# Daniel E. Bauer
**Daniel E. Bauer** (full name Daniel Evan Bauer) is an American physician-scientist in genome editing who directs the Gene Therapy Program and attends at the Dana-Farber/Boston Children's Cancer and Blood Disorders Center, and holds the [Donald S. Fredrickson](https://www.edgepedia.org/donald-s-fredrickson), MD Associate Professor of Pediatrics chair at Harvard Medical School.[1](https://research.childrenshospital.org/researchers/daniel-bauer) He is known for identifying the erythroid enhancer of the *BCL11A* gene as a therapeutic genome-editing target for sickle cell disease and beta-thalassemia, work that underlies approved CRISPR therapies.[1](https://research.childrenshospital.org/researchers/daniel-bauer) • [2](https://www.hsci.harvard.edu/people/daniel-e-bauer-md-phd)
| Fact | Detail |
|---|---|
| Current roles | Director, Gene Therapy Program; attending physician, Dana-Farber/Boston Children's Cancer and Blood Disorders Center[1](https://research.childrenshospital.org/researchers/daniel-bauer) |
| Academic chair | Donald S. Fredrickson, MD Associate Professor of Pediatrics, Harvard Medical School[1](https://research.childrenshospital.org/researchers/daniel-bauer) |
| Signature work | BCL11A erythroid enhancer editing to reactivate fetal hemoglobin (Science 2013; Nature 2015; Nature Medicine 2019, 2020)[1](https://research.childrenshospital.org/researchers/daniel-bauer) |
| Training | B.S. Brown University; M.D./Ph.D. University of Pennsylvania (thesis with Craig Thompson); postdoc with Stuart Orkin[2](https://www.hsci.harvard.edu/people/daniel-e-bauer-md-phd) |
| Awards | NIH Director's New Innovator Award (2016); ASGCT Outstanding New Investigator Award (2020)[2](https://www.hsci.harvard.edu/people/daniel-e-bauer-md-phd) • [3](https://www.danafarberbostonchildrens.org/news/bauer-earns-outstanding-new-investigator-award-asgct) |
| Clinical translation | Lead sponsor-investigator of phase 1 BCL11A enhancer-editing trial NCT06647979 (started December 2025)[4](https://clinicaltrials.gov/study/NCT06647979) |
| Lab | Opened July 2014, Karp Family Research Building, Boston Children's Hospital[5](https://www.bauerlab.org/) |
## Education and training
Bauer received a B.S. in Biology from [Brown University](https://www.edgepedia.org/brown-university) and his M.D. and Ph.D. from the University of Pennsylvania.[2](https://www.hsci.harvard.edu/people/daniel-e-bauer-md-phd) His doctoral thesis in Cell and Molecular Biology was under [Craig Thompson](https://www.edgepedia.org/craig-thompson), investigating growth factor regulation of hematopoietic cell metabolism.[2](https://www.hsci.harvard.edu/people/daniel-e-bauer-md-phd) He then trained clinically in pediatrics at [Boston Children's Hospital](https://www.edgepedia.org/boston-childrens-hospital) and in pediatric hematology/oncology at Boston Children's/Dana-Farber Cancer Institute.[1](https://research.childrenshospital.org/researchers/daniel-bauer) His postdoctoral work was in Stuart Orkin's laboratory at Harvard, studying the role of common genetic variation in the regulation of fetal hemoglobin.[2](https://www.hsci.harvard.edu/people/daniel-e-bauer-md-phd) He is Principal Faculty at the Harvard Stem Cell Institute and an Associate Member of the Broad Institute.[2](https://www.hsci.harvard.edu/people/daniel-e-bauer-md-phd)
## Research on BCL11A and fetal hemoglobin
[Fetal hemoglobin](https://www.edgepedia.org/fetal-hemoglobin) (HbF) is the oxygen carrier of the newborn, and people who retain elevated levels of it are protected from sickle cell disease and beta-thalassemia. According to *CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β-Thalassemia*, BCL11A is a zinc-finger transcription factor that represses gamma-globin expression and fetal hemoglobin in erythroid cells, and SNPs in its erythroid-specific enhancer associated with increased fetal hemoglobin lower disease severity.[6](https://www.nejm.org/doi/full/10.1056/NEJMoa2031054) Bauer's 2013 Science paper identified an erythroid enhancer of *BCL11A* subject to genetic variation that determines fetal hemoglobin level.[1](https://research.childrenshospital.org/researchers/daniel-bauer) His 2015 Nature paper dissected this enhancer by Cas9-mediated in situ saturating mutagenesis.[1](https://research.childrenshospital.org/researchers/daniel-bauer) The enhancer is active only in red blood cells, so disrupting it silences BCL11A where it represses HbF while sparing B-cell function.[7](https://www.danafarberbostonchildrens.org/news/researchers-dana-farberboston-childrens-and-umass-medical-school-optimize-gene-editing-sickle)
