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https://www.readbyqxmd.com/read/29342249/splice-expression-variation-analysis-seva-for-inter-tumor-heterogeneity-of-gene-isoform-usage-in-cancer
#1
Bahman Afsari, Theresa Guo, Michael Considine, Liliana Florea, Luciane T Kagohara, Genevieve L Stein-O'Brien, Dylan Kelley, Emily Flam, Kristina D Zambo, Patrick K Ha, Donald Geman, Michael F Ochs, Joseph A Califano, Daria A Gaykalova, Alexander V Favorov, Elana J Fertig
Motivation: Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in normal tissues, which have stable regulation of gene splicing. Pathological conditions, such as cancer, can have broken regulation of splicing that increases the heterogeneity of the expression of splice variants. Inferring events with such differential heterogeneity in gene isoform usage requires new statistical approaches...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#2
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342108/different-lipid-regulation-in-ovarian-cancer-inhibition-of-the-immune-system
#3
Christina Wefers, Tjitske Duiveman-de Boer, Petra L M Zusterzeel, Leon F A G Massuger, David Fuchs, Ruurd Torensma, Craig E Wheelock, I Jolanda M de Vries
Lipid metabolism is altered in several cancer settings leading to different ratios of intermediates. Ovarian cancer is the most lethal gynecological malignancy. Cancer cells disperse in the abdominal space and ascites occurs. T cells obtained from ascites are unable to proliferate after an antigenic stimulus. The proliferation of ascites-derived T cells can be restored after culturing the cells for ten days in normal culture medium. No pathway aberrancies were detected. The acellular fraction of ascites can inhibit the proliferation of autologous as well as allogeneic peripheral blood lymphocytes, indicating the presence of soluble factors that interfere with T cell functionality...
January 17, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29341930/activation-of-estrogen-receptor-beta-er%C3%AE-regulates-the-expression-of-n-cadherin-e-cadherin-and-%C3%AE-catenin-in-androgen-independent-prostate-cancer-cells
#4
Rafael de Souza Silva, Ana Paola G Lombardi, Deborah Simão de Souza, Carolina M Vicente, Catarina S Porto
The aim of the present study was to investigate the impact of the activation of estrogen receptors on expression and localization of N-cadherin, E-cadherin and non-phosphorylated β-catenin in androgen-independent prostate cancer cells (PC-3 and DU-145) and in human post pubertal prostate epithelial cells (PNT1A). Expression of N-cadherin was detected in PNT1A and PC-3 cells, but not in DU-145 cells. E-cadherin was detected only in DU-145 cells and β-catenin was detected in all cells studied. N-cadherin and β-catenin were located preferentially in the cellular membrane of PNT1A cells and in the cytoplasm of PC-3 cells...
January 13, 2018: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29341851/underutilization-of-supplemental-magnetic-resonance-imaging-screening-among-patients-at-high-breast-cancer-risk
#5
Randy Miles, Fei Wan, Tracy L Onega, Amanda Lenderink-Carpenter, Ellen S O'Meara, Weiwei Zhu, Louise M Henderson, Jennifer S Haas, Deirdre A Hill, Anna N A Tosteson, Karen J Wernli, Jennifer Alford-Teaster, Janie M Lee, Constance D Lehman, Christoph I Lee
BACKGROUND: Women at high lifetime breast cancer risk may benefit from supplemental breast magnetic resonance imaging (MRI) screening, in addition to routine mammography screening for earlier cancer detection. MATERIALS AND METHODS: We performed a cross-sectional study of 422,406 women undergoing routine mammography screening across 86 Breast Cancer Surveillance Consortium (BCSC) facilities during calendar year 2012. We determined availability and use of on-site screening breast MRI services based on woman-level characteristics, including >20% lifetime absolute risk using the National Cancer Institute risk assessment tool...
