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https://www.readbyqxmd.com/read/29676642/immunomethylomics-a-novel-cancer-risk-prediction-tool
#1
Karl T Kelsey, John K Wiencke
There is emerging evidence that the immune biology associated with lung and other solid tumors, as well as patient immune genetic traits, contributes to individual survival. At this time, dramatic advances in immunologic approaches to the study and management of human cancers are taking place, including lung and head and neck squamous cell carcinoma. However, major obstacles for therapies are the profound immune alterations in blood and in the tumor microenvironment that arise in tandem with the cancer. Although there is a significant current effort underway across the cancer research community to probe the tumor environment to uncover the dynamics of the immune response, little similar work is being done to understand the dynamics of immune alterations in peripheral blood, despite evidence showing the prognostic relevance of the neutrophil/lymphocyte ratio for these cancers...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29676376/an-unusual-presentation-of-large-b-cell-lymphoma-with-interferon-regulatory-factor-4-gene-rearrangement
#2
Anuj Verma, Sridhar Epari, Sumeet Gujral, Tanuja Shet
Rearrangements involving interferon regulatory factor 4 (IRF4) gene has been recently described in a subtype of diffuse large B-cell lymphoma (DLBCL). They occur in a typical clinical setting of a pediatric age group, predominantly with tonsillar mass, usually as a low-stage disease and with good response to chemotherapy. Histomorphologically, they show nodular/follicular architecture with diffuse strong immunopositivity for multiple myeloma oncogene 1. Here, the authors describe one such unusual case of large B-cell lymphoma with IRF4 gene rearrangement in a young child with the unusual location of inguinal region and detailed pathological (histological, immunohistochemical, and molecular) findings...
April 2018: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/29676353/interobserver-reproducibility-of-tumor-infiltrating-lymphocyte-evaluations-in-breast-cancer
#3
Fatmagul Kusku Cabuk, Fatma Aktepe, Fatma Nilgun Kapucuoglu, Ipek Coban, Dauren Sarsenov, Vahit Ozmen
Aim: Tumor-infiltrating lymphocytes (TILs) have a prognostic value in breast cancer (BC); however, because of the lack of standard evaluation methods, we aimed to assess the interobserver agreement of stromal TILs (sTILs) and intratumoral TILs (iTILs) as well as the effect of hot spot areas and molecular subtyping on the overall agreement. Methods: The study consisted of 121 haematoxylin and eosin (H and E)-stained slides of invasive BC samples obtained from the pathology archives...
April 2018: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/29676340/progesterone-receptor-expression-and-ki-67-labelling-index-of-meningiomas-in-the-lagos-university-teaching-hospital
#4
Nzechukwu Zimudo Ikeri, Charles Chidozie Anunobi, Olufemi B Bankole
Background: Meningioma in Nigeria has been poorly studied. Its location within the intracranial cavity is associated with significant morbidity and mortality. Even when completely excised, it has a tendency to recur and this is associated with repeat operations and shortened survival. The World Health Organization (WHO) grade, progesterone receptor (PR) expression and Ki-67 index are predictive for recurrence and are, therefore, useful for individualised management. The aim of this study was therefore to determine the PR expression and Ki-67 index of meningiomas received in our institution...
January 2018: Nigerian Postgraduate Medical Journal
https://www.readbyqxmd.com/read/29675946/plasma-proteomics-identifies-a-chemokine-storm-in-idiopathic-multicentric-castleman-disease
#5
Sheila K Pierson, Aaron J Stonestrom, Dustin Shilling, Jason Ruth, Christopher S Nabel, Amrit Singh, Yue Ren, Katie Stone, Hongzhe Li, Frits van Rhee, David C Fajgenbaum
Human Herpesvirus-8 (HHV-8)-negative/idiopathic multicentric Castleman disease (iMCD) is a poorly understood disease involving polyclonal lymphoproliferation with dysmorphic germinal centers, constitutional symptoms, and multi-organ failure. Patients can experience thrombocytopenia, anasarca, reticulin fibrosis, renal dysfunction, organomegaly, and normal immunoglobulin levels, - iMCD-TAFRO. Others experience thrombocytosis, milder effusions, and hypergammaglobulinemia, -iMCD-Not Otherwise Specified (iMCD-NOS)...
