Feng Pan

All Publications

• High-efficiency CRISPR induction of t(9;11) chromosomal translocations and acute leukemias in human blood stem cells. Blood advances Jeong, J., Jager, A., Domizi, P., Pavel-Dinu, M., Gojenola, L., Iwasaki, M., Wei, M. C., Pan, F., Zehnder, J. L., Porteus, M. H., Davis, K. L., Cleary, M. L. 2019; 3 (19): 2825–35

  Abstract

  Chromosomal rearrangements involving the mixed lineage leukemia (MLL) gene, also known as KMT2A, are often observed in human leukemias and are generally associated with a poor prognosis. To model these leukemias, we applied clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing to induce MLL chromosomal rearrangements in human hematopoietic stem and progenitor cells purified from umbilical cord blood. Electroporation of ribonucleoprotein complexes containing chemically modified synthetic single guide RNAs and purified Cas9 protein induced translocations between chromosomes 9 and 11 [t(9;11)] at an efficiency >1%. Transplantation of gene-edited cells into immune-compromised mice rapidly induced acute leukemias of different lineages and often with multiclonal origins dictated by the duration of in vitro culture prior to transplantation. Breakpoint junction sequences served as biomarkers to monitor clonal selection and progression in culture and in vivo. High-dimensional cell surface and intracellular protein analysis by mass cytometry (CyTOF) revealed that gene-edited leukemias recapitulated disease-specific protein expression observed in human patients and showed that MLL-rearranged (MLLr) mixed phenotype acute leukemias (MPALs) were more similar to acute myeloid leukemias (AMLs) than to acute lymphoblastic leukemias (ALLs). Therefore, highly efficient generation of MLL chromosomal translocations in primary human blood stem cells using CRISPR/Cas9 reliably models human acute MLLr leukemia and provides an experimental platform for basic and translational studies of leukemia biology and therapeutics.

  View details for DOI 10.1182/bloodadvances.2019000450

  View details for PubMedID 31582391

• Consecutive epigenetically-active agent combinations act inID1-RUNX3-TET2andHOXApathways forFlt3ITD+veAML. Oncotarget Sayar, H., Liu, Y., Gao, R., Zaid, M. A., Cripe, L. D., Weisenbach, J., Sargent, K. J., Nassiri, M., Li, L., Konig, H., Suvannasankha, A., Pan, F., Shanmugam, R., Goswami, C., Kapur, R., Xu, M., Boswell, H. S. 2018; 9 (5): 5703–15

  Abstract

  Co-occurrence ofFlt3ITDandTET2mutations provoke an animal model of AML by epigenetic repression of Wnt pathway antagonists, includingRUNX3,and by hyperexpression ofID1,encoding Wnt agonist. These affectHOXAover-expression and treatment resistance. A comparable epigenetic phenotype was identified among adult AML patients needing novel intervention. We chose combinations of targeted agents acting on distinct effectors, at the levels of both signal transduction and chromatin remodeling, in relapsed/refractory AML's, includingFlt3ITD+ve,described with a signature of repressed tumor suppressor genes, involving Wnt antagonistRUNX3, occurring along withID1andHOXAover-expressions. We tracked patient response to combination of Flt3/Raf inhibitor, Sorafenib, and Vorinostat, pan-histone deacetylase inhibitor, without or with added Bortezomib, in consecutive phase I trials. A striking association of rapid objective remissions (near-complete, complete responses) was noted to accompany induced early pharmacodynamic changes within patient blasts in situ, involving these effectors, significantly linkingRUNX3/Wnt antagonist de-repression (80%) andID1downregulation (85%), to a response, also preceded by profoundHOXA9repression. Response occurred in context of concurrentTET2mutation/hypomorphy andFlt3ITD+vemutation (83% of complete responses). Addition of Bortezomib to the combination was vital to attainment of complete response inFlt3ITD+vecases exhibiting such Wnt pathway dysregulation.

  View details for DOI 10.18632/oncotarget.23655

  View details for PubMedID 29464028

  View details for PubMedCentralID PMC5814168

• RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells. Nature genetics Guallar, D., Bi, X., Pardavila, J. A., Huang, X., Saenz, C., Shi, X., Zhou, H., Faiola, F., Ding, J., Haruehanroengra, P., Yang, F., Li, D., Sanchez-Priego, C., Saunders, A., Pan, F., Valdes, V. J., Kelley, K., Blanco, M. G., Chen, L., Wang, H., Sheng, J., Xu, M., Fidalgo, M., Shen, X., Wang, J. 2018

