My lab’s long-term research is to enhance genetic therapies by understanding how genes are regulated and how genomes remain stable. We’re focusing on two key areas: the functional genomics of hemoglobin switching, which improves our clinical and biological understanding of β-hemoglobinopathies and studying how blood stem cells respond to DNA damage, particularly from genome editing tools like CRISPR-Cas9. This work is crucial for improving the safety and effectiveness of genetic therapies.

Functional genomics of hemoglobin switching

Hemoglobin switching is the developmental process where different globin genes are activated at specific stages. Around six months after birth, the fetal γ-globin genes are silenced and the adult β-globin gene is activated, which prompts symptoms of β-hemoglobinopathies like sickle cell disease and β-thalassemia. By studying this switching mechanism, we aim to develop therapies that reactivate γ-globin to treat these conditions. Our research focuses on the genetic elements involved in this switch and how this knowledge can inform genome editing strategies for effective treatments.

DNA damage responses in blood stem cells

Our lab focuses on how blood stem cells respond to DNA damage, particularly from genome editing tools like CRISPR-Cas9. We found that genome editing with CRISPR in blood stem cells can cause significant chromosomal damage, including the formation of micronuclei and chromosome bridges. Micronuclei contain fragmented chromosomes and can lead to chromothripsis, a massive and chaotic rearrangement of chromosomes, which poses dangerous risks and can potentially lead to cancer. Our lab is focused on thorough safety studies in CRISPR-based gene therapies to mitigate these serious risks and ensure their safe application.

• NIDDK K01 “Defining the mechanisms of hemoglobin switching and genotoxicities associated with its manipulation”

Sibabalo Sokupa
Research Technologist I

Iliana Hunsberger
Research Technologist I

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Selected Publications

1. Mayuranathan T, Newby GA, Feng R, Yao Y, Mayberry KD, Lazzarotto CR, Li Y, Levine RM, Nimmagadda N, Dempsey E, Kang G, Porter SN, Doerfler PA, Zhang J, Jang Y, Chen J, Bell HW, Crossley M, Bhoopalan SV, Sharma A, Tisdale JF, Pruett-Miller SM, Cheng Y, Tsai SQ, Liu DR, Weiss MJ, Yen JS. Potent and uniform fetal hemoglobin induction via base editing. Nat Genet. 2023 Jul;55(7):1210-1220. Epub 2023 Jul 3. PMID: 37400614; PMCID: PMC10722557.
2. Feng R, Mayuranathan T, Huang P, Doerfler PA, Li Y, Yao Y, Zhang J, Palmer LE, Mayberry K, Christakopoulos GE, Xu P,Li C, Cheng Y, Blobel GA, Simon MC, Weiss MJ. Activation of γ-globin expression by hypoxia-inducible factor 1α. Nature Oct;610(7933):783-790, 2022. Epub 2022 Oct 12. PMID: 36224385; PMCID: PMC9773321
3. Woodard KJ, Doerfler PA, Mayberry KD, Sharma A, Levine R, Yen J, Valentine V, Palmer LE, Valentine M, Weiss MJ. Limitations of mouse models for sickle cell disease conferred by their human globin transgene configurations. Dis Model Mech Jun 1;15(6):dmm049463, 2022. PMID: 35793591; PMCID: PMC9277148.
4. Qin K, Huang P, Feng R, Keller CA, Peslak SA, Khandros E, Saari MS, Lan X, Mayuranathan T, Doerfler PA, Abdulmalik O, Giardine B, Chou ST, Shi J, Hardison RC, Weiss MJ, Blobel GA. Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells. Nat Genet Jun;54(6):874-884, 2022. PMID: 35618846; PMCID: PMC9203980
5. Doerfler PA, Feng R, Li Y, Palmer LE, Porter SN, Bell HW, Crossley M, Pruett-Miller SM, Cheng Y, Weiss MJ. Activation of γ-globin gene expression by GATA1 and NF-Y in hereditary persistence of fetal hemoglobin. Nat Genet Aug 2;53(8):1177-1186, 2021. PMID: 34341563; PMCID: PMC8610173
6. Leibowitz ML†, Papathanasiou S†, Doerfler PA‡, Blaine LJ‡, Sun L, Yao Y, Zhang CZ, Weiss MJ, Pellman D. Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing. Nat Genet Jun;53(6):895-905, 2021. PMID: 33846636; PMCID: PMC8192433. †‡Denotes equal contribution
7. Doerfler PA*, Sharma A*, Porter JS, Zheng Y, Tisdale JF, Weiss MJ. Genetic therapies for the first molecular disease. J Clin Invest Apr 15;131(8), 2021. PMID: 33855970; PMCID: PMC8262557. *Denotes equal contribution
8. Métais JY*, Doerfler PA*, Mayuranathan T*, Bauer DE, Fowler SC, Hsieh MM, Katta V, Keriwala S, Lazzarotto CR, Luk K, Neel MD, Perry SS, Peters ST, Porter SN, Ryu BY, Sharma A, Shea D, Tisdale JF, Uchida N, Wolfe SA, Woodard KJ, Wu Y, Yao Y, Zeng J, Pruett-Miller S, Tsai SQ, Weiss MJ. Genome editing of HBG1 and HBG2 to induce fetal hemoglobin. Blood Adv Nov 12;3(21):3379-3392, 2019. PMID: 31698466; PMCID: PMC6855127. *Denotes equal contribution

Linkedin
https://www.linkedin.com/in/pdoerfler/