Laboratory of Glial Biology and Omics Technologies

At the GliaOmics Lab, we explore the fundamental roles of glial cells—astrocytes, microglia, and oligodendrocytes—in the health, disease, and injury responses of the central nervous system. Using cutting-edge omics technologies, we investigate the molecular and cellular mechanisms that regulate glial function, diversity, and interactions. Our goal is to advance the understanding of neurological disorders and contribute to the development of novel glial-oriented therapeutic strategies.

Research Areas

• Glial Cell Function & Heterogeneity – Investigating the roles of astrocytes, microglia, and oligodendrocytes in the physiological and pathological processes of the central nervous system.
• Glia in Neurological Disorders – Understanding glial contributions to conditions such as stroke, Alzheimer’s disease, amyotrophic lateral sclerosis, multiple sclerosis, Alexander disease, and spinal cord injury.
• Single-Cell & Spatial Transcriptomics – Leveraging high-resolution omics techniques to map glial activity and communication networks.
• Therapeutic Strategies – Identifying and targeting pathophysiological mechanisms of glial cells to develop next-generation therapeutics.

Key Research Projects

• Mapping the Pathology of Ischemic Brain Injury – Characterizing glial responses and identifying therapeutic targets for stroke treatment using single-cell and spatial transcriptomics.
• Glial Cells as Therapeutic Targets – Modulating astrocyte-microglia communication, the complement system, and mTOR signaling in glial cells to modify disease progression.
• Advanced Modeling of Neurological Disorders – Developing humanized organoid models for studying stroke and Alzheimer’s disease and exploring the potential of mRNA-based interventions as a therapeutic strategy.

Collaboration

We actively collaborate with academic and industry partners to advance glial biology research and omics-based discovery. Our laboratory maintains a close connection with the GeneCore Facility, which provides advanced single-cell and spatial transcriptomic services.

2025

• Genotype-driven sensitivity of mice to tick-borne encephalitis virus correlates with differential host responses in peripheral macrophages and brain. Berankova M, Holoubek J, Hönig V, Matusova Z, Palus M, Salat J, Krayem I, Vojtiskova J, Svoboda P, Pranclova V, Valihrach L, Demant P, Lipoldova M, Ruzek D. J Neuroinflammation. 2025 Jan 28;22(1):22. doi: 10.1186/s12974-025-03354-1.

2024

• Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia. Zucha D, Abaffy P, Kirdajova D, Jirak D, Kubista M, Anderova M, Valihrach L. Proc Natl Acad Sci U S A. 2024 Nov 12;121(46):e2404203121. doi: 10.1073/pnas.2404203121.
• Aberrant neurodevelopment in human iPS cell-derived models of Alexander disease. Matusova Z, Dykstra W, de Pablo Y, Zetterdahl OG, Canals I, van Gelder CAGH, Vos HR, Pérez-Sala D, Kubista M, Abaffy P, Ahlenius H, Valihrach L, Hol EM, Pekny M. Glia. 2025 Jan;73(1):57-79. doi: 10.1002/glia.24618.
• The deletion of AQP4 and TRPV4 affects astrocyte swelling/volume recovery in response to ischemia-mimicking pathologies. Hermanova Z, Valihrach L, Kriska J, Maheta M, Tureckova J, Kubista M, Anderova M. Front Cell Neurosci. 2024 May 15;18:1393751. doi: 10.3389/fncel.2024.1393751.
• A practical guide to spatial transcriptomics. Valihrach L, Zucha D, Abaffy P, Kubista M. Mol Aspects Med. 2024 Jun;97:101276. doi: 10.1016/j.mam.2024.101276.

