Publications

2026:3

1. Blood

   The GATA1 N terminus coordinates metabolic reprogramming in erythropoiesis

   Ling Te, Bezavada Lavanya, Mehmood Rashid, Zhang Kevin, Cotton Anitria, Crawford Jeremy Chase, Jin Hongjian, Sona Surbhi, Li Lei, Ju Yan, Han Lei, Liu Nana, Tran Tam, Vu Hieu S., Jin Yan, Zhai Jinbin, Pruett-Miller Shondra M., Bhoopalan Senthil Velan, Xu Jian, Ni Min, Crispino John D.

   Blood 2026

   Abstract DOI

   Mutations in GATA1 that cause skipping of exon 2, which encodes the N terminus, are associated with the myeloid leukemia of Down syndrome and Diamond-Blackfan anemia (DBA). To elucidate the molecular function of this N-terminal region, we used single-cell RNA sequencing (scRNA-seq) on fetal liver cells from Gata1-mutant embryos that express only the short isoform of GATA1 (GATA1s) lacking the N terminus of full-length GATA1 (GATA1FL). scRNA-seq revealed defects in erythropoiesis and aberrant upregulation of glycolytic genes, including PKM, which encodes pyruvate kinase to catalyze the final and irreversible step of glycolysis. Using precision nuclear run-on sequencing and cleavage under targets and release using nuclease (CUT&RUN) after acute GATA1 deletion in erythroid cells, we identified PKM as a direct target of GATA1. Substitution of GATA1FL with GATA1s induced histone lactylation at the PKM promoter, increased pyruvate kinase M (PKM) expression and activity, and enhanced glycolytic flux in erythroid progenitors, without affecting mitochondrial respiration. Importantly, PKM expression is also significantly elevated in patients with DBA with RPS19 mutations, which is associated with reduced levels of GATA1, further supporting a link between GATA1s-driven defective erythropoiesis and dysregulated glycolysis. Together, these findings reveal that GATA1 controls not only heme metabolism but also glycolytic reprogramming.

2. Cell Reports

   Developmental reprogramming underlies chemotherapy resistance in favorable-histology Wilms tumor

   Fleming Andrew M., Jablonowski Carolyn M., Jin Hongjian, Zhang Siwei, Sona Surbhi, Lee Ha Won, Dieseldorff Jones Karissa M., Cheng Changde, Xu Beisi, Morton Christopher L., Woolard Mary A., Pichavaram Prahalathan, Gehle Daniel B., Natarajan Sivaraman, Kodali Kiran, Pagala Vishwajeeth, High Anthony A., Kumar Yogesh, Burden Steven, Valentine Virginia, Daria Deidre, Harbour Jake, Vocelle Daniel, Chang Ti-Cheng, Easton John, Olsen Scott R., Neale Geoffrey, Pinto Emilia M., Rehg Jerold E., Janke Laura, Santiago Teresa, George Rani E., Ma Xiaotu, Zambetti Gerard P., Davidoff Andrew M., Chen Taosheng, Wu Gang, Chen Xiang, Yang Jun, Murphy Andrew J.

   Cell Reports 2026

   Abstract DOI

   Children with favorable-histology Wilms tumor (FHWT) who relapse or whose tumors show blastemal predominance post-chemotherapy often face poor outcomes. The purpose of this study is to identify mechanisms of chemotherapy resistance in FHWT. We induce a patient-derived xenograft model (KT-47) to develop blastemal predominance after chemotherapy and to become resistant to vincristine, actinomycin-D, and doxorubicin (VAD). Multi-omics analyses reveal chromatin and transcriptional changes, including increased H3K4me3 and decreased H3K27me3 at stem cell and nephrogenesis gene loci. LIN28B is the most upregulated resistance-associated gene, linked to MYCN copy gain/upregulation and chromatin remodeling. ABCB1 expression correlates with interchromosomal enhancer interactions and functions as the mediator of chemotherapy resistance in vitro. These findings are validated in additional Wilms tumor models. Overall, resistance is associated with de-differentiation to a stem-like state and is driven by ABCB1 upregulation, suggesting that therapeutic strategies targeting chromatin regulation and drug efflux may be relevant in therapy-resistant Wilms tumor.

