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Journal articles on the topic 'Mutation spatiale'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 February 2022

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1

Beauregard, Ludger, and Normand Dupont. "La réorganisation spatiale du commerce dans la région métropolitaine de Montréal." Cahiers de géographie du Québec 27, no. 71 (2005): 277–305. http://dx.doi.org/10.7202/021612ar.

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Depuis une trentaine d'années, la géographie du commerce a connu une profonde mutation dans la région de Montréal. Le déploiement des commerces a suivi celui de la population vers la banlieue en s'accompagnant d'une transformation structurelle et spatiale. L'article analyse la nouvelle armature commerciale de la métropole et fait le point sur la concurrence qu'exercent les grands centres commerciaux sur le centre-ville. Il constate un état d'équilibre presque parfait dans la répartition spatiale des supercentres.

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2

Dureau, Françoise, Vincent Gouëset, Guillaume Le Roux, and Thierry Lulle. "Les inégalités d’accès aux ressources urbaines dans des quartiers périphériques en mutation nouvellement desservis par le Transmilenio à Bogotá (Colombie)." Cahiers de géographie du Québec 58, no. 163 (2015): 7–38. http://dx.doi.org/10.7202/1028937ar.

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L’ampleur des changements urbains et de l’amélioration de l’offre de transport dans le secteur de la Calle 80, qui a bénéficié d’une des premières lignes de bus à haut niveau de service construites en Amérique latine, font de ce quartier périphérique de Bogotá un lieu privilégié pour étudier les inégalités d’accès aux ressources urbaines. L’analyse de deux recensements et d’une enquête biographique sur les mobilités spatiales montre que l’accessibilité des habitants aux ressources de la ville est caractérisée par une double évolution. D’un côté, les populations peu mobiles trouvent aujourd’hui

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Marois, Claude. "Étude typologique des migrations nettes au Québec (1961-1966)." Cahiers de géographie du Québec 19, no. 46 (2005): 209–27. http://dx.doi.org/10.7202/021254ar.

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Cette recherche est une étude, à l'échelle du Québec, de la structure du phénomène migratoire avec une emphase sur une typologie spatiale. Le but principal de l'article vise à établir des comparaisons montrant que certains comtés, bien que différents, peuvent provenir d'une structure semblable. Pour ce faire nous avons constitué une matrice permettant d'étudier les caractéristiques pathologiques des aires de refoulement et les conditions ou les éléments constitutifs des zones d'accueil. Cette matrice concerne les conditions socio-démographiques et socio-économiques des comtés vis-à-vis leur po

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Faber, Matthew S., Emily E. Wrenbeck, Laura R. Azouz, Paul J. Steiner, and Timothy A. Whitehead. "Impact of In Vivo Protein Folding Probability on Local Fitness Landscapes." Molecular Biology and Evolution 36, no. 12 (2019): 2764–77. http://dx.doi.org/10.1093/molbev/msz184.

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Abstract It is incompletely understood how biophysical properties like protein stability impact molecular evolution and epistasis. Epistasis is defined as specific when a mutation exclusively influences the phenotypic effect of another mutation, often at physically interacting residues. In contrast, nonspecific epistasis results when a mutation is influenced by a large number of nonlocal mutations. As most mutations are pleiotropic, the in vivo folding probability—governed by basal protein stability—is thought to determine activity-enhancing mutational tolerance, implying that nonspecific epis

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Mithraprabhu, Sridurga, Tiffany Khong, Malarmathy Ramachandran, et al. "Mutational Characterisation and Tracking Disease Progression Using Circulating Cell-Free Tumor DNA in Multiple Myeloma Patients." Blood 128, no. 22 (2016): 3280. http://dx.doi.org/10.1182/blood.v128.22.3280.3280.

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Abstract Background: Multiple myeloma (MM) currently relies on bone marrow (BM) biopsy for mutational characterisation, which does not capture the putative spatial and genetic heterogeneity of this multi-focal disease. Circulating cell-free tumour DNA (ctDNA) is a powerful non-invasive biomarker, which is being utilised to monitor tumor dynamics in a number of cancers. In this study, analysis of peripheral blood plasma (PL) - derived ctDNA and contemporaneously sourced BM MM cells was undertaken to determine if ctDNA can be utilised as an adjunct to BM biopsy for mutational characterisation an

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Ploquin, Anne, Michael Genin, Mohamed Hebbar, et al. "Spatial heterogeneity of KRAS mutations in colorectal cancers: A population-based study in northern France." Journal of Clinical Oncology 37, no. 15_suppl (2019): e15101-e15101. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e15101.