January 17, 2018: Journal of Women's Health
https://www.readbyqxmd.com/read/29341459/multicenter-study-of-diagnostic-procedures-genetic-aberration-analysis-and-first-line-treatment-of-lung-cancer-in-jiangsu-province-china
#6
YangBo Hu, Huan Hu, LiYun Miao, Xin Zhao, Wei Gu, Wei Heng, ZiLi Meng, Jian Feng, Yi You, XingXiang Xu, Rong Hu, HaiQuan Li, Jie Zhao, XiaoLi Zhu, MeiQi Shi, Li Shen, XiuWei Zhang, XiaoWei Yin, Hang Ma, MinHua Shi, Yong Yu, Hong Lv, LiMing Cai, GaoHua Feng, YeQing Zhang, Feng Wu, TangFeng Lv, Yong Song
BACKGROUND: Jiangsu Province, China, is highly developed economically and culturally, and has a high prevalence of lung cancer. We aimed to evaluate the diagnostic procedures, genetic aberration analysis status, and first-line treatment models of lung cancer in Jiangsu Province. METHODS: Lung cancer patients diagnosed in 2016 at 22 tertiary care hospitals were evaluated. Demographic characteristics, tumor histology, staging, family history of lung cancer, auxiliary examinations, genetic testing, and first-line treatment were collected on discharge...
January 17, 2018: Thoracic Cancer
https://www.readbyqxmd.com/read/29341453/mechanism-underlying-the-negative-effect-of-prostate-volume-on-the-outcome-of-extensive-transperineal-ultrasound-guided-template-prostate-biopsy
#7
Takayoshi Demura, Takenori Takada, Naohiko Shimoda, Takaya Hioka, Yoshihumi Iwaguchi, Shin Ichihara, Hiroko Gotoda
Previous studies have indicated a possible relationship between increased prostate volume (PV) and decreased biopsy yield, although the mechanism involved is unclear. We evaluated 1650 patients who underwent template biopsy. The distribution of 993 cancer lesions in 302 prostatectomy specimens was compared with the biopsy data to determine whether each lesion was detected. A receiver operating characteristic (ROC) model was used to determine the diagnostic accuracy of prostate-specific antigen (PSA) and related markers...
January 17, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29341428/epigenetic-silencing-of-tap1-in-aldefluor-breast-cancer-stem-cells-contributes-to-their-enhanced-immune-evasion
#8
Mohammad Sultan, Dejan Vidovic, Arianne S Paine, Thomas T Huynh, Krysta M Coyle, Margaret L Thomas, Brianne M Cruickshank, Cheryl A Dean, Derek R Clements, Youra Kim, Kristin Lee, Shashi A Gujar, Ian C Weaver, Paola Marcato
Avoiding detection and destruction by immune cells is key for tumor initiation and progression. The important role of cancer stem cells (CSC) in tumor initiation has been well established, yet their ability to evade immune detection and targeting is only partly understood. To investigate the ability of breast CSCs to evade immune detection we identified a highly tumorigenic population in a spontaneous murine mammary tumor based on increased aldehyde dehydrogenase (ALDH) activity. We performed tumor growth studies in immunocompetent and immunocompromised mice...
January 17, 2018: Stem Cells
https://www.readbyqxmd.com/read/29341374/validation-of-the-digital-pcr-system-in-tyrosine-kinase-inhibitor-resistant-egfr-mutant-non-small-cell-lung-cancer
#9
Katsuhiro Masago, Shiro Fujita, Akito Hata, Chiyuki Okuda, Yuko Yoshizumi, Reiko Kaji, Nobuyuki Katakami, Yukio Hirata, Yasushi Yatabe
The aim of this study was to compare the accuracy of the QuantStudio 3D Digital polymerase chain reaction (dPCR) system and a PCR-based next generation sequencing (NGS) system for detecting a secondary mutation in the epidermal growth factor receptor (EGFR) gene T790M in non-small cell lung cancer (NSCLC) patients previously diagnosed with EGFR-activating mutations. Twenty-five patients with NSCLC previously treated with EGFR-TKIs were examined. The patients were treated daily with either erlotinib or gefitinib...
January 17, 2018: Pathology International
https://www.readbyqxmd.com/read/29341356/all-over-the-map-an-interobserver-agreement-study-of-tumor-location-based-on-the-pi-radsv2-sector-map
#10
Matthew D Greer, Joanna H Shih, Tristan Barrett, Sandra Bednarova, Ismail Kabakus, Yan Mee Law, Haytham Shebel, Maria J Merino, Bradford J Wood, Peter A Pinto, Peter L Choyke, Baris Turkbey
BACKGROUND: Prostate imaging reporting and data system version 2 (PI-RADSv2) recommends a sector map for reporting findings of prostate cancer mulitparametric MRI (mpMRI). Anecdotally, radiologists may demonstrate inconsistent reproducibility with this map. PURPOSE: To evaluate interobserver agreement in defining prostate tumor location on mpMRI using the PI-RADSv2 sector map. STUDY TYPE: Retrospective. POPULATION: Thirty consecutive patients who underwent mpMRI between October, 2013 and March, 2015 and who subsequently underwent prostatectomy with whole-mount processing...