2023

• A view of the genetic and proteomic profile of extracellular matrix molecules in aging and stroke. Chmelova M, Androvic P, Kirdajova D, Tureckova J, Kriska J, Valihrach L, Anderova M, Vargova L. Front Cell Neurosci. 2023 Nov 30;17:1296455. doi: 10.3389/fncel.2023.1296455. eCollection 2023.
• NEUROD1 reinforces endocrine cell fate acquisition in pancreatic development. Bohuslavova R, Fabriciova V, Smolik O, Lebrón-Mora L, Abaffy P, Benesova S, Zucha D, Valihrach L, Berkova Z, Saudek F, Pavlinkova G. Nat Commun. 2023 Sep 9;14(1):5554. doi: 10.1038/s41467-023-41306-6.
• Reactive astrogliosis in the era of single-cell transcriptomics. Matusova Z, Hol EM, Pekny M, Kubista M, Valihrach L. Front Cell Neurosci. 2023 Apr 20;17:1173200. doi: 10.3389/fncel.2023.1173200.
• Cortical glia in SOD1(G93A) mice are subtly affected by ALS-like pathology. Filipi T, Matusova Z, Abaffy P, Vanatko O, Tureckova J, Benesova S, Kubiskova M, Kirdajova D, Zahumensky J, Valihrach L, Anderova M. Sci Rep. 2023 Apr 21;13(1):6538. doi: 10.1038/s41598-023-33608-y.
• Complement C3a treatment accelerates recovery after stroke via modulation of astrocyte reactivity and cortical connectivity. Stokowska A, Aswendt M, Zucha D, Lohmann S, Wieters F, Morán Suarez J, Atkins AL, Li Y, Miteva M, Lewin J, Wiedermann D, Diedenhofen M, Torinsson Naluai Å, Abaffy P, Valihrach L, Kubista M, Hoehn M, Pekny M, Pekna M. J Clin Invest. 2023 May 15;133(10):e162253. doi: 10.1172/JCI162253.
• ISL1 controls pancreatic alpha cell fate and beta cell maturation. Bohuslavova R, Fabriciova V, Lebrón-Mora L, Malfatti J, Smolik O, Valihrach L, Benesova S, Zucha D, Berkova Z, Saudek F, Evans SM, Pavlinkova G. Cell Biosci. 2023 Mar 10;13(1):53. doi: 10.1186/s13578-023-01003-9.
• β-Lactoglobulin affects the oxidative status and viability of equine endometrial progenitor cells via lncRNA-mRNA-miRNA regulatory associations. Data K, Marcinkowska K, Buś K, Valihrach L, Pawlak E, Śmieszek A. J Cell Mol Med. 2023 Apr;27(7):927-938. doi: 10.1111/jcmm.17694.
• Glioblastoma and cerebral organoids: development and analysis of an in vitro model for glioblastoma migration. Fedorova V, Pospisilova V, Vanova T, Amruz Cerna K, Abaffy P, Sedmik J, Raska J, Vochyanova S, Matusova Z, Houserova J, Valihrach L, Hodny Z, Bohaciakova D. Mol Oncol. 2023 Apr;17(4):647-663. doi: 10.1002/1878-0261.13389.

2022

• Recent advances in deciphering oligodendrocyte heterogeneity with single-cell transcriptomics. Valihrach L, Matusova Z, Zucha D, Klassen R, Benesova S, Abaffy P, Kubista M, Anderova M. Front Cell Neurosci. 2022 Oct 13;16:1025012. doi: 10.3389/fncel.2022.1025012.
• ISL1 is necessary for auditory neuron development and contributes toward tonotopic organization. Filova I, Pysanenko K, Tavakoli M, Vochyanova S, Dvorakova M, Bohuslavova R, Smolik O, Fabriciova V, Hrabalova P, Benesova S, Valihrach L, Cerny J, Yamoah EN, Syka J, Fritzsch B, Pavlinkova G. Proc Natl Acad Sci U S A. 2022 Sep 13;119(37):e2207433119. doi: 10.1073/pnas.2207433119.
• Obesity Affects the Proliferative Potential of Equine Endometrial Progenitor Cells and Modulates Their Molecular Phenotype Associated with Mitochondrial Metabolism. Smieszek A, Marcinkowska K, Pielok A, Sikora M, Valihrach L, Carnevale E, Marycz K. Cells. 2022 Apr 24;11(9):1437. doi: 10.3390/cells11091437.
• Compromised Astrocyte Swelling/Volume Regulation in the Hippocampus of the Triple Transgenic Mouse Model of Alzheimer's Disease. Tureckova J, Kamenicka M, Kolenicova D, Filipi T, Hermanova Z, Kriska J, Meszarosova L, Pukajova B, Valihrach L, Androvic P, Zucha D, Chmelova M, Vargova L, Anderova M. Front Aging Neurosci. 2022 Jan 27;13:783120. doi: 10.3389/fnagi.2021.783120.
• Small RNA-Sequencing for Analysis of Circulating miRNAs: Benchmark Study. Androvic P, Benesova S, Rohlova E, Kubista M, Valihrach L. J Mol Diagn. 2022 Apr;24(4):386-394. doi: 10.1016/j.jmoldx.2021.12.006.

