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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
Petra Vychytilova-Faltejskova, Martin Pesta, Lenka Radova, Vaclav Liska, Ondrej Daum, Zdenek Kala, Marek Svoboda, Igor Kiss, Ondrej Slaby
BACKGROUND: Primary tumor spread to the liver is the major cause of disease progression and death in patients with colorectal cancer (CRC). MicroRNAs (miRNAs) are small non-coding RNAs that are involved in cancer development and progression, but their role in metastasis has not been extensively investigated. MATERIALS AND METHODS: Firstly, expression profiling of 752 miRNAs in 20 primary tumors and their corresponding liver metastases was performed. Secondly, validation of the results was carried out on an independent cohort of 66 patients with metastatic CRC using reverse transcription-quantitative polymerase chain (RT-qPCR) reaction...
July 2016: Cancer Genomics & Proteomics
Tomoki Sumida, Akiko Ishikawa, Yoshihide Mori
BACKGROUND: Salivary gland cancer is a common type of head and neck cancer characterized by occasional deep invasion and lung metastasis. The precise role of sex steroid hormones in salivary gland cancer is unclear. To address this issue, we investigated whether the estrogen axis modulates salivary adenocarcinoma (SAC) and whether hormone therapy can be an effective treatment. MATERIALS AND METHODS: The estrogen receptor (ER) was overexpressed in HSG human SAC cells that lack endogenous ER and the cells were treated with and without 17β-estradiol (E2)...
July 2016: Cancer Genomics & Proteomics
Aslihan Dagdemir, Gaëlle Judes, André Lebert, Maureen Echegut, Seher Karsli-Ceppioglu, Khaldoun Rifaï, Marine Daures, Marjolaine Ngollo, Lucas Dubois, Frédérique Penault-Llorca, Yves-Jean Bignon, Dominique Bernard-Gallon
BACKGROUND/AIM: Numerous studies have shown that breast cancer and epigenetic mechanisms have a very powerful interactive relation. The MCF7 cell line, representative of luminal subtype and the MDA-MB 231 cell line representative of mesenchymal-like subtype were treated respectively with a Histone Methyl Transferase Inhibitors (HMTi), 3-Deazaneplanocin hydrochloride (DZNep), two histone deacetylase inhibitors (HDACi), sodium butyrate (NaBu), and suberoylanilide hydroxamic acid (SAHA) for 48 h...
July 2016: Cancer Genomics & Proteomics
Inga Flor, Meike Spiekermann, Thomas Löning, Klaus-Peter Dieckmann, Gazanfer Belge, Jörn Bullerdiek
BACKGROUND: Testicular germ cell tumours (TGCTs) are the most common tumours in men aged from 20 to 40 years, with a steadily increasing incidence. This study aimed to characterize the expression of the miRNA cluster C19MC in TGCT and to evaluate the suitability of a C19MC miRNA as a serum biomarker. MATERIALS AND METHODS: By quantitative reverse transcription PCR, we measured the expression of miR-517a-3p, miR-519a-3p, and miR-519c 3p in tissue samples of 25 TGCTs and the level of miR-517a-3p in serum samples obtained pre- and postoperatively from the same patients...
July 2016: Cancer Genomics & Proteomics
Michael Medinger, Jörg Halter, Dominik Heim, Andreas Buser, Sabine Gerull, Claudia Lengerke, Jakob Passweg
BACKGROUND/AIM: Novel agents such as thalidomide, lenalidomide and bortezomib have in part anti-angiogenic properties. In this study, we examined gene expression of angiogenic molecules in patients with plasma cell myeloma (PCM). MATERIALS AND METHODS: We included 93 patients with PCM treated with novel agents (immunomodulatory drugs (IMiDs), bortezomib or a combination of both). The mRNA levels of angiogenic molecules were measured using the Human Angiogenesis RT2 Profiler PCR Array...
July 2016: Cancer Genomics & Proteomics
Whitney Evans, Maria Filippova, Valery Filippov, Svetlana Bashkirova, Guangyu Zhang, Mark E Reeves, Penelope Duerksen-Hughes
BACKGROUND: High-risk human papillomaviruses (HPV) cause nearly all cases of cervical cancer, as well as many types of oral and anogenital cancer. Alternative splicing increases the capacity of the HPV genome to encode the proteins necessary for successful completion of its infectious life cycle. However, the roles of these splice variants, including E6*, the smaller splice isoform of the E6 oncogene, in carcinogenesis are not clear. MATERIALS AND METHODS: SiHa (HPV16(+)) and C33A (HPV(-)) cells were transfected with the E6* plasmid, and tandem mass tag-labeled protein levels were quantified by mass spectrometry...