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e15101 Background: Somatic mutations in the KRAS gene are present in about 40% of tumors from colorectal cancer (CRC) patients and are associated with a resistance to anti-EGFR therapies. However, no clinical features have been linked to KRAS mutations in CRC. In this study, we attempted to identify the potential geographical population clusters of KRAS mutations in CRC patients in northern France. Methods: All patients with CRC who were identified to have KRAS mutations performed by pyrosequencing between 2008 and 2014 at the Regional Molecular Biology Platform at Lille University Hospital we

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Legeard, Emmanuel. "Saint-Gilles, Laon, Germigny : Iconologie d'une représentation politique de la Vierge dans le "style 1200"." De Medio Aevo 15, no. 1 (2021): 231–40. http://dx.doi.org/10.5209/dmae.73298.

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Selon le concept énoncé par Carl Schmitt, le critère de démarcation du politique, c'est la discrimination entre l'ami et l'ennemi. Au Moyen Âge, Pierre le Vénérable (1092-1156) fut le premier à concevoir l'Eglise comme une entité spatiale cernée et modelée par contraste avec la personnalité de ses assaillants : Juifs, musulmans et hérétiques. Dès lors, l'Ecclesia se perçoit et s'impose comme une forteresse constamment assiégée, mais illuminée intérieurement par la Sapientia, la lumière intime du Saint-Esprit. Dans le même temps, la "vraie mutation sociale de l'an 1100" (D. Barthélémy) qui a re

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Heong, Valerie, Darwin Tay, Shane Ee Goh, et al. "Whole Exome Sequencing of Multi-Regional Biopsies from Metastatic Lesions to Evaluate Actionable Truncal Mutations Using a Single-Pass Percutaneous Technique." Cancers 12, no. 6 (2020): 1599. http://dx.doi.org/10.3390/cancers12061599.

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We investigate the feasibility of obtaining multiple spatially-separated biopsies from a single lesion to explore intratumor heterogeneity and identify actionable truncal mutations using whole exome sequencing (WES). A single-pass radiologically-guided percutaneous technique was used to obtain four spatially-separated biopsies from a single metastatic lesion. WES was performed to identify putative truncal variants (PTVs), defined as a non-synonymous somatic (NSS) variant present in all four spatially separated biopsies. Actionable truncal mutations—filtered using the FoundationOne panel—were d

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Won Choi, Seung, Yeri Lee, Kayoung Shin, et al. "CBIO-04. MUTATION-SPECIFIC NON-CANONICAL PATHWAY OF PTEN AS A DISTINCT THERAPEUTIC TARGET FOR GLIOBLASTOMA." Neuro-Oncology 22, Supplement_2 (2020): ii16. http://dx.doi.org/10.1093/neuonc/noaa215.064.

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Abstract The dominant-negative effect of PTEN mutation has been described previously, suggesting that aberrant gain of function attributed to mutation might be more disastrous than deletion in respect to malignant potential. In present study, we explored the functional implications of hot spot mutations of PTEN in GBM tumors. Subcellular location of PTEN is important for its distinct function and spatial distribution within the cytoplasm is known to be associated with cellular locomotion. We evaluated the subcellular compartmentalization of different PTEN mutants and found that some PTEN mutan

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KOMAROVA, NATALIA L. "STOCHASTIC MODELING OF LOSS- AND GAIN-OF-FUNCTION MUTATIONS IN CANCER." Mathematical Models and Methods in Applied Sciences 17, supp01 (2007): 1647–73. http://dx.doi.org/10.1142/s021820250700242x.

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Here we review some spatial and non-spatial stochastic methods developed to study the dynamics of cancer progression. We illustrate the methodology with applications to the two most common patterns in cancer initiation and progression: loss-of-function and gain-of-function mutations. An example of a gain-of-function mutation is an activation of an oncogene; for such mutations we are interested in the process of mutant take-over. An example of a loss-of-function mutation is an inactivation of a tumor suppressor gene; for such processes we calculate the rate of production of double-hit mutants.

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Danilenko, Marina, Masood Zaka, Claire Keeling, et al. "MBRS-59. SINGLE-CELL WHOLE-GENOME SEQUENCING DISSECTS INTRA-TUMOURAL GENOMIC HETEROGENEITY AND CLONAL EVOLUTION IN CHILDHOOD MEDULLOBLASTOMA." Neuro-Oncology 22, Supplement_3 (2020): iii408. http://dx.doi.org/10.1093/neuonc/noaa222.563.

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Abstract Medulloblastomas harbor clinically-significant intra-tumoral heterogeneity for key biomarkers (e.g. MYC/MYCN, β-catenin). Recent studies have characterized transcriptional heterogeneity at the single-cell level, however the underlying genomic copy number and mutational architecture remains to be resolved. We therefore sought to establish the intra-tumoural genomic heterogeneity of medulloblastoma at single-cell resolution. Copy number patterns were dissected by whole-genome sequencing in 1024 single cells isolated from multiple distinct tumour regions within 16 snap-frozen medulloblas

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Oldenburg, Anja, Nolwenn Briand, Anita L. Sørensen, et al. "A lipodystrophy-causing lamin A mutant alters conformation and epigenetic regulation of the anti-adipogenic MIR335 locus." Journal of Cell Biology 216, no. 9 (2017): 2731–43. http://dx.doi.org/10.1083/jcb.201701043.