2021

• Tutorial: Guidelines for Single-Cell RT-qPCR. Zucha D, Kubista M, Valihrach L. Cells. 2021 Sep 30;10(10):2607. doi: 10.3390/cells10102607.
• Transient astrocyte-like NG2 glia subpopulation emerges solely following permanent brain ischemia. Kirdajova D, Valihrach L, Valny M, Kriska J, Krocianova D, Benesova S, Abaffy P, Zucha D, Klassen R, Kolenicova D, Honsa P, Kubista M, Anderova M. Glia. 2021 Nov;69(11):2658-2681. doi: 10.1002/glia.24064.
• Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. Benesova S, Kubista M, Valihrach L. Diagnostics (Basel). 2021 May 27;11(6):964. doi: 10.3390/diagnostics11060964.

2020

• Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain. Androvic P, Kirdajova D, Tureckova J, Zucha D, Rohlova E, Abaffy P, Kriska J, Valny M, Anderova M, Kubista M, Valihrach L. Cell Rep. 2020 Jun 16;31(11):107777. doi: 10.1016/j.celrep.2020.107777.
• The Role of miR-21 in Osteoblasts-Osteoclasts Coupling In Vitro. Smieszek A, Marcinkowska K, Pielok A, Sikora M, Valihrach L, Marycz K. Cells. 2020 Feb 19;9(2):479. doi: 10.3390/cells9020479.
• High potassium exposure reveals the altered ability of astrocytes to regulate their volume in the aged hippocampus of GFAP/EGFP mice. Kolenicova D, Tureckova J, Pukajova B, Harantova L, Kriska J, Kirdajova D, Vorisek I, Kamenicka M, Valihrach L, Androvic P, Kubista M, Vargova L, Anderova M. Neurobiol Aging. 2020 Feb;86:162-181. doi: 10.1016/j.neurobiolaging.2019.10.009.
• Performance Comparison of Reverse Transcriptases for Single-Cell Studies. Zucha D, Androvic P, Kubista M, Valihrach L. Clin Chem. 2020 Jan 1;66(1):217-228. doi: 10.1373/clinchem.2019.307835.
• Circulating miRNA analysis for cancer diagnostics and therapy. Valihrach L, Androvic P, Kubista M. Mol Aspects Med. 2020 Apr;72:100825. doi: 10.1016/j.mam.2019.10.002.

GAČR: GA25-16979S, L. Valihrach: Prostorová transkriptomická mapa ischemické cévní příhody. 2025 – 2027.

GAČR: GA24-11364S, L. Valihrach: Humanizovaná platforma založená na organoidech pro modelování mozkové mrtvice a terapeutické intervence na bázi mRNA. 2024 – 2026.

GAČR: GA24-12028S, L. Valihrach: Atlas Alzheimerovy choroby: Mapování vývoje demence u cerebrálních organoidů pomocí single-cell transkriptomiky. 2024 -2026.

GAČR: GA23-05327S, L. Valihrach: Komunikace astrocytů a mikroglií jako cíl terapie cévní mozkové příhody. 2023 – 2025.

GAČR: GA23-06269S, M. Kubista: Narušená regulace mTOR signálni dráhy u gliových buněk po ischemickém poškození mozku. 2023 – 2025.

AZV: NU21-08-00286, L. Valihrach: Monitorace biomarkerů séra u pacientů s akutním poraněním míchy. 2021-2024.

MŠMT (Project ALEXANDER): EJPRD19-256, M. Kubista, L. Valihrach: The astrocyte nanofilament system in Alexander disease – from molecules to function, uncovering new leads for therapy. 2020-2022.

GAČR: GA20-05770S, M. Kubista: Úloha gliálních TRPV4 kanálů ve vzniku mozkového edému a post-ischemické regeneraci. 2020-2022.

GAČR: GA19-02046S, L. Valihrach: Gliové buňky - klíčoví hráči v progresi amyotrofické laterální sklerózy. 2019-2021.

GAČR: GA18-21942S, M. Kubista: MikroRNA v poranění nervové soustavy: potenciální úloha a terapeutický význam. 2018-2020.

GAČR: GA17-0403, 4S, M. Kubista: Klíčové signální dráhy regulující proliferaci a diferenciaci NG2 gliových buněk v poškozené nervové tkáni mozku. 2017-2019.

GAČR: GA16-10214S, L. Valihrach: Změny difuzivity mozku, složení extracelulární matrix a fyziologie gliových buněk v průběhu stárnutí - dopad na patogenezi ischemického poškození. 2016-2018.

MŠMT (program OP VK): CZ.1.07/2.3.00/30.0045, Bařinka, Nováková, Kubista, Valihrach, Hejnalová: Biotechnologický expert v oblasti strukturní biologie a genové exprese. 2012-2015.