Yang Feng

All Publications

• DNMT3AR882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency. bioRxiv : the preprint server for biology Köhnke, T., Karigane, D., Hilgart, E., Fan, A. C., Kayamori, K., Miyauchi, M., Collins, C. T., Suchy, F. P., Rangavajhula, A., Feng, Y., Nakauchi, Y., Martinez-Montes, E., Fowler, J. L., Loh, K. M., Nakauchi, H., Koldobskiy, M. A., Feinberg, A. P., Majeti, R. 2024

  Abstract

  Genetic mutations are being thoroughly mapped in human cancers, yet a fundamental question in cancer biology is whether such mutations are functionally required for cancer initiation, maintenance of established cancer, or both. Here, we study this question in the context of human acute myeloid leukemia (AML), where DNMT3A R882 missense mutations often arise early, in pre-leukemic clonal hematopoiesis, and corrupt the DNA methylation landscape to initiate leukemia. We developed CRISPR-based methods to directly correct DNMT3A R882 mutations in leukemic cells obtained from patients. Surprisingly, DNMT3A R882 mutations were largely dispensable for disease maintenance. Replacing DNMT3A R882 mutants with wild-type DNMT3A did not impair the ability of AML cells to engraft in vivo, and minimally altered DNA methylation. Taken together, DNMT3A R882 mutations are initially necessary for AML initiation, but are largely dispensable for disease maintenance. The notion that initiating oncogenes differ from those that maintain cancer has important implications for cancer evolution and therapy.

  View details for DOI 10.1101/2024.10.26.620318

  View details for PubMedID 39553934

  View details for PubMedCentralID PMC11565803

• A New Era of Functional Experimentation in Human Hematopoiesis and Leukemia Research. Experimental hematology Köhnke, T., Feng, Y., Majeti, R. 2024: 104652

  Abstract

  Functional experimentation has laid the foundation for our understanding of hematopoietic and leukemic stem cells. Yet, most recently, a flurry of descriptive studies of primary human cells, fueled by rapid technological advances in sequencing technologies, have emerged. These increasing opportunities to describe at great detail have taken precedence over rigorously interrogating functional mediators of biology, particularly in primary human cells. Here, we argue that an improved toolset of gene editing and stem cell biology technologies will allow the field to expand beyond extensive descriptive studies to more functional studies.

  View details for DOI 10.1016/j.exphem.2024.104652

  View details for PubMedID 39362578

• IDH1-Mutant Preleukemic Hematopoietic Stem Cells Can Be Eliminated by Inhibition of Oxidative Phosphorylation. Blood cancer discovery Landberg, N., Köhnke, T., Feng, Y., Nakauchi, Y., Fan, A. C., Linde, M. H., Karigane, D., Lim, K., Sinha, R., Malcovati, L., Thomas, D., Majeti, R. 2024: OF1-OF18

  Abstract

  Rare preleukemic hematopoietic stem cells (pHSC) harboring only the initiating mutations can be detected at the time of acute myeloid leukemia (AML) diagnosis. pHSCs are the origin of leukemia and a potential reservoir for relapse. Using primary human samples and gene editing to model isocitrate dehydrogenase 1 (IDH1) mutant pHSCs, we show epigenetic, transcriptional, and metabolic differences between pHSCs and healthy hematopoietic stem cells (HSC). We confirm that IDH1-driven clonal hematopoiesis is associated with cytopenia, suggesting an inherent defect to fully reconstitute hematopoiesis. Despite giving rise to multilineage engraftment, IDH1-mutant pHSCs exhibited reduced proliferation, blocked differentiation, downregulation of MHC class II genes, and reprogramming of oxidative phosphorylation metabolism. Critically, inhibition of oxidative phosphorylation resulted in the complete eradication of IDH1-mutant pHSCs but not IDH2-mutant pHSCs or wild-type HSCs. Our results indicate that IDH1-mutant preleukemic clones can be targeted with complex I inhibitors, offering a potential strategy to prevent the development and relapse of leukemia.A high burden of pHSCs is associated with worse overall survival in AML. Using single-cell sequencing, metabolic assessment, and gene-edited human models, we find human pHSCs with IDH1 mutations to be metabolically vulnerable and sensitive to eradication by complex I inhibition. See related commentary by Steensma.

