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https://www.readbyqxmd.com/read/29146883/a-landscape-of-germline-mutations-in-a-cohort-of-inherited-bone-marrow-failure-patients
#1
Olivier Bluteau, Marie Sebert, Thierry Leblanc, Régis Peffault de Latour, Samuel Quentin, Elodie Lainey, Lucie Hernandez, Jean-Hugues Dalle, Flore Sicre de Fontbrune, Etienne Lengline, Raphael Itzykson, Emmanuelle Clappier, Nicolas Boissel, Naddia Vasquez, Mélanie Da Costa, Julien Masliah-Planchon, Wendy Cuccuini, Anna Raimbault, Louis De Jaegere, Lionel Adès, Pierre Fenaux, Sébastien Maury, Claudine Schmitt, Marc Muller, Carine Domenech, Nicolas Blin, Bénédicte Bruno, Isabelle Pellier, Mathilde Hunault, Stéphane Blanche, Arnaud Petit, Guy Leverger, Gérard Michel, Yves Bertrand, André Baruchel, Gérard Socié, Jean Soulier
Bone marrow failure (BMF) in children and young adults is often suspected to be inherited, but in many cases diagnosis remains uncertain. We studied a cohort of 179 patients (from 173 families) with BMF of suspected inherited origin but unresolved diagnosis after medical evaluation and Fanconi anemia exclusion. All patients had cytopenias, and 12.0% presented ≥5% bone marrow blast cells. Median age at genetic evaluation was 11 years; 20.7% of patients were aged ≤2 years and 36.9% were ≥18 years. We analyzed genomic DNA from skin fibroblasts using whole-exome sequencing, and were able to assign a causal or likely causal germline mutation in 86 patients (48...
November 16, 2017: Blood
https://www.readbyqxmd.com/read/29146193/detection-of-relationships-among-multi-modal-brain-imaging-meta-features-via-information-flow
#2
Robyn L Miller, Victor M Vergara, Vince D Calhoun
BACKGROUND: Neuroscientists and clinical researchers are awash in data from an ever-growing number of imaging and other bio-behavioral modalities. This flow of brain imaging data, taken under resting and various task conditions, combines with available cognitive measures, behavioral information, genetic data plus other potentially salient biomedical and environmental information to create a rich but diffuse data landscape. The conditions being studied with brain imaging data are often extremely complex and it is common for researchers to employ more than one imaging, behavioral or biological data modality (e...
November 13, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/29144541/genetic-landscape-of-papillary-thyroid-carcinoma-in-the-chinese-population
#3
Jialong Liang, Wanshi Cai, Dongdong Feng, Huajing Teng, Fengbiao Mao, Yi Jiang, Shanshan Hu, Xianfeng Li, Yujie Zhang, Baoguo Liu, Zhong Sheng Sun
Improvement in the clinical outcome of human cancers requires characterization of genetic alterations underlying their pathogenesis. Large-scale genomic and transcriptomic characterization of papillary thyroid carcinomas (PTCs) in Western populations has revealed multiple oncogenic drivers which are essential for understanding pathogenic mechanisms of this disease; while so far, the genetic landscape in Chinese patients with PTC remains uncharacterized. Here, we conducted a largescale genetic analysis of PTCs from patients in China to determine the mutational landscape of this cancer...
November 16, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29143176/the-treatment-landscape-and-new-opportunities-of-molecular-targeted-therapies-in-gastroenteropancreatic-neuroendocrine-tumors
#4
REVIEW
Fabiola Amair-Pinedo, Ignacio Matos, Tamara Saurí, Jorge Hernando, Jaume Capdevila
Neuroendocrine neoplasms (NENs) are a heterogeneous group of neoplasms that originate from neuroendocrine stem cells and express both neural and endocrine markers. They are found in almost every organ, and while NENs are mostly associated with slow growth, complications due to the uncontrolled secretion of active peptides, and metastatic disease, may significantly impair the quality of life and can ultimately lead to the death of affected individuals. Expanding knowledge of the genetic, epigenetic, and proteomic landscapes of NENs has led to a better understanding of their molecular pathology and consequently increased treatment options for patients...