April 20, 2018: American Journal of Hematology
https://www.readbyqxmd.com/read/29675884/specific-breast-cancer-prognosis-subtype-distinctions-based-on-dna-methylation-patterns
#6
Shumei Zhang, Yihan Wang, Yue Gu, Jiang Zhu, Ce Ci, Zhongfu Guo, Chuangeng Chen, Yanjun Wei, Wenhua Lv, Hongbo Liu, Dongwei Zhang, Yan Zhang
Tumor heterogeneity is an obstacle to effective breast cancer diagnosis and therapy. DNA methylation is an important regulator of gene expression, thus characterizing tumor heterogeneity by epigenetic features can be clinically informative. In this study, we explored specific prognosis-subtypes based on DNA methylation status using 669 breast cancers from TCGA database. Nine subgroups were distinguished by consensus clustering using 3869 CpGs that significantly influenced survival. The specific DNA methylation patterns were reflected by different races, ages, tumor stages, receptor status, histological types, metastasis status and prognosis...
April 19, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/29675864/molecular-based-identification-and-detection-of-salmonella-in-food-production-systems-current-perspectives
#7
REVIEW
Steven C Ricke, Sun Ae Kim, Zhaohao Shi, Si Hong Park
Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies has greatly improved the resolution for differentiating strains within a particular serovar...
April 19, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29674445/druggable-negative-allosteric-site-of-p2x3-receptors
#8
Jin Wang, Yao Wang, Wen-Wen Cui, Yichen Huang, Yang Yang, Yan Liu, Wen-Shan Zhao, Xiao-Yang Cheng, Wang-Sheng Sun, Peng Cao, Michael X Zhu, Rui Wang, Motoyuki Hattori, Ye Yu
Allosteric modulation provides exciting opportunities for drug discovery of enzymes, ion channels, and G protein-coupled receptors. As cation channels gated by extracellular ATP, P2X receptors have attracted wide attention as new drug targets. Although small molecules targeting P2X receptors have entered into clinical trials for rheumatoid arthritis, cough, and pain, negative allosteric modulation of these receptors remains largely unexplored. Here, combining X-ray crystallography, computational modeling, and functional studies of channel mutants, we identified a negative allosteric site on P2X3 receptors, fostered by the left flipper (LF), lower body (LB), and dorsal fin (DF) domains...
April 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29672479/protracted-outbreak-of-salmonella-newport-infections-linked-to-ground-beef-possible-role-of-dairy-cows-21-states-2016-2017
#9
Katherine E Heiman Marshall, Mackenzie Tewell, Selam Tecle, Molly Leeper, Jennifer Sinatra, Bonnie Kissler, Adrienne Fung, Kerri Brown, Darlene Wagner, Eija Trees, Kelley B Hise, Vishnu Chaturvedi, Linda K Schlater, Brenda R Morningstar-Shaw, Laura Whitlock, Kristin Holt, Karen Becker, Megin Nichols, Ian T Williams, Michael Jhung, Matthew E Wise, Laura Gieraltowski
In January 2017, CDC identified a cluster of Salmonella enterica serotype Newport infections with isolates sharing an indistinguishable pulsed-field gel electrophoresis (PFGE) pattern, JJPX01.0010 (pattern 10), through PulseNet, the national molecular subtyping network for foodborne disease surveillance. This report summarizes the investigation by CDC, state and local health and agriculture departments, and the U.S. Department of Agriculture's Food Safety and Inspection Service (USDA-FSIS) and discusses the possible role of dairy cows as a reservoir for strains of Salmonella that persistently cause human illness...
April 20, 2018: MMWR. Morbidity and Mortality Weekly Report
https://www.readbyqxmd.com/read/29670256/deviations-of-the-immune-cell-landscape-between-healthy-liver-and-hepatocellular-carcinoma
#10
Nataliya Rohr-Udilova, Florian Klinglmüller, Rolf Schulte-Hermann, Judith Stift, Merima Herac, Martina Salzmann, Francesca Finotello, Gerald Timelthaler, Georg Oberhuber, Matthias Pinter, Thomas Reiberger, Erika Jensen-Jarolim, Robert Eferl, Michael Trauner
Tumor-infiltrating immune cells are highly relevant for prognosis and identification of immunotherapy targets in hepatocellular carcinoma (HCC). The recently developed CIBERSORT method allows immune cell profiling by deconvolution of gene expression microarray data. By applying CIBERSORT, we assessed the relative proportions of immune cells in 41 healthy human livers, 305 HCC samples and 82 HCC adjacent tissues. The obtained immune cell profiles provided enumeration and activation status of 22 immune cell subtypes...