  View details for DOI 10.1158/2643-3230.BCD-23-0195

  View details for PubMedID 38261864

• IDH1-mutant preleukemic hematopoietic stem cells can be eliminated by inhibition of oxidative phosphorylation. Blood cancer discovery Landberg, N., Köhnke, T., Feng, Y., Nakauchi, Y., Fan, A. C., Linde, M. H., Karigane, D., Lim, K., Sinha, R., Malcovati, L., Thomas, D., Majeti, R. 2023

  Abstract

  Rare preleukemic hematopoietic stem cells (pHSCs) harboring only the initiating mutations can be detected at the time of AML diagnosis. pHSCs are the origin of leukemia and a potential reservoir for relapse. Using primary human samples and gene-editing to model isocitrate dehydrogenase 1 (IDH1) mutant pHSCs, we show epigenetic, transcriptional, and metabolic differences between pHSCs and healthy hematopoietic stem cells (HSCs). We confirm that IDH1 driven clonal hematopoiesis is associated with cytopenia, suggesting an inherent defect to fully reconstitute hematopoiesis. Despite giving rise to multilineage engraftment, IDH1-mutant pHSCs exhibited reduced proliferation, blocked differentiation, downregulation of MHC Class II genes, and reprogramming of oxidative phosphorylation metabolism. Critically, inhibition of oxidative phosphorylation resulted in complete eradication of IDH1-mutant pHSCs but not IDH2-mutant pHSCs or wildtype HSCs. Our results indicate that IDH1-mutant preleukemic clones can be targeted with complex I inhibitors, offering a potential strategy to prevent development and relapse of leukemia.

  View details for DOI 10.1158/2643-3230.BCD-23-0195

  View details for PubMedID 38091010

• Gene Correction of DNMT3A:R882H in Primary Human AML Demonstrates That This Mutation Is Not Required for Disease Maintenance, but Is Associated with Increased Leukemia Stem Cell Frequency Koehnke, T., Karigane, D., Hilgart, E., Kayamori, K., Fan, A. C., Collins, C. T., Suchy, F. P., Rangavajhula, A. S., Feng, Y., Nakauchi, Y., Martinez-Montes, E., Koldobskiy, M., Feinberg, A., Majeti, R. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-186440

  View details for Web of Science ID 001159306702092

• Hematopoietic-specific heterozygous loss of Dnmt3a exacerbates colitis-associated colon cancer. The Journal of experimental medicine Feng, Y., Yuan, Q., Newsome, R. C., Robinson, T., Bowman, R. L., Zuniga, A. N., Hall, K. N., Bernsten, C. M., Shabashvili, D. E., Krajcik, K. I., Gunaratne, C., Zaroogian, Z. J., Venugopal, K., Casellas Roman, H. L., Levine, R. L., Chatila, W. K., Yaeger, R., Riva, A., Jobin, C., Kopinke, D., Avram, D., Guryanova, O. A. 2023; 220 (11)

  Abstract

  Clonal hematopoiesis (CH) is defined as clonal expansion of mutant hematopoietic stem cells absent diagnosis of a hematologic malignancy. Presence of CH in solid tumor patients, including colon cancer, correlates with shorter survival. We hypothesized that bone marrow-derived cells with heterozygous loss-of-function mutations of DNMT3A, the most common genetic alteration in CH, contribute to the pathogenesis of colon cancer. In a mouse model that combines colitis-associated colon cancer (CAC) with experimental CH driven by Dnmt3a+/Delta, we found higher tumor penetrance and increased tumor burden compared with controls. Histopathological analysis revealed accentuated colonic epithelium injury, dysplasia, and adenocarcinoma formation. Transcriptome profiling of colon tumors identified enrichment of gene signatures associated with carcinogenesis, including angiogenesis. Treatment with the angiogenesis inhibitor axitinib eliminated the colon tumor-promoting effect of experimental CH driven by Dnmt3a haploinsufficiency and rebalanced hematopoiesis. This study provides conceptually novel insights into non-tumor-cell-autonomous effects of hematopoietic alterations on colon carcinogenesis and identifies potential therapeutic strategies.