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Mutations in the Lamin A/C (LMNA) gene-encoding nuclear LMNA cause laminopathies, which include partial lipodystrophies associated with metabolic syndromes. The lipodystrophy-associated LMNA p.R482W mutation is known to impair adipogenic differentiation, but the mechanisms involved are unclear. We show in this study that the lamin A p.R482W hot spot mutation prevents adipogenic gene expression by epigenetically deregulating long-range enhancers of the anti-adipogenic MIR335 microRNA gene in human adipocyte progenitor cells. The R482W mutation results in a loss of function of differentiation-de

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Guttery, David S., Karen Page, Allison Hills, et al. "Noninvasive Detection of Activating Estrogen Receptor 1 (ESR1) Mutations in Estrogen Receptor–Positive Metastatic Breast Cancer." Clinical Chemistry 61, no. 7 (2015): 974–82. http://dx.doi.org/10.1373/clinchem.2015.238717.

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Abstract BACKGROUND Activating mutations in the estrogen receptor 1 (ESR1) gene are acquired on treatment and can drive resistance to endocrine therapy. Because of the spatial and temporal limitations of needle core biopsies, our goal was to develop a highly sensitive, less invasive method of detecting activating ESR1 mutations via circulating cell-free DNA (cfDNA) and tumor cells as a “liquid biopsy.” METHODS We developed a targeted 23-amplicon next-generation sequencing (NGS) panel for detection of hot-spot mutations in ESR1, phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit

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14

Vanichtanankul, Jarunee, Supannee Taweechai, Chayasith Uttamapinant, et al. "Combined Spatial Limitation around Residues 16 and 108 of Plasmodium falciparum Dihydrofolate Reductase Explains Resistance to Cycloguanil." Antimicrobial Agents and Chemotherapy 56, no. 7 (2012): 3928–35. http://dx.doi.org/10.1128/aac.00301-12.

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ABSTRACTNatural mutations ofPlasmodium falciparumdihydrofolate reductase (PfDHFR) at A16V and S108T specifically confer resistance to cycloguanil (CYC) but not to pyrimethamine (PYR). In order to understand the nature of CYC resistance, the effects of various mutations at A16 on substrate and inhibitor binding were examined. Three series of mutations at A16 with or without the S108T/N mutation were generated. Only three mutants with small side chains at residue 16 (G, C, and S) were viable from bacterial complementation assay in the S108 series, whereas these three and an additional four mutan

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Ryser, Marc D., Byung-Hoon Min, Kimberly D. Siegmund, and Darryl Shibata. "Spatial mutation patterns as markers of early colorectal tumor cell mobility." Proceedings of the National Academy of Sciences 115, no. 22 (2018): 5774–79. http://dx.doi.org/10.1073/pnas.1716552115.

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A growing body of evidence suggests that a subset of human cancers grows as single clonal expansions. In such a nearly neutral evolution scenario, it is possible to infer the early ancestral tree of a full-grown tumor. We hypothesized that early tree reconstruction can provide insights into the mobility phenotypes of tumor cells during their first few cell divisions. We explored this hypothesis by means of a computational multiscale model of tumor expansion incorporating the glandular structure of colorectal tumors. After calibrating the model to multiregional and single gland data from 19 hum

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Zhao, Zhenyu, Cheng Zhang, Mi Li, et al. "Applications of cerebrospinal fluid circulating tumor DNA in the diagnosis of gliomas." Japanese Journal of Clinical Oncology 50, no. 3 (2020): 325–32. http://dx.doi.org/10.1093/jjco/hyz156.

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Abstract Objective The 2016 World Health Organization (WHO) Classification of Tumors of the Central Nervous System (CNS) was revised to include molecular biomarkers as diagnostic criteria. However, conventional biopsies of gliomas were spatially and temporally limited. This study aimed to determine whether circulating tumor DNA (ctDNA) from cerebrospinal fluid (CSF) could provide more comprehensive diagnostic information to gliomas. Methods Combined with clinical data, we analyzed gene alterations from CSF and tumor tissues of newly diagnosed patients, and detected mutations of ctDNA in recurr

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Yuan, Qiu, Haihong Yang, Hanzhang Chen, et al. "Clinical and patho-genomic characteristics of concomitant mutated status of TP53, EGFR, KRAS genes in Chinese patients with resected lung adenocarcinoma." Journal of Clinical Oncology 38, no. 15_suppl (2020): e21024-e21024. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e21024.