April 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29668721/ultra-high-field-mri-of-human-hippocampi-morphological-and-multiparametric-differentiation-of-hippocampal-sclerosis-subtypes
#11
Clarissa Gillmann, Roland Coras, Karl Rössler, Arnd Doerfler, Michael Uder, Ingmar Blümcke, Tobias Bäuerle
The aim of the present study is to differentiate subtypes of hippocampal sclerosis (HS) using ex vivo ultra-high field magnetic resonance imaging (MRI). Included were 14 surgically resected hippocampi of patients with medically intractable temporal lobe epilepsy. The resected hippocampi were histologically categorized into subtypes of hippocampal sclerosis (HS type 1 (n = 10), HS type 2 (n = 2) and no-HS (n = 2)) and subsequently scanned on a preclinical 7T MRI acquiring T2-weighted morphology, relaxometry and diffusion tensor imaging...
2018: PloS One
https://www.readbyqxmd.com/read/29668675/correlated-metabolomic-genomic-and-histologic-phenotypes-in-histologically-normal-breast-tissue
#12
Xuezheng Sun, Delisha A Stewart, Rupninder Sandhu, Erin L Kirk, Wimal W Pathmasiri, Susan L McRitchie, Robert F Clark, Melissa A Troester, Susan J Sumner
Breast carcinogenesis is a multistep process accompanied by widespread molecular and genomic alterations, both in tumor and in surrounding microenvironment. It is known that tumors have altered metabolism, but the metabolic changes in normal or cancer-adjacent, nonmalignant normal tissues and how these changes relate to alterations in gene expression and histological composition are not well understood. Normal or cancer-adjacent normal breast tissues from 99 women of the Normal Breast Study (NBS) were evaluated...
2018: PloS One
https://www.readbyqxmd.com/read/29668342/sequencing-the-next-generation-of-glioblastomas
#13
Ivana Jovčevska
The most aggressive brain malignancy, glioblastoma, accounts for 60-70% of all gliomas and is uniformly fatal. According to the molecular signature, glioblastoma is divided into four subtypes (proneural, neural, classical, and mesenchymal), each with its own genetic background. The Cancer Genome Atlas project provides information about the most common genetic changes in glioblastoma. They involve mutations in TP53, TERT, and PTEN, and amplifications in EFGR, PDGFRA, CDK4, CDK6, MDM2, and MDM4. Recently, epigenetics was used to demonstrate the oncogenic roles of miR-124, miR-137, and miR-128...
April 18, 2018: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29667086/contrast-enhancement-predicting-survival-in-integrated-molecular-subtypes-of-diffuse-glioma-an-observational-cohort-study
#14
Johann-Martin Hempel, Cornelia Brendle, Benjamin Bender, Georg Bier, Marco Skardelly, Irina Gepfner-Tuma, Franziska Eckert, Ulrike Ernemann, Jens Schittenhelm
INTRODUCTION: To assess the predictive value of magnetic resonance imaging (MRI) gadolinium enhancement as a prognostic factor in the 2016 World Health Organization Classification of Tumors of the Central Nervous System integrated glioma groups. METHODS: Four-hundred fifty patients with histopathologically confirmed glioma were retrospectively assessed between 07/1997 and 06/2014 using gadolinium enhancement, survival, and relevant prognostic molecular data [isocitrate dehydrogenase (IDH); alpha-thalassemia/mental retardation syndrome X-linked (ATRX); chromosome 1p/19q loss of heterozygosity; and O6-methylguanine DNA methyltransferase (MGMT)]...
