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Molecular classification

Lev M Berstein, Aglaya G Iyevleva, Alexander O Ivantsov, Dmitry A Vasilyev, Tatyana E Poroshina, Igor V Berlev
AIM: To compare endocrine characteristics of  endometrial cancer (EC) patients based on recent molecular EC types classification. MATERIALS & METHODS:  A total of 234 treatment-naive EC patients as well their tumors were studied. RESULTS: Patients with POLE mutations demonstrated tendency to lower body mass index (BMI) and higher serum estradiol. Patients with p53 overexpression were older and had higher diabetes incidence. In the without characteristic molecular profile group there was no difference in fasting serum insulin, estradiol and testosterone levels between women with BMI ≥30...
March 19, 2019: Future Oncology
Nivedita Saxena, Ka-Wai Mok, Michael Rendl
Hair follicle formation in developing embryonic skin requires stepwise signaling between the epithelial epidermis and mesenchymal dermis, and their specialized derivatives, the placode/germ/peg and dermal condensate/papilla, respectively. Classically, distinct stages of hair follicle morphogenesis have been defined, in the mouse model, based on 1) changes in cell morphology and aggregation, 2) expression of few known molecular markers, 3) the extent of follicle downgrowth, and 4) the presence of differentiating cell types...
March 19, 2019: Experimental Dermatology
Emily A Quinn, Jamie L Maciaszek, Emilia M Pinto, Aaron H Phillips, David Berdy, Mohammad Khandwala, Santhosh A Upadhyaya, Gerard P Zambetti, Richard W Kriwacki, David W Ellison, Kim E Nichols, Chimene Kesserwan
Li-Fraumeni syndrome (LFS) is a highly penetrant cancer predisposition syndrome caused by heterozygous germline mutations in the TP53 gene. Although several missense and null TP53 mutations are well established as disease-causing, little is known about the pathogenicity and cancer risks associated with small in-frame deletions. This leads to challenges in variant classification and subsequent difficulty making a molecular diagnosis. We report the genetic testing process for a pediatric patient diagnosed with an undifferentiated high-grade brain tumor following his mother's diagnosis of early-onset bilateral breast cancer...
March 18, 2019: Cold Spring Harbor Molecular Case Studies
Juliette Thariat, Muriel Hourseau, Anne-Catherine Baglin, Laurence Digue, Noémie Vulquin, Cécile Badoual, Bertrand Baujat, Francois Janot, Francois-Régis Ferrand, Beatrix Barry
Among the 20,000 new cases of head and neck neoplasms in France each year, squamous cell carcinomas (HNSCC) represent about 90 % of the cases. Among these, variants of conventional squamous cell carcinomas represent between 5% and 10% of cases. Patient history and risk factors are often similar from those of conventional HSNCC. Variants may, however, be misdiagnosed, which can lead to therapeutic mismanagement due to confusion with sarcomas, glandular tumors or even benign tumors. Diagnostic workup needs to be more cautionary or to include additional exams not to omit their most aggressive component in the case of composite tumors or to under stage the tumor...
March 13, 2019: Bulletin du Cancer
Farzaneh Sharifzad, Saeid Ghavami, Soura Mardpour, Mahsa Mollapour, Zahra Azizi, Adeleh Taghikhani, Marek J Łos, Javad Verdi, Esmail Fakharian, Marzieh Ebrahimi, Amir Ali Hamidieh
Glioblastoma multiforme (GBM) is among the most incurable cancers. GBMs survival rate has not markedly improved, despite new radical surgery protocols, the introduction of new anticancer drugs, new treatment protocols, and advances in radiation techniques. The low efficacy of therapy, and short interval between remission and recurrence, could be attributed to the resistance of a small fraction of tumorigenic cells to treatment. The existence and importance of cancer stem cells (CSCs) is perceived by some as controversial...
March 8, 2019: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
Fan Wu, Rui-Chao Chai, Zhiliang Wang, Yu-Qing Liu, Zheng Zhao, Guan-Zhang Li, Hao-Yu Jiang
Isocitrate dehydrogenase (IDH) mutant glioblastoma (GBM), accounts for ~10% GBMs, arises from lower grade diffuse glioma and preferentially appears in younger patients. Here, we aim to establish a robust gene expression-based molecular classification of IDH-mutant GBM. A total of 33 samples from the Chinese Glioma Genome Atlas RNA-sequencing data were selected as training set, and 21 cases from Chinese Glioma Genome Atlas microarray data were used as validation set. Consensus clustering identified three groups with distinguished prognostic and molecular features...
February 13, 2019: Carcinogenesis
Jin Li, Ailing Fu, Le Zhang
Currently, molecular docking is becoming a key tool in drug discovery and molecular modeling applications. The reliability of molecular docking depends on the accuracy of the adopted scoring function, which can guide and determine the ligand poses when thousands of possible poses of ligand are generated. The scoring function can be used to determine the binding mode and site of a ligand, predict binding affinity and identify the potential drug leads for a given protein target. Despite intensive research over the years, accurate and rapid prediction of protein-ligand interactions is still a challenge in molecular docking...
