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958 Publications visible to you, out of a total of 958
RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas.
Leipzig Melanoma Studies

Abstract (Expand)

Recent studies revealed trajectories of mutational events in early melanomagenesis, but the accompanying changes in gene expression are far less understood. Therefore, we performed a comprehensive … RNA-seq analysis of laser-microdissected melanocytic nevi (n = 23) and primary melanoma samples (n = 57) and characterized the molecular mechanisms of early melanoma development. Using self-organizing maps, unsupervised clustering, and analysis of pseudotime (PT) dynamics to identify evolutionary trajectories, we describe here two transcriptomic types of melanocytic nevi (N1 and N2) and primary melanomas (M1 and M2). N1/M1 lesions are characterized by pigmentation-type and MITF gene signatures, and a high prevalence of NRAS mutations in M1 melanomas. N2/M2 lesions are characterized by inflammatory-type and AXL gene signatures with an equal distribution of wild-type and mutated BRAF and low prevalence of NRAS mutations in M2 melanomas. Interestingly, N1 nevi and M1 melanomas and N2 nevi and M2 melanomas, respectively, cluster together, but there is no clustering in a stage-dependent manner. Transcriptional signatures of M1 melanomas harbor signatures of BRAF/MEK inhibitor resistance and M2 melanomas harbor signatures of anti-PD-1 antibody treatment resistance. Pseudotime dynamics of nevus and melanoma samples are suggestive for a switch-like immune-escape mechanism in melanoma development with downregulation of immune genes paralleled by an increasing expression of a cell cycle signature in late-stage melanomas. Taken together, the transcriptome analysis identifies gene signatures and mechanisms underlying development of melanoma in early and late stages with relevance for diagnostics and therapy.

Authors: M. Kunz, H. Loffler-Wirth, M. Dannemann, E. Willscher, G. Doose, J. Kelso, T. Kottek, B. Nickel, L. Hopp, J. Landsberg, S. Hoffmann, T. Tuting, P. Zigrino, C. Mauch, J. Utikal, M. Ziemer, H. J. Schulze, M. Holzel, A. Roesch, S. Kneitz, S. Meierjohann, A. Bosserhoff, H. Binder, M. Schartl

Date Published: 12th Jul 2018

Publication Type: Not specified

Human Diseases: melanoma

A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer
GC-HBOC - German Consortium for Hereditary Breast and Ovarian Cancer

Abstract (Expand)

The breast cancer risk variants identified in genome-wide association studies explain only a small fraction of the familial relative risk, and the genes responsible for these associations remain largely … unknown. To identify novel risk loci and likely causal genes, we performed a transcriptome-wide association study evaluating associations of genetically predicted gene expression with breast cancer risk in 122,977 cases and 105,974 controls of European ancestry. We used data from the Genotype-Tissue Expression Project to establish genetic models to predict gene expression in breast tissue and evaluated model performance using data from The Cancer Genome Atlas. Of the 8,597 genes evaluated, significant associations were identified for 48 at a Bonferroni-corrected threshold of P \textless 5.82 \times 10-6, including 14 genes at loci not yet reported for breast cancer. We silenced 13 genes and showed an effect for 11 on cell proliferation and/or colony-forming efficiency. Our study provides new insights into breast cancer genetics and biology.