April 17, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29666783/development-of-neuroendocrine-prostate-cancers-by-the-ser-arg-repetitive-matrix-4-mediated-rna-splicing-network
#15
Ahn R Lee, Nicole Che, Jessica M Lovnicki, Xuesen Dong
While the use of next-generation androgen receptor pathway inhibition (ARPI) therapy has significantly increased the survival of patients with metastatic prostate adenocarcinoma (AdPC), several groups have reported a treatment-resistant mechanism, whereby cancer cells can become androgen receptor (AR) indifferent and gain a neuroendocrine (NE)-like phenotype. This subtype of castration-resistant prostate cancer has been termed "treatment-induced castration-resistant neuroendocrine prostate cancer" (CRPC-NE)...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29666373/a-geometric-approach-to-characterize-the-functional-identity-of-single-cells
#16
Shahin Mohammadi, Vikram Ravindra, David F Gleich, Ananth Grama
Single-cell transcriptomic data has the potential to radically redefine our view of cell-type identity. Cells that were previously believed to be homogeneous are now clearly distinguishable in terms of their expression phenotype. Methods for automatically characterizing the functional identity of cells, and their associated properties, can be used to uncover processes involved in lineage differentiation as well as sub-typing cancer cells. They can also be used to suggest personalized therapies based on molecular signatures associated with pathology...
April 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29666255/digitizing-omics-profiles-by-divergence-from-a-baseline
#17
Wikum Dinalankara, Qian Ke, Yiran Xu, Lanlan Ji, Nicole Pagane, Anching Lien, Tejasvi Matam, Elana J Fertig, Nathan D Price, Laurent Younes, Luigi Marchionni, Donald Geman
Data collected from omics technologies have revealed pervasive heterogeneity and stochasticity of molecular states within and between phenotypes. A prominent example of such heterogeneity occurs between genome-wide mRNA, microRNA, and methylation profiles from one individual tumor to another, even within a cancer subtype. However, current methods in bioinformatics, such as detecting differentially expressed genes or CpG sites, are population-based and therefore do not effectively model intersample diversity...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29666172/genetic-editing-of-colonic-organoids-provides-a-molecularly-distinct-and-orthotopic-preclinical-model-of-serrated-carcinogenesis
#18
Tamsin R M Lannagan, Young K Lee, Tongtong Wang, Jatin Roper, Mark L Bettington, Lochlan Fennell, Laura Vrbanac, Lisa Jonavicius, Roshini Somashekar, Krystyna Gieniec, Miao Yang, Jia Q Ng, Nobumi Suzuki, Mari Ichinose, Josephine A Wright, Hiroki Kobayashi, Tracey L Putoczki, Yoku Hayakawa, Simon J Leedham, Helen E Abud, Ömer H Yilmaz, Julie Marker, Sonja Klebe, Pratyaksha Wirapati, Siddhartha Mukherjee, Sabine Tejpar, Barbara A Leggett, Vicki L J Whitehall, Daniel L Worthley, Susan L Woods
OBJECTIVE: Serrated colorectal cancer (CRC) accounts for approximately 25% of cases and includes tumours that are among the most treatment resistant and with worst outcomes. This CRC subtype is associated with activating mutations in the mitogen-activated kinase pathway gene, BRAF , and epigenetic modifications termed the CpG Island Methylator Phenotype, leading to epigenetic silencing of key tumour suppressor genes. It is still not clear which (epi-)genetic changes are most important in neoplastic progression and we begin to address this knowledge gap herein...
April 17, 2018: Gut
https://www.readbyqxmd.com/read/29666150/epigenetics-and-epitranscriptomics-in-temporal-patterning-of-cortical-neural-progenitor-competence
#19
REVIEW
Ki-Jun Yoon, Caroline Vissers, Guo-Li Ming, Hongjun Song
During embryonic brain development, neural progenitor/stem cells (NPCs) sequentially give rise to different subtypes of neurons and glia via a highly orchestrated process. To accomplish the ordered generation of distinct progenies, NPCs go through multistep transitions of their developmental competence. The molecular mechanisms driving precise temporal coordination of these transitions remains enigmatic. Epigenetic regulation, including changes in chromatin structures, DNA methylation, and histone modifications, has been extensively investigated in the context of cortical neurogenesis...
April 17, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29666114/chronic-lymphocytic-leukemia-and-mantle-cell-lymphoma-crossroads-of-genetic-and-microenvironment-interactions
#20
Xose S Puente, Pedro Jares, Elias Campo
Chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) are two well defined entities that diverge in their basic pathogenic mechanisms and clinical evolution but they share epidemiological characteristics, cells of origin, molecular alterations, and clinical features that differ from other lymphoid neoplasms. CLL and MCL are classically considered indolent and aggressive neoplasms, respectively. However, the clinical evolution of both tumors is very heterogeneous, with subsets of patients having a stable disease for long time whereas others require immediate intervention...
April 17, 2018: Blood
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