Published in Blood, co-corresponding author Jian Xu, PhD, and co-first author Kaili Wang, PhD, St. Jude Department of Pathology, in a collaborative effort with Northwestern University, found a novel treatment opportunity for sickle cell disease and β-thalassemia by probing the mechanism for gene therapy.
Scientists at St. Jude Children’s Research Hospital and Northwestern University identified a previously unknown treatment opportunity for sickle cell disease and β-thalassemia. The discovery, published in Blood, is based on a new understanding of how CRISPR-based gene therapy works. In these therapies, CRISPR-Cas9 targets a regulatory DNA element, called an enhancer, which controls expression of BCL11A, a key gene responsible for switching hemoglobin production from fetal to adult forms. The researchers found that doing so disrupts a three-dimensional genome structure required for maintaining high-level BCL11A expression in red blood cell precursors. As a result, BCL11A is silenced, leading to reactivation of fetal hemoglobin, which compensates for defective adult hemoglobin in sickle cell disease and β-thalassemia. The researchers further found that targeting a specific RNA produced by the BCL11A enhancer could have similar effects to gene therapy.
BCL11A represses fetal hemoglobin expression, which is typically produced at low levels in the red blood cells of healthy adults. Inactivating BCL11A can reactivate fetal hemoglobin expression, compensating for mutant sickle hemoglobin in sickle cell disease or for the loss of the β-globin genes in β-thalassemia. Recently approved gene therapies for these disorders employ CRISPR-based genome editing to target the BCL11A enhancer in blood stem cells, achieving transformative outcomes for patients. A more detailed understanding of how gene therapy works to disrupt BCL11A expression, however, has been an ongoing question.
The high costs, limited availability, and potential risks associated with current gene therapies make them inaccessible to most patients. Developing alternative, scalable and affordable approaches are therefore needed to reduce the overall disease burden.
“Our motivation for this study was twofold,” said co-corresponding author Jian Xu, PhD, St. Jude Department of Pathology and Center of Excellence for Leukemia Studies. “First, to find out how CRISPR genome editing effectively inactivates BCL11A for fetal hemoglobin reactivation. And second, to identify more cost-effective and accessible therapeutic strategies.”
Gene therapy breaks up three-dimensional DNA structure
The team investigated how BCL11A is regulated during hematopoiesis (blood cell growth) and identified a key control mechanism: the enhancer region targeted by the gene therapy was folding into a three-dimensional structure. “We found that this enhancer forms a chromatin ‘rosette’ structure, making multiple contacts with critical regulatory elements of the gene,” Xu explained. “This ensures high-level BCL11A expression and prevents its silencing in red blood cell precursors.”
When CRISPR-Cas9 makes a DNA break in this enhancer as part of the therapy, it disrupts the chromatin rosette structure. Without this structure, other repressive proteins can enter and silence the BCL11A gene.
Further, the researchers discovered that the formation of this complex structure requires a special type of RNA known as “enhancer” RNA. They tested whether targeting this enhancer RNA with antisense oligonucleotides, a more cost-effective type of therapy that does not modify the genome, might produce the same therapeutic benefit. “By delivering antisense oligonucleotides to both normal and sickle red blood cell precursors, we found we can selectively degrade the enhancer RNA, causing BCL11A silencing and fetal hemoglobin reactivation,” Xu said. “We think this could offer a more affordable, accessible and scalable alternative to current gene therapies.”
Authors and funding
The study’s first authors are Kaili Wang, St. Jude, and Juan Wang, Northwestern University. The study’s other co-corresponding author is Feng Yue, Northwestern University. The study’s other authors are Kseniia Dudnyk, Yoon Jung Kim, Jun Yi Stanley Lim, Michael Lee Jr. and Jian Zhou, University of Texas Southwestern Medical Center; Stuart Orkin, Harvard Medical School; and Ruopeng Feng, Yuannyu Zhang, Xiaofei Gao, Yong Cheng and Mitchell Weiss, St. Jude.
The study was supported by the National Institutes of Health (R01DK111430, R01CA230631, R01CA259581, R35GM124820, DP2GM146336 and R01HL165798), the Cancer Prevention and Research Institute of Texas (RR190071) and the American Lebanese Syrian Associated Charities (ALSAC), the fundraising and awareness organization of St. Jude.
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