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https://www.readbyqxmd.com/read/28230789/fungal-ribotoxins-a-review-of-potential-biotechnological-applications
#1
REVIEW
Miriam Olombrada, Rodrigo Lázaro-Gorines, Juan C López-Rodríguez, Álvaro Martínez-Del-Pozo, Mercedes Oñaderra, Moisés Maestro-López, Javier Lacadena, José G Gavilanes, Lucía García-Ortega
Fungi establish a complex network of biological interactions with other organisms in nature. In many cases, these involve the production of toxins for survival or colonization purposes. Among these toxins, ribotoxins stand out as promising candidates for their use in biotechnological applications. They constitute a group of highly specific extracellular ribonucleases that target a universally conserved sequence of RNA in the ribosome, the sarcin-ricin loop. The detailed molecular study of this family of toxic proteins over the past decades has highlighted their potential in applied research...
February 21, 2017: Toxins
https://www.readbyqxmd.com/read/28229366/mining-cancer-transcriptomes-bioinformatic-tools-and-the-remaining-challenges
#2
Thomas Milan, Brian T Wilhelm
The development of next-generation sequencing technologies has had a profound impact on the field of cancer genomics. With the enormous quantities of data being generated from tumor samples, researchers have had to rapidly adapt tools or develop new ones to analyse the raw data to maximize its value. While much of this effort has been focused on improving specific algorithms to get faster and more precise results, the accessibility of the final data for the research community remains a significant problem. Large amounts of data exist but are not easily available to researchers who lack the resources and experience to download and reanalyze them...
February 22, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28227013/pan-cancer-analysis-for-studying-cancer-stage-using-protein-and-gene-expression-data
#3
Sameer Mishra, Chanchala D Kaddi, May D Wang, Sameer Mishra, Chanchala D Kaddi, May D Wang, Sameer Mishra, Chanchala D Kaddi, May D Wang
Pan-cancer analyses attempt to discover similar features among multiple cancers to identify fundamental patterns common to cancer development and progression. A pan-cancer analysis integrating both protein expression and transcriptomic data is important because it can identify genes that are linked to proteins potentially responsible for a patient's status. This study aims to identify differentially expressed (DE) genes between early and advanced cases of multiple cancer types through the usage of RNA sequencing data...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28224040/massilioclostridium-coli-gen-nov-sp-nov-a-new-member-of-the-clostridiaceae-family-isolated-from-the-left-colon-of-a-27-year-old-woman
#4
C I Lo, M Mailhe, D Ricaboni, V Vitton, A Benezech, C Michelle, N Armstrong, F Bittar, P-E Fournier, D Raoult, J-C Lagier
Massilioclostridium coli strain Marseille-P2976(T) (= CSUR P2976 = DSM 103344) is a new bacterial genus isolated from the left colon of a patient who underwent colonoscopy for colorectal cancer screening. Massilioclostridium coli is a Gram-negative bacillus, strict anaerobic, nonsporogenous and nonmotile organism. We describe here the strain Marseille-P2976(T) and provide its complete annotated genome sequence according to taxonogenomics concepts. Its genome is 2 985 330 bp long and contains 2562 predicted genes and 75 RNA genes...
March 2017: New Microbes and New Infections
https://www.readbyqxmd.com/read/28223711/identification-of-novel-cancer-therapeutic-targets-using-a-designed-and-pooled-shrna-library-screen
#5
David Oliver, Hao Ji, Piaomu Liu, Alexander Gasparian, Ellen Gardiner, Samuel Lee, Adrian Zenteno, Lillian O Perinskaya, Mengqian Chen, Phillip Buckhaults, Eugenia Broude, Michael D Wyatt, Homayoun Valafar, Edsel Peña, Michael Shtutman
Targeted cancer therapeutics aim to exploit tumor-specific, genetic vulnerabilities specifically affecting neoplastic cells without similarly affecting normal cells. Here we performed sequencing-based screening of an shRNA library on a panel of cancer cells of different origins as well as normal cells. The shRNA library was designed to target a subset of genes previously identified using a whole genome screening approach. This focused shRNA library was infected into cells followed by analysis of enrichment and depletion of the shRNAs over the course of cell proliferation...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223310/overexpression-of-vitamin-d-receptor-mrna-correlates-with-poor-prognosis-in-ptc
#6
June Young Choi, Jin Wook Yi, Joon-Hyop Lee, Ra-Yeong Song, Hyeong Won Yu, Hyungju Kwon, Young Jun Chai, Su-Jin Kim, Kyu Eun Lee
The purpose of this study was to assess the relationship between vitamin D receptor (VDR) mRNA expression and prognosis in papillary thyroid cancer. RNA sequencing and somatic mutation data from TCGA (the Cancer Genome Atlas) were analyzed. VDR mRNA expression was compared to clinicopathologic variables by linear regression. Tree-based classification was applied to find VDR cutoff and patients were split into low and high VDR group. Logistic regression, Kaplan-Meier analysis, differentially expressed gene (DEG) test, and pathway analysis were performed to assess differences between groups...
