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https://www.readbyqxmd.com/read/28550183/somatic-mutation-spectrum-in-monoclonal-gammopathy-of-undetermined-significance-indicates-a-less-complex-genomic-landscape-compared-to-multiple-myeloma
#1
Aneta Mikulasova, Christopher P Wardell, Alexander Murison, Eileen M Boyle, Graham H Jackson, Jan Smetana, Zuzana Kufova, Ludek Pour, Viera Sandecka, Martina Almasi, Pavla Vsianska, Evzen Gregora, Petr Kuglik, Roman Hajek, Faith E Davies, Gareth J Morgan, Brian A Walker
Monoclonal gammopathy of undetermined significance (MGUS) is a premalignant precursor of multiple myeloma with a 1% risk of progression per year. Although targeted analyses have shown the presence of specific genetic abnormalities such as IGH translocations, RB1 deletion, 1q gain, hyperdiploidy or RAS genes mutations, little is known about the molecular mechanism of malignant transformation. We have performed whole exome sequencing together with CGH+SNP array analysis in 33 flow-cytometry separated abnormal plasma cell samples from MGUS patients to describe somatic gene mutations and chromosome changes at the genome-wide level...
May 26, 2017: Haematologica
https://www.readbyqxmd.com/read/28550046/genome-instability-a-conserved-mechanism-of-ageing
#2
REVIEW
Jan Vijg, Xiao Dong, Brandon Milholland, Lei Zhang
DNA is the carrier of genetic information and the primary template from which all cellular information is ultimately derived. Changes in the DNA information content through mutation generate diversity for evolution through natural selection but are also a source of deleterious effects. It has since long been hypothesized that mutation accumulation in somatic cells of multicellular organisms could causally contribute to age-related cellular degeneration and death. Assays to detect different types of mutations, from base substitutions to large chromosomal aberrations, have been developed and show unequivocally that mutations accumulate in different tissues and cell types of ageing humans and animals...
May 26, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/28548104/genomic-analysis-of-oesophageal-squamous-cell-carcinoma-identifies-alcohol-drinking-related-mutation-signature-and-genomic-alterations
#3
Jiang Chang, Wenle Tan, Zhiqiang Ling, Ruibin Xi, Mingming Shao, Mengjie Chen, Yingying Luo, Yanjie Zhao, Yun Liu, Xiancong Huang, Yuchao Xia, Jinlin Hu, Joel S Parker, David Marron, Qionghua Cui, Linna Peng, Jiahui Chu, Hongmin Li, Zhongli Du, Yaling Han, Wen Tan, Zhihua Liu, Qimin Zhan, Yun Li, Weimin Mao, Chen Wu, Dongxin Lin
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28546842/opportunities-and-challenges-for-the-sustainable-production-of-structurally-complex-diterpenoids-in-recombinant-microbial-systems
#4
REVIEW
Katarina Kemper, Max Hirte, Markus Reinbold, Monika Fuchs, Thomas Brück
With over 50.000 identified compounds terpenes are the largest and most structurally diverse group of natural products. They are ubiquitous in bacteria, plants, animals and fungi, conducting several biological functions such as cell wall components or defense mechanisms. Industrial applications entail among others pharmaceuticals, food additives, vitamins, fragrances, fuels and fuel additives. Central building blocks of all terpenes are the isoprenoid compounds isopentenyl diphosphate and dimethylallyl diphosphate...
2017: Beilstein Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28542345/ancient-mtdna-diversity-reveals-specific-population-development-of-wild-horses-in-switzerland-after-the-last-glacial-maximum
#5
Julia Elsner, Michael Hofreiter, Jörg Schibler, Angela Schlumbaum
On large geographical scales, changes in animal population distribution and abundance are driven by environmental change due to climatic and anthropogenic processes. However, so far, little is known about population dynamics on a regional scale. We have investigated 92 archaeological horse remains from nine sites mainly adjacent to the Swiss Jura Mountains dating from c. 41,000-5,000 years BP. The time frame includes major environmental turning points such as the Last Glacial Maximum (LGM), followed by steppe vegetation, afforestation and initial re-opening of the landscape by human agricultural activities...
