About

Gerd A. Blobel, MD, PhD, is a Professor of Pediatrics (Hematology) and the Frank E. Weise III Professor of Pediatrics at the Children's Hospital of Philadelphia (CHOP). He is affiliated with the Department of Pediatrics and holds graduate group affiliations in Pharmacology, Genomics and Computational Biology, Cell and Molecular Biology, and Immunology. His research focuses on understanding how genetic regulatory elements are organized spatially within the nucleus and how transcription programs and chromatin architecture are maintained throughout the cell cycle to preserve lineage identity. A major aspect of his work involves studying the regulation of globin gene expression and developing approaches to modify globin gene expression to treat sickle cell disease. His research bridges basic science with pre-clinical studies, employing molecular, genomic, biochemical, and imaging techniques, and utilizing studies in normal and gene-targeted mice.

Research topics

• Cell biology
• Biology
• Biochemistry
• Genetics
• Molecular biology
• Cancer research
• Endocrinology

Selected publications

• An optimized CRISPR-Cas12a genome-wide screen reveals PTPA phosphatase pathway in fetal hemoglobin silencing

  Blood · 2026-01-12 · 1 citations

  articleOpen accessSenior author

  ABSTRACT: Reactivating the fetal globin genes HBG1 and HBG2 in adult erythroid cells represents a validated therapeutic approach for hemoglobinopathies. Central mediators of the fetal-to-adult hemoglobin transition include the direct transcriptional HBG1/2 repressors BCL11A, LRF, and NFIA/X. Limited-scale screens have expanded the regulatory circuity surrounding fetal globin silencing, but systematic genome-wide dissection of such pathways is lacking. We used a 2-tiered genetic screening strategy, a novel CRISPR-Cas12a-based screening platform followed by a domain-focused CRISPR-Cas9 screen, to interrogate all known human protein-coding genes for their impact on HBG1/2 regulation and erythroid cellular fitness, generating a comprehensive resource for the field. Among the top new hits was protein phosphatase 2A (PP2A) phosphatase activator (PTPA), an activator of the serine-threonine phosphatase PP2A whose loss elevates HBG1/2 levels while preserving erythroid differentiation. Phenotypic rescue experiments revealed that PTPA silences HBG1/2 expression primarily by regulating BCL11A expression. To our knowledge, this study represents the most comprehensive CRISPR dissection of HBG regulation to date, highlighting the power of Cas12a-based genome-scale screening for uncovering disease-relevant pathways.

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• Dissecting polycomb complexes for enhanced fetal hemoglobin production

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-18

  articleOpen accessSenior authorCorresponding

  Abstract Polycomb repressive complexes PRC1 and PRC2 regulate diverse developmental processes, including the fetal-to-adult switch in hemoglobin production, a process whose reversal is a goal for the treatment of sickle cell disease and β-thalassemia. PRC inhibitors show promise for various disorders, but use is limited because of pleiotropic PRC activities. We explored whether fetal hemoglobin (HbF) can be reactivated in adult erythroid cells by selective perturbations of PRC1 or PRC2 components without complete loss of PRC function. A high-density CRISPR-Cas9 mutagenesis screen identified a region in the EZH2 subunit where Cas9 induced exon 14 skipping (EZH2Δ14). EZH2Δ14, which lacks a portion of the CXC domain, relieves HbF repression while largely maintaining cellular fitness. EZH2Δ14 retains H3K27 methylation and repression of a PRC target gene subset. Experiments in cells derived from mice bearing human β-globin genes confirm that pathways mediating EZH2 control of HbF expression can function in a mouse model of HBG switching. These findings demonstrate that partial disruption of PRC can yield selective phenotypes, highlighting the therapeutic potential of targeting non-enzymatic domains within chromatin-modifying complexes. Key Points CRISPR-Cas9 screen across PRC1 and a saturating mutagenesis screen of PRC2 found the EZH2 CXC domain a desirable target for HbF induction the EZH2-CXC domain leads to exon 14 exclusion, resulting in de-repression of HbF but maintenance of cell fitness.

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• De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion

  Nature Genetics · 2026-04-01 · 2 citations

  articleSenior author
  PublisherDOI

• Abstract 7237: LDB1-dependent enhancer connectivity constrains a metabolic synthetic lethality in T-cell acute lymphoblastic leukemia