  View details for DOI 10.1084/jem.20230011

  View details for PubMedID 37615936

• miR-196b-TLR7/8 Signaling Axis Regulates Innate Immune Signaling and Myeloid Maturation in DNMT3A-Mutant AML CLINICAL CANCER RESEARCH Gamlen, H. A., Romer-Seibert, J. S., Lawler, M. E., Versace, A. M., Goetz, M. L., Feng, Y., Guryanova, O. A., Palmisiano, N., Meyer, S. E. 2022; 28 (20): 4574-4586

  Abstract

  DNMT3A mutations confer a poor prognosis in acute myeloid leukemia (AML), but the molecular mechanisms downstream of DNMT3A mutations in disease pathogenesis are not completely understood, limiting targeted therapeutic options. The role of miRNA in DNMT3A-mutant AML pathogenesis is understudied.DNA methylation and miRNA expression was evaluated in human AML patient samples and in Dnmt3a/Flt3-mutant AML mice. The treatment efficacy and molecular mechanisms of TLR7/8-directed therapies on DNMT3A-mutant AML were evaluated in vitro on human AML patient samples and in Dnmt3a/Flt3-mutant AML mice.miR-196b is hypomethylated and overexpressed in DNMT3A-mutant AML and is associated with poor patient outcome. miR-196b overexpression in DNMT3A-mutant AML is important to maintain an immature state and leukemic cell survival through repression of TLR signaling. The TLR7/8 agonist resiquimod induces dendritic cell-like differentiation with costimulatory molecule expression in DNMT3A-mutant AML cells and provides a survival benefit to Dnmt3a/Flt3-mutant AML mice. The small molecule bryostatin-1 augments resiquimod-mediated AML growth inhibition and differentiation.DNMT3A loss-of-function mutations cause miRNA locus-specific hypomethylation and overexpression important for mutant DNMT3A-mediated pathogenesis and clinical outcomes. Specifically, the overexpression of miR-196b in DNMT3A-mutant AML creates a novel therapeutic vulnerability by controlling sensitivity to TLR7/8-directed therapies.

  View details for DOI 10.1158/1078-0432.CCR-22-1598

  View details for Web of Science ID 000874100900001

  View details for PubMedID 35943291

  View details for PubMedCentralID PMC9588567

• Combination strategies to promote sensitivity to cytarabine-induced replication stress in acute myeloid leukemia with and without DNMT3A mutations EXPERIMENTAL HEMATOLOGY Shabashvili, D. E., Feng, Y., Kaur, P., Venugopal, K., Guryanova, O. A. 2022; 110: 20-27

  Abstract

  Cytarabine and other chain-terminating nucleoside analogs that damage replication forks in rapidly proliferating cells are a cornerstone of leukemia chemotherapy, yet the outcomes remain unsatisfactory because of resistance and toxicity. Better understanding of DNA damage repair and downstream effector mechanisms in different disease subtypes can guide combination strategies that sensitize leukemia cells to cytarabine without increasing side effects. We have previously found that mutations in DNMT3A, one of the most commonly mutated genes in acute myeloid leukemia and associated with poor prognosis, predisposed cells to DNA damage and cell killing by cytarabine, cladribine, and other nucleoside analogs, which coincided with PARP1 dysfunction and DNA repair defect (Venugopal K, Feng Y, Nowialis P, et al. Clin Cancer Res 2022;28:756-769). In this article, we first overview DNA repair mechanisms that remove aberrant chain-terminating nucleotides as determinants of sensitivity or resistance to cytarabine and other nucleoside analogs. Next, we discuss PARP inhibition as a rational strategy to increase cytarabine efficacy in cells without DNMT3A mutations, while considering the implications of PARP inhibitor resistance for promoting clonal hematopoiesis. Finally, we examine the utility of p53 potentiators to boost leukemia cell killing by cytarabine in the context of mutant DNMT3A. Systematic profiling of DNA damage repair proficiency has the potential to uncover subtype-specific therapeutic dependencies in AML.

  View details for DOI 10.1016/j.exphem.2022.03.008

  View details for Web of Science ID 000814700800003

  View details for PubMedID 35306047

  View details for PubMedCentralID PMC9133110

• DNMT3A Harboring Leukemia-Associated Mutations Directs Sensitivity to DNA Damage at Replication Forks CLINICAL CANCER RESEARCH Venugopal, K., Feng, Y., Nowialis, P., Xu, H., Shabashvili, D. E., Berntsen, C. M., Kaur, P., Krajcik, K., Taragjini, C., Zaroogian, Z., Roman, H., Posada, L. M., Gunaratne, C., Li, J., Dupere-Richer, D., Bennett, R. L., Pondugula, S., Riva, A., Cogle, C. R., Opavsky, R., Law, B. K., Bhaduri-McIntosh, S., Kubicek, S., Staber, P. B., Licht, J. D., Bird, J. E., Guryanova, O. A. 2022; 28 (4): 756-769