2017: PloS One
https://www.readbyqxmd.com/read/28540598/parp-inhibitors-in-prostate-cancer
#6
REVIEW
Praveen Ramakrishnan Geethakumari, Matthew J Schiewer, Karen E Knudsen, Wm Kevin Kelly
The genomic landscape of metastatic prostate cancer (mPCa) reveals that up to 90% of patients harbor actionable mutations and >20% have somatic DNA repair gene defects (DRD). This provides the therapeutic rationale of PARP inhibition (PARPi) to achieve "synthetic lethality" in treating this fatal disease. Clinical trials with PARP inhibitors have shown significant response rates up to 88% for PCa patients having DRD like BRCA1/2 or ATM mutations. The FDA has awarded "breakthrough designation" to develop the PARPi olaparib in treating this subset of metastatic PCa patients...
June 2017: Current Treatment Options in Oncology
https://www.readbyqxmd.com/read/28538662/maternal-factors-that-induce-epigenetic-changes-contribute-to-neurological-disorders-in-offspring
#7
REVIEW
Avijit Banik, Deepika Kandilya, Seshadri Ramya, Walter Stünkel, Yap Seng Chong, S Thameem Dheen
It is well established that the regulation of epigenetic factors, including chromatic reorganization, histone modifications, DNA methylation, and miRNA regulation, is critical for the normal development and functioning of the human brain. There are a number of maternal factors influencing epigenetic pathways such as lifestyle, including diet, alcohol consumption, and smoking, as well as age and infections (viral or bacterial). Genetic and metabolic alterations such as obesity, gestational diabetes mellitus (GDM), and thyroidism alter epigenetic mechanisms, thereby contributing to neurodevelopmental disorders (NDs) such as embryonic neural tube defects (NTDs), autism, Down's syndrome, Rett syndrome, and later onset of neuropsychological deficits...
May 24, 2017: Genes
https://www.readbyqxmd.com/read/28536306/chronic-lymphocytic-leukemia-with-mutated-ighv4-34-receptors-shared-and-distinct-immunogenetic-features-and-clinical-outcomes
#8
Aliki Xochelli, Panagiotis Baliakas, Ioannis Kavakiotis, Andreas Agathangelidis, Lesley-Ann Sutton, Eva Minga, Stavroula Ntoufa, Eugen Tausch, Xiao-Jie Yan, Tait D Shanafelt, Karla Plevova, Myriam Boudjogra, Davide Rossi, Zadie Davis, Alba Navarro, Yorick Sandberg, Fie Juhl Vojdeman, Lydia Scarfò, Niki Stavroyianni, Andrey Sudarikov, Silvio Veronese, Tatiana Tzenou, Teodora Karan Djurasevic, Mark A Catherwood, Dirk Kienle, Maria Chatzouli, Monica Facco, Jasmin Bahlo, Christiane Pott, Lone Bredo Pedersen, Larry Mansouri, Karin E Smedby, Charles C Chu, Véronique Giudicelli, Marie-Paule Lefranc, Panagiotis Panagiotidis, Gunnar Juliusson, Achilles Anagnostopoulos, Ioannis Vlahavas, Darko Antic, Livio Trentin, Marco Montillo, Carsten U Niemann, Hartmut Dohner, Anton W Langerak, Sarka Pospisilova, Michael Hallek, Elias Campo, Nicholas- Chiorazzi, Nikos Maglaveras, David Oscier, Gianluca Gaidano, Diane F Jelinek, Stephan Stilgenbauer, Ioanna Chouvarda, Nikos Darzentas, Chrysoula Belessi, Frédéric Davi, Anastasia Hadzidimitriou, Richard Rosenquist, Paolo Ghia, Kostas Stamatopoulos
We sought to investigate if B cell receptor immunoglobulin (BcR IG) stereotypy is associated with particular clinicobiological features amongst chronic lymphocytic leukemia (CLL) patients expressing mutated BcR IG (M-CLL) encoded by the IGHV4-34 gene, and also ascertain whether these associations could refine prognostication.<br /> <p>Experimental Design: In a series of 19,907 CLL cases with available immunogenetic information, we identified 339 IGHV4-34 expressing cases assigned to one of the four largest stereotyped M-CLL subsets, namely subsets #4, #16, #29 and #201, and investigated in detail their clinicobiological characteristics and disease outcomes...
May 23, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28535939/gene-expression-profiling-of-large-cell-lung-cancer-links-transcriptional-phenotypes-to-the-new-histological-who2015-classification
#9
Anna Karlsson, Hans Brunnström, Patrick Micke, Srinivas Veerla, Johanna Mattsson, Linnea La Fleur, Johan Botling, Mats Jönsson, Christel Reuterswärd, Maria Planck, Johan Staaf
INTRODUCTION: Large cell carcinoma with or without neuroendocrine features (LCNEC and LC, respectively) constitutes a small proportion of non-small cell lung cancer (NSCLC). The WHO2015 classification guidelines changed the definition of the debated histological subtype LC to be based on immunomarkers for adenocarcinoma and squamous cancer. We sought to determine if these new guidelines translate also to the transcriptional landscape of lung cancer, and LC specifically. METHODS: Gene expression profiling was performed using Illumina V4 HT12 microarrays on 159 cases (comprising all histological subtypes including 10 WHO2015 LC and 14 LCNEC tumors), with complimentary mutational and IHC data...