  Cancer Research · 2026-04-03

  articleSenior author

  Abstract LDB1 and LMO2, two proteins frequently overexpressed in T-cell acute lymphoblastic leukemia (T-ALL), form a chromatin architectural complex that promotes chromatin looping between enhancers and/or promoters. Here, we defined LDB1-driven oncogenic enhancer connectivity in T-ALL and examined its impact on therapeutic vulnerabilities. To identify proximal LDB1 targets in T-ALL, we engineered isogenic T-ALL cell lines (LOUCY [ETP-ALL] and KOPT K1 [non-ETP-ALL]) with dTAG degrons at the endogenous LDB1 loci. Treatment with dTAG-V1 ligand for 4 hours reduced LDB1 protein levels and chromatin occupancy by >90%. Acute LDB1 loss disrupted spatial enhancer connectivity at critical leukemic oncogenes in both LOUCY (e.g. HHEX, MYB, MYCN) and KOPT K1 (e.g. DUSP6, STAT4), resulting in their downregulation and subsequent reduction in cell growth. CRISPRa-mediated restoration of select LDB1-dependent oncogenes, such as MYB, in LDB1-depleted cells rescued cell expansion. Nascent transcript profiling further revealed that acute LDB1 loss affected distinct gene sets in LOUCY and KOPT K1, consistent with their distinct identities. Notably, however, several cholesterol biosynthetic genes (HMGCS1, MVD, MVK) were upregulated in both cell types. These changes were not driven by altered expression or subcellular localization of SREBP2—the canonical transcriptional regulator of these genes. Instead, they were caused by altered enhancer-promoter connectivity in the absence of LDB1. Specifically, LDB1 loss disrupted connectivity of nearby enhancers for different genes, thereby liberating them to form de novo contacts with HMGCS1, MVK, and MVD gene promoters to activate them. Hence, by clustering regulatory elements, LDB1 not only enables the expression of genes but also constrains enhancers from making inappropriate contacts. Importantly, the native LDB1-dependent loops are detected in primary samples from patients with T-ALL based on published H3K27ac HiChIP data. Functionally, we found that cholesterol flux and expression of upstream regulators, like SREBP2, increased with prolonged LDB1 depletion, suggesting a feed-forward regulatory mechanism on cholesterol homeostasis in T-ALL. Using both LDB1 degron and knockout models, we observed that LDB1 loss sensitizes leukemic cells to rosuvastatin and pitavastatin by 2-5-fold. This was recapitulated in several T-ALL cell lines with distinct molecular drivers upon LDB1 knockout. Furthermore, statin sensitization was rescued by spike-in of mevalonate or geranylgeranyl pyrophosphate, confirming that this phenotype is driven by altered cholesterol metabolism. Together, our study illustrates a paradigm by which LDB1 loss enables illegitimate spatial connections of enhancers with cholesterol biosynthetic gene promoters. This, in turn, creates a new metabolic addiction in leukemic cells, which may be targeted with statins. Citation Format: Rahul S. Bhansali, Juan S. Long, Siqing Wang, Ahnaf Tausif, Shuo Zhang, Petri Pölönen, Sarah Skuli, Nicholas Aboreden, Zhuangzhuang Geng, Belinda M. Giardine, Cheryl A. Keller, Ross C. Hardison, Charles G. Mullighan, Gerd A. Blobel. LDB1-dependent enhancer connectivity constrains a metabolic synthetic lethality in T-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7237.

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• Expansion of human hematopoietic stem cells by inhibiting translation

  Blood · 2025-11-03

  articleOpen access

  Abstract Hematopoietic stem cell (HSC) transplantation using umbilical cord blood (UCB) is a potentially life-saving treatment for leukemia and bone marrow failure but is limited by the low number of HSCs in UCB. The loss of HSCs after ex vivo manipulation is also a major obstacle to gene editing for inherited blood disorders. HSCs require a low rate of translation to maintain their capacity for self-renewal, but hematopoietic cytokines used to expand HSCs stimulate protein synthesis and impair long-term self-renewal. We previously described cytokine-free conditions that maintain human and mouse HSCs ex vivo using inhibitors of GSK-3 (CHIR) and mTOR (Rapamycin), referred to hereafter as “CR”. Here we performed a high throughput screen of 2,240 FDA approved and/or bioactive compounds and found that the translation inhibitor 4E1RCat allows ex vivo expansion of human HSCs from UCB in CR medium with minimal cytokine exposure. Single cell transcriptomic analysis demonstrates maintenance of HSCs expressing mediators of the unfolded protein stress response, further supporting the potential importance of regulated proteostasis in HSC maintenance and expansion. We confirmed that these culture conditions promote the expansion of long-term HSCs by limiting dilution analysis (LDA) and secondary transplantation. The LDA shows a ~5-fold expansion of functional HSCs from UCB after one week of culture in CR with low cytokines and 4E1RCat. Secondary transplantation assays confirm expansion of long-term HSCs with multilineage potential. CRISPR/Cas9 editing of the BCL11A+58 enhancer is now an FDA approved therapy for sickle cell disease and transfusion-dependent β-thalassemia. However, loss of functional HSCs after ex vivo manipulation and culture remains a major obstacle to therapeutic gene editing. Our culture conditions maintain and expand human adult HSCs after gene editing by both electroporation and lipid nanoparticles (LNPs) delivery methods. After 7 days of culture in CR with low cytokines and 4E1RCat, phenotypic HSCs expanded ~35-78-fold compared to day 0 for HSCs undergoing electroporation or exposure to LNPs. Fetal hemoglobin (HbF) expression increased substantially after BCL11A editing in erythroid cells derived from day 7 expansion after electroporation or LNP delivery. Transplant of BCL11A-edited HSCs cultured in CR and low cytokines with 4E1RCat showed high engraftment comparable to freshly isolated HSCs, indicating maintenance of HSCs after culture in these conditions. Culturing edited HSCs under these conditions may therefore overcome a major obstacle to ex vivo gene correction for human hemoglobinopathies by maintaining functional HSCs.