Authors: Lang Wu, Wei Shi, Jirong Long, Xingyi Guo, Kyriaki Michailidou, Jonathan Beesley, Manjeet K. Bolla, Xiao-Ou Shu, Yingchang Lu, Qiuyin Cai, Fares Al-Ejeh, Esdy Rozali, Qin Wang, Joe Dennis, Bingshan Li, Chenjie Zeng, Helian Feng, Alexander Gusev, Richard T. Barfield, Irene L. Andrulis, Hoda Anton-Culver, Volker Arndt, Kristan J. Aronson, Paul L. Auer, Myrto Barrdahl, Caroline Baynes, Matthias W. Beckmann, Javier Benitez, Marina Bermisheva, Carl Blomqvist, Natalia V. Bogdanova, Stig E. Bojesen, Hiltrud Brauch, Hermann Brenner, Louise Brinton, Per Broberg, Sara Y. Brucker, Barbara Burwinkel, Trinidad Caldés, Federico Canzian, Brian D. Carter, J. Esteban Castelao, Jenny Chang-Claude, Xiaoqing Chen, Ting-Yuan David Cheng, Hans Christiansen, Christine L. Clarke, Margriet Collée, Sten Cornelissen, Fergus J. Couch, David Cox, Angela Cox, Simon S. Cross, Julie M. Cunningham, Kamila Czene, Mary B. Daly, Peter Devilee, Kimberly F. Doheny, Thilo Dörk, Isabel Dos-Santos-Silva, Martine Dumont, Miriam Dwek, Diana M. Eccles, Ursula Eilber, A. Heather Eliassen, Christoph Engel, Mikael Eriksson, Laura Fachal, Peter A. Fasching, Jonine Figueroa, Dieter Flesch-Janys, Olivia Fletcher, Henrik Flyger, Lin Fritschi, Marike Gabrielson, Manuela Gago-Dominguez, Susan M. Gapstur, Montserrat García-Closas, Mia M. Gaudet, Maya Ghoussaini, Graham G. Giles, Mark S. Goldberg, David E. Goldgar, Anna González-Neira, Pascal Guénel, Eric Hahnen, Christopher A. Haiman, Niclas Håkansson, Per Hall, Emily Hallberg, Ute Hamann, Patricia Harrington, Alexander Hein, Belynda Hicks, Peter Hillemanns, Antoinette Hollestelle, Robert N. Hoover, John L. Hopper, Guanmengqian Huang, Keith Humphreys, David J. Hunter, Anna Jakubowska, Wolfgang Janni, Esther M. John, Nichola Johnson, Kristine Jones, Michael E. Jones, Audrey Jung, Rudolf Kaaks, Michael J. Kerin, Elza Khusnutdinova, Veli-Matti Kosma, Vessela N. Kristensen, Diether Lambrechts, Loic Le Marchand, Jingmei Li, Sara Lindström, Jolanta Lissowska, Wing-Yee Lo, Sibylle Loibl, Jan Lubinski, Craig Luccarini, Michael P. Lux, Robert J. MacInnis, Tom Maishman, Ivana Maleva Kostovska, Arto Mannermaa, JoAnn E. Manson, Sara Margolin, Dimitrios Mavroudis, Hanne Meijers-Heijboer, Alfons Meindl, Usha Menon, Jeffery Meyer, Anna Marie Mulligan, Susan L. Neuhausen, Heli Nevanlinna, Patrick Neven, Sune F. Nielsen, Børge G. Nordestgaard, Olufunmilayo I. Olopade, Janet E. Olson, Håkan Olsson, Paolo Peterlongo, Julian Peto, Dijana Plaseska-Karanfilska, Ross Prentice, Nadege Presneau, Katri Pylkäs, Brigitte Rack, Paolo Radice, Nazneen Rahman, Gad Rennert, Hedy S. Rennert, Valerie Rhenius, Atocha Romero, Jane Romm, Anja Rudolph, Emmanouil Saloustros, Dale P. Sandler, Elinor J. Sawyer, Marjanka K. Schmidt, Rita K. Schmutzler, Andreas Schneeweiss, Rodney J. Scott, Christopher G. Scott, Sheila Seal, Mitul Shah, Martha J. Shrubsole, Ann Smeets, Melissa C. Southey, John J. Spinelli, Jennifer Stone, Harald Surowy, Anthony J. Swerdlow, Rulla M. Tamimi, William Tapper, Jack A. Taylor, Mary Beth Terry, Daniel C. Tessier, Abigail Thomas, Kathrin Thöne, Rob A. E. M. Tollenaar, Diana Torres, Thérèse Truong, Michael Untch, Celine Vachon, David van den Berg, Daniel Vincent, Quinten Waisfisz, Clarice R. Weinberg, Camilla Wendt, Alice S. Whittemore, Hans Wildiers, Walter C. Willett, Robert Winqvist, Alicja Wolk, Lucy Xia, Xiaohong R. Yang, Argyrios Ziogas, Elad Ziv, Alison M. Dunning, Paul D. P. Pharoah, Jacques Simard, Roger L. Milne, Stacey L. Edwards, Peter Kraft, Douglas F. Easton, Georgia Chenevix-Trench, Wei Zheng

Date Published: 1st Jul 2018

Publication Type: Journal article

Human Diseases: hereditary breast ovarian cancer syndrome

Common variants in the CLDN2-MORC4 and PRSS1-PRSS2 loci confer susceptibility to acute pancreatitis
Genetical Statistics and Systems Biology

Abstract (Expand)