March 15, 2019: Interdisciplinary Sciences, Computational Life Sciences
Radosław W Piast, Radosław Piast
The quest for defining life has lasted since the beginning of modern science. During the last century, we have reached a lot of milestones toward the understanding of life and its molecular basis. Also, as living creatures, we have imprinted awareness about what is life and what is not. It seems like we have everything we need to formulate the definition of life. If so, why has one, that would satisfy everybody, not yet been announced? What is holding us back? Although we seem to know what life is, our understanding of its edges is still blurry...
March 12, 2019: Journal of Theoretical Biology
Otília Menyhárt, Felice Giangaspero, Balázs Győrffy
Childhood medulloblastomas (MB) are heterogeneous and are divided into four molecular subgroups. The provisional non-wingless-activated (WNT)/non-sonic hedgehog-activated (SHH) category combining group 3 and group 4 represents over two thirds of all MBs, coupled with the highest rates of metastases and least understood pathology. The molecular era expanded our knowledge about molecular aberrations involved in MB tumorigenesis, and here, we review processes leading to non-WNT/non-SHH MB formations.The heterogeneous group 3 and group 4 MBs frequently harbor rare individual genetic alterations, yet the emerging profiles suggest that infrequent events converge on common, potentially targetable signaling pathways...
March 15, 2019: Journal of Hematology & Oncology
Oliver P Stuart, Matthew Binns, Paul A Umina, Joanne Holloway, Dustin Severtson, Michael Nash, Thomas Heddle, Maarten van Helden, Ary A Hoffmann
Dermaptera (earwigs) from the Anisolabididae family may be important for pest control but their taxonomy and status in Australia is poorly studied. Here we used taxonomic information to assess the diversity of southern Australian Anisolabididae and then applied cox1 barcodes as well as additional gene fragments (mitochondrial and nuclear) to corroborate classification and assess the monophyly of the putative genera. Anisolabididae morphospecies fell into two genera, Anisolabis Fieber and Gonolabis Burr, based on paramere morphology...
March 14, 2019: Insects
Igor Tsaur, Isabel Heidegger, Alexander Kretschmer, Hendrik Borgmann, Giorgio Gandaglia, Alberto Briganti, Pieter de Visschere, Romain Mathieu, Massimo Valerio, Roderick van den Bergh, Piet Ost, Cristian Mirvald, Derya Tilki, Guillaume Ploussard, Cristian Surcel
Recently, adoption of novel drugs for systemic treatment of metastatic prostate cancer has led to a striking improvement of response rate and survival in both hormone-sensitive and castration-resistant disease. In most cases, prostate cancer essentially depends on androgen receptor signaling axis, even in castration-resistant setting, and hence may be targeted by second generation hormonal therapy. However, a subset of patients bears androgen-independent cancer biology with a short-term response to hormonal treatment, early and extensive visceral metastases, low PSA levels and poor outcomes...
March 11, 2019: Cancer Treatment Reviews
Vishesh Dubey, Azeem Ahmad, Ankit Butola, Darakhshan Qaiser, Anurag Srivastava, Dalip Singh Mehta
Early-stage detection of breast cancer is the primary requirement in modern healthcare as it is the most common cancer among women worldwide. Histopathology is the most widely preferred method for the diagnosis of breast cancer, but it requires long processing time and involves qualitative assessment of cancer by a trained person/doctor. Here, we present an alternate technique based on white light interference microscopy (WLIM) and Raman spectroscopy, which has the capability to differentiate between cancerous and normal breast tissue...
February 10, 2019: Applied Optics
Jiahao Lin, Lie Ma, Di Zhang, Jiafeng Gao, Yipeng Jin, Zhihai Han, Degui Lin
In recent years, with the increase in cancer mortality caused by metastasis, and with the development of individualized and precise medical treatment, early diagnosis with precision becomes the key to decrease the death rate. Since detecting tumour biomarkers in body fluids is the most non-invasive way to identify the status of tumour development, it has been widely investigated for the usage in clinic. These biomarkers include different expression or mutation in microRNAs (miRNAs), circulating tumour DNAs (ctDNAs), proteins, exosomes and circulating tumour cells (CTCs)...
March 14, 2019: Cell Proliferation
Laura Follia, Giulio Ferrero, Giorgia Mandili, Marco Beccuti, Daniele Giordano, Rosella Spadi, Maria Antonietta Satolli, Andrea Evangelista, Hiroyuki Katayama, Wang Hong, Amin A Momin, Michela Capello, Samir M Hanash, Francesco Novelli, Francesca Cordero
Background: Most of the patients with Pancreatic Ductal Adenocarcinoma (PDA) are not eligible for a curative surgical resection. For this reason there is an urgent need for personalized therapies. PDA is the result of complex interactions between tumor molecular profile and metabolites produced by its microenvironment. Despite recent studies identified PDA molecular subtypes, its metabolic classification is still lacking. Methods: We applied an integrative analysis on transcriptomic and genomic data of glycolytic genes in PDA...