  Abstract

  In acute myeloid leukemia (AML), recurrent DNA methyltransferase 3A (DNMT3A) mutations are associated with chemoresistance and poor prognosis, especially in advanced-age patients. Gene-expression studies in DNMT3A-mutated cells identified signatures implicated in deregulated DNA damage response and replication fork integrity, suggesting sensitivity to replication stress. Here, we tested whether pharmacologically induced replication fork stalling, such as with cytarabine, creates a therapeutic vulnerability in cells with DNMT3A(R882) mutations.Leukemia cell lines, genetic mouse models, and isogenic cells with and without DNMT3A(mut) were used to evaluate sensitivity to nucleoside analogues such as cytarabine in vitro and in vivo, followed by analysis of DNA damage and signaling, replication restart, and cell-cycle progression on treatment and after drug removal. Transcriptome profiling identified pathways deregulated by DNMT3A(mut) expression.We found increased sensitivity to pharmacologically induced replication stress in cells expressing DNMT3A(R882)-mutant, with persistent intra-S-phase checkpoint activation, impaired PARP1 recruitment, and elevated DNA damage, which was incompletely resolved after drug removal and carried through mitosis. Pulse-chase double-labeling experiments with EdU and BrdU after cytarabine washout demonstrated a higher rate of fork collapse in DNMT3A(mut)-expressing cells. RNA-seq studies supported deregulated cell-cycle progression and p53 activation, along with splicing, ribosome biogenesis, and metabolism.Together, our studies show that DNMT3A mutations underlie a defect in recovery from replication fork arrest with subsequent accumulation of unresolved DNA damage, which may have therapeutic tractability. These results demonstrate that, in addition to its role in epigenetic control, DNMT3A contributes to preserving genome integrity during replication stress. See related commentary by Viny, p. 573.

  View details for DOI 10.1158/1078-0432.CCR-21-2863

  View details for Web of Science ID 000756665300001

  View details for PubMedID 34716195

  View details for PubMedCentralID PMC8866212

• HOXBLINC long non-coding RNA activation promotes leukemogenesis in NPM1-mutant acute myeloid leukemia NATURE COMMUNICATIONS Zhu, G., Luo, H., Feng, Y., Guryanova, O. A., Xu, J., Chen, S., Lai, Q., Sharma, A., Xu, B., Zhao, Z., Feng, R., Ni, H., Claxton, D., Guo, Y., Mesa, R. A., Qiu, Y., Yang, F., Li, W., Nimer, S. D., Huang, S., Xu, M. 2021; 12 (1): 1956

  Abstract

  Nucleophosmin (NPM1) is the most commonly mutated gene in acute myeloid leukemia (AML) resulting in aberrant cytoplasmic translocation of the encoded nucleolar protein (NPM1c+). NPM1c+ maintains a unique leukemic gene expression program, characterized by activation of HOXA/B clusters and MEIS1 oncogene to facilitate leukemogenesis. However, the mechanisms by which NPM1c+ controls such gene expression patterns to promote leukemogenesis remain largely unknown. Here, we show that the activation of HOXBLINC, a HOXB locus-associated long non-coding RNA (lncRNA), is a critical downstream mediator of NPM1c+-associated leukemic transcription program and leukemogenesis. HOXBLINC loss attenuates NPM1c+-driven leukemogenesis by rectifying the signature of NPM1c+ leukemic transcription programs. Furthermore, overexpression of HoxBlinc (HoxBlincTg) in mice enhances HSC self-renewal and expands myelopoiesis, leading to the development of AML-like disease, reminiscent of the phenotypes seen in the Npm1 mutant knock-in (Npm1c/+) mice. HoxBlincTg and Npm1c/+ HSPCs share significantly overlapped transcriptome and chromatin structure. Mechanistically, HoxBlinc binds to the promoter regions of NPM1c+ signature genes to control their activation in HoxBlincTg HSPCs, via MLL1 recruitment and promoter H3K4me3 modification. Our study reveals that HOXBLINC lncRNA activation plays an essential oncogenic role in NPM1c+ leukemia. HOXBLINC and its partner MLL1 are potential therapeutic targets for NPM1c+ AML.