  Abstract

  Ten-eleven translocation (TET) proteins play key roles in the regulation of DNA-methylation status by oxidizing 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), which can both serve as a stable epigenetic mark and participate in active demethylation. Unlike the other members of the TET family, TET2 does not contain a DNA-binding domain, and it remains unclear how it is recruited to chromatin. Here we show that TET2 is recruited by the RNA-binding protein Paraspeckle component 1 (PSPC1) through transcriptionally active loci, including endogenous retroviruses (ERVs) whose long terminal repeats (LTRs) have been co-opted by mammalian genomes as stage- and tissue-specific transcriptional regulatory modules. We found that PSPC1 and TET2 contribute to ERVL and ERVL-associated gene regulation by both transcriptional repression via histone deacetylases and post-transcriptional destabilization of RNAs through 5hmC modification. Our findings provide evidence for a functional role of transcriptionally active ERVs as specific docking sites for RNA epigenetic modulation and gene regulation.

  View details for DOI 10.1038/s41588-018-0060-9

  View details for PubMedID 29483655

• Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells NATURE COMMUNICATIONS Pan, F., Wingo, T. S., Zhao, Z., Gao, R., Makishima, H., Qu, G., Lin, L., Yu, M., Ortega, J. R., Wang, J., Nazha, A., Chen, L., Yao, B., Liu, C., Chen, S., Weeks, O., Ni, H., Phillips, B. L., Huang, S., Wang, J., He, C., Li, G., Radivoyevitch, T., Aifantis, I., Maciejewski, J. P., Yang, F., Jin, P., Xu, M. 2017; 8

  Abstract

  TET2 is a dioxygenase that catalyses multiple steps of 5-methylcytosine oxidation. Although TET2 mutations frequently occur in various types of haematological malignancies, the mechanism by which they increase risk for these cancers remains poorly understood. Here we show that Tet2(-/-) mice develop spontaneous myeloid, T- and B-cell malignancies after long latencies. Exome sequencing of Tet2(-/-) tumours reveals accumulation of numerous mutations, including Apc, Nf1, Flt3, Cbl, Notch1 and Mll2, which are recurrently deleted/mutated in human haematological malignancies. Single-cell-targeted sequencing of wild-type and premalignant Tet2(-/-) Lin(-)c-Kit(+) cells shows higher mutation frequencies in Tet2(-/-) cells. We further show that the increased mutational burden is particularly high at genomic sites that gained 5-hydroxymethylcytosine, where TET2 normally binds. Furthermore, TET2-mutated myeloid malignancy patients have significantly more mutational events than patients with wild-type TET2. Thus, Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells, suggesting a novel TET2 loss-mediated mechanism of haematological malignancy pathogenesis.

  View details for DOI 10.1038/ncomms15102

  View details for Web of Science ID 000400109400001

  View details for PubMedID 28440315

  View details for PubMedCentralID PMC5414116

• Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis. Nature communications Li, X., Yao, B., Chen, L., Kang, Y., Li, Y., Cheng, Y., Li, L., Lin, L., Wang, Z., Wang, M., Pan, F., Dai, Q., Zhang, W., Wu, H., Shu, Q., Qin, Z., He, C., Xu, M., Jin, P. 2017; 8: 15903

  Abstract

  Emerging evidence suggests that active DNA demethylation machinery plays important epigenetic roles in mammalian adult neurogenesis; however, the precise molecular mechanisms and critical functional players of DNA demethylation in this process remain largely unexplored. Ten-eleven translocation (Tet) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and its downstream derivatives. Here we show that 5hmC is elevated during the differentiation of adult neural stem cells (aNSCs), and Tet2 is primarily responsible for modulating 5hmC dynamics. Depletion of Tet2 leads to increased aNSC proliferation and reduced differentiation in vitro and in vivo. Genome-wide transcriptional analyses reveal important epigenetic roles of Tet2 in maintaining the transcriptome landscape related to neurogenesis. Mechanistically, transcription factor forkhead box O3 (Foxo3a) physically interacts with Tet2 and regulates the expression of genes related to aNSC proliferation. These data together establish an important role for the Tet2-Foxo3a axis in epigenetically regulating critical genes in aNSCs during adult neurogenesis.

  View details for DOI 10.1038/ncomms15903

  View details for PubMedID 28660881

• The catalytic activity of TET2 is essential for its myeloid malignancy-suppressive function in hematopoietic stem/progenitor cells. Leukemia Zhao, Z., Chen, S., Zhu, X., Pan, F., Li, R., Zhou, Y., Yuan, W., Ni, H., Yang, F. C., Xu, M. 2016

  View details for DOI 10.1038/leu.2016.56

  View details for PubMedID 27003514

• Combined Loss of Tet1 and Tet2 Promotes B Cell, but Not Myeloid Malignancies, in Mice CELL REPORTS Zhao, Z., Chen, L., Dawlaty, M. M., Pan, F., Weeks, O., Zhou, Y., Cao, Z., Shi, H., Wang, J., Lin, L., Chen, S., Yuan, W., Qin, Z., Ni, H., Nimer, S. D., Yang, F., Jaenisch, R., Jin, P., Xu, M. 2015; 13 (8): 1692-1704