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e21024 Background: Alterations of TP53, EGFR, KRAS genes are of importance in LUAD etiology, vital prognostic markers as well as therapeutic targets as recently reported. In addition, in advanced or metastatic NSCLC, concomitant mutations of TP53 with EGFR or KRAS closely associated with prognosis and TKIs’ efficacy. While, distribution of concomitant mutations of TP53, EGFR and KRAS in early stage or resectable LUAD remained to be elucidated. Methods: 434 patients with defined pathological diagnosis of LUAD were recruited from 1st.Jan.2019-31st.Dec.2019, which made 468 FFPE blocks for the stu

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Chen, Ting, Haiying Wu, Chenxi Zhang, et al. "Clinical, Genetics, and Bioinformatic Characterization of Mutations Affecting an Essential Region of PLS3 in Patients with BMND18." International Journal of Endocrinology 2018 (October 14, 2018): 1–9. http://dx.doi.org/10.1155/2018/8953217.

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Background. Bone mineral density quantitative trait locus 18 (BMND18, OMIM #300910) is a type of early-onset osteogenesis imperfecta (OI) caused by loss-of-function mutations in the PLS3 gene, which encodes plastin-3, a key protein in the formation of actin bundles throughout the cytoskeleton. Here, we report a patient with PLS3 mutation caused BMND18 and evaluated all the reported disease-causing mutations by bioinformatic analysis. Methods. Targeted gene sequencing was performed to find the disease-causing mutation in our patient. Bioinformatic analyses mainly including homology modelling an

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Bauske, Mitchell J., Ipsita Mallik, S. K. R. Yellareddygari, and Neil C. Gudmestad. "Spatial and Temporal Distribution of Mutations Conferring QoI and SDHI Resistance in Alternaria solani Across the United States." Plant Disease 102, no. 2 (2018): 349–58. http://dx.doi.org/10.1094/pdis-06-17-0852-re.

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The application of succinate dehydrogenase inhibiting (SDHI) and quinone outside inhibiting (QoI) fungicide chemistries is a primary tactic in the management of early blight of potato, caused by Alternaria solani. Resistance to QoIs in A. solani has been attributed to the F129L mutation, while resistance to SDHIs is conferred by five different known point mutations on three AsSdh genes. In total, 1,323 isolates were collected from 2013 through 2015 across 11 states to determine spatial and temporal frequency distribution of these mutations. A real-time polymerase chain reaction (PCR) was used

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Soe, Myat Han, Chienying Liu, Aaron Barak Neinstein, and Elizabeth J. Murphy. "Biochemical and Genomic Changes of a Devastating Metastatic Medullary Thyroid Cancer." Journal of the Endocrine Society 5, Supplement_1 (2021): A1038. http://dx.doi.org/10.1210/jendso/bvab048.2124.

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Abstract Introduction: Medullary thyroid carcinoma (MTC) is a neuroendocrine tumor of thyroid parafollicular C cells. About 25% of cases are hereditary, associated with MEN2 syndromes. RET M918 mutation (somatic or germline) is associated with the most aggressive form of MTC. If MTC is hereditary, further tumor genomic analysis is not routinely performed. Therefore, the somatic mutational landscape of hereditary MTCs is not frequently described in the literature. We present an unusual case of MTC with a germline M918 RET mutation, displaying an initial smoldering course followed by rapidly fat

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McInerny, G. J., J. R. G. Turner, H. Y. Wong, J. M. J. Travis, and T. G. Benton. "How range shifts induced by climate change affect neutral evolution." Proceedings of the Royal Society B: Biological Sciences 276, no. 1661 (2009): 1527–34. http://dx.doi.org/10.1098/rspb.2008.1567.

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We investigate neutral evolution during range shifts in a strategic model of a metapopulation occupying a climate gradient. Using heritable, neutral markers, we track the spatio-temporal fate of lineages. Owing to iterated founder effects (‘mutation surfing’), survival of lineages derived from the leading range limit is enhanced. At trailing limits, where habitat suitability decreases, survival is reduced (mutations ‘wipe out’). These processes alter (i) the spatial spread of mutations, (ii) origins of persisting mutations and (iii) the generation of diversity. We show that large changes in ne

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Nagy, Ákos, Bence Bátai, Alexandra Balogh, et al. "Quantitative Analysis and Monitoring of EZH2 Mutations Using Liquid Biopsy in Follicular Lymphoma." Genes 11, no. 7 (2020): 785. http://dx.doi.org/10.3390/genes11070785.