3. Developmental Cell

   Non-cell-autonomous tumor promotion in DICER1 cancer predisposition

   Larsen Randolph K., Hanna Jason A., Jin Hongjian, Reed Kristin B., Kimbrough Darden W., Vuong Kyna, Hwang Jongchan, Adkins Grace E., Hopkins Jack D., Stevens Bradley T., Evans Myron K., Langdon Casey G., Drummond Catherine J., Garcia Matthew R., Wiggins Kristin B., Iverson Amy R., Finkelstein David, Schreiner Patrick A., Rosch Jason W., Rehg Jerold E., Schultz Kris Ann P., Hatley Mark E.

   Developmental Cell 2026

   Abstract DOI

   DICER1-related tumors are characterized by germline loss-of-function mutations in one DICER1 allele (DICER1+/-) and a somatic "second hit" mutation in the remaining DICER1 allele. Whether the germline DICER1+/- mutation participates in tumorigenesis is unknown. We show that germline heterozygous loss of Dicer1 promotes tumor formation via aberrant neutrophil function in spontaneous and allograft mouse models of rhabdomyosarcoma. Germline heterozygous deletion of Dicer1 decreased tumor latency and increased tumor penetrance, while conditional heterozygous deletion in tumor cells did not, illustrating that non-cell-autonomous contributions were required for tumor promotion. We show that Dicer1+/- murine and human tumors were enriched for neutrophils and that tumor-bearing mice had abundant circulating neutrophil extracellular traps (NETs). Genetically and pharmacologically preventing NET release reduced tumor promotion in Dicer1+/- mice, suggesting NETs promote tumor growth. These findings demonstrate that germline DICER1+/- mutations promote tumor growth and suggest that targeting neutrophils/NET release may reduce cancer risk in DICER1+/- individuals.

2025:7

1. Scientific Data

   Transcriptomic and epigenetic profiling of neuroblastoma states in response to RBM39 degrader

   Jin Hongjian, Fang Jie, Myers Jason, Singh Shivendra, Yang Jun

   Scientific Data 2025

   Abstract DOI

   Neuroblastoma accounts for approximately 15% of all pediatric cancer-related deaths, largely due to disease relapse following intensive multimodal therapy. A critical barrier to cure neuroblastoma is the emergence of therapy-resistant tumor cells. Neuroblastoma comprises two major cell states, adrenergic (ADRN) and mesenchymal (MES), which are believed to interconvert and contribute to therapeutic resistance through lineage plasticity. To investigate the mechanisms underlying this plasticity, we subjected human and murine neuroblastoma models to repeated treatment with indisulam, a molecular glue compound that selectively degrades the splicing factor RBM39, until full drug resistance emerged. We then generated datasets from these models, including bulk transcriptomic data, ATAC-seq, and H3K27ac CUT&Tag. These data comprehensively characterize transcriptomic and epigenetic landscapes of resistant ADRN and MES neuroblastoma cell states. We present this resource to facilitate reuse by the scientific community. These datasets may support efforts to decipher lineage switching, identify regulators of therapy resistance, and discover potential therapeutic vulnerabilities in resistant neuroblastoma.

2. Blood

   Venetoclax plus gilteritinib is effective in preclinical models of FLT3-mutant BCL11B-a lineage-ambiguous leukemia

   Montefiori Lindsey E., Iacobucci Ilaria, Gao Qingsong, Moore Jamila, Wright William C., Wei Huimei, Baviskar Pradyumna, Sona Surbhi, Jin Hongjian, Budhraja Amit, Lott Josi, Tatarata Qi Zhang, Cheng Zhongshan, Khan Tanya, Backhaus Wagner Emily A., Johnson Melissa, Mehr Cyrus M., Freeman Burgess, Janke Laura, Haferlach Torsten, Geeleher Paul, Mead Paul E., Konopleva Marina, Opferman Joseph T., Mullighan Charles G.

   Blood 2025

   Abstract DOI

   Aberrant activation of BCL11B (BCL11B-a) defines a subtype of lineage-ambiguous leukemias with T-lymphoid and myeloid features, co-occurring activating FLT3 mutations, and a stem/progenitor immunophenotype and gene expression profile. Similar to other lineage-ambiguous leukemias, optimal treatment is unclear, and there are limited targeted therapeutic options. Here, we investigated the efficacy of B-cell lymphoma 2 (BCL-2) and FMS-like tyrosine kinase 3 (FLT3) inhibition with venetoclax and gilteritinib, respectively, in preclinical models of BCL11B-a leukemia. Despite variation in response to single-agent therapies, the combination of venetoclax plus gilteritinib (VenGilt) was highly effective in all models evaluated. BH3 profiling suggested that resistance to venetoclax monotherapy was due to the tumor-intrinsic dependence on additional BCL-2 family proteins before drug treatment. Longitudinal single-cell RNA sequencing analysis identified mitochondrial pathways and a pro-lymphoid gene expression signature as potential drivers of rare cell survival on VenGilt therapy. These data support clinical evaluation of venetoclax in combination with gilteritinib in BCL11B-a lineage-ambiguous leukemias.