## Therapeutic gene editing of hematopoietic stem cells
His 2019 [Nature Medicine](https://www.edgepedia.org/nature-medicine) paper showed that electroporating Cas9 ribonucleoproteins targeting the +58 BCL11A erythroid enhancer into human CD34+ hematopoietic stem and progenitor cells achieved indel frequencies of 66.1 to 90.7 percent, up to 98.1 percent with an optimized 3xNLS-Cas9 RNP.[8](https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6512986&blobtype=pdf) In edited cells, BCL11A expression was preserved in B-lymphocytes but reduced by more than 80 percent in erythroid cells, and gamma-globin rose from about 2 to over 70 percent of total beta-like globin; edited marrow supported secondary transplantation at a mean indel frequency of over 95 percent, consistent with editing of self-renewing HSCs.[8](https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6512986&blobtype=pdf)
His 2020 Nature Medicine paper moved to base editing, which converts a single DNA letter without making a double-strand break. Using purified A3A(N57Q)-BE3 base editor protein delivered by RNP electroporation, a single cytidine edit within the core [GATA1](https://www.edgepedia.org/gata1) motif of the enhancer produced HbF induction similar to Cas9 nuclease indels and ameliorated sickling in sickle cell disease and globin-chain imbalance in beta-thalassemia patient-derived cells.[9](https://pmc.ncbi.nlm.nih.gov/articles/PMC7869435/) In mobilized CD34+ cells from two sickle cell donors, two electroporation cycles achieved over 70 percent editing at the target cytosine, raising bulk erythroid HbF to roughly 30 percent from baselines of about 5 and 6 percent.[9](https://pmc.ncbi.nlm.nih.gov/articles/PMC7869435/) A related 2019 Blood abstract reported 81 percent on-target allele editing with low indels and reduced sickling from 84 to 29 percent of erythrocytes.[10](https://doi.org/10.1182/blood-2019-129173)
## Translation and comparison with other sickle cell gene therapies
The enhancer target moved to the clinic as exagamglogene autotemcel (exa-cel, Casgevy), a nonviral autologous therapy that edits the erythroid enhancer of BCL11A ex vivo in patients' own CD34+ cells.[11](https://www.nejm.org/doi/full/10.1056/NEJMoa2309676) In the phase 3 study, nearly all of 30 evaluable patients were free of severe vaso-occlusive crises for at least 12 consecutive months, with mean allelic editing of about 86 percent; no graft-versus-host disease or hematologic cancer occurred, and adverse events were mostly attributed to busulfan conditioning.[11](https://www.nejm.org/doi/full/10.1056/NEJMoa2309676)
Alternatives differ in mechanism. [Adenine base editing](https://www.edgepedia.org/adenine-base-editing) converting the sickle HBB S allele to the benign Makassar variant reached 80 percent conversion in patient HSPCs and avoided the p53 activation and larger deletions seen after Cas9 nuclease treatment.[12](https://www.nature.com/articles/s41586-021-03609-w) [Prime editing](https://www.edgepedia.org/prime-editing) corrected HBB S to wild type at 15 to 41 percent frequencies without double-strand breaks or donor templates, with desired edit-to-indel ratios of 5.9 to 6.7 versus 0.74 to 1.6 for Cas9-HDR correction.[13](https://doi.org/10.1038/s41551-023-01026-0) A comparative murine analysis found base editing preserved about 20 percent of edited beta-globin alleles versus about 6 percent for BCL11A enhancer editing, attributed to double-strand-break-induced p53 responses, and, per the study, both approved autologous products leave about 45 percent HbS in erythrocytes, which direct allele correction could alleviate.[14](https://pmc.ncbi.nlm.nih.gov/articles/PMC12828757/)
## Representative work
- **"BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis"**, *Nature* (2015), [doi:10.1038/nature15521](https://doi.org/10.1038/nature15521).
