We are interested in understanding the epigenetic and transcriptional regulation of cell state transition in cancer and immunology. We employ next-generation sequencing methods to investigate genetic and epigenetic aspects of cancer pathogenesis, metastasis and cancer immunotherapy.
Dr. Sarina Halm
Chromatin regulation of embryonic stem cells
We aim to understand chromatin dynamics during cell state transition in the context of regenerative medicine. Using multi-omics techniques, such as Chromatin-immunoprecipitation coupled with next generation sequencing (ChIP-Seq), we interrogate the roles of polycomb proteins and histone variants in various stem cells and cancer cells.
Heterogeneity of regulatory T cells
Using single cell RNA-Seq techniques, we have discovered heterogeneity in regulatory T cells. Each Treg subset represents differential transcriptional signatures. We continue to explore and identify additional subsets to understand their functions.
Assay Development for Clinical Cancer Diagnostics
We develop clinical diagnostic next-generation sequencing methodologies to investigate gene mutations and epigenomes in pediatric cancers.
Google Scholar: https://scholar.google.com/citations?user=x5bquwoAAAAJ&hl=en
*equal contribution, ^corresponding author.
- Ku M*^, Ke E*, Sabouri-Ghomi M, Abadejos JR, Freeman B, Nham A, Phillips N, Yang KY, Lui KO, Kirak O^. Deconstructive somatic cell nuclear transfer reveals novel regulatory T-cell subsets. J Allergy Clin Immunol. 2018 142(3): 997-1000.e4. DOI: 10.1016/j.jaci.2018.04.038
- Ku M, Chang S-E, Hernandez J, Abadejos JR, Sabouri-Ghomi M, Muenchmeier NJ, Schwarz A, Valencia AM, Kirak O. Nuclear Transfer nTreg Model Reveals Fate-Determining TCR-b and Novel Peripheral nTreg precursors. PNAS 2016 Apr 19;113(16):E2316-25. DOI: 10.1073/pnas.1523664113
- Mertens J, Paquola ACM, Ku M, Hatch E, Böhnke L, Ladjevardi S, McGrath S, Campbell B, Lee H, Herdy JR, Gonçalves JT, Toda T, Kim Y, Winkler J, Yao J, Hetzer MW, Gage FH. Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects. Cell Stem Cell 2015 17 (6), 705-718. DOI: 10.1016/j.stem.2015.09.001
- Ku M^, Jaffe JD, Koche RP, Rheinbay E, Endoh M, Koseki H, Carr SA, Bernstein BE^. H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biology 2012 13:R85. DOI: 10.1186/gb-2012-13-10-r85
- Ku M*, Koche RP*, Rheinbay R*, Mendenhall E, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki K, Bernstein BE^. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 2008 Oct; 4(10). DOI: 10.1371/journal.pgen.1000242
- Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O’Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE^. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007 Aug 2; 448(7153): 553-60. DOI: 10.1038/nature06008
Dr. med. Oktay Kirak, Freiburg Center for Pediatrics and Adolescent Medicine
Prof. Melanie Boerries, University of Freiburg
PD Dr. med. Simone Hettmer, Freiburg Center for Pediatrics and Adolescent Medicine
Prof. Tak Sing Wong, Pennsylvania State University
Prof. Kathy Lui, Chinese University of Hong Kong
Dr. Jerome Mertens, University Innsbruck
DAAD German Academic Exchange Service
University of Freiburg / Penn State University Global Programs
Qiagen NGS Sponsorship Award