November 15, 2017: Targeted Oncology
https://www.readbyqxmd.com/read/29141960/rapid-molecular-assays-to-study-human-centromere-genomics
#5
Rafael Contreras-Galindo, Sabrina Fischer, Anjan K Saha, John D Lundy, Patrick W Cervantes, Mohamad Mourad, Claire Wang, Brian Qian, Manhong Dai, Fan Meng, Arul Chinnaiyan, Gilbert S Omenn, Mark H Kaplan, David M Markovitz
The centromere is the structural unit responsible for the faithful segregation of chromosomes. Although regulation of centromeric function by epigenetic factors has been well-studied, the contributions of the underlying DNA sequences have been much less well defined, and existing methodologies for studying centromere genomics in biology are laborious. We have identified specific markers in the centromere of 23 of the 24 human chromosomes that allow for rapid PCR assays capable of capturing the genomic landscape of human centromeres at a given time...
November 15, 2017: Genome Research
https://www.readbyqxmd.com/read/29138459/the-genomic-landscape-of-nepalese-tibeto-burmans-reveals-new-insights-into-the-recent-peopling-of-southern-himalayas
#6
Guido A Gnecchi-Ruscone, Choongwon Jeong, Sara De Fanti, Stefania Sarno, Michela Trancucci, Davide Gentilini, Anna M Di Blasio, Mingma G Sherpa, Phurba T Sherpa, Giorgio Marinelli, Marco Di Marcello, Luca Natali, Davide Peluzzi, Davide Pettener, Anna Di Rienzo, Donata Luiselli, Marco Sazzini
While much research attention has focused on demographic processes that enabled human diffusion on the Tibetan plateau, little is known about more recent colonization of Southern Himalayas. In particular, the history of migrations, admixture and/or isolation of populations speaking Tibeto-Burman languages, which is supposed to be quite complex and to have reshaped patterns of genetic variation on both sides of the Himalayan arc, remains only partially elucidated. We thus described the genomic landscape of previously unsurveyed Tibeto-Burman (i...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138394/critical-mutation-rate-has-an-exponential-dependence-on-population-size-for-eukaryotic-length-genomes-with-crossover
#7
Elizabeth Aston, Alastair Channon, Roman V Belavkin, Danna R Gifford, Rok Krašovec, Christopher G Knight
The critical mutation rate (CMR) determines the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness ("flattest"). We identify an inverse relationship between CMR and sequence length in an in silico system with a two-peak fitness landscape; CMR decreases to no more than five orders of magnitude above estimates of eukaryotic per base mutation rate. We confirm the CMR reduces exponentially at low population sizes, irrespective of peak radius and distance, and increases with the number of genetic crossovers...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138304/refactoring-the-genetic-code-for-increased-evolvability
#8
Gur Pines, James D Winkler, Assaf Pines, Ryan T Gill
The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29136202/a-conceptual-framework-for-cell-identity-transitions-in-plants
#9
Idan Efroni
Multicellular organisms develop from a single cell that proliferates to form different cell types with specialized functions. Sixty years ago, Waddington's suggested the "epigenetic landscape" as a useful metaphor for the process. According to this view, cells move through a rugged identity space along genetically-encoded trajectories, until arriving at one of possible final fates. In plants in particular, these trajectories also have strong spatial correlates, as cell identity is intimately linked to its relative position within the plant...
November 9, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29134741/contemporary-evolution-of-a-lepidopteran-species-heliothis-virescens-in-response-to-modern-agricultural-practices
#10
Megan L Fritz, Alexandra M DeYonke, Alexie Papanicolaou, Stephen Micinski, John Westbrook, Fred Gould
Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve: 1) shifts in host plant selection mechanisms to avoid cotton, 2) changes in detoxification mechanisms required for cotton-feeding versus feeding on other hosts, or 3) loss of resistance to previously used management practices including insecticides...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29132555/considerations-in-testing-for-inherited-breast-cancer-predisposition-in-the-era-of-personalized-medicine
#11
REVIEW
Benjamin Powers, Tuya Pal, Christine Laronga
Technological advances realized through next-generation sequencing technologies coupled with the loss of the ability to patent genes have led to reduction in costs for genetic testing. As a result, more people are being identified with inherited breast cancer syndromes that may affect recommendations for surveillance and risk reduction. Surgeons, at the forefront for patients newly diagnosed with breast cancer, must keep current with the changing landscape of genetics to continue to provide appropriate counsel and care...