3. Cell Reports

   Transdifferentiation of endothelial progenitor cells into rhabdomyosarcoma defined by hedgehog signaling competence

   Gadek Katherine E., Drummond Catherine J., Jin Hongjian, Garcia Matthew R., Mathew Edwin D., Adkins Grace E., Langdon Casey G., Evans Myron, Searcy Madeline B., Schreiner Patrick, Maguire Matthew, Rehg Jerold E., Ogden Stacey K., Hatley Mark E.

   Cell Reports 2025

   Abstract DOI

   Rhabdomyosarcoma (RMS) is a pediatric soft tissue sarcoma resembling developing skeletal muscle, but tumors are found in sites devoid of skeletal muscle, suggesting a non-myogenic cell of origin. We previously described an endothelial progenitor cell-derived model of RMS by activating a conditional, constitutively active Smoothened mutant (SmoM2) with aP2-Cre. We sought to further identify the endothelial progenitor cell of origin in our aP2-Cre;R26SmoM2 model using mice with more endothelial-specific Cre recombinase expression. Using lineage tracing of embryonic endothelial progenitor cells and mature, adult endothelial cells, we show that a selected subset of endothelial progenitor cells can transform into RMS. These endothelial progenitor cells have a specific window during embryogenesis with a capacity for transformation into RMS that is dictated by the presence of primary cilia and Sonic Hedgehog signaling pathway competency. These findings deepen our understanding of endothelial differentiation and the connections between normal development and oncogenesis in children.

4. Nature Communication

   RBM39 degrader invigorates innate immunity to eradicate neuroblastoma despite cancer cell plasticity

   Singh Shivendra, Fang Jie, Jin Hongjian, Van De Velde Lee-Ann, Cortes Andrew, Chen Jiani, Natarajan Sivaraman, Poon Evon, Wu Qiong, Morton Christopher L., Woolard Mary A., Quarni Waise, Steele Jacob A., Connelly Jon P., He Liusheng, Thorne Rebecca, Turner Gregory, Confer Thomas, Johnson Melissa, Caufield William V., Freeman Burgess B., Lockey Timothy, Murphy Andrew J., Murray Peter J., Owa Takashi, Pruett-Miller Shondra M., Wang Ruoning, Chesler Louis, Park Julie R., Davidoff Andrew M., Easton John, Chen Xiang, Thomas Paul G., Yang Jun

   Nature Communications 2025

   Abstract DOI

   The cellular plasticity of neuroblastoma is defined by a mixture of two major cell states, adrenergic and mesenchymal, which may contribute to therapy resistance. However, how neuroblastoma cells switch cellular states during therapy remains largely unknown, and how to eradicate neuroblastoma regardless of its cell state is a clinical challenge. To better understand the cellular plasticity of neuroblastoma in chemoresistance, we define the transcriptomic and epigenetic map of adrenergic and mesenchymal types of neuroblastomas using human and murine models treated with indisulam, a selective RBM39 degrader. We show that cancer cells not only undergo a bidirectional switch between adrenergic and mesenchymal states, but also acquire additional cellular states, reminiscent of the developmental pliancy of neural crest cells. These cell state alterations are coupled with epigenetic reprogramming and dependency switching of cell state-specific transcription factors, epigenetic modifiers, and targetable kinases. Through targeting RNA splicing, indisulam induces an inflammatory tumor microenvironment and enhances the anticancer activity of natural killer cells. The combination of indisulam with anti-GD2 immunotherapy results in a durable, complete response in high-risk transgenic neuroblastoma models, providing an innovative, rational therapeutic approach to eradicate tumor cells regardless of their potential to switch cell states.