May 20, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28534435/genome-editing-technologies-and-patent-landscape-overview
#10
Fairouz Benahmed-Miniuk, Mat Kresz, Jitendra K Kanaujiya, Christopher D Southgate
Unlike with zinc finger nuclease and transcriptional activator-like effector nuclease DNA modification technologies that rely on lead proteins, developed through expensive and time-consuming processes, the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system has rapidly emerged as the most promising gene-editing technology to date for the modification of any selected DNA sequence. CRISPR is receiving tremendous fanfare due, in part, to its potential to provide a means to fundamentally alter medical genetics and especially cancer medicine...
May 23, 2017: Pharmaceutical Patent Analyst
https://www.readbyqxmd.com/read/28530655/a-quantitative-and-multiplexed-approach-to-uncover-the-fitness-landscape-of-tumor-suppression-in-vivo
#11
Zoë N Rogers, Christopher D McFarland, Ian P Winters, Santiago Naranjo, Chen-Hua Chuang, Dmitri Petrov, Monte M Winslow
Cancer growth is a multistage, stochastic evolutionary process. While cancer genome sequencing has been instrumental in identifying the genomic alterations that occur in human tumors, the consequences of these alterations on tumor growth remain largely unexplored. Conventional genetically engineered mouse models enable the study of tumor growth in vivo, but they are neither readily scalable nor sufficiently quantitative to unravel the magnitude and mode of action of many tumor-suppressor genes. Here, we present a method that integrates tumor barcoding with ultradeep barcode sequencing (Tuba-seq) to interrogate tumor-suppressor function in mouse models of human cancer...
May 22, 2017: Nature Methods
https://www.readbyqxmd.com/read/28530509/genotyping-toxoplasma-gondii-with-the-b1-gene-in-naturally-infected-sheep-from-an-endemic-region-in-the-pacific-coast-of-mexico
#12
Williams Arony Martínez-Flores, José Manuel Palma-García, Heriberto Caballero-Ortega, Alejandra Del Viento-Camacho, Eduardo López-Escamilla, Fernando Martínez-Hernández, Pablo Vinuesa, Dolores Correa, Pablo Maravilla
Toxoplasma gondii is a protozoan parasite with a broad ecological valence, which has been detected in a wide range of hosts and landscapes. Although the genus is considered monospecific, in recent years it has been demonstrated to exhibit more genetic variability than previously known. In Mexico, there are few genotyping studies, which suggest that classical, autochthonous, and atypical strains are circulating. The goal of this study was to describe T. gondii genetic diversity in naturally infected sheep from Colima, Mexico...
May 22, 2017: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/28529228/-the-absence-doubled-photo-poetic-narratives-of-prophylactic-mastectomy
#13
Stella Bolaki
This essay considers Clare Best's poetic sequence Self-portrait without Breasts (2011) and her collaboration with photographer Laura Stevens, which explore preventive surgery and questions of genetics/hereditary breast cancer. In an era when risk and cosmetic reconstruction guide treatment and the development of new breast cancer subjects, Best reclaims the "flat simple scarred chest with no extras." I situate her poems in the context of statistics and the neoliberal postfeminist subject as well as in a poetic tradition about the post-mastectomy body as landscape...
2017: Literature and Medicine
https://www.readbyqxmd.com/read/28528024/structure-diverse-phylomer-libraries-as-a-rich-source-of-bioactive-hits-from-phenotypic-and-target-directed-screens-against-intracellular-proteins
#14
REVIEW
Paul M Watt, Nadia Milech, Shane R Stone
Phylomers are peptides derived from biodiverse protein fragments. Genetically encoded Phylomer libraries have been constructed, containing hundreds of billions of peptides derived from virtually all of the few thousand fold families found in the protein universe. They offer a rich source of high quality hits against diverse target sequences and have been used for three main purposes: firstly, to identify and validate targets in phenotypic screens; secondly, to block protein interactions with nanomolar potency binding affinities; thirdly as a source of more efficient cell penetrating peptides for the delivery of a wide range of biologics...