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• Dynamics of microcompartment formation at the mitosis-to-G1 transition

  Nature Structural & Molecular Biology · 2025-10-17 · 11 citations

  articleOpen access

  As cells exit mitosis and enter G1, chromosomes decompact and transcription is reestablished. Hi-C studies have indicated that all interphase three-dimensional genome features, including A/B compartments, topologically associating domains and CCCTC-binding factor loops, are lost during mitosis. However, Hi-C is insensitive to features such as microcompartments, nested focal interactions between cis-regulatory elements. Here we apply region capture Micro-C to mouse erythroblasts from mitosis to G1. We unexpectedly observe microcompartments in prometaphase, which strengthen in anaphase and telophase before weakening throughout G1. Microcompartment anchors coincide with transcriptionally spiking promoters during mitosis. Loss of condensin loop extrusion differentially impacts microcompartments and A/B compartments, suggesting that they are partially distinct. Polymer modeling shows that microcompartment formation is favored by chromatin compaction and disfavored by loop extrusion, providing a basis for strong microcompartmentalization in anaphase and telophase. Our results suggest that compaction and homotypic affinity drive microcompartment formation, which may explain transient transcriptional spiking at mitotic exit.

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• SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity

  Cell Reports · 2025-03-31 · 1 citations

  articleOpen access

  The clustering of multiple transcription factor binding sites (TFBSs) for the same TF has proved to be a pervasive feature of cis-regulatory elements in the eukaryotic genome. However, the contribution of binding sites within the homotypic clusters of TFBSs (HCTs) to TF binding and target gene expression remains to be understood. Here, we characterize the CHD4 enhancers that harbor unique functional ZNF410 HCTs genome wide. We uncover that ZNF410 controls chromatin accessibility and activity of the CHD4 enhancer regions. We demonstrate that ZNF410 binds to the HCTs in a collaborative fashion, further conferring transcriptional activation. In particular, three ZNF410 motifs (sub-HCTs) located at 3' end of the distal enhancer act as "switch motifs" to control chromatin accessibility and enhancer activity. Mechanistically, the SWI/SNF complex is selectively required to mediate cooperative ZNF410 binding for CHD4 expression. Together, our findings expose a complex functional hierarchy of homotypic clustered motifs, which cooperate to fine-tune target gene expression.

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• Supp Fig S3 from Ubiquitin-Specific Protease 6 mRNA Lipid Nanoparticles Ignite Antitumor Immunity and Suppress Tumorigenesis in Ewing Sarcoma

  2025-11-03

  articleOpen access

  <p>IVT USP6 mRNA recapitulates immunostimulatory effects</p>

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• Keep your distance or lose control

  Blood · 2025-08-07

  letterOpen access1st authorCorresponding

  Finally, Khatib-Massalha et al show that the increased number of senescent neutrophils seems to be restricted to JAK2V617F MPN as it was absent in CALR-mutated MPN.Thus, these results suggest that the physiopathology of bone marrow fibrosis and of thrombocytosis differs among MPNs and depends on the driver mutation despite the common constitutive activation of the MPL/JAK2/STAT pathway.

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• LDB1-dependent enhancer networks drive high-risk transcriptional programs in T-cell acute lymphoblastic leukemia

