Resistance to modulation of in vivo gene expression by genomic editing.
8 affiliations
- 1Department of Stem Cell Biology and Regenerative Medicine, Mount Sinai School of Medicine, New York, NY, USA.
- 2Tisch Cancer Center, Mount Sinai School of Medicine, New York, NY, USA.
- 3Division of Hematology and Medical Oncology, Mount Sinai School of Medicine, New York, NY, USA.
- 4Department of Emergency Medicine, Mount Sinai School of Medicine, New York, NY, USA.
- 5Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA.
- 6Department of Stem Cell Biology and Regenerative Medicine, Mount Sinai School of Medicine, New York, NY, USA. [email protected].
- 7Tisch Cancer Center, Mount Sinai School of Medicine, New York, NY, USA. [email protected].
- 8Mindich Child Health the Development Institute, Mount Sinai School of Medicine, New York, NY, USA. [email protected].
Abstract
Enhancer editing is widely proposed as a strategy to modulate gene dosage therapeutically. EKLF/KLF1, a master erythroid transcription factor, is an attractive target because haploinsufficiency is benign and associated with hereditary persistence of fetal hemoglobin (HPFH). Here we test whether enhancer disruption can recapitulate this state by targeting two KLF1 regulatory elements, EHS1 and INT1. EHS1 editing reduces KLF1 expression and increases γ-globin, and combined INT1/EHS1 targeting produces additional increases in some samples, although responses are variable. In xenotransplantation models, edited cells engraft and retain indels but fail to sustain consistent γ-globin induction. Epigenetic profiling across the KLF1 genetic locus reveals a remarkable resistance to loss of hypersensitive sites. These results establish a key principle: the transcriptional consequences of enhancer editing are strongly constrained by local genomic architecture. Attempts to mimic KLF1 haploinsufficiency by non-coding indels are blunted by dense regulatory architecture, enhancer redundancy, and long-range interaction. Thus, it may be difficult to develop KLF1 as a target for gene therapy for hemoglobinopathies until tools for recapitulating natural mutations via heterozygous edits are developed. Our findings underscore the observation that disruption of non-coding elements may not always recapitulate the biology of haploinsufficiency from heterozygous loss-of-function mutations.
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BibTeX
@article{planutis2026resistance,
title = {{Resistance to modulation of in vivo gene expression by genomic editing.}},
author = {Antanas Planutis and Sanjana Pillay and Babu Mia and Christoph Schaniel and Huihui Li and Sean T Campbell and Ronald Hoffman and Julian A Waksal and Jeffrey A Glassberg and James J Bieker},
journal = {Communications biology},
year = {2026},
month = sep,
doi = {10.1038/s42003-026-10868-8},
url = {https://europepmc.org/article/MED/42957769},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Resistance to modulation of in vivo gene expression by genomic editing.
AU - Antanas Planutis
AU - Sanjana Pillay
AU - Babu Mia
AU - Christoph Schaniel
AU - Huihui Li
AU - Sean T Campbell
AU - Ronald Hoffman
AU - Julian A Waksal
AU - Jeffrey A Glassberg
AU - James J Bieker
PY - 2026
DA - 2026/09/02
JO - Communications biology
DO - 10.1038/s42003-026-10868-8
UR - https://europepmc.org/article/MED/42957769
AB - Enhancer editing is widely proposed as a strategy to modulate gene dosage therapeutically. EKLF/KLF1, a master erythroid transcription factor, is an attractive target because haploinsufficiency is benign and associated with hereditary persistence of fetal hemoglobin (HPFH). Here we test whether enhancer disruption can recapitulate this state by targeting two KLF1 regulatory elements, EHS1 and INT1. EHS1 editing reduces KLF1 expression and increases γ-globin, and combined INT1/EHS1 targeting produces additional increases in some samples, although responses are variable. In xenotransplantation models, edited cells engraft and retain indels but fail to sustain consistent γ-globin induction. Epigenetic profiling across the KLF1 genetic locus reveals a remarkable resistance to loss of hypersensitive sites. These results establish a key principle: the transcriptional consequences of enhancer editing are strongly constrained by local genomic architecture. Attempts to mimic KLF1 haploinsufficiency by non-coding indels are blunted by dense regulatory architecture, enhancer redundancy, and long-range interaction. Thus, it may be difficult to develop KLF1 as a target for gene therapy for hemoglobinopathies until tools for recapitulating natural mutations via heterozygous edits are developed. Our findings underscore the observation that disruption of non-coding elements may not always recapitulate the biology of haploinsufficiency from heterozygous loss-of-function mutations.
SN - 2399-3642
ER -