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Recent advances in molecular technologies enable sensitive and quantitative assessment of circulating tumor DNA, offering a noninvasive disease monitoring tool for patients with malignant disorders. Here, we demonstrated on four follicular lymphoma cases that circulating tumor DNA based EZH2 mutation analysis performed by a highly sensitive droplet digital PCR method may be a valuable treatment monitoring approach in EZH2 mutant follicular lymphoma. EZH2 variant allele frequencies changed in parallel with the volume of metabolically active tumor sites observed on 18F-fluorodeoxyglucose positro

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Pan, Tingting, Yu Zhang, Fenzhen Su, Vincent Lyne, Fei Cheng, and Han Xiao. "Practical Efficient Regional Land-Use Planning Using Constrained Multi-Objective Genetic Algorithm Optimization." ISPRS International Journal of Geo-Information 10, no. 2 (2021): 100. http://dx.doi.org/10.3390/ijgi10020100.

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Practical efficient regional land-use planning requires planners to balance competing uses, regional policies, spatial compatibilities, and priorities across the social, economic, and ecological domains. Genetic algorithm optimization has progressed complex planning, but challenges remain in developing practical alternatives to random initialization, genetic mutations, and to pragmatically balance competing objectives. To meet these practical needs, we developed a Land use Intensity-restricted Multi-objective Spatial Optimization (LIr-MSO) model with more realistic patch size initialization, n

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Lebecque, S. G., and P. J. Gearhart. "Boundaries of somatic mutation in rearranged immunoglobulin genes: 5' boundary is near the promoter, and 3' boundary is approximately 1 kb from V(D)J gene." Journal of Experimental Medicine 172, no. 6 (1990): 1717–27. http://dx.doi.org/10.1084/jem.172.6.1717.

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To investigate why somatic mutations are spatially restricted to a region around the rearranged V(D)J immunoglobulin gene, we compared the distribution of mutations flanking murine V gene segments that had rearranged next to either proximal or distal J gene segments. 124 nucleotide substitutions, nine deletions, and two insertions were identified in 32,481 bp of DNA flanking the coding regions from 17 heavy and kappa light chain genes. Most of the mutations occurred within a 2-kb region centered around the V(D)J gene, regardless of which J gene segment was used, suggesting that the structural

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Kondratiev, Yuri, Oleksandr Kutoviy, Robert Minlos, and Sergey Pirogov. "On spatial mutation-selection models." Journal of Mathematical Physics 54, no. 11 (2013): 113504. http://dx.doi.org/10.1063/1.4828856.

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Savy, Michel. "Mutation économique et changement spatial." Les Annales de la recherche urbaine 46, no. 1 (1990): 106–12. http://dx.doi.org/10.3406/aru.1990.1514.

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Parl, Fritz F., William D. Dupont, and Philip S. Crooke. "Interchromosomal Translocations as a Means to Map Chromosome Territories in Breast Cancer." Cancer Informatics 18 (January 2019): 117693511984257. http://dx.doi.org/10.1177/1176935119842573.

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The genome-wide identification of mutated genes is an important advance in our understanding of tumor biology, but several fundamental questions remain open. How do these genes act together to promote cancer development and, a related question, how are they spatially arranged in the nucleus to allow coordinated expression? We examined the nuclear topography of mutated genes in breast cancer and their relation to chromosome territories (CTs). We performed a literature review and analyzed 1 type of mutation, interchromosomal translocations, in 1546 primary breast cancers to infer the spatial arr

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Casanova, Jordi, Ernesto Sánchez-Herrero, and Ginés Morata. "Contrabithorax and the control of spatial expression of the bithorax complex genes of Drosophila." Development 90, no. 1 (1985): 179–96. http://dx.doi.org/10.1242/dev.90.1.179.

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Cbx 1 is a dominant mutation of the bithorax complex (BX-C) of Drosophila partially transforming the second thoracic (T2) segment towards the third one (T3). Molecular analysis has shown that Cbx1 arose from a transposition within the BX-C of a DNA fragment of 17 kb containing pbx+ inserted into the Ubx area. In addition to the dominant phenotype, the Cbx1 mutation produces a set of recessive homeotic transformations that we show are characteristic of the Ubx mutations. We present evidence that the dominant and the recessive transformations arise from different mechanisms and suggest the domin

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Laborde, Pierre. "Mutations spatiales et mutations commerciales à Bayonne." Revue géographique des Pyrénées et du Sud-Ouest 58, no. 3 (1987): 277–84. http://dx.doi.org/10.3406/rgpso.1987.3089.

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Henn, Brenna M., Laura R. Botigué, Stephan Peischl, et al. "Distance from sub-Saharan Africa predicts mutational load in diverse human genomes." Proceedings of the National Academy of Sciences 113, no. 4 (2015): E440—E449. http://dx.doi.org/10.1073/pnas.1510805112.

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The Out-of-Africa (OOA) dispersal ∼50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We s

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Epperson, B. K. "Spatial autocorrelation of genotypes under directional selection." Genetics 124, no. 3 (1990): 757–71. http://dx.doi.org/10.1093/genetics/124.3.757.

