NEW YORK – New research by Northwestern University researchers is providing a look at the genes and cell types affected by genetic risk variants for uterine fibroids, also known as leiomyomas.
"Our study shows the power of integrating multiple data modalities to address the two critical challenges of GWAS studies: identifying the gene targets and identifying the cell type targets of risk loci," Mazhar Adli, a researcher at the Feinberg School of Medicine at Northwestern University's Robert Lurie Comprehensive Cancer Center, said in an email.
"Now that we have a better understanding of these two critical mediators of GWAS risk loci in fibroid development," he explained, "we can experimentally validate these genes and cell types."
As they reported in in Nature Communications on Wednesday, Adli and his colleagues analyzed epigenetic and gene expression, as well as chromatin state and structure data alongside findings from a GWAS meta-analysis, building on findings from past studies of uterine fibroid heritability.
Past research suggests that more than 70 percent of women develop one or more uterine fibroid tumors by the time they reach the age of 50, the team noted. While most cases are symptom-free and nonmalignant, roughly 20 to 25 percent of affected individuals experience symptoms ranging from uterine bleeding and anemia to pregnancy problems such as poor embryo implantation, recurrent pregnancy loss, preterm labor, or labor obstruction.
"Few medical treatments are available for [uterine fibroids], and many patients undergo extreme measures such as surgical hysterectomy," the authors explained, noting that "such procedures create significant emotional stress on patients and a substantial financial burden on society."
While uterine fibroid tumor sequencing studies have uncovered recurrent somatic mutations affecting genes such as MED12, HMGA1/2, FH, and collagen genes, Adli noted, many of the germline genetic risk variants found in uterine fibroid/leiomyoma GWAS have turned up in noncoding portions of the genome.
The noncoding risk variant component "creates a formidable challenge to know why these variants are associated with fibroid development because we don't know which genes are being aberrantly regulated by these variants and we don't know which cell types in the tumor micro-environment are being affected by these aberrantly regulated genes," he said.
For the current study, the team started with risk SNPs and candidate genes unearthed in a GWAS meta-analysis published in Nature Communications in 2019, which included 20,406 individuals with uterine fibroids and more than 223,900 unaffected controls.
With the help of a data analysis platform known as FUMA, the researchers incorporated epigenomic clues from the ENCODE database and Roadmap Epigenomics Project. They also integrated gene expression data from the GTEx project, together with published maps of three-dimensional chromatin organization data across cell types.
The team further included chromatin immunoprecipitation sequencing-based chromatin state data, Hi-C chromatin organization profiles, and single-cell gene expression profiles from studies that specifically assessed uterine fibroids and matched normal uterine myometrium tissues.
"We integrated GWAS-identified risk loci with gene expression (both single-cell and bulk), epigenetic, and chromatin architecture datasets from fibroid tumors," Adli wrote, noting that they "initially identified potential gene targets of these genetic variants" and "significantly expanded the number of target genes by including 3D genome organization data."
In the process, the investigators tracked down two dozen uterine fibroid risk loci and nearly 400 potential target genes, including 168 genes that appear to be differentially expressed in uterine fibroid tumors — findings they explored further with CRISPR-based experiments focused on expression changes found when targeting epigenetic factors with activating or repressive functions.
By bringing in single-cell gene expression data, meanwhile, the team highlighted cell types with enhanced expression of GWAS target genes, from smooth muscle cells found in uterine fibroid tumors to neighboring immune cell types.
Together, Adli explained, the results suggest that "the effect of GWAS risk loci may be mediated through a cell type, such as immune cells, that is not directly linked to fibroid tumorigenesis."
More broadly, he and his coauthors suggested that the current findings and approach "indicate the effectiveness of integrating multiomics data with locus-specific epigenetic editing approaches for identifying gene and [cell] type targets of disease-relevant risk loci."