Enhancer biology
Foundational work on enhancers and enhancer RNAs in transcriptional regulation and inflammatory gene expression.
Projects · Kaikkonen Lab
From genetic discovery to cardiovascular mechanisms
The Kaikkonen Lab investigates how genetic variation, regulatory elements, cellular states, and tissue context shape atherosclerotic cardiovascular disease. Our research connects functional genomics, single-cell and spatial biology, computational modelling, and translational cardiovascular medicine.
Ongoing programs
Current research projects
01
Ongoing · 2023–2027
MIRACLE
MIRACLE focuses on understanding how genetic risk contributes to cardiovascular disease mechanisms and disease progression. The project integrates genetic, functional, and multi-omics data to identify causal variants, regulatory mechanisms, and pathways that shape cardiovascular risk.
genetic risk
causal variants
multi-omics
pathways
risk prediction
02
ERC-funded project
SECRET
SECRET aims to functionally dissect causal regulatory variants in atherosclerotic cardiovascular disease. The project connects non-coding disease variants to enhancer activity, target genes, cellular phenotypes, and disease-relevant regulatory networks.
non-coding variants
CRISPRi/a
endothelial cells
smooth muscle cells
regulatory networks
03
Single-cell · Spatial biology
Single-cell and spatial genomics
This research direction maps cardiovascular disease at cell-type and spatial resolution, identifying disease-associated cell states, regulatory programs, and spatial tissue organization in vascular pathology.
scRNA-seq
scATAC-seq
multiome
spatial transcriptomics
cell states
04
Variant-to-function
Functional fine-mapping of GWAS variants
This project area translates statistical disease associations into experimentally testable biological mechanisms by identifying causal regulatory elements, target genes, and functional effects of non-coding variants.
GWAS interpretation
fine-mapping
MPRA
CRISPR validation
target genes
05
Computational · Translational
Multimodal translational cardiovascular genomics
This emerging direction integrates molecular, cellular, spatial, genetic, and clinical data to connect disease mechanisms with phenotype and support mechanism-aware prediction.
genomics
epigenomics
spatial data
clinical integration
machine learning
06
Core biology
Gene regulatory mechanisms in cardiovascular disease
A central goal of the lab is to understand how regulatory elements, enhancers, enhancer RNAs, chromatin programs, and transcriptional networks control disease-relevant cellular phenotypes.
enhancers
eRNAs
chromatin regulation
inflammation
variant-to-gene mechanisms
Foundations
Previous and foundational research
Genomic dissection of atherosclerosis
Application of next-generation sequencing technologies to identify regulatory mechanisms in cardiovascular disease.
Polygenic disease architecture
Research linking genetic variation, disease-associated cell states, and heritability in cardiovascular disease.
Variant-to-function mapping
Frameworks connecting non-coding variants to regulatory elements, target genes, and disease mechanisms.
Research vision
Bridging genetic association and disease mechanism
Genetic variation → Regulatory function → Cellular mechanisms → Disease biology → Clinical translation
The long-term goal is to bridge the gap between genetic association and disease mechanism by combining experimental genomics, single-cell technologies, computational biology, and translational cardiovascular research.