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Abstract The spatial distributions of genetic variation under selection-mutation equilibrium within populations that have limited dispersal are investigated. The results show that directional selection with moderate strength rapidly reduces the amount of genetic structure and spatial autocorrelations far below that predicted for selectively neutral loci. For the latter, homozygotes are spatially clustered into separate areas or patches, each consisting of several hundred homozygotes. When selection is added the patches of the deleterious homozygotes are much smaller, in the range of 25 to 50 i

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Anandalakshmi, Venkatraman, Guillaume Hochart, David Bonnel, et al. "Targeted Expression of TGFBIp Peptides in Mouse and Human Tissue by MALDI-Mass Spectrometry Imaging." Separations 8, no. 7 (2021): 97. http://dx.doi.org/10.3390/separations8070097.

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Stromal corneal dystrophies are a group of hereditary disorders caused by mutations in the TGFBI gene. The mutant TGFBIp is prone to protein aggregation and the mutant protein gets deposited in the cornea, leading to severe visual impairment. The mutations lead to a corneal specific protein aggregation suggesting the involvement of tissue-specific factors. The exact molecular mechanism of the process of tissue-specific protein aggregation remains to be elucidated. Differential proteolysis of mutant TGFBIp is a critical component of the disease pathology. The differential proteolysis gives rise

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Cheng, Michael L., Maha Shady, Catharine Kline Cipolla, et al. "Comparison of somatic mutation profiles from cell free DNA (cfDNA) versus tissue in metastatic urothelial carcinoma (mUC)." Journal of Clinical Oncology 35, no. 15_suppl (2017): 4533. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.4533.

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4533 Background: Next-generation sequencing (NGS) of cfDNA is an emerging non-invasive strategy to define tumor mutation profiles that counters spatial and temporal limitations of sequencing single tissue specimens. We examined the feasibility of NGS of cfDNA in mUC and compared mutation profiles from cfDNA to results of tissue NGS previously performed in the clinical setting. Methods: Plasma cfDNA was collected in mUC pts and analyzed using a capture-based NGS assay (MSK-IMPACT) targeting 341-468 genes. NGS profiles from cfDNA and archival tumor tissue (using the same assay) were analyzed in

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Stein, Matthew K., Manjari Pandey, Joanne Xiu, et al. "Tumor Mutational Burden Is Site Specific in Non–Small-Cell Lung Cancer and Is Highest in Lung Adenocarcinoma Brain Metastases." JCO Precision Oncology, no. 3 (December 2019): 1–13. http://dx.doi.org/10.1200/po.18.00376.

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PURPOSE Tumor mutational burden (TMB) is a developing biomarker in non–small-cell lung cancer (NSCLC). Little is known regarding differences between TMB and sample location, histology, or other biomarkers. METHODS A total of 3,424 unmatched NSCLC samples, including 2,351 lung adenocarcinomas (LUADs) and 1,073 lung squamous cell carcinomas (LUSCs), underwent profiling, including next-generation sequencing of 592 cancer-related genes, programmed death ligand 1 immunohistochemistry, and TMB. The rate TMB of 10 mutations per megabase (Mb) or greater was compared between primary and metastatic LUAD

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Picouet, Patrick, and Jean-Pierre Renard. "Discontinuités et mutations spatiales." Territoire en mouvement, no. 1 (December 1, 2006): 68–77. http://dx.doi.org/10.4000/tem.965.

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Kiss, Richárd, Donát Alpár, Ambrus Gángó, et al. "Spatial Convergent Clonal Evolution Leading to Ibrutinib Resistance and Disease Progression in Chronic Lymphocytic Leukemia." Blood 132, Supplement 1 (2018): 5539. http://dx.doi.org/10.1182/blood-2018-99-115937.

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Abstract Introduction: Bruton tyrosine kinase inhibitor ibrutinib has altered the therapeutic landscape of chronic lymphocytic leukemia (CLL) with remarkable responses in relapsed or refractory CLL. Despite mostly durable responses, approximately 20% of patients experience disease progression with, in many cases, BTK or phospholipase Cg2 (PLCG2) resistance mutations predating the clinical progression by up to 15 months. Longitudinal studies have shed some light on the temporal aspects of clonal evolution processes leading to ibrutinib resistance, however, the spatial heterogeneity within the v

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Krochmalnek, E., A. Accogli, J. St-Onge, et al. "P.048 Characterization of somatic mutations in mTOR pathway genes in focal cortical dysplasias." Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques 46, s1 (2019): S26—S27. http://dx.doi.org/10.1017/cjn.2019.148.