February 21, 2017: Endocrine Connections
https://www.readbyqxmd.com/read/28221941/the-hap-complex-governs-fumonisin-biosynthesis-and-maize-kernel-pathogenesis-in-fusarium-verticillioides
#7
John B Ridenour, Jonathon E Smith, Burton H Bluhm
Contamination of maize ( Zea mays ) with fumonisins produced by the fungus Fusarium verticillioides is a global concern for food safety. Fumonisins are a group of polyketide-derived secondary metabolites linked to esophageal cancer and neural tube birth defects in humans and numerous toxicoses in livestock. Despite the importance of fumonisins in global maize production, the regulation of fumonisin biosynthesis during kernel pathogenesis is poorly understood. The HAP complex is a conserved, heterotrimeric transcriptional regulator that binds the consensus sequence CCAAT to modulate gene expression...
September 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221868/somatic-brca1-2-recovery-as-a-resistance-mechanism-after-exceptional-response-to-poly-adp-ribose-polymerase-inhibition
#8
Stephanie Lheureux, Jeff P Bruce, Julia V Burnier, Katherine Karakasis, Patricia A Shaw, Blaise A Clarke, S Y Cindy Yang, Rene Quevedo, Tiantian Li, Mark Dowar, Valerie Bowering, Trevor J Pugh, Amit M Oza
Purpose Durable and long-term responses to the poly (ADP-ribose) polymerase inhibitor olaparib are observed in patients without BRCA1/2 mutations. However, beyond BRCA1/2 mutations, there are no approved biomarkers for olaparib in high-grade serous ovarian cancer (HGSOC). To determine mechanisms of durable response and resistance to olaparib therapy, we performed an analysis of HGSOC tumors from three patients without germline BRCA1/2 mutations who experienced exceptional responses to olaparib. Patients and Methods We performed integrated exome, low-pass genome, and RNA sequence analysis of tumors at diagnosis and upon relapse from patients with platinum-sensitive HGSOC recurrence who were treated > 5 years with olaparib therapy as a single agent...
February 21, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28219123/identification-of-core-gene-networks-and-hub-genes-associated-with-progression-of-nonalcoholic-fatty-liver-disease-by-rna-sequencing
#9
Kikuko Hotta, Masataka Kikuchi, Takuya Kitamoto, Aya Kitamoto, Yuji Ogawa, Yasushi Honda, Takaomi Kessoku, Kaori Kobayashi, Masato Yoneda, Kento Imajo, Wataru Tomeno, Akihiro Nakaya, Yutaka Suzuki, Satoru Saito, Atsushi Nakajima
AIM: Nonalcoholic fatty liver disease (NAFLD) progresses because of the interaction between numerous genes. Thus, we performed weighted gene co-expression network analysis to identify core gene networks and key genes associated with NAFLD progression. METHODS: We enrolled 39 patients with mild NAFLD (fibrosis stages 0 to 2) and 21 with advanced NAFLD (fibrosis stages 3 or 4). Total RNA was extracted from frozen liver biopsies, and sequenced to capture a large dynamic range of expression levels...
February 20, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
https://www.readbyqxmd.com/read/28218725/treating-cancer-by-targeting-telomeres-and-telomerase
#10
REVIEW
Marko Ivancich, Zachary Schrank, Luke Wojdyla, Brandon Leviskas, Adijan Kuckovic, Ankita Sanjali, Neelu Puri
Telomerase is expressed in more than 85% of cancer cells. Tumor cells with metastatic potential may have a high telomerase activity, allowing cells to escape from the inhibition of cell proliferation due to shortened telomeres. Human telomerase primarily consists of two main components: hTERT, a catalytic subunit, and hTR, an RNA template whose sequence is complimentary to the telomeric 5'-dTTAGGG-3' repeat. In humans, telomerase activity is typically restricted to renewing tissues, such as germ cells and stem cells, and is generally absent in normal cells...