January 2018: Surgical Oncology Clinics of North America
https://www.readbyqxmd.com/read/29132298/population-genetic-structure-is-shaped-by-historical-geographic-and-environmental-factors-in-the-leguminous-shrub-caragana-microphylla-on-the-inner-mongolia-plateau-of-china
#12
Bo Xu, Guoli Sun, Xuemin Wang, Jingwei Lu, Ian J Wang, Zan Wang
BACKGROUND: Understanding how landscape factors, including suites of geographic and environmental variables, and both historical and contemporary ecological and evolutionary processes shape the distribution of genetic diversity is a primary goal of landscape and conservation genetics and may be particularly consequential for species involved in ecological restoration. In this study, we examine the factors that shape the distribution of genetic variation in a leguminous shrub (Caragana microphylla) important for restoration efforts on the Mongolian Plateau in China...
November 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29131160/human-primary-liver-cancer-derived-organoid-cultures-for-disease-modeling-and-drug-screening
#13
Laura Broutier, Gianmarco Mastrogiovanni, Monique Ma Verstegen, Hayley E Francies, Lena Morrill Gavarró, Charles R Bradshaw, George E Allen, Robert Arnes-Benito, Olga Sidorova, Marcia P Gaspersz, Nikitas Georgakopoulos, Bon-Kyoung Koo, Sabine Dietmann, Susan E Davies, Raaj K Praseedom, Ruby Lieshout, Jan N M IJzermans, Stephen J Wigmore, Kourosh Saeb-Parsy, Mathew J Garnett, Luc Jw van der Laan, Meritxell Huch
Human liver cancer research currently lacks in vitro models that can faithfully recapitulate the pathophysiology of the original tumor. We recently described a novel, near-physiological organoid culture system, wherein primary human healthy liver cells form long-term expanding organoids that retain liver tissue function and genetic stability. Here we extend this culture system to the propagation of primary liver cancer (PLC) organoids from three of the most common PLC subtypes: hepatocellular carcinoma (HCC), cholangiocarcinoma (CC) and combined HCC/CC (CHC) tumors...
November 13, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29130200/padlock-probes-to-detect-single-nucleotide-polymorphisms
#14
Tomasz Krzywkowski, Mats Nilsson
Rapid development of high-throughput DNA analyzation methods has enabled global characterization of genetic landscapes and aberrations in study subjects in a time and cost effective fashion. In most methods, however, spatial tissue context is lost since sample preparation requires isolation of nucleic acids out of their native environment. We hereby present the most recent protocol for multiplexed, in situ detection of mRNAs and single nucleotide polymorphisms using padlock probes and rolling circle amplification...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29128937/epigenetics-in-diabetic-nephropathy-immunity-and-metabolism
#15
REVIEW
Samuel T Keating, Janna A van Diepen, Niels P Riksen, Assam El-Osta
When it comes to the epigenome, there is a fine line between clarity and confusion-walk that line and you will discover another fascinating level of transcription control. With the genetic code representing the cornerstone of rules for information that is encoded to proteins somewhere above the genome level there is a set of rules by which chemical information is also read. These epigenetic modifications show a different side of the genetic code that is diverse and regulated, hence modifying genetic transcription transiently, ranging from short- to long-term alterations...
November 11, 2017: Diabetologia
https://www.readbyqxmd.com/read/29128259/role-of-dysregulated-cytokine-signaling-and-bacterial-triggers-in-the-pathogenesis-of-cutaneous-t-cell-lymphoma
#16
Melania H Fanok, Amy Sun, Laura K Fogli, Vijay Narendran, Miriam Eckstein, Kasthuri Kannan, Igor Dolgalev, Charalampos Lazaris, Adriana Heguy, Mary E Laird, Mark S Sundrud, Cynthia Liu, Jeff Kutok, Rodrigo S Lacruz, Jo-Ann Latkowski, Iannis Aifantis, Niels Ødum, Kenneth B Hymes, Swati Goel, Sergei B Koralov
Cutaneous T cell lymphoma is a heterogeneous group of lymphomas characterized by the accumulation of malignant T cells in the skin. The molecular and cellular etiology of this malignancy remains enigmatic and what role antigenic stimulation plays in the initiation and/or progression of the disease remains to be elucidated. Deep sequencing of the tumor genome revealed a highly heterogeneous landscape of genetic perturbations and transcriptome analysis of transformed T cells further highlighted the heterogeneity of this disease...