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Background: Focal cortical dysplasias (FCDs) are congenital structural abnormalities of the brain, and represent the most common cause of medication-resistant focal epilepsy in children and adults. Recent studies have shown that somatic mutations (i.e. mutations arising in the embryo) in mTOR pathway genes underlie some FCD cases. Specific therapies targeting the mTOR pathway are available. However, testing for somatic mTOR pathway mutations in FCD tissue is not performed on a clinical basis, and the contribution of such mutations to the pathogenesis of FCD remains unknown. Aim: To investigate

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Hilz, Stephanie, Chibo Hong, Llewellyn Jalbert, et al. "GENE-47. A 3D ATLAS TO EVALUATE THE SPATIAL PATTERNING OF GENETIC ALTERATIONS AND TUMOR CELL STATES IN GLIOMA." Neuro-Oncology 21, Supplement_6 (2019): vi107—vi108. http://dx.doi.org/10.1093/neuonc/noz175.449.

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Abstract BACKGROUND Previous studies of solid tumors have been restricted in their ability to map how heterogeneous cell populations evolved within the tumor in three-dimensional (3D) space due to insufficient sampling, typically one sample per tumor, and a lack of knowledge of where within the tumor the sample was obtained. Knowledge of the extensivity of heterogeneity and how it is spatially distributed is crucial for assessing whether a therapeutic target is truly tumor-wide, and for exploring how mutations relate to heterogeneity in the local microenvironment. METHODS We developed a novel

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JAISSER, FRÉDÉRIC. "Inducible Gene Expression and Gene Modification in Transgenic Mice." Journal of the American Society of Nephrology 11, suppl 2 (2000): S95—S100. http://dx.doi.org/10.1681/asn.v11suppl_2s95.

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Abstract. Animal transgenesis has proven to be useful for physiologic as well as pathophysiologic studies. Animal models with conditional expression of a transgene of interest or with a conditional gene mutation can be generated. This permits spatial and temporal control of the expression of the transgene or of gene mutations previously introduced by gene targeting. These approaches allow the generation of models suitable for physiologic analysis or models mimicking disease states.

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Moore, Ariane L., Aashil A. Batavia, Jack Kuipers, et al. "Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma." Cancers 13, no. 9 (2021): 2163. http://dx.doi.org/10.3390/cancers13092163.

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Intra-tumour heterogeneity is the molecular hallmark of renal cancer, and the molecular tumour composition determines the treatment outcome of renal cancer patients. In renal cancer tumourigenesis, in general, different tumour clones evolve over time. We analysed intra-tumour heterogeneity and subclonal mutation patterns in 178 tumour samples obtained from 89 clear cell renal cell carcinoma patients. In an initial discovery phase, whole-exome and transcriptome sequencing data from paired tumour biopsies from 16 ccRCC patients were used to design a gene panel for follow-up analysis. In this sec

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Galen, Spencer C., Chandrasekhar Natarajan, Hideaki Moriyama, et al. "Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens." Proceedings of the National Academy of Sciences 112, no. 45 (2015): 13958–63. http://dx.doi.org/10.1073/pnas.1507300112.

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A key question in evolutionary genetics is why certain mutations or certain types of mutation make disproportionate contributions to adaptive phenotypic evolution. In principle, the preferential fixation of particular mutations could stem directly from variation in the underlying rate of mutation to function-altering alleles. However, the influence of mutation bias on the genetic architecture of phenotypic evolution is difficult to evaluate because data on rates of mutation to function-altering alleles are seldom available. Here, we report the discovery that a single point mutation at a highly

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Simon, Helmut, and Gavin Huttley. "Quantifying Influences on Intragenomic Mutation Rate." G3: Genes|Genomes|Genetics 10, no. 8 (2020): 2641–52. http://dx.doi.org/10.1534/g3.120.401335.

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We report work to quantify the impact on the probability of human genome polymorphism both of recombination and of sequence context at different scales. We use population-based analyses of data on human genetic variants obtained from the public Ensembl database. For recombination, we calculate the variance due to recombination and the probability that a recombination event causes a mutation. We employ novel statistical procedures to take account of the spatial auto-correlation of recombination and mutation rates along the genome. Our results support the view that genomic diversity in recombina

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Barton, N. H. "Genetic linkage and natural selection." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1552 (2010): 2559–69. http://dx.doi.org/10.1098/rstb.2010.0106.

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The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill–Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence

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Brossier, Nicole, Olivia Cobb, and David Gutmann. "PDTM-07. DEFINING THE MECHANISMS UNDERLYING NF1 OPTIC GLIOMA PENETRANCE." Neuro-Oncology 21, Supplement_6 (2019): vi188. http://dx.doi.org/10.1093/neuonc/noz175.783.

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Abstract While most children develop cancer without a clear etiology, some pediatric cancers arise in the context of tumor predisposition syndromes, typically caused by germline mutations in genes that regulate cell growth. The most common of these syndromes, Neurofibromatosis type 1 (NF1), affects ~1:3,000 individuals worldwide, 15% of whom will develop low-grade tumors of the optic pathway (optic pathway gliomas; OPGs). However, it is currently unclear which children with NF1 will develop an OPG, making risk assessment for each individual child difficult. Recent evidence suggests that the sp

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Bosshard, Lars, Stephan Peischl, Martin Ackermann, and Laurent Excoffier. "Mutational and Selective Processes Involved in Evolution during Bacterial Range Expansions." Molecular Biology and Evolution 36, no. 10 (2019): 2313–27. http://dx.doi.org/10.1093/molbev/msz148.