January 17, 2018: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/29341317/apoptosis-induction-in-k562-human-myelogenous-leukaemia-cells-is-connected-to-the-modulation-of-wnt-%C3%AE-catenin-signalling-by-bhx-a-novel-pyrazoline-derivative
#11
Hanmei Bao, Qing Zhang, Yibo Du, Cai Zhang, Hui Xu, Zhongling Zhu, Zhao Yan
OBJECTIVES: The goal of this study was to explore the effects of BHX on human chronic myeloid leukaemia (CML) cells and to elucidate the underlying molecular mechanism. MATERIALS AND METHODS: CML cell line K562 cells were treated with BHX. The effects of BHX on cell proliferation, apoptosis and cell cycle were detected. Subsequently, the caspase, ATP activity, Ca2+ , ROS and mitochondrial membrane potential (MMP) levels treated with various concentrations of BHX were analysed...
January 16, 2018: Cell Proliferation
https://www.readbyqxmd.com/read/29341162/impact-of-genomics-on-the-surgical-management-of-melanoma
#12
REVIEW
P M Ferguson, G V Long, R A Scolyer, J F Thompson
BACKGROUND: Although surgery for early-stage melanoma offers the best chance of cure, recent advances in molecular medicine have revolutionized the management of late-stage melanoma, leading to significant improvements in clinical outcomes. Research into the genomic drivers of disease and cancer immunology has not only ushered in a new era of targeted and immune-based therapies for patients with metastatic melanoma, but has also provided new tools for monitoring disease recurrence and selecting therapeutic strategies...
January 2018: British Journal of Surgery
https://www.readbyqxmd.com/read/29341161/modalities-for-image-and-molecular-guided-cancer-surgery
#13
REVIEW
M A Stammes, S L Bugby, T Porta, K Pierzchalski, T Devling, C Otto, J Dijkstra, A L Vahrmeijer, L-F de Geus-Oei, J S D Mieog
BACKGROUND: Surgery is the cornerstone of treatment for many solid tumours. A wide variety of imaging modalities are available before surgery for staging, although surgeons still rely primarily on visual and haptic cues in the operating environment. Image and molecular guidance might improve the adequacy of resection through enhanced tumour definition and detection of aberrant deposits. Intraoperative modalities available for image- and molecular-guided cancer surgery are reviewed here...
January 2018: British Journal of Surgery
https://www.readbyqxmd.com/read/29341153/circulating-tumour-cells-and-dna-as-liquid-biopsies-in-gastrointestinal-cancer
#14
REVIEW
O Nordgård, K Tjensvoll, B Gilje, K Søreide
BACKGROUND: Blood is the most extensively studied body fluid and, because it contains circulating tumour cells (CTCs) and circulating tumour-derived cell-free DNA (ctDNA), it may represent a liquid biopsy for cancer. Methods for enrichment and detection of CTCs and ctDNA, their clinical applications and future opportunities in gastrointestinal cancers were the focus of this review. METHODS: The PubMed database was searched for literature up to 24 June 2017, with a focus on the past 10 years...
January 2018: British Journal of Surgery
https://www.readbyqxmd.com/read/29341110/eurogin-roadmap-2017-triage-strategies-for-the-management-of-hpv-positive-women-in-cervical-screening-programmes
#15
REVIEW
K Cuschieri, G Ronco, A Lorincz, L Smith, G Ogilvie, L Mirabello, F Carozzi, H Cubie, N Wentzensen, P Snijders, M Arbyn, J Monsonego J, S Franceschi
Cervical cancer screening will rely, increasingly, on HPV testing as a primary screen. The requirement for triage tests which can delineate clinically significant infection is thus prescient. In this EUROGIN 2017 roadmap, justification behind the most evidenced triages is outlined, as are challenges for implementation. Cytology is the triage with the most follow-up data; the existence of an HR-HPV positive, cytology negative group presents a challenge and re-testing intervals for this group (and choice of re-test) require careful consideration...