  Blood · 2025-11-03

  articleOpen accessSenior author

  Abstract In T-cell acute lymphoblastic leukemia (T-ALL), LMO2 (Lim domain only 2) is frequently overexpressed due to chromosomal translocations or epigenetic changes. LMO2 is a molecular scaffold connecting LDB1 (Lim domain binding 1) to DNA-binding transcription factors. LDB1 is a major chromatin architectural factor involved in long-range enhancer-promoter interactions. Given the prevalence of aberrant LMO2 expression in T-ALL, we hypothesized that LDB1 promotes T-ALL proliferation/survival by connecting oncogenic enhancers to their target genes. We performed LDB1 ChIP-seq in 2 T-ALL cell lines with high LMO2 expression: LOUCY (early thymic precursor [ETP]; SET::NUP214) and KOPT K1 (non-ETP; TCRG::LMO2). LDB1 is predominantly recruited to cis-regulatory elements, with 40-60% of peaks localizing to enhancers. However, LDB1 enhancer occupancy differed significantly between cell lines, suggesting subtype-specific regulation of transcriptional programs. Indeed, motif enrichment analysis at LDB1-occupied enhancers demonstrated distinct recruiting factors in LOUCY versus KOPT K1. To enable rapid LDB1 degradation, we tagged endogenous LDB1 with dTAG in both cell lines. Treatment with dTAG-V1 ligand for 4hrs depleted LDB1 by >90%. To assess LDB1-dependent enhancer-promoter connectivity, we treated cells with dTAG-V1 for 4hrs and performed Micro-C sequenced to a depth of ~1 billion valid contacts. Globally, compartmentalization and topologically associated domains remained largely intact in the absence of LDB1. However, we observed widespread changes to loops involving LDB1-occupied enhancers and/or promoters. Importantly, histone modifications and chromatin accessibility at enhancers remained intact upon acute LDB1 depletion, suggesting that architectural changes were directly due to loss of LDB1's looping function rather than indirect consequences of enhancer loss. To explore how architectural changes impact gene expression, we measured nascent transcription using TT-seq upon acute LDB1 depletion and observed 328 and 134 differentially expressed genes in LOUCY and KOPT K1, respectively. LDB1-dependent transcripts in LOUCY included critical hematopoietic oncogenes (HHEX, MYB, MYCN, ERG, MEF2C) while those in KOPT K1 were enriched in immune activation pathways (DUSP6, BACH2, CD69). Reduced transcriptional output at these loci was associated with weakened enhancer-promoter connectivity. We analyzed 26 H3K27ac HiChIP datasets from patients with T-ALL and found that LDB1-dependent loops at these oncogenic loci are recapitulated and often correlate with T-ALL differentiation state. These findings suggest that LDB1 connects enhancers with oncogenic driver genes in both cultured and primary T-ALL cells. To determine if LDB1 is required for T-ALL proliferation/survival, we passaged LOUCY and KOPT K1 cells in the presence of dTAG-V1 for 15 days and observed loss of cell expansion. Loss of LDB1 in LOUCY induced apoptosis, while in KOPT K1 it elicited a senescent phenotype characterized by beta-galactosidase activation, cell cycle exit, and senescence-associated gene expression. To determine which gene expression changes accounted for these phenotypes, we restored expression of several LDB1-dependent genes in LDB1-depleted cells using CRISPRa. Reactivation of oncogenes like MYB partially rescued cell expansion, suggesting that LDB1 dependency in T-ALL may in part be conveyed through MYB. Finally, we compared LDB1-dependent transcriptional signatures from LOUCY and KOPT K1 to transcriptomic data from >1300 patients with T-ALL. The LOUCY signature was enriched in several high-risk T-ALL subtypes, including the recently defined ETP-like and LMO2 γδ-like entities. The KOPT K1 signature was conversely enriched in more differentiated subtypes such as TAL1/DP-like, together suggesting that LDB1 may be required to maintain transcriptional identity of T-ALL subtypes in vivo. Notably, LOUCY signature enrichment conferred worse overall survival (p=0.026) and event-free survival (p=0.00032), driven in part due to LDB1 regulation of high-risk transcriptional features in the ETP-like subtype. Together, our study highlights LDB1 as a critical architectural factor that connects T-ALL subtype-specific enhancers and promoters to regulate transcriptional programs required for T-ALL cell expansion. Analyses of patient-derived data corroborate our findings and implicate the prognostic and therapeutic value of LDB1 regulatory networks.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R56DK065806

  NIH · $224k · 2015

• NIH Grant R21DK075731

  NIH · $449k · 2009

• Epigenetic Control of Hematopoietic Gene Expression

  NIH · $3.7M · 2000–2020

• Epigenetic Control of Hematopoietic Gene Expression

  NIH · $4.5M · 2002–2025

• NIH Grant R01DK065806

  NIH · $5.3M · 2014

Frequent coauthors

• Ross C. Hardison

  Pennsylvania State University

  133 shared

• Cheryl A. Keller

  108 shared

• Belinda Giardine

  95 shared

• Mitchell J. Weiss

  St. Jude Children's Research Hospital

  91 shared

• Mortimer Poncz

  Children's Hospital of Philadelphia

  70 shared

• Ian C. Henrich

  Baruch S. Blumberg Institute

  67 shared

• Robert Young

  University of Pennsylvania

  66 shared

• Kanika Jain

  63 shared

Labs

• Blobel LabPI