  Abstract

  TET1/2/3 are methylcytosine dioxygenases that regulate cytosine hydroxymethylation. Tet1/2 are abundantly expressed in HSC/HPCs and are implicated in hematological malignancies. Tet2 deletion in mice causes myeloid malignancies, while Tet1-null mice develop B cell lymphoma after an extended period of latency. Interestingly, TET1/2 are often concomitantly downregulated in acute B-lymphocytic leukemia. Here, we investigated the overlapping and non-redundant functions of Tet1/2 using Tet1/2 double-knockout (DKO) mice. DKO and Tet2(-/-) HSC/HPCs show overlapping and unique 5 hmC and 5 mC profiles. DKO mice exhibit strikingly decreased incidence and delayed onset of myeloid malignancies in comparison to Tet2(-/-) mice and in contrast develop lethal B cell malignancies. Transcriptome analysis of DKO tumors reveals expression changes in many genes dysregulated in human B cell malignancies, including LMO2, BCL6, and MYC. These results highlight the critical roles of TET1/2 individually and together in the pathogenesis of hematological malignancies.

  View details for DOI 10.1016/j.celrep.2015.10.037

  View details for Web of Science ID 000365404900018

  View details for PubMedID 26586431

• The TET2 interactors and their links to hematological malignancies IUBMB LIFE Pan, F., Weeks, O., Yang, F., Xu, M. 2015; 67 (6): 438-445

  Abstract

  Ten-eleven translocation (TET) family proteins are dioxygenases that oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in DNA, early steps of active DNA demethylation. TET2, the second member of TET protein family, is frequently mutated in patients with hematological malignancies, leading to aberrant DNA methylation profiling and decreased 5hmC levels. Located in the nucleus and acting as a DNA-modifying enzyme, TET2 is thought to exert its function via TET2-containing protein complexes. Identifying the interactome network of TET2 likely holds the key to uncover the mechanisms by which TET2 exerts its function in cells. Here, we review recent literature on TET2 interactors and discuss their possible roles in TET2 loss-mediated dysregulation of hematopoiesis and pathogenesis of hematological malignancies.

  View details for DOI 10.1002/iub.1389

  View details for Web of Science ID 000356969600005

  View details for PubMedID 26099018

• Loss of Asxl1 leads to myelodysplastic syndrome-like disease in mice. Blood Wang, J., Li, Z., He, Y., Pan, F., Chen, S., Rhodes, S., Nguyen, L., Yuan, J., Jiang, L., Yang, X., Weeks, O., Liu, Z., Zhou, J., Ni, H., Cai, C., Xu, M., Yang, F. 2014; 123 (4): 541-553

  Abstract

  ASXL1 is mutated/deleted with high frequencies in multiple forms of myeloid malignancies, and its alterations are associated with poor prognosis. De novo ASXL1 mutations cause Bohring-Opitz syndrome characterized by multiple congenital malformations. We show that Asxl1 deletion in mice led to developmental abnormalities including dwarfism, anophthalmia, and 80% embryonic lethality. Surviving Asxl1(-/-) mice lived for up to 42 days and developed features of myelodysplastic syndrome (MDS), including dysplastic neutrophils and multiple lineage cytopenia. Asxl1(-/-) mice had a reduced hematopoietic stem cell (HSC) pool, and Asxl1(-/-) HSCs exhibited decreased hematopoietic repopulating capacity, with skewed cell differentiation favoring granulocytic lineage. Asxl1(+/-) mice also developed mild MDS-like disease, which could progress to MDS/myeloproliferative neoplasm, demonstrating a haploinsufficient effect of Asxl1 in the pathogenesis of myeloid malignancies. Asxl1 loss led to an increased apoptosis and mitosis in Lineage(-)c-Kit(+) (Lin(-)c-Kit(+)) cells, consistent with human MDS. Furthermore, Asxl1(-/-) Lin(-)c-Kit(+) cells exhibited decreased global levels of H3K27me3 and H3K4me3 and altered expression of genes regulating apoptosis (Bcl2, Bcl2l12, Bcl2l13). Collectively, we report a novel ASXL1 murine model that recapitulates human myeloid malignancies, implying that Asxl1 functions as a tumor suppressor to maintain hematopoietic cell homeostasis. Future work is necessary to clarify the contribution of microenvironment to the hematopoietic phenotypes observed in the constitutional Asxl1(-/-) mice.

  View details for DOI 10.1182/blood-2013-05-500272

  View details for PubMedID 24255920