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AbstractBacterial populations have been shown to accumulate deleterious mutations during spatial expansions that overall decrease their fitness and ability to grow. However, it is unclear if and how they can respond to selection in face of this mutation load. We examine here if artificial selection can counteract the negative effects of range expansions. We examined the molecular evolution of 20 mutator lines selected for fast expansions (SEL) and compared them to 20 other mutator lines freely expanding without artificial selection (CONTROL). We find that the colony size of all 20 SEL lines ha

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Click, Eleanor S., Tim Stearns, and David Botstein. "Systematic Structure-Function Analysis of the Small GTPase Arf1 in Yeast." Molecular Biology of the Cell 13, no. 5 (2002): 1652–64. http://dx.doi.org/10.1091/mbc.02-01-0007.

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Members of the ADP-ribosylation factor (Arf) family of small GTPases are implicated in vesicle traffic in the secretory pathway, although their precise function remains unclear. We generated a series of 23 clustered charge-to-alanine mutations in the Arf1 protein ofSaccharomyces cerevisiae to determine the portions of this protein important for its function in cells. These mutants display a number of phenotypes, including conditional lethality at high or low temperature, defects in glycosylation of invertase, dominant lethality, fluoride sensitivity, and synthetic lethality with thearf2 null m

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Carico, Zachary M., Holden C. Stefan, Megan Justice, Askar Yimit, and Jill M. Dowen. "A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression." PLOS Genetics 17, no. 3 (2021): e1009435. http://dx.doi.org/10.1371/journal.pgen.1009435.

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The cohesin complex spatially organizes interphase chromatin by bringing distal genomic loci into close physical proximity, looping out the intervening DNA. Mutation of cohesin complex subunits is observed in cancer and developmental disorders, but the mechanisms through which these mutations may contribute to disease remain poorly understood. Here, we investigate a recurrent missense mutation to the hinge domain of the cohesin subunit SMC1A, observed in acute myeloid leukemia. Engineering this mutation into murine embryonic stem cells caused widespread changes in gene expression, including dy

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Bian, Chang, Yu Wang, Zhihao Lu, et al. "ImmunoAIzer: A Deep Learning-Based Computational Framework to Characterize Cell Distribution and Gene Mutation in Tumor Microenvironment." Cancers 13, no. 7 (2021): 1659. http://dx.doi.org/10.3390/cancers13071659.

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Spatial distribution of tumor infiltrating lymphocytes (TILs) and cancer cells in the tumor microenvironment (TME) along with tumor gene mutation status are of vital importance to the guidance of cancer immunotherapy and prognoses. In this work, we developed a deep learning-based computational framework, termed ImmunoAIzer, which involves: (1) the implementation of a semi-supervised strategy to train a cellular biomarker distribution prediction network (CBDPN) to make predictions of spatial distributions of CD3, CD20, PanCK, and DAPI biomarkers in the tumor microenvironment with an accuracy of

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Williams, Stephen, Cedric Uytingco, Neil Weisenfeld, et al. "50 Spatially resolved molecular investigation of triple negative breast cancer and its immune microenvironment." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (2020): A53. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0050.

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BackgroundTriple negative breast cancer (TNBC) accounts for 10–20% of all diagnosed breast cancer cases in the US and is characterized by loss of HER2, estrogen receptors, and progesterone receptors. TNBC is an aggressive, complex disease with a poor prognosis due to resistance to traditional therapies. Understanding the underlying biology and tumor microenvironment is critical to the development of diagnostic biomarkers and to guide the search for effective therapies. Here, we demonstrated the ability of the 10x Genomics Visium Spatial Gene Expression Solution to elucidate the immunological p

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Morrow, Zachary, Alexander Cicala, Evan Flietner, et al. "Reconstructing the Clonal and Mutational Architecture of Myeloma through Avian Leukosis Virus (ALV)-Mediated Genome Editing." Blood 132, Supplement 1 (2018): 4480. http://dx.doi.org/10.1182/blood-2018-99-115288.

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Abstract Background and Aims. Despite the fact that the myeloma mutational landscape was elucidated several years ago, there are yet no approved precision therapies targeting specific driver mutations. The role of common, but somewhat enigmatic, mutational events remains elusive, for example, the loss-of-function mutation of the RNA-processing exosome ribonuclease, DIS3, the third most-common mutation after KRAS and NRAS mutations. Furthermore, complex clonal architectural patterns (such as subclonal BRAF mutations nested within RAS-mutant clones) complicate the design of targeted therapy tria

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