February 19, 2017: Antioxidants (Basel, Switzerland)
https://www.readbyqxmd.com/read/28214867/the-novel-long-noncoding-rna-tusc7-inhibits-proliferation-by-sponging-mir-211-in-colorectal-cancer
#11
Jian Xu, Rui Zhang, Jian Zhao
BACKGROUND/AIMS: The novel long noncoding RNA (lncRNA) tumor suppressor candidate 7 (TUSC7) has been reported as a potential tumor suppressor, while the functional role of TUSC7 is still unknown in colorectal cancer (CRC). Here, we characterized TUSC7 expression profile in CRC patients and investigated its biological function and potential molecular mechanism. METHODS: RNA isolation, qRT-PCR, cell counter kit-8 assay, cell cycle assay, EdU assay, and western blot were performed...
February 8, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28213378/prognostic-role-of-circulating-exosomal-mirnas-in-multiple-myeloma
#12
Salomon Manier, Chia-Jen Liu, Hervé Avet-Loiseau, Jihye Park, Jiantao Shi, Federico Campigotto, Karma Z Salem, Daisy Huynh, Siobhan V Glavey, Bradley Rivotto, Antonio Sacco, Aldo M Roccaro, Juliette Bouyssou, Stéphane Minvielle, Philippe Moreau, Thierry Facon, Xavier Leleu, Edie Weller, Lorenzo Trippa, Irene M Ghobrial
Exosomes, secreted by several cell types, including cancer cells, can be isolated from the peripheral blood and have been shown to be powerful markers of disease progression in cancer. In this study, we examined the prognostic significance of circulating exosomal microRNAs (miRNAs) in multiple myeloma (MM). A cohort of 156 patients with newly diagnosed MM, uniformly treated and followed, was studied. Circulating exosomal miRNAs were isolated and used to perform small RNA sequencing analysis on 10 samples and a qRT-PCR array on 156 samples...
February 17, 2017: Blood
https://www.readbyqxmd.com/read/28213328/an-integrated-dual-functional-recognition-amplification-bio-label-for-the-one-step-impedimetric-detection-of-micro-rna-21
#13
Sawsen Azzouzi, Wing Cheung Mak, Kamalodin Kor, Anthony P F Turner, Mounir Ben Ali, Valerio Beni
Alteration in expression of miRNAs has been correlated with different cancer types, tumour stage and response to treatments. In this context, a structurally responsive oligonucleotide-based electrochemical impedimetric biosensor has been developed for the simple and sensitive detection of miRNA-21. A highly specific biotinylated DNA/LNA molecular beacon (MB) probe was conjugated with gold nanoparticles (AuNPs) to create an integrated, dual function bio-label (biotin-MB-AuNPs) for both biorecognition and signal generation...
February 10, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28211871/expression-level-is-a-key-determinant-of-e2f1-mediated-cell-fate
#14
Igor Shats, Michael Deng, Adam Davidovich, Carolyn Zhang, Jungeun S Kwon, Dinesh Manandhar, Raluca Gordân, Guang Yao, Lingchong You
The Rb/E2F network has a critical role in regulating cell cycle progression and cell fate decisions. It is dysfunctional in virtually all human cancers, because of genetic lesions that cause overexpression of activators, inactivation of repressors, or both. Paradoxically, the downstream target of this network, E2F1, is rarely strongly overexpressed in cancer. E2F1 can induce both proliferation and apoptosis but the factors governing these critical cell fate decisions remain unclear. Previous studies have focused on qualitative mechanisms such as differential cofactors, posttranslational modification or state of other signaling pathways as modifiers of the cell fate decisions downstream of E2F1 activation...
February 17, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28210977/genetic-characterization-of-adenoid-cystic-carcinoma-of-the-minor-salivary-glands-a-potential-familial-occurrence-in-first-degree-relatives
#15
Hani Ibrahim Channir, Thomas van Overeem Hansen, Simon Andreasen, Christina Westmose Yde, Katalin Kiss, Birgitte Wittenborg Charabi
Adenoid cystic carcinoma (AdCC) is a malignant salivary gland tumor. To date, no cases of AdCC in first-degree relatives have been reported in the literature. We present a 50-year-old female (Case 1) and this patients' father (Case 2), both of whom were diagnosed with AdCC of the minor salivary glands. Histology of Case 1 demonstrated a tubulocribriform AdCC whereas Case 2 primarily was an AdCC of solid type. Both cases harbored the MYB-NFIB gene fusion as demonstrated by FISH and RNA-sequencing. After filtering and selection of putative deleterious variants, whole exome sequencing identified 18 germline variants in common between Case 1 and Case 2...