July 2016: Cancer Genomics & Proteomics
Ulrich H Weidle, Fabian Birzele, Gwendlyn Kollmorgen, Rüdiger Rüger
Brain metastases outnumber the incidence of brain tumors by a factor of ten. Patients with brain metastases have a dismal prognosis and current treatment modalities achieve only a modest clinical benefit. We discuss the process of brain metastasis with respect to mechanisms and involved targets to outline options for therapeutic intervention and focus on breast and lung cancer, as well as melanoma. We describe the process of penetration of the blood-brain-barrier (BBB) by disseminated tumor cells, establishment of a metastatic niche, colonization and outgrowth in the brain parenchyma...
July 2016: Cancer Genomics & Proteomics
Martin Purdy, Merja Kokki, Maarit Anttila, Samuli Aspinen, Petri Juvonen, Tuomas Selander, Hannu Kokki, Kari Pulkki, Matti Eskelinen
BACKGROUND: The aim of the study was to evaluate whether the post-surgery placement of the rectus sheath block (RSB) analgesia could alter the oxidative stress response. The main hypothesis of our study was to find some correlation between patients' pain experience, numeric rating scale (NRS) and the concentration of oxidative stress marker, 8-OHdG (8-hydroxy-2'-deoxyguanosine) in patients with benign disease and cancer. MATERIALS AND METHODS: Initially, 46 patients were randomized to the placebo group (n=11) and to one of the three active groups; single-dose (n=12), repeated-dose (n=12) and continuous infusion (n=11) RSB analgesia group...
May 2016: Cancer Genomics & Proteomics
Huili Zheng, Yan Wang, Chuanning Tang, Lindsey Jones, Hua Ye, Guangchun Zhang, Weihai Cao, Jingwen Li, Lifeng Liu, Zhencong Liu, Chao Zhang, Feng Lou, Zhiyuan Liu, Yangyang Li, Zhenfen Shi, Jingbo Zhang, Dandan Zhang, Hong Sun, Haichao Dong, Zhishou Dong, Baishuai Guo, H E Yan, Qingyu Lu, Xue Huang, Si-Yi Chen
BACKGROUND/AIM: Esophageal cancer (EC) is a common malignancy with significant morbidity and mortality. As individual cancers exhibit unique mutation patterns, identifying and characterizing gene mutations in EC that may serve as biomarkers might help predict patient outcome and guide treatment. Traditionally, personalized cancer DNA sequencing was impractical and expensive. Recent technological advancements have made targeted DNA sequencing more cost- and time-effective with reliable results...
May 2016: Cancer Genomics & Proteomics
Kuo-Chiang Chen, Chih-Ming Lin, Chi-Jung Huang, Shao-Kuan Chen, Sheng-Tang Wu, Han-Sun Chiang, Wei-Chi Ku
BACKGROUND: It has been proposed that 17-β-estradiol (E2) activates estrogen receptor and inhibits renal cell carcinoma (RCC) growth. In the present study we explored the role of E2 and ER in the regulation of RCC growth. MATERIALS AND METHODS: The RCC cell line ACHN was treated by E2 combining with E2 antagonist Fulvestrant or ER knockdown, and cell growth was monitored. Quantitative phosphoproteomics was applied to study the E2 regulated non-genomic phosphorylation changes...
May 2016: Cancer Genomics & Proteomics
Anna E Kowalczyk, Bartlomiej E Krazinski, Janusz Godlewski, Jedrzej Grzegrzolka, Jolanta Kiewisz, Przemyslaw Kwiatkowski, Agnieszka Sliwinska-Jewsiewicka, Piotr Dziegiel, Zbigniew Kmiec
BACKGROUND: Altered expression of special AT-rich sequence binding protein 1 (SATB1) was reported in several types of human cancers. This study aimed to determine the expression levels of SATB1, as well as miR-21-5p -the post-transcriptional repressor of SATB1 expression- in clear cell renal cell carcinoma (ccRCC) and to investigate their association with the progression of ccRCC. MATERIALS AND METHODS: Immunohistochemistry and quantitative polymerase chain reaction were used to assess the expression of SATB1 protein and mRNA as well as miR-21-5p in tumor and matched normal kidney tissues collected from 56 ccRCC patients...
May 2016: Cancer Genomics & Proteomics
Baobei Lv, Fei Xie, Pengxiang Zhao, Xuemei Ma, Wen G Jiang, Jing Yu, Xiaodong Zhang, Jun Jia
BACKGROUND: Fibroblast activation protein-alpha (FAPα) is a type-II integral membrane serine protease and is expressed in most stromal fibroblasts. Recent studies showed that FAPα is also expressed in certain cancer cells but its role is still uncertain. MATERIALS AND METHODS: We analyzed the non-enzymatic activity of FAPα in breast cancer cells by introducing an enzymatic mutant FAPα (FAPS624A), in which the serine catalytic triad was destroyed. FAPα overexpression and knockdown cells were generated as controls...
May 2016: Cancer Genomics & Proteomics
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