Genetic Variation Associated with Thyroid Autoimmunity Shapes the Systemic Immune Response to PD-1 Checkpoint Blockade

The authors studied endocrine immune related adverse events from seven clinical trials across six cancers where atezolizumab was combined with chemotherapies and compared to standard of care.
[Nature Communications]
Khan, Z., Hammer, C., Carroll, J., Di Nucci, F., Acosta, S. L., Maiya, V., Bhangale, T., Hunkapiller, J., Mellman, I., Albert, M. L., McCarthy, M. I., & Chandler, G. S. (2021). Genetic variation associated with thyroid autoimmunity shapes the systemic immune response to PD-1 checkpoint blockade. Nature Communications, 12(1), 3355. https://doi.org/10.1038/s41467-021-23661-4 Cite
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Transcriptome-Wide Association Study Uncovers the Role of Essential Genes in Anthracycline-Induced Cardiotoxicity

Scientists identified a genetic association between decreased expression of GDF5 and anthracycline-induced cardiotoxicity, and found that cell viability of GDF5-silenced human cardiac myocytes was significantly decreased in response to anthracycline treatment.
[NPJ Genomic Medicine]
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Genetic Effects on Liver Chromatin Accessibility Identify Disease Regulatory Variants

Researchers mapped caQTLs in human liver tissue in 20 liver samples and identified 3,123 caQTLs.
[The American Journal of Human Genetics]
Currin, K. W., Erdos, M. R., Narisu, N., Rai, V., Vadlamudi, S., Perrin, H. J., Idol, J. R., Yan, T., Albanus, R. D., Broadaway, K. A., Etheridge, A. S., Bonnycastle, L. L., Orchard, P., Didion, J. P., Chaudhry, A. S., Barnabas, B. B., Black, S., Bouffard, G. G., Brooks, S. Y., … Mohlke, K. L. (2021). Genetic effects on liver chromatin accessibility identify disease regulatory variants. The American Journal of Human Genetics, 0(0). https://doi.org/10.1016/j.ajhg.2021.05.001 Cite
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Whole-Genome Sequencing Association Analysis of Quantitative Red Blood Cell Phenotypes: The NHLBI TOPMed Program

Researchers discovered 14 single variant-red blood cell trait associations at 12 genomic loci, which have not been reported previously.
[American Journal of Human Genetics]
Hu, Y., Stilp, A. M., McHugh, C. P., Rao, S., Jai, D., Zheng, X., Lane, J., Bellefon, S. M. de, Raffield, L. M., Chen, M.-H., Yanek, L. R., Wheeler, M., Yao, Y., Ren, C., Broome, J., Moon, J.-Y., Vries, P. S. de, Hobbs, B. D., Sun, Q., … Reiner, A. P. (2021). Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. The American Journal of Human Genetics, 0(0). https://doi.org/10.1016/j.ajhg.2021.04.003 Cite
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APOE2 Mitigates Disease-Related Phenotypes in an Isogenic hiPSC-Based Model of Alzheimer’s Disease

Investigators utilized an isogenic human induced pluripotent stem cell (hiPSC)-based system to demonstrate that conversion of APOE3 to APOE2 greatly reduced the production of amyloid-beta peptides in hiPSC-derived neural cultures.
[Molecular Psychiatry]
Brookhouser, N., Raman, S., Frisch, C., Srinivasan, G., & Brafman, D. A. (2021). APOE2 mitigates disease-related phenotypes in an isogenic hiPSC-based model of Alzheimer’s disease. Molecular Psychiatry, 1–18. https://doi.org/10.1038/s41380-021-01076-3 Cite
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Integration of Alzheimer’s Disease Genetics and Myeloid Genomics Identifies Disease Risk Regulatory Elements and Genes