2019: Frontiers in Oncology
Ling Hao, Yatao Shi, Samuel Thomas, Chad M Vezina, Sagar Bajpai, Arya Ashok, Charles J Bieberich, William A Ricke, Lingjun Li
Dysfunction of the lower urinary tract commonly afflicts the middle-aged and aging male population. The etiology of lower urinary tract symptoms (LUTS) is multifactorial. Benign prostate hyperplasia, fibrosis, smooth muscle contractility, and inflammation likely contribute. Here we aim to characterize the urinary metabolomic profile associated with prostatic inflammation, which could inform future personalized diagnosis or treatment, as well as mechanistic research. Quantitative urinary metabolomics was conducted to examine molecular changes following induction of inflammation via conditional Interleukin-1β expression in prostate epithelia using a novel transgenic mouse strain...
November 2018: International Journal of Mass Spectrometry
Scott P Morton, Julie B Phillips, Joshua L Phillips
Decades of research has yet to provide a vaccine for HIV, the virus which causes AIDS. Recent theoretical research has turned attention to mucosa pH levels over systemic pH levels. Previous research in this field developed a computational approach for determining pH sensitivity that indicated higher potential for transmission at mucosa pH levels present during intercourse. The process was extended to incorporate a principal component analysis (PCA)-based machine learning technique for classification of gp120 proteins against a known transmitted variant called Biomolecular Electro-Static Indexing (BESI)...
2019: Evolutionary Bioinformatics Online
Roby P Bhattacharyya, Mark Walker, Rich Boykin, Sophie S Son, Jamin Liu, Austin C Hachey, Peijun Ma, Lidan Wu, Kyungyong Choi, Kaelyn C Cummins, Maura Benson, Jennifer Skerry, Hyunryul Ryu, Sharon Y Wong, Marcia B Goldberg, Jongyoon Han, Virginia M Pierce, Lisa A Cosimi, Noam Shoresh, Jonathan Livny, Joseph Beechem, Deborah T Hung
Rapid bacterial identification remains a critical challenge in infectious disease diagnostics. We developed a novel molecular approach to detect and identify a wide diversity of bacterial pathogens in a single, simple assay, exploiting the conservation, abundance, and rich phylogenetic content of ribosomal RNA in a rapid fluorescent hybridization assay that requires no amplification or enzymology. Of 117 isolates from 64 species across 4 phyla, this assay identified bacteria with >89% accuracy at the species level and 100% accuracy at the family level, enabling all critical clinical distinctions...
March 14, 2019: Scientific Reports
Pu Liu, Yue Zou, Jiangan Hou, Steven L Stephenson, Yu Li
BACKGROUND: Dictyostelid cellular slime molds (dictyostelids) are microscopic throughout their entire life cycle. The vegetative phase consists of single-celled amoeboid forms which live in the soil/leaf litter microhabitat of fields and forests along with animal dung, where they feed upon bacteria and other microbes, grow, and multiply until the available food supply is exhausted. When this happens, the amoeboid forms aggregate together in large numbers to form multi-celled pseudoplasmodia, which then give rise to fruiting bodies (sorocarps) that consist of supportive stalks and unwalled sori containing propagative spores...
March 14, 2019: BMC Evolutionary Biology
Sujoy Roy, Kazi I Zaman, Robert W Williams, Ramin Homayouni
BACKGROUND: Gene co-expression studies can provide important insights into molecular and cellular signaling pathways. The GeneNetwork database is a unique resource for co-expression analysis using data from a variety of tissues across genetically distinct inbred mice. However, extraction of biologically meaningful co-expressed gene sets is challenging due to variability in microarray platforms, probe quality, normalization methods, and confounding biological factors. In this study, we tested whether literature derived functional cohesion could be used as an objective metric in lieu of 'ground truth' to evaluate the quality of probes and microarray datasets...
March 14, 2019: BMC Bioinformatics
Anna Puiggalí-Jou, Luis J Del Valle, Carlos Alemán
Molecular sensing, water purification and desalination, drug delivery, and DNA sequencing are some striking applications of biomimetic hybrid membranes. These devices take advantage of biomolecules, which have gained excellence in their specificity and efficiency during billions of years, and of artificial materials that load the purified biological molecules and provide technological properties, such as robustness, scalability, and suitable nanofeatures to confine the biomolecules. Recent methodological advances allow more precise control of polymer membranes that support the biomacromolecules, and are expected to improve the design of the next generation of membranes as well as their applicability...
March 14, 2019: Soft Matter
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