Novel genomic screening tool enables precision reverse-engineering of genetic programming in cells

Collaborative research led by investigators at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center defines a novel approach to understanding how certain proteins called transcription factors determine which genetic programs will drive cell growth and maturation. The study is published in the journal Science.

The method, called “Perturb-multiome,” uses CRISPR to knock out the function of individual transcription factors across many blood cells at once. The researchers then perform single-cell analyses on each cell to measure the effects of the editing, including identifying which genes have been turned on or off and which genes are accessible (based on epigenetic markers). The team applied this tool to immature blood cells to identify the important transcription factors—and DNA regions that code for them—that strongly affect how blood cells develop.

They discovered that many of the DNA regions they identified as important for driving blood cell production are also regions known to harbor mutations linked to blood disorders. The DNA regions they identified as important occupy less than 0.3% of the genome, but they explain a disproportionately large share of the genetic influence on blood cell features and specialization.

In earlier work, investigators from this team and other collaborators used genome-wide association studies to identify the transcription factor responsible for switching off fetal hemoglobin after birth, laying the groundwork for the development of gene therapy for sickle cell disease and beta thalassemia.

This new Perturb-multiome approach enables researchers to systematically reveal how thousands of transcription factor variants influence blood cell production and influence disease risk, creating opportunities for finding many more novel targeted therapies for blood disorders.

Collaborative research led by investigators at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center defines a novel approach to understanding how certain proteins called transcription factors determine which genetic programs will drive cell growth and maturation. The study is published in the journal Science.

The method, called “Perturb-multiome,” uses CRISPR to knock out the function of individual transcription factors across many blood cells at once. The researchers then perform single-cell analyses on each cell to measure the effects of the editing, including identifying which genes have been turned on or off and which genes are accessible (based on epigenetic markers). The team applied this tool to immature blood cells to identify the important transcription factors—and DNA regions that code for them—that strongly affect how blood cells develop.

They discovered that many of the DNA regions they identified as important for driving blood cell production are also regions known to harbor mutations linked to blood disorders. The DNA regions they identified as important occupy less than 0.3% of the genome, but they explain a disproportionately large share of the genetic influence on blood cell features and specialization.

In earlier work, investigators from this team and other collaborators used genome-wide association studies to identify the transcription factor responsible for switching off fetal hemoglobin after birth, laying the groundwork for the development of gene therapy for sickle cell disease and beta thalassemia.

This new Perturb-multiome approach enables researchers to systematically reveal how thousands of transcription factor variants influence blood cell production and influence disease risk, creating opportunities for finding many more novel targeted therapies for blood disorders.