February 16, 2017: Head and Neck Pathology
https://www.readbyqxmd.com/read/28210664/fibronectin-and-androgen-receptor-expression-data-in-prostate-cancer-obtained-from-a-rna-sequencing-bioinformatics-analysis
#16
Dibash K Das, Thahmina Ali, Konstantinos Krampis, Olorunseun O Ogunwobi
Prostate cancer is the second most commonly diagnosed male cancer in the world. The molecular mechanisms underlying its development and progression are still unclear. Here we show analysis of a prostate cancer RNA-sequencing dataset that was originally generated by Ren et al. [3] from the prostate tumor and adjacent normal tissues of 14 patients. The data presented here was analyzed using our RNA-sequencing bioinformatics analysis pipeline implemented on the bioinformatics web platform, Galaxy. The relative expression of fibronectin (FN1) and the androgen receptor (AR) were calculated in fragments per kilobase of transcript per million mapped reads, and represented in FPKM unit...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28210624/rna-sequencing-analysis-reveals-interactions-between-breast-cancer-or-melanoma-cells-and-the-tissue-microenvironment-during-brain-metastasis
#17
Ryo Sato, Teppei Nakano, Mari Hosonaga, Oltea Sampetrean, Ritsuko Harigai, Takashi Sasaki, Ikuko Koya, Hideyuki Okano, Jun Kudoh, Hideyuki Saya, Yoshimi Arima
Metastasis is the main cause of treatment failure and death in cancer patients. Metastasis of tumor cells to the brain occurs frequently in individuals with breast cancer, non-small cell lung cancer, or melanoma. Despite recent advances in our understanding of the causes and in the treatment of primary tumors, the biological and molecular mechanisms underlying the metastasis of cancer cells to the brain have remained unclear. Metastasizing cancer cells interact with their microenvironment in the brain to establish metastases...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28205537/her2-alterations-in-muscle-invasive-bladder-cancer-patient-selection-beyond-protein-expression-for-targeted-therapy
#18
Bernhard Kiss, Alexander W Wyatt, James Douglas, Veronika Skuginna, Fan Mo, Shawn Anderson, Diana Rotzer, Achim Fleischmann, Vera Genitsch, Tetsutaro Hayashi, Maja Neuenschwander, Christine Buerki, Elai Davicioni, Colin Collins, George N Thalmann, Peter C Black, Roland Seiler
Although the introduction of novel targeted agents has improved patient outcomes in several human cancers, no such advance has been achieved in muscle-invasive bladder cancer (MIBC). However, recent sequencing efforts have begun to dissect the complex genomic landscape of MIBC, revealing distinct molecular subtypes and offering hope for implementation of targeted therapies. Her2 (ERBB2) is one of the most established therapeutic targets in breast and gastric cancer but agents targeting Her2 have not yet demonstrated anti-tumor activity in MIBC...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28202522/histone-acetyltransferase-activity-of-mof-is-required-for-mll-af9-leukemogenesis
#19
Daria G Valerio, Haiming Xu, Chun-Wei Chen, Takayuki Hoshii, Meghan E Eisold, Christopher Delaney, Monica Cusan, Aniruddha J Deshpande, Chun-Hao Huang, Amaia Lujambio, Y George G Zheng, Johannes Zuber, Tej K Pandita, Scott W Lowe, Scott A Armstrong
Chromatin-based mechanisms offer therapeutic targets in acute myeloid leukemia (AML) that are of great current interest. In this study, we conducted an RNAi-based screen to identify druggable chromatin regulator-based targets in leukemias marked by oncogenic rearrangements of the MLL gene. In this manner, we discovered the H4K16 histone acetyltransferase (HAT) MOF to be a potent suppressor of leukemia cell growth. Conditional deletion of Mof in a mouse model of MLL-AF9-driven leukemogenesis reduced tumor burden and prolonged host survival...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28202495/expression-of-grk2-and-igf1r-in-hepatocellular-carcinoma-clinicopathological-and-prognostic-significance
#20
Song-Bai Lin, Li Zhou, Zhi-Yong Liang, Wei-Xun Zhou, Ye Jin
AIM: It has been shown that G-protein-coupled receptor kinase 2 (GRK2) negatively regulates the insulin-like growth factor 1 receptor (IGF1R) signalling pathway in hepatocellular carcinoma (HCC). The aim of this study was to evaluate the clinicopathological and prognostic significance of GRK2 and IGF1R in HCC. METHODS: Expression of GRK2 and IGF1R was first detected by tissue microarray-based immunohistochemistry in 156 patients with HCC. Staining results, termed the H-score, were then correlated with clinicopathological variables and patient survival...
February 15, 2017: Journal of Clinical Pathology
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