January 17, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29341018/magnetic-resonance-spectroscopy-studies-of-mouse-models-of-cancer
#16
Menglin Cheng, Kristine Glunde
Magnetic resonance spectroscopy (MRS) or spectroscopic imaging (MRSI) enables the detection of metabolites, amino acids, and lipids, among other biomolecules, in tumors of live mouse models of cancer. Tumor-bearing mice are anesthetized by breathing isoflurane in a magnetic resonance (MR) scanner dedicated to small animal MR. Here we describe the overall setup and steps for measuring 1H and 31P MRS and 1H MRSI of orthotopic breast tumor models in mice with surface coils. This protocol can be adapted to the use of volume coils to measure 1H and 31P MRS(I) of tumor models that grow inside the body...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29340992/prospective-comparative-study-of-laparoscopic-narrow-band-imaging-nbi-versus-standard-imaging-in-gynecologic-oncology
#17
Alessia Aloisi, Yukio Sonoda, Ginger J Gardner, Kay J Park, Sarah L Elliott, Qin C Zhou, Alexia Iasonos, Nadeem R Abu-Rustum
BACKGROUND: Narrow band imaging (NBI) is an optic filtration enhancement for endoscopy that uses two wavelengths of light (415 and 540 nm) to highlight superficial microvascular patterns. It has been successfully utilized to improve identification of lesions with abnormal vasculature, which is associated with endometriosis and endometrial cancer. Case studies suggest it may also facilitate surgical staging of gynecologic cancer, which is critical in determining appropriate adjuvant therapies...
January 16, 2018: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/29340821/a-novel-and-safe-approach-middle-cranial-approach-for-laparoscopic-right-hemicolon-cancer-surgery-with-complete-mesocolic-excision
#18
Songtao Du, Bomiao Zhang, Yanlong Liu, Peng Han, Chengxin Song, Fangjie Hu, Tianyi Xia, Xiangxin Wu, Binbin Cui
BACKGROUND: Mastering right hemicolectomy techniques using laparoscopy in colorectal cancer surgery is very difficult. Although the long-term prognosis of laparoscopic right hemicolectomy (LRH) and complete mesocolic excision is unquestionable, different surgeons have their own opinions on routes of conducting LRH. OBJECTIVES: LRH surgery is very complex due to the upper abdominal anatomical structure and vascular variation. Therefore, it has been considered the most difficult of all colorectal cancer surgeries...
January 16, 2018: Surgical Endoscopy
https://www.readbyqxmd.com/read/29340818/changes-in-plasma-albumin-levels-in-early-detection-of-infectious-complications-after-laparoscopic-colorectal-cancer-surgery-with-eras-protocol
#19
Mateusz Wierdak, Magdalena Pisarska, Beata Kuśnierz-Cabala, Jan Witowski, Jadwiga Dworak, Piotr Major, Piotr Małczak, Piotr Ceranowicz, Andrzej Budzyński, Michał Pędziwiatr
BACKGROUND: Combination of laparoscopic approach with ERAS protocol in colorectal surgery allows for an early discharge. However there is a risk that some of the discharged patients are developing, asymptomatic at the time, infectious complications. This may lead to a delay in diagnostics and proper treatment introduction. We aimed to assess the usefulness of preoperative plasma albumin concentration and their changes as indicators of infectious complications in patients undergoing colorectal cancer surgery...
January 16, 2018: Surgical Endoscopy
https://www.readbyqxmd.com/read/29340817/adenoma-detection-rate-metrics-in-colorectal-cancer-surveillance-colonoscopy
#20
Jamie M Tjaden, Jessica A Hause, Daniel Berger, Samantha K Duveneck, Shriram M Jakate, Bruce A Orkin, Elizabeth L Hubbard, Joshua E Melson
BACKGROUND: A target goal for screening adenoma detection rate (S-ADR) of ≥ 25% has been set to define high-quality colonoscopy performance. However, there is no current accepted target goal for ADR in colorectal cancer (CRC) surveillance. This makes quality assessment challenging when physicians perform cancer surveillance colonoscopy but minimal screening procedures. METHODS: In this cohort study, consecutive colonoscopies performed at either Rush University Medical Center or Rush Oak Park Hospital by a gastroenterologist or colorectal surgeon in average risk screening population and CRC surveillance population were reviewed retrospectively from 2006 to 2012 and prospectively from 2013 to 2016...
January 16, 2018: Surgical Endoscopy
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