May 18, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28526922/advances-in-systemic-therapy-for-metastatic-breast-cancer-future-perspectives
#15
REVIEW
S P Corona, N Sobhani, A Ianza, G Roviello, G Mustacchi, M Bortul, F Zanconati, D Generali
Breast cancer (BC) is the most common cancer in women worldwide. One in eight women will develop the disease in her lifetime. Notwithstanding the incredible progress made in this field, BC still represents the second most common cause of cancer-related death in women. Targeted drugs have revolutionised breast cancer treatment and improved the prognosis as well as the life expectancy of millions of women. However, the phenomenon of primary and secondary pharmacological resistance is becoming increasingly evident, limiting the efficacy of these agents and calling for a better in-depth knowledge and understanding of the biology as well as the biochemical crosstalk underlying the disease...
July 2017: Medical Oncology
https://www.readbyqxmd.com/read/28525307/exploiting-genetic-information-to-trace-plant-virus-dispersal-in-landscapes
#16
Coralie Picard, Sylvie Dallot, Kirstyn Brunker, Karine Berthier, Phillipe Roumagnac, Samuel Soubeyrand, Emmanuel Jacquot, Gaël Thébaud
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology...
May 19, 2017: Annual Review of Phytopathology
https://www.readbyqxmd.com/read/28524737/utilizing-next-generation-sequencing-in-the-management-of-multiple-myeloma
#17
Marta Lionetti, Antonino Neri
Multiple myeloma (MM) is a bone marrow plasma cell malignancy characterized by wide clinical presentation and heterogeneous genetic background. Despite the recent advances in patient outcome, new markers are needed for improving risk prediction and choice of a more appropriate therapy. In this perspective, the genetic makeup of MM cells is being better characterized by means of next-generation sequencing (NGS) technologies. Areas covered: The authors discuss how the application of NGS has improved our knowledge of MM biology by discovering its mutational landscape, identifying the operating mutational processes, and revealing the clonal composition of tumors and the dynamics of its evolution; and how this can have important clinical implications in terms of prognostication, therapeutic choices, and response assessment...
May 26, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28524624/pulmonary-arterial-hypertension-progress-in-understanding-the-disease-and-prioritizing-strategies-for-drug-development
#18
REVIEW
P Ghataorhe, C J Rhodes, L Harbaum, M Attard, J Wharton, M R Wilkins
Pulmonary arterial hypertension (PAH), at one time a largely overlooked disease, is now the subject of intense study in many academic and biotech groups. The availability of new treatments has increased awareness of the condition. This in turn has driven a change in the demographics of PAH, with an increase in the mean age at diagnosis. The diagnosis of PAH in more elderly patients has highlighted the need for careful phenotyping of patients and for further studies to understand how best to manage pulmonary hypertension associated with, for example, left heart disease...
May 19, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28523791/genetic-assessment-of-the-effects-of-streamscape-succession-on-coho-salmon-oncorhynchus-kisutch-colonization-in-recently-deglaciated-streams
#19
K T Scribner, C Soiseth, J McGuire, G K Sage, L Thorsteinson, J L Nielsen, E Knudsen
Measures of genetic diversity within and among populations and historical geomorphological data on stream landscapes were used in model simulations based on approximate Bayesian computation (ABC) to examine hypotheses of the relative importance of stream features (geomorphology and age) associated with colonization events and gene flow for coho salmon Oncorhynchus kisutch breeding in recently deglaciated streams (50-240 years b.p.) in Glacier Bay National Park (GBNP), Alaska. Population estimates of genetic diversity including heterozygosity and allelic richness declined significantly and monotonically from the oldest and largest to youngest and smallest GBNP streams...
May 19, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28523552/epigenetics-of-huntington-s-disease
#20
Silvia Bassi, Takshashila Tripathi, Alan Monziani, Francesca Di Leva, Marta Biagioli
Huntington's disease (HD) is a genetic, fatal autosomal dominant neurodegenerative disorder typically occurring in midlife with symptoms ranging from chorea, to dementia, to personality disturbances (Philos Trans R Soc Lond Ser B Biol Sci 354:957-961, 1999). HD is inherited in a dominant fashion, and the underlying mutation in all cases is a CAG trinucleotide repeat expansion within exon 1 of the HD gene (Cell 72:971-983, 1993). The expanded CAG repeat, translated into a lengthened glutamine tract at the amino terminus of the huntingtin protein, affects its structural properties and functional activities...
2017: Advances in Experimental Medicine and Biology
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