taiwan. MATERIALS AND METHODS: In this case-control study, MMP-7 A-181G and C-153T promoter genotypes were determined and their association with CRC risk were investigated among 362 CRC patients and 362 age- and gender-matched healthy controls...
May 2018: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29695402/egfr-l861q-mutation-in-a-metastatic-solid-pseudopapillary-neoplasm-of-the-pancreas
#3
Kevin G Neill, James Saller, Sameer Al Diffalha, Barbara A Centeno, Mokenge P Malafa, Domenico Coppola
Solid-pseudopapillary neoplasm of the pancreas (SPN) is a rare neoplasm that is typically indolent in nature. Surgical resection is the preferred method of treatment and often associated with a good prognosis. Local invasion and metastasis have been reported in a small subset of patients. Currently, there are limited data on the molecular mutation profile of invasive and metastatic SPN. In this report, we present the case of a 38-year-old female with a locally-invasive and unresectable SPN that, despite exhaustive chemoradiotherapy, progressed to liver metastasis...
May 2018: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29695401/cytogenetics-of-spindle-cell-pleomorphic-lipomas-karyotyping-and-fish-analysis-of-31-tumors
#4
Ioannis Panagopoulos, Ludmila Gorunova, Marius Lund-Iversen, Kristin Andersen, Hege Kilen Andersen, Ingvild Lobmaier, Bodil Bjerkehagen, Sverre Heim
BACKGROUND: Spindle cell/pleomorphic lipomas are benign tumors. Here, we present our cytogenetic data on 31 such tumors. MATERIALS AND METHODS: G-banding chromosome analysis and (in selected cases) fluorescence in situ hybridization (FISH) using probes for FOXO1, RB1, and HMGA2 were performed. RESULTS: Rearrangements of chromosome 13 were found in 58% of tumors. Chromosomes 6, 1, 12, and 11 were also involved in 42%, 26%, 26%, and 23% of tumors, respectively...
May 2018: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29695400/admixture-mapping-links-racgap1-regulation-to-prostate-cancer-in-african-americans
#5
Bradford D Wilson, Luisel J Ricks-Santi, Tshela E Mason, Muneer Abbas, Rick A Kittles, Georgia M Dunston, Yasmine M Kanaan
BACKGROUND/AIM: Prostate cancer is the most common malignancy in US males. African American men have higher incidence and mortality rates than European Americans. Five single nucleotide polymorphisms are associated with PCa. We hypothesized haplotypes inferred from these SNPs are also associated with PCa. PATIENTS AND METHODS: We genotyped SNPs in a case-control admixture mapping study. SNP haplotypes inferred for 157 PCa cases and 150 controls were used in the regression analysis...
May 2018: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29695399/hif-1%C3%AE-and-mtor-possible-novel-strategies-of-targeted-therapies-in-p16-positive-and-negative-hnscc
#6
Benedikt Kramer, Max Polit, Richard Birk, Nicole Rotter, Christoph Aderhold
BACKGROUND/AIM: Targeted therapy in head and neck squamous cell carcinoma (HNSCC) is limited. HIF-1α and mTOR are involved in the formation of local tumor progression and distant metastasis. The present study analyzed the influence of well-established tyrosine kinase inhibitors nilotinib, dasatinib, erlotinib and gefitinib on the expression of HIF-1α and mTOR in p16-positive and -negative squamous cancer cells (SCC) in vitro in order to develop novel strategies in the treatment of HNSCC...
May 2018: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29695398/chromatin-immunoprecipitation-and-dna-sequencing-identified-a-lims1-ilk-pathway-regulated-by-lmo1-in-neuroblastoma
#7
Norihisa Saeki, Akira Saito, Yuki Sugaya, Mitsuhiro Amemiya, Hiroe Ono, Rie Komatsuzaki, Kazuyoshi Yanagihara, Hiroki Sasaki
BACKGROUND/AIM: Overall survival for the high-risk group of neuroblastoma (NB) remains at 40-50%. An integrative genomics study revealed that LIM domain only 1 (LMO1) encoding a transcriptional regulator to be an NB-susceptibility gene with a tumor-promoting activity, that needs to be revealed. MATERIALS AND METHODS: We conducted chromatin immunoprecipitation and DNA sequencing analyses and cell proliferation assays on two NB cell lines. RESULTS: We identified three genes regulated by LMO1 in the cells, LIM and senescent cell antigen-like domains 1 (LIMS1), Ras suppressor protein 1 (RSU1) and relaxin 2 (RLN2)...
May 2018: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29496694/insights-into-novel-prognostic-and-possible-predictive-biomarkers-of-lung-neuroendocrine-tumors
#8
REVIEW
Dimitrios Moris, Ioannis Ntanasis-Stathopoulos, Diamantis I Tsilimigras, Mohamad A Adam, Chi-Fu 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
https://www.readbyqxmd.com/read/29496693/line-1-orf1-protein-is-up-regulated-by-reactive-oxygen-species-and-associated-with-bladder-urothelial-carcinoma-progression
#9
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
https://www.readbyqxmd.com/read/29496692/ilk-expression-in-colorectal-cancer-is-associated-with-emt-cancer-stem-cell-markers-and-chemoresistance
#10
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
https://www.readbyqxmd.com/read/29496691/genetic-landscape-of-acute-myeloid-leukemia-interrogated-by-next-generation-sequencing-a-large-cancer-center-experience
#11
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
https://www.readbyqxmd.com/read/29496690/novel-germline-pten-mutation-associated-with-cowden-syndrome-and-osteosarcoma
#12
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
https://www.readbyqxmd.com/read/29496689/characterization-of-camptothecin-induced-genomic-changes-in-the-camptothecin-resistant-t-all-derived-cell-line-cpt-k5
#13
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
https://www.readbyqxmd.com/read/29275365/2-methoxyestradiol-affects-mitochondrial-biogenesis-pathway-and-succinate-dehydrogenase-complex-flavoprotein-subunit-a-in-osteosarcoma-cancer-cells
#14
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
#15
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
#16
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
#17
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
#18
REVIEW
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
https://www.readbyqxmd.com/read/29275360/the-role-of-micro-rnas-in-breast-cancer-metastasis-preclinical-validation-and-potential-therapeutic-targets
#19
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
#20
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
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