November 8, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29127217/adding-landscape-genetics-and-individual-traits-to-the-ecosystem-function-paradigm-reveals-the-importance-of-species-functional-breadth
#17
Antonio R Castilla, Nathaniel S Pope, Megan O'Connell, María F Rodriguez, Laurel Treviño, Alonso Santos, Shalene Jha
Animal pollination mediates both reproduction and gene flow for the majority of plant species across the globe. However, past functional studies have focused largely on seed production; although useful, this focus on seed set does not provide information regarding species-specific contributions to pollen-mediated gene flow. Here we quantify pollen dispersal for individual pollinator species across more than 690 ha of tropical forest. Specifically, we examine visitation, seed production, and pollen-dispersal ability for the entire pollinator community of a common tropical tree using a series of individual-based pollinator-exclusion experiments followed by molecular-based fractional paternity analyses...
November 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29126208/influence-of-range-position-on-locally-adaptive-gene-environment-associations-in-populus-flowering-time-genes
#18
Stephen R Keller, Vikram E Chhatre, Matthew C Fitzpatrick
Local adaptation is pervasive in forest trees, which are characterized by large effective population sizes spanning broad climatic gradients. In addition to having relatively contiguous populations, many species also form isolated populations along the rear edge of their range. These rear-edge populations may contain unique adaptive diversity reflecting a history of selection in marginal environments. Thus, discovering genomic regions conferring local adaptation in rear edge populations is a key priority for landscape genomics to ensure conservation of genetic resources under climate change...
November 8, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29123967/ionizing-radiation-sensitizes-tumors-to-pd-l1-immune-checkpoint-blockade-in-orthotopic-murine-head-and-neck-squamous-cell-carcinoma
#19
Ayman Oweida, Shelby Lennon, Dylan Calame, Sean Korpela, Shilpa Bhatia, Jaspreet Sharma, Caleb Graham, David Binder, Natalie Serkova, David Raben, Lynn Heasley, Eric Clambey, Raphael Nemenoff, Sana D Karam
Immunotherapy clinical trials targeting the programmed-death ligand axis (PD-1/PD-L1) show that most head and neck squamous cell carcinoma (HNSCC) patients are resistant to PD-1/PD-L1 inhibition. We investigated whether local radiation to the tumor can transform the immune landscape and render poorly immunogenic HNSCC tumors sensitive to PD-L1 inhibition. We used the first novel orthotopic model of HNSCC with genetically distinct murine cell lines. Tumors were resistant to PD-L1 checkpoint blockade, harbored minimal PD-L1 expression and tumor infiltrating lymphocytes at baseline, and were resistant to radiotherapy...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29123614/the-roles-of-ros-in-cancer-heterogeneity-and-therapy
#20
REVIEW
Paulo Luiz de Sá Junior, Diana Aparecida Dias Câmara, Allan Saj Porcacchia, Pâmela Maria Moreira Fonseca, Salomão Doria Jorge, Rodrigo Pinheiro Araldi, Adilson Kleber Ferreira
Cancer comprises a group of heterogeneous diseases encompassing high rates of morbidity and mortality. Heterogeneity, which is a hallmark of cancer, is one of the main factors related to resistance to chemotherapeutic agents leading to poor prognosis. Heterogeneity is profoundly affected by increasing levels of ROS. Under low concentrations, ROS may function as signaling molecules favoring tumorigenesis and heterogeneity, while under high ROS concentrations, these species may work as cancer modulators due to their deleterious, genotoxic or even proapoptotic effect on cancer cells...
2017: Oxidative Medicine and Cellular Longevity
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