Transcriptional networks and genomics​
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By focusing primarily on ER stress we are exploring how gene expression networks are modulated to attain homeostasis. Beyond ER stress, our approaches are applied to other conditions and pathologies such as aging and cancer, as well as for the study of traits at the level of whole populations.
In parallel, we are actively engaged in genomic and transcriptomic studies in Peromyscus.
More recently we introduced the composite Pearson's correlation index (Pc) which reflects the degree of coordination for every gene with the whole transcriptome, between 2 experimental conditions. Its calculation implies if and at which extent the functionality of a given gene changes in 2 conditions and can be used to predict biological processes that are altered.
Datasets
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GSE146846 Whole Transcriptome Sequencing of Peromyscus maniculatus in Response to High Fat Diet
GSE131429 Whole Transcriptome RNA-seq in Peromyscus maniculatus fibroblasts
PRJEB41333 Whole Genome Sequencing for genetic variants between the Peromyscus maniculatus subspecies, bairdii and sonoriensis
GSE167827 RNAseq of A549 human lung cancer cells cultured with sera from P. californicus with different bonding experiences.
Pc articles
Zhang, Y., Chatzistamou, I. & Kiaris, H. Transcriptomic coordination at hepatic steatosis indicates robust immune cell engagement prior to inflammation. BMC Genomics 22, 454 (2021). https://doi.org/10.1186/s12864-021-07784-y
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Soltanmohammadi E*, Zhang Y*, Chatzistamou I, Kiaris H. Resilience, plasticity and robustness in gene expression during aging in the brain of outbred deer mice. BMC Genomics 22, 291 (2021). https://doi.org/10.1186/s12864-021-07613-2. (*, equal contribution)
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Zhang Y, Chatzistamou I, Kiaris H. Identification of frailty-associated genes by coordination analysis of gene expression. Aging (Albany NY). 2020; . https://doi.org/10.18632/aging.102875
Recent papers
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​Zhang Y, Huynh-Dam KT, Ding X, Sikirzhytski V, Lim CU, Broude E, Kiaris H. RASSF1 is identified by transcriptome coordination analysis as a target of ATF4. FEBS Open Bio. 2023 Feb 1. doi: 10.1002/2211-5463.13569. Epub ahead of print. PMID: 36723232.
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Horvath S, Haghani A, Zoller JA, Naderi A, Soltanmohammadi E, Farmaki E, Kaza V, Chatzistamou I, Kiaris H. Methylation studies in Peromyscus: aging, altitude adaptation, and monogamy. GeroScience 2021. https://doi.org/10.1007/s11357-021-00472-5 [bioRxiv 2021. 10.1101/2021.03.15.435544 https://doi.org/10.1101/2021.03.15.435544]
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Lucius MD, Ji H, Altomare D, Doran R, Torkian B, Havighorst A, Kaza V, Zhang Y, Gasparian AV, Shankar V, Shtutman M, and Kiaris H. Genomic variation in captive deer mouse (Peromyscus maniculatus) populations. BMC Genomics 22, 662 (2021). https://doi.org/10.1186/s12864-021-07956-w
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Zhang, Y., Chatzistamou, I. & Kiaris, H. Transcriptomic coordination at hepatic steatosis indicates robust immune cell engagement prior to inflammation. BMC Genomics 22, 454 (2021). https://doi.org/10.1186/s12864-021-07784-y
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Soltanmohammadi E*, Zhang Y*, Chatzistamou I, Kiaris H. Resilience, plasticity and robustness in gene expression during aging in the brain of outbred deer mice. BMC Genomics 22, 291 (2021). https://doi.org/10.1186/s12864-021-07613-2. (*, equal contribution)
Balderrama-Gutierrez G, Milovic A, Cook VJ, Islam NM, Zhang Y, Kiaris H, Belisle JT, Mortazavi A, Barbour AG. An infection-tolerant mammalian reservoir for several zoonotic agents broadly counters the inflammatory effects of endotoxin. mBio. 2021 Apr 13;12(2):e00588-21. doi: 10.1128/mBio.00588-21. [bioRxiv 2020.12.13.422519; doi: https://doi.org/10.1101/2020.12.13.422519]
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Zhang Y, Chatzistamou I, Kiaris H. Coordination of the unfolded protein response during hepatic steatosis identifies CHOP as a specific regulator of hepatocyte ballooning. Cell Stress Chaperones. 2020 Jun 23. doi: 10.1007/s12192-020-01132-x
Chavez B, Farmaki E, Zhang Y, Altomare D, Hao J, Soltnamohammadi E, Shtutman M, Chatzistamou I, & Kiaris H. A strategy for the Identification of Paracrine Regulators of Cancer Cell Migration. Clin Exp Pharmacol Physiol. 2020 Jun 25. doi: 10.1111/1440-1681.13366. Selected for the Journal's Cover
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Soltanmohammadi E, Farmaki E, Zhang Y, Naderi A, Kaza V, Chatzistamou I, Kiaris H. Coordination in the unfolded protein response during aging in outbred deer mice. Experimental Gerontology. 2020 Dec 5;144:111191. doi: 10.1016/j.exger.2020.111191
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Zhang Y, Chatzistamou I, Kiaris H. Identification of frailty-associated genes by coordination analysis of gene expression. Aging (Albany NY). 2020; . https://doi.org/10.18632/aging.102875
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Zhang Y, Lucius M, Altomare D, Havighorst A, Farmaki E, Chatzistamou I, Shtutman M, and Kiaris H. Coordination analysis of gene expression points to the relative impact of different regulators during endoplasmic reticulum stress. DNA and Cell Biology. 2019 Jul 29. doi: 10.1089/dna.2019.4910
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