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Cancer Genomics & Proteomics

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November 2016: Cancer Genomics & Proteomics
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
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
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
Mónica Molano, Pablo Moreno-Acosta, Nicolás Morales, Marcela Burgos, Lina Buitrago, Oscar Gamboa, Rayner Alvarez, Suzanne M Garland, Sepehr N Tabrizi, Renske D M Steenbergen, Juan Carlos Mejía
BACKGROUND: There exists limited information on the role of hTERT methylation, and its association with type-specific HPV infections in cervical cancer. MATERIALS AND METHODS: Eighty-seven frozen samples were analyzed for type-specific HPV infection using a GP5(+)/GP6(+) PCR-RLB assay (RLB). hTERT DNA methylation analysis was performed using a newly developed PCR-RLB-hTERT. RESULTS: Ninety-three percent of samples were HPV-positive and fifteen different types were detected...
November 2016: Cancer Genomics & Proteomics
Kazutoshi Isobe, Atsushi Kakimoto, Tetsuo Mikami, Kyohei Kaburaki, Hiroshi Kobayashi, Takahiro Yoshizawa, Takashi Makino, Hajime Otsuka, G O Sano, Keishi Sugino, Susumu Sakamoto, Yujiro Takai, Naobumi Tochigi, Akira Iyoda, Sakae Homma
AIM: This pilot study assessed the association of BIM deletion polymorphism and BIM RNA isoform in patients with EGFR-positive non-small cell lung cancer (NSCLC). PATIENTS AND METHODS: The study included 33 patients with EGFR-positive NSCLC treated with gefitinib. BIM deletion polymorphism and BIM RNA isoform (EL/L/S/γ) were determined by polymerase chain reaction (PCR). RESULTS: BIM-γ expression was significantly higher in patients with BIM deletion polymorphism than among those without BIM deletion polymorphism inside tumors (p=0...
November 2016: Cancer Genomics & Proteomics
Jie Lu, Mark G Burnett, Max Shpak
BACKGROUND: Familial cancers are those that co-occur among first-degree relatives without showing Mendelian patterns of inheritance. MATERIALS AND METHODS: In this analysis, we compare the genomic characteristics of familial and sporadic cancers, with a focus on low-grade gliomas (LGGs) using sequence and expression data from the Cancer Genome Atlas. RESULTS: Familial cancers show similar genomic and molecular biomarker profiles to sporadic cancers, consistent with the similarity in their clinical features...
November 2016: Cancer Genomics & Proteomics
Ali Azimi, Kimberley L Kaufman, Marina Ali, Steven Kossard, Pablo Fernandez-Penas
BACKGROUND: Cutaneous squamous cell carcinoma (cSCC) is a common type of skin cancer but there are no comprehensive proteomic studies on this entity. MATERIALS AND METHODS: We employed liquid chromatography coupled with tandem mass spectrometry (MS/MS) using formalin-fixed paraffin-embedded (FFPE) cSCC material to study the tumor and normal skin tissue proteomes. Ingenuity Pathway Analysis (IPA) was used to interpret the role of altered proteins in cSCC pathophysiology...
November 2016: Cancer Genomics & Proteomics
Katarzyna A Podyma-Inoue, Takuya Moriwaki, Anupama R Rajapakshe, Kazue Terasawa, Miki Hara-Yokoyama
BACKGROUND: Heparan sulfate proteoglycans (HSPGs)-dependent endocytic events have been involved in glioma progression. Thus, comprehensive understanding of the intracellular trafficking complexes formed in presence of HSPGs would be important for development of glioma treatments. MATERIALS AND METHODS: Subcellular fractionation was used to separate vesicles containing HSPGs from the rat C6 glioma cell line. Isolated HSPG-positive vesicles were further characterized with liquid chromatography-mass spectrometry...