BACKGROUND/OBJECTIVES Acute pancreatitis (AP) is one of the most common gastrointestinal disorders often requiring hospitalization. Frequent aetiologies are gallstones and alcohol abuse. In contrast …t to chronic pancreatitis (CP) few robust genetic associations have been described. Here we analysed whether common variants in the CLDN2-MORC4 and the PRSS1-PRSS2 locus that increase recurrent AP and CP risk associate with AP. METHODS We screened 1462 AP patients and 3999 controls with melting curve analysis for SNPs rs10273639 (PRSS1-PRSS2), rs7057398 (RIPPLY), and rs12688220 (MORC4). Calculations were performed for the overall group, aetiology, and gender sub-groups. To examine genotype-phenotype relationships we performed several meta-analyses. RESULTS Meta-analyses of all AP patients depicted significant (p-value \textless 0.05) associations for rs10273639 (odds ratio (OR) 0.88, 95% confidence interval (CI) 0.81-0.97, p-value 0.01), rs7057398 (OR 1.27, 95% CI 1.07-1.5, p-value 0.005), and rs12688220 (OR 1.32, 95% CI 1.12-1.56, p-value 0.001). For the different aetiology groups a significant association was shown for rs10273639 (OR 0.76, 95% CI 0.63-0.92, p-value 0.005), rs7057398 (OR 1.43, 95% CI 1.07-1.92, p-value 0.02), and rs12688220 (OR 1.44, 95% CI 1.07-1.93, p-value 0.02) in the alcoholic sub-group only. CONCLUSIONS The association of CP risk variants with different AP aetiologies, which is strongest in the alcoholic AP group, might implicate common pathomechanisms most likely between alcoholic AP and CP.

Authors: Frank Ulrich Weiss, Nico Hesselbarth, Andrea Párniczky, Dora Mosztbacher, Felix Lämmerhirt, Claudia Ruffert, Peter Kovacs, Sebastian Beer, Katharina Seltsam, Heidi Griesmann, Richard Böhme, Tom Kaune, Marcus Hollenbach, Hans-Ulrich Schulz, Peter Simon, Julia Mayerle, Markus M. Lerch, Giulia Martina Cavestro, Raffaella Alessia Zuppardo, Milena Di Leo, Pier Alberto Testoni, Ewa Malecka-Panas, Anita Gasirowska, Stanislaw Głuszek, Peter Bugert, Andrea Szentesi, Joachim Mössner, Heiko Witt, Patrick Michl, Peter Hégyi, Markus Scholz, Jonas Rosendahl

Date Published: 1st Jul 2018

Publication Type: Journal article

Combined SOM-portrayal of gene expression and DNA methylation landscapes disentangles modes of epigenetic regulation in glioblastoma.
GGN - German Glioma Network

Abstract (Expand)

AIM: We present here a novel method that enables unraveling the interplay between gene expression and DNA methylation in complex diseases such as cancer. MATERIALS & METHODS: The method is based … on self-organizing maps and allows for analysis of data landscapes from 'governed by methylation' to 'governed by expression'. RESULTS: We identified regulatory modules of coexpressed and comethylated genes in high-grade gliomas: two modes are governed by genes hypermethylated and underexpressed in IDH-mutated cases, while two other modes reflect immune and stromal signatures in the classical and mesenchymal subtypes. A fifth mode with proneural characteristics comprises genes of repressed and poised chromatin states active in healthy brain. Two additional modes enrich genes either in active or repressed chromatin states. CONCLUSION: The method disentangles the interplay between gene expression and methylation. It has the potential to integrate also mutation and copy number data and to apply to large sample cohorts.

Authors: L. Hopp, H. Loffler-Wirth, J. Galle, H. Binder

Date Published: 12th Jun 2018

Publication Type: Not specified

Human Diseases: glioblastoma multiforme

User Expectations of Metadata Repositories for Clinical Research
Evaluation Metadata Repository

Abstract (Expand)

Metadata Repositories (MDR) are databases for data elements that can be utilized in research as well as in medical care. These data elements are not the actual patient data (facts), but a complete … definition of the variables or characteristics used, including coding, unit of measurement, data type and other aspects. The aim of the project described here was to evaluate possible application scenarios for MDRs by a larger group of experts. The focus was not on specific software, but on the community's basic expectation of such a database of data elements. To achieve this goal, a questionnaire was designed that contained questions on general aspects of setting up a registry for data elements in biomedical research as well as more specific points with regard to necessary functionalities, desired contents, tools for community work and the quality of data elements. One of the main results was that the users attach more importance to the quality of the content than to the efficiency in implementing their documentation concepts. At the same time, they consider the effort involved in using existing software systems to be too much compared with the benefits and have concerns about the use of their designs by third parties.