## Awards, funding and clinical trial
Bauer's honors include the American Society of Clinical Investigation Young Physician-Scientist Award (2014), the NIH Director's New Innovator Award (2016), the Society for Pediatric Research Young Investigator Award (2017), finalist for the Foundation for the NIH Trailblazer Prize (2018),[2](https://www.hsci.harvard.edu/people/daniel-e-bauer-md-phd) and the 2020 Outstanding New Investigator Award from the American Society of Gene & Cell Therapy.[3](https://www.danafarberbostonchildrens.org/news/bauer-earns-outstanding-new-investigator-award-asgct) He held NIH K08 DK093705 (2012–2017) on epigenetic regulation of BCL11A in the hemoglobin switch[15](https://grantome.com/grant/NIH/K08-DK093705-05) and R01 HL150669 (2019–2023) developing Cas9 and Cas12a editing to correct splicing mutations in beta-thalassemia and [Shwachman-Diamond syndrome](https://www.edgepedia.org/shwachman-diamond-syndrome).[16](https://grantome.com/grant/NIH/R01-HL150669-02)
He is lead sponsor-investigator of a phase 1 adaptive basket trial (NCT06647979) at Boston Children's Hospital, started December 1, 2025, testing a single infusion of autologous bone-marrow-derived CD34+ cells electroporated with BCL11A enhancer-targeting Cas9 ribonucleoprotein in up to 14 subjects, seven with sickle cell disease and seven with beta-thalassemia, with primary completion expected in December 2028.[4](https://clinicaltrials.gov/study/NCT06647979)
## References
1. Daniel Bauer | Boston Children's Research. https://research.childrenshospital.org/researchers/daniel-bauer
2. Daniel E. Bauer, M.D., Ph.D. | Harvard Stem Cell Institute. https://www.hsci.harvard.edu/people/daniel-e-bauer-md-phd
3. Bauer earns Outstanding New Investigator Award from ASGCT. https://www.danafarberbostonchildrens.org/news/bauer-earns-outstanding-new-investigator-award-asgct
4. NCT06647979. https://clinicaltrials.gov/study/NCT06647979
5. Daniel Bauer Lab. https://www.bauerlab.org/
6. CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β-Thalassemia | NEJM. https://www.nejm.org/doi/full/10.1056/NEJMoa2031054
7. Researchers optimize gene editing for sickle cell disease and beta thalassemia. https://www.danafarberbostonchildrens.org/news/researchers-dana-farberboston-childrens-and-umass-medical-school-optimize-gene-editing-sickle
8. Highly efficient therapeutic gene editing of human hematopoietic stem cells (PMC full text). https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6512986&blobtype=pdf
9. Therapeutic base editing of human hematopoietic stem cells (Nature Medicine, 2020). https://pmc.ncbi.nlm.nih.gov/articles/PMC7869435/
10. Therapeutic Base Editing of Human Hematopoietic Stem Cells (Blood, 2019). https://doi.org/10.1182/blood-2019-129173
11. Exagamglogene Autotemcel for Severe Sickle Cell Disease | NEJM. https://www.nejm.org/doi/full/10.1056/NEJMoa2309676
12. Base editing of haematopoietic stem cells rescues sickle cell disease in mice (Nature, 2021). https://www.nature.com/articles/s41586-021-03609-w
13. Ex vivo prime editing of patient haematopoietic stem cells (Nature Biomedical Engineering, 2023). https://doi.org/10.1038/s41551-023-01026-0
14. Comparative analysis of CRISPR-Cas9, lentiviral transduction, and base editing for sickle cell disease (2025). https://pmc.ncbi.nlm.nih.gov/articles/PMC12828757/
15. NIH K08 DK093705. https://grantome.com/grant/NIH/K08-DK093705-05
16. NIH R01 HL150669. https://grantome.com/grant/NIH/R01-HL150669-02
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*Topic: Encyclopedia › Life and health › Life and health scientists › Life scientists › Researchers in genetics, genomics, and genome engineering › Genome engineering and gene editing*
*Initially written Sep 21, 2026 · Reviewed: Sep 25, 2026 · Edited: Sep 25, 2026 · Last review: Sep 25, 2026*
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License: Edgepedia Community License 1.0, https://www.edgepedia.org/edgepedia/license