November 2016: Cancer Genomics & Proteomics
Manpreet S Chahal, H Teresa Ku, Zhihong Zhang, Christian M Legaspi, Angela Luo, Mandi M Hopkins, Kathryn E Meier
BACKGROUND: Previous work characterized variants of the EL4 murine lymphoma cell line. Some are non-metastatic, and others metastatic, in syngenic mice. In addition, metastatic EL4 cells were stably transfected with phospholipase D2 (PLD2), which further enhanced metastasis. MATERIALS AND METHODS: Microarray analyses of mRNA expression was performed for non-metastatic, metastatic, and PLD2-expressing metastatic EL4 cells. RESULTS: Many differences were observed between non-metastatic and metastatic cell lines...
November 2016: Cancer Genomics & Proteomics
Lei Shi, Jeyna Resaul, Sioned Owen, Lin Ye, Wen G Jiang
Follistatin (FST), as a single-chain glycosylated protein, has two major isoforms, FST288 and FST315. The FST315 isoform is the predominant form whilst the FST288 variant accounts for less than 5% of the encoded mRNA. FST is differentially expressed in human tissues and aberrant expression has been observed in a variety of solid tumours, including gonadal, gastric and lung cancer, hepatocellular carcinoma, basal cell carcinoma and melanoma. Based on the current evidence, FST is an antagonist of transforming growth factor beta family members, such as activin and bone morphogenetic proteins (BMPs)...
November 2016: Cancer Genomics & Proteomics
Ulrich H Weidle, Fabian Birzele, Gwendlyn Kollmorgen, Rüdiger Rueger
Ovarian carcinoma is associated with the highest death rate of all gynecological tumors. On one hand, its aggressiveness is based on the rapid dissemination of ovarian cancer cells to the peritoneum, the omentum, and organs located in the peritoneal cavity, and on the other hand, on the rapid development of resistance to chemotherapeutic agents. In this review, we focus on the metastatic process of ovarian cancer, which involves dissemination of, homing to and growth of tumor cells in distant organs, and describe promising molecular targets for possible therapeutic intervention...
November 2016: Cancer Genomics & Proteomics
Asmaa Al-Attas, Mourad Assidi, Jaudah Al-Maghrabi, Ashraf Dallol, Hans-Juergen Schulten, Muhammad Abu-Elmagd, Adeel Chaudhary, Adel Abuzenadah, Bruce Budowle, Abdelbaset Buhmeida, Mohammed Al-Qahtani
BACKGROUND/AIM: To date, the conventional formalin-fixed, paraffin-embedded (FFPE) technique is the gold-standard for preserving histomorphology. Once FFPE tissues are stained, slides are routinely archived along with their blocks at biobanks/hospitals. However, the reuse of fixed and stained biospecimens as DNA source is not a common routine practice worldwide and, thus, indicates the need of studies to investigate the feasibility of extracting DNA from already immunohistochemistry (IHC) FFPE-stained slides and its possible reuse in subsequent downstream molecular analyses...
September 2016: Cancer Genomics & Proteomics
Parunya Chaiyawat, Churat Weeraphan, Pukkavadee Netsirisawan, Daranee Chokchaichamnankit, Chantragan Srisomsap, Jisnuson Svasti, Voraratt Champattanachai
BACKGROUND: O-GlcNAcylation is a single sugar attachment of serine and/or threonine residues on intracellular proteins. Recent reports reveal that it can modify several secretory proteins; however, the underlying mechanisms are largely unexplored. MATERIALS AND METHODS: To investigate whether extracellular vesicles (EVs) carry secretory O-GlcNAc-modified proteins that were isolated from colorectal cancer (CRC) cells, two-dimensional gel electrophoresis followed with O-GlcNAc immunoblotting and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were applied...
September 2016: Cancer Genomics & Proteomics
Tai-Long Chen, John Wen-Cheng Chang, Jia-Juan Hsieh, Hsin-Yi Cheng, Chiuan-Chian Chiou
Mutated v-Raf murine sarcoma viral oncogene homolog B (BRAF) is an important biomarker for the prediction of therapeutic efficacy of several anticancer drugs. The detection of BRAF mutation faces two challenges: Firstly, there are multiple types of mutations, and secondly, tumor samples usually contain various amounts of wild-type, normal tissues. Here, we describe a newly established method for sensitive detection of multiple types of BRAF V600 mutations in excess wild-type background. The method introduced a fluorophore-tagged peptide nucleic acid (PNA) to serve as both polymerase chain reaction (PCR) clamp and sensor probe, which inhibited the amplification of wild-type templates during PCR and revealed multiple types of mutant signals during melting analysis...
