Karla Plevová Group
Genomics of Immune Cells
About us
We are an interdisciplinary team of biologists and bioinformaticians exploring the complexity of the human genome, with a special focus on immune cells and hematological malignancies. By combining cutting-edge laboratory experiments with advanced computational analyses, we aim to understand how changes in genome structure and regulation contribute to the development and progression of cancer.
What we do
Cancer genomes are often highly complex, with structural changes that span multiple chromosomes and reshape the 3D architecture of the nucleus, reprogram gene regulation, and alter the epigenomic state of cells. Understanding these alterations is key to deciphering how tumors evolve, why they resist therapy, and how they can be more effectively targeted.
We focus on hematological malignancies and primarily on chronic lymphocytic leukemia (CLL) as a model system to investigate how genome and epigenome regulation drive disease development. By integrating advanced genomic technologies with computational innovation, we want to connect fundamental biological and genomics discoveries with clinical applications. Working mainly with primary patient samples, we bridge basic research with translational impact. In parallel, we develop and implement user-friendly software and tools that make complex genomic data more accessible for both researchers and clinicians.
Research focus and ongoing projects
- Chromatin architecture in leukemia. Using Micro-C and integrative omics (RNA-seq, ATAC-seq), we explore how nuclear organization, topologically associating domains (TADs), compartments, and chromatin loops are altered in CLL, and how these changes correlate with shifts in gene expression.
- Structural variants and methylation. Applying Oxford Nanopore sequencing (ONT), we investigate complex genome rearrangements, repetitive elements, and DNA methylation patterns.
- Clonal evolution in CLL. Through transcriptome and exome sequencing, we study how genetic alterations shape tumor heterogeneity and disease progression.
- Multiclonal expansions in CLL. Using NGS and single-cell approaches (scRNA-seq, scATAC-seq), we study clonal transformation and selection of cellular clones bearing distinct B-cell receptors.
- Computational tool development. We create platforms such as LYNX and ARResT/Interrogate to enable the analysis and visualization of genomic data, making interpretation more straightforward.