Scientists showed that Alzheimer’s disease risk alleles were specifically enriched in active enhancers of monocytes, macrophages and microglia.
[Nature Communications]
Novikova, G., Kapoor, M., Tcw, J., Abud, E. M., Efthymiou, A. G., Chen, S. X., Cheng, H., Fullard, J. F., Bendl, J., Liu, Y., Roussos, P., Björkegren, J. L., Liu, Y., Poon, W. W., Hao, K., Marcora, E., & Goate, A. M. (2021). Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes. Nature Communications, 12(1), 1610. https://doi.org/10.1038/s41467-021-21823-y Cite
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Forkhead Box F1 Induces Columnar Phenotype and Epithelial-to-Mesenchymal Transition in Esophageal Squamous Cells To Initiate Barrett’s Like Metaplasia

Initiation of a Barrett’s esophagus-like metaplastic change was evaluated by measuring characteristic cytokeratins and global gene expression profiling and by culturing organoids.
[Laboratory Investigation]
De, A., Zhou, J., Liu, P., Huang, M., Gunewardena, S., Mathur, S. C., Christenson, L. K., Sharma, M., Zhang, Q., & Bansal, A. (2021). Forkhead box F1 induces columnar phenotype and epithelial-to-mesenchymal transition in esophageal squamous cells to initiate Barrett’s like metaplasia. Laboratory Investigation, 1–15. https://doi.org/10.1038/s41374-021-00534-4 Cite
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Genetic Mechanisms of Critical Illness in COVID-19

Scientists report the results of the Genetics Of Mortality In Critical Care genome-wide association study in 2244 critically ill Covid-19 patients from 208 UK intensive care units.
[Nature]
Pairo-Castineira, E., Clohisey, S., Klaric, L., Bretherick, A. D., Rawlik, K., Pasko, D., Walker, S., Parkinson, N., Fourman, M. H., Russell, C. D., Furniss, J., Richmond, A., Gountouna, E., Wrobel, N., Harrison, D., Wang, B., Wu, Y., Meynert, A., Griffiths, F., … Baillie, J. K. (2020). Genetic mechanisms of critical illness in Covid-19. Nature, 1–1. https://doi.org/10.1038/s41586-020-03065-y Cite
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Transcriptome and Regulatory Maps of Decidua-Derived Stromal Cells Inform Gene Discovery in Preterm Birth

Researchers generated transcriptome (RNA-seq), epigenome (ChIP-seq of H3K27ac, H3K4me1, and H3K4me3 histone modifications), open chromatin (ATAC-seq), and chromatin interaction (promoter capture Hi-C) annotations of cultured primary decidua-derived MSCs and in vitro differentiated decidual stromal cells and developed a computational framework to integrate these functional annotations with results from a GWAS of gestational duration in 56,384 women.
[Science Advances]

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Altered Transcriptional and Chromatin Responses to Rhinovirus in Bronchial Epithelial Cells from Adults with Asthma

Scientists demonstrated that cultured primary bronchial epithelial cells from adults with asthma showed different transcriptional and chromatin responses to rhinovirus infection compared to those without asthma.
[Communications Biology]
Helling, B. A., Sobreira, D. R., Hansen, G. T., Sakabe, N. J., Luo, K., Billstrand, C., Laxman, B., Nicolae, R. I., Nicolae, D. L., Bochkov, Y. A., Gern, J. E., Nobrega, M. A., White, S. R., & Ober, C. (2020). Altered transcriptional and chromatin responses to rhinovirus in bronchial epithelial cells from adults with asthma. Communications Biology, 3(1), 1–11. https://doi.org/10.1038/s42003-020-01411-4 Cite
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Identification of Candidate Genetic Variants and Altered Protein Expression in Neural Stem and Mature Neural Cells Support Altered Microtubule Function to Be an Essential Component in Bipolar Disorder

Quantitative proteomics revealed NLRP2 as the most significantly up-regulated protein in neural stem cells and mature neural cells obtained from bipolar disorder-patient cell samples.
[Translational Psychiatry]
Truvé, K., Parris, T. Z., Vizlin-Hodzic, D., Salmela, S., Berger, E., Ågren, H., & Funa, K. (2020). Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder. Translational Psychiatry, 10(1), 1–12. https://doi.org/10.1038/s41398-020-01056-1 Cite
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