September 2016: Cancer Genomics & Proteomics
Rosaria Viola Abbritti, Francesca Polito, Maria Cucinotta, Claudio Lo Giudice, Maria Caffo, Chiara Tomasello, Antonino Germanò, Mohammed Aguennouz
Meningiomas are one of the most common tumors affecting the central nervous system, exhibiting a great heterogeneity in grading, treatment and molecular background. This article provides an overview of the current literature regarding the molecular aspect of meningiomas. Analysis of potential biomarkers in serum, cerebrospinal fluid (CSF) and pathological tissues was reported. Applying bioinformatic methods and matching the common proteic profile, arising from different biological samples, we highlighted the role of nine proteins, particularly related to tumorigenesis and grading of meningiomas: serpin peptidase inhibitor alpha 1, ceruloplasmin, hemopexin, albumin, C3, apolipoprotein, haptoglobin, amyloid-P-component serum and alpha-1-beta-glycoprotein...
September 2016: Cancer Genomics & Proteomics
Candace Johnson, Briana Segovia, Raj P Kandpal
Erythropoietin-producing hepatocellular carcinoma cell (EPH) receptors comprise the most abundant receptor tyrosine kinase family characterized to date in mammals including humans. These proteins are involved in axon guidance, tissue organization, vascular development and the intricate process of various diseases including cancer. These diverse functions of EPH receptors are attributed, in part, to their abilities for heterodimerization. While the interacting partners of kinase-deficient EPHB6 receptor have been characterized, the interaction of the kinase-dead EPHA10 with any other receptor has not been identified...
September 2016: Cancer Genomics & Proteomics
Nu T Lu, Natalie M Liu, James Q Vu, Darshil Patel, Whitaker Cohn, Joe Capri, Mary Ziegler, Nikita Patel, Angela Tramontano, Roger Williams, Julian Whitelegge, Samuel W French
BACKGROUND: Patients with chronic hepatitis C virus (HCV) infection are at risk of serious complications of cirrhosis and hepatocellular carcinoma (HCC). Mass spectrometry (MS) is a versatile methodology that produces a global proteomic landscape for analysis of cancer mechanisms. MATERIALS AND METHODS: Using multiplex peptide stable isotopic labeling and immobilized metal affinity chromatography (IMAC), we enriched and quantified the phosphoproteome of HCC, with and without HCV...
September 2016: Cancer Genomics & Proteomics
José Schneider, Noemí Eiró, Román Pérez-Fernández, Anxo Martínez-Ordóñez, Francisco Vizoso
Our research team has recently isolated and characterized a new stromal stem cell line (hUCESCs) obtained from cytological smears, as routinely performed for cervical cancer screening. We have, furthermore, described that both hUCESCs directly, as well as the secretome contained in the conditioned medium used for growing them (hUCESCs-CM) have potent antitumoral, anti-inflammatory, antibiotic, antimycotic and re-epitheliasation-enhancing properties. The scientific explanation our team proposes for these pleiotropic effects are directly related to the site of origin of hUCESCs, the human cervical transition zone, which has unique features that biologically justify the different actions of hUCESCs and hUCESCs-CM...
September 2016: Cancer Genomics & Proteomics
Michael Medinger, Claudia Lengerke, Jakob Passweg
Acute myeloid leukemia (AML) is a biologically complex and molecularly and clinically heterogeneous disease, and its incidence increases with age. Cytogenetics and mutation testing remain important prognostic tools for treatment after induction therapy. The post-induction treatment is dependent on risk stratification. Despite rapid advances in determination of gene mutations involved in the pathophysiology and biology of AML, and the rapid development of new drugs, treatment improvements changed slowly over the past 30 years, with the majority of patients eventually experiencing relapse and dying of their disease...
September 2016: Cancer Genomics & Proteomics
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