Author: Matthias Löbe

Date Published: 9th May 2018

Publication Type: Misc

Towards Phenotyping of Clinical Trial Eligibility Criteria.
NLP4CR - Natural Language Processing for Clinical Research

Abstract (Expand)

BACKGROUND: Medical plaintext documents contain important facts about patients, but they are rarely available for structured queries. The provision of structured information from natural language texts … in addition to the existing structured data can significantly speed up the search for fulfilled inclusion criteria and thus improve the recruitment rate. OBJECTIVES: This work is aimed at supporting clinical trial recruitment with text mining techniques to identify suitable subjects in hospitals. METHOD: Based on the inclusion/exclusion criteria of 5 sample studies and a text corpus consisting of 212 doctor's letters and medical follow-up documentation from a university cancer center, a prototype was developed and technically evaluated using NLP procedures (UIMA) for the extraction of facts from medical free texts. RESULTS: It was found that although the extracted entities are not always correct (precision between 23% and 96%), they provide a decisive indication as to which patient file should be read preferentially. CONCLUSION: The prototype presented here demonstrates the technical feasibility. In order to find available, lucrative phenotypes, an in-depth evaluation is required.

Authors: M. Lobe, S. Staubert, C. Goldberg, I. Haffner, A. Winter

Date Published: 5th May 2018

Publication Type: Journal article

Human Diseases: breast cancer

Systemic and Ocular Determinants of Peripapillary Retinal Nerve Fiber Layer Thickness Measurements in the European Eye Epidemiology (E3) Population.
LIFE Adult

Abstract (Expand)

PURPOSE: To investigate systemic and ocular determinants of peripapillary retinal nerve fiber layer thickness (pRNFLT) in the European population. DESIGN: Cross-sectional meta-analysis. PARTICIPANTS: … A total of 16 084 European adults from 8 cohort studies (mean age range, 56.9+/-12.3-82.1+/-4.2 years) of the European Eye Epidemiology (E3) consortium. METHODS: We examined associations with pRNFLT measured by spectral-domain OCT in each study using multivariable linear regression and pooled results using random effects meta-analysis. MAIN OUTCOME MEASURES: Determinants of pRNFLT. RESULTS: Mean pRNFLT ranged from 86.8+/-21.4 mum in the Rotterdam Study I to 104.7+/-12.5 mum in the Rotterdam Study III. We found the following factors to be associated with reduced pRNFLT: Older age (beta = -0.38 mum/year; 95% confidence interval [CI], -0.57 to -0.18), higher intraocular pressure (IOP) (beta = -0.36 mum/mmHg; 95% CI, -0.56 to -0.15), visual impairment (beta = -5.50 mum; 95% CI, -9.37 to -1.64), and history of systemic hypertension (beta = -0.54 mum; 95% CI, -1.01 to -0.07) and stroke (beta = -1.94 mum; 95% CI, -3.17 to -0.72). A suggestive, albeit nonsignificant, association was observed for dementia (beta = -3.11 mum; 95% CI, -6.22 to 0.01). Higher pRNFLT was associated with more hyperopic spherical equivalent (beta = 1.39 mum/diopter; 95% CI, 1.19-1.59) and smoking (beta = 1.53 mum; 95% CI, 1.00-2.06 for current smokers compared with never-smokers). CONCLUSIONS: In addition to previously described determinants such as age and refraction, we found that systemic vascular and neurovascular diseases were associated with reduced pRNFLT. These may be of clinical relevance, especially in glaucoma monitoring of patients with newly occurring vascular comorbidities.

Authors: M. M. Mauschitz, P. W. M. Bonnemaijer, K. Diers, F. G. Rauscher, T. Elze, C. Engel, M. Loeffler, J. M. Colijn, M. A. Ikram, J. R. Vingerling, K. M. Williams, C. J. Hammond, C. Creuzot-Garcher, A. M. Bron, R. Silva, S. Nunes, C. Delcourt, A. Cougnard-Gregoire, F. G. Holz, C. C. W. Klaver, M. M. B. Breteler, R. P. Finger

Date Published: 3rd May 2018

Publication Type: Journal article

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