  View details for DOI 10.1038/s41467-021-22095-2

  View details for Web of Science ID 000636294300001

  View details for PubMedID 33782403

  View details for PubMedCentralID PMC8007823

• DNMT3A alterations associated with myeloid malignancies dictate differential responses to hypomethylating agents LEUKEMIA RESEARCH Roman, H., Venugopal, K., Feng, Y., Shabashvili, D. E., Posada, L. M., Li, J., Guryanova, O. A. 2020; 94: 106372

  View details for DOI 10.1016/j.leukres.2020.106372

  View details for Web of Science ID 000564127700009

  View details for PubMedID 32445940

  View details for PubMedCentralID PMC7481860

• Inhibition of Polo-like kinase 2 ameliorates pathogenesis in Alzheimer's disease model mice PLOS ONE Lee, J., Lee, Y., Andre, E. A., Lee, K., Thien Nguyen, Feng, Y., Jia, N., Harris, B. T., Burns, M. P., Pak, D. S. 2019; 14 (7): e0219691

  Abstract

  Alzheimer disease (AD) is a neurodegenerative disorder characterized by pathological hallmarks of neurofibrillary tangles and amyloid plaques. The plaques are formed by aggregation and accumulation of amyloid β (Aβ), a cleavage fragment of amyloid precursor protein (APP). Enhanced neuronal activity and seizure events are frequently observed in AD, and elevated synaptic activity promotes Aβ production. However, the mechanisms that link synaptic hyperactivity to APP processing and AD pathogenesis are not well understood. We previously found that Polo-like kinase 2 (Plk2), a homeostatic repressor of neuronal overexcitation, promotes APP β-processing in vitro. Here, we report that Plk2 stimulates Aβ production in vivo, and that Plk2 levels are elevated in a spatiotemporally regulated manner in brains of AD mouse models and human AD patients. Genetic disruption of Plk2 kinase function reduces plaque deposits and activity-dependent Aβ production. Furthermore, pharmacological Plk2 inhibition hinders Aβ formation, synapse loss, and memory decline in an AD mouse model. Thus, Plk2 links synaptic overactivity to APP β-processing, Aβ production, and disease-relevant phenotypes in vivo, suggesting that Plk2 may be a potential target for AD therapeutics.

  View details for DOI 10.1371/journal.pone.0219691

  View details for Web of Science ID 000484968200030

  View details for PubMedID 31306446

  View details for PubMedCentralID PMC6629081

• Kappa opioid receptors regulate hippocampal synaptic homeostasis and epileptogenesis EPILEPSIA Queenan, B. N., Dunn, R. L., Santos, V. R., Feng, Y., Huizenga, M. N., Hammack, R. J., Vicini, S., Forcelli, P. A., Pak, D. S. 2018; 59 (1): 106-122

  Abstract

  Homeostatic synaptic plasticity (HSP) serves as a gain control mechanism at central nervous system (CNS) synapses, including those between the dentate gyrus (DG) and CA3. Improper circuit control of DG-CA3 synapses is hypothesized to underlie epileptogenesis. Here, we sought to (1) identify compounds that preferentially modulate DG-CA3 synapses in primary neuronal culture and (2) determine if these compounds would delay or prevent epileptogenesis in vivo.We previously developed and validated an in vitro assay to visualize the behavior of DG-CA3 synapses and predict functional changes. We used this "synapse-on-chip" assay (quantification of synapse size, number, and type using immunocytochemical markers) to dissect the mechanisms of HSP at DG-CA3 synapses. Using chemogenetic constructs and pharmacological agents we determined the signaling cascades necessary for gain control at DG-CA3 synapses. Finally, we tested the implicated cascades (using kappa opioid receptor (OR) agonists and antagonists) in two models of epileptogenesis: electrical amygdala kindling in the mouse and chemical (pentylenetetrazole) kindling in the rat.In vitro, synapses between DG mossy fibers (MFs) and CA3 neurons are the primary homeostatic responders during sustained periods of activity change. Kappa OR signaling is both necessary and sufficient for the homeostatic elaboration of DG-CA3 synapses, induced by presynaptic DG activity levels. Blocking kappa OR signaling in vivo attenuates the development of seizures in both mouse and rat models of epilepsy.This study elucidates mechanisms by which synapses between DG granule cells and CA3 pyramidal neurons undergo activity-dependent homeostatic compensation, via OR signaling in vitro. Modulation of kappa OR signaling in vivo alters seizure progression, suggesting that breakdown of homeostatic closed-loop control at DG-CA3 synapses contributes to seizures, and that targeting endogenous homeostatic mechanisms at DG-CA3 synapses may prove useful in combating epileptogenesis.

  View details for DOI 10.1111/epi.13941

  View details for Web of Science ID 000419634500011

  View details for PubMedID 29114861

  View details for PubMedCentralID PMC5774867