5. eLife

   The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells

   Fang Jie, Singh Shivendra, Wells Brennan, Wu Qiong, Jin Hongjian, Janke Laura J., Wan Shibiao, Steele Jacob A., Connelly Jon P., Murphy Andrew J., Wang Ruoning, Davidoff Andrew, Ashcroft Margaret, Pruett-Miller Shondra M., Yang Jun

   eLife 2025

   Abstract DOI

   3D cellular-specific epigenetic and transcriptomic reprogramming is critical to organogenesis and tumorigenesis. Here, we dissect the distinct cell fitness in 2D (normoxia vs. chronic hypoxia) vs 3D (normoxia) culture conditions for an MYC-driven murine liver cancer model. We identify over 600 shared essential genes and additional context-specific fitness genes and pathways. Knockout of the VHL-HIF1 pathway results in incompatible fitness defects under normoxia vs. 1% oxygen or 3D culture conditions. Moreover, deletion of each of the mitochondrial respiratory electron transport chain complex has distinct fitness outcomes. Notably, multicellular organogenesis signaling pathways including TGFβ-SMAD, which is upregulated in 3D culture, specifically constrict the uncontrolled cell proliferation in 3D while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3, and Mettl14) has opposite outcomes in 2D vs. 3D. We further identify a 3D-dependent synthetic lethality with partial loss of Prmt5 due to a reduction of Mtap expression resulting from 3D-specific epigenetic reprogramming. Our study highlights unique epigenetic, metabolic, and organogenesis signaling dependencies under different cellular settings.

6. Cancer Research

   Conditional Activation of c-MYC in Distinct Catecholaminergic Cells Drives Development of Neuroblastoma or Somatostatinoma

   Wang Tingting, Liu Lingling, Fang Jie, Jin Hongjian, Natarajan Sivaraman, Sheppard Heather, Lu Meifen, Turner Gregory, Confer Thomas, Johnson Melissa, Steinberg Jeffrey, Ha Larry, Yadak Nour, Jain Richa, Picketts David J., Ma Xiaotu, Murphy Andrew, Davidoff Andrew M., Glazer Evan S., Easton John, Chen Xiang, Wang Ruoning, Yang Jun

   Cancer Research 2025

   Abstract DOI

   c-MYC is an important driver of high-risk neuroblastoma. A lack of c-MYC-driven genetically engineered mouse models (GEMM) has hampered the ability to better understand mechanisms of neuroblastoma oncogenesis and to develop effective therapies. In this study, we showed that conditional c-MYC induction via Cre recombinase driven by a tyrosine hydroxylase promoter led to a preponderance of PDX1+ somatostatinoma, a type of pancreatic neuroendocrine tumor. However, c-MYC activation via an improved Cre recombinase driven by a dopamine β-hydroxylase promoter resulted in neuroblastoma development. The c-MYC murine neuroblastoma tumors recapitulated the pathologic and genetic features of human neuroblastoma and responded to anti-GD2 immunotherapy and difluoromethylornithine, an FDA-approved inhibitor targeting the MYC transcriptional target ODC1. Thus, c-MYC overexpression results in different but related tumor types depending on the targeted cell. The GEMMs represent valuable tools for testing immunotherapies and targeted therapies for these diseases. Significance: The development of c-MYC-driven genetically engineered neuroblastoma and somatostatinoma mouse models provides useful tools for understanding the tumor cell origin and investigating treatment strategies.

7. Frontiers in Cell an

   Hedgehog signaling controls astral microtubules and mitotic spindle orientation in neural progenitors and iPSCs

   Liu Fengming, Medyukhina Anna, Olesen Kris M., Shirinifard Abbas, Jin Hongjian, Li Lei, Mapelli Marina, Khairy Khaled, Han Young-Goo

   Frontiers in Cell and Developmental Biology 2025

   Abstract DOI

   Mitotic spindle orientation is crucial for cell fate determination and tissue organization. Although the intracellular machinery governing spindle orientation is well characterized, whether and how secreted factors, such as morphogens, regulate this process remains poorly understood. This study investigated the role of Hedgehog (HH) signaling in modulating mitotic spindle orientation in neural progenitor cells and in induced pluripotent stem cells (iPSCs). Time-lapse microscopy of cerebral organoids and iPSCs revealed that HH signaling increases the angle of the mitotic spindle relative to the apical surface, prolongs mitosis, and enhances spindle rotation. Mechanistically, HH signaling reduces both the number and the length of astral microtubules, key regulators of spindle orientation. This reduction correlates with increased spindle angle in iPSCs. Furthermore, we show that canonical HH signaling, involving GLI-dependent transcriptional regulation, contributes to these effects. RNA sequencing and gene set enrichment analysis (GSEA) revealed that HH signaling upregulates genes associated with microtubule depolymerization, suggesting a transcriptional mechanism by which HH signaling influences astral microtubule dynamics and, consequently, mitotic spindle orientation. These findings highlight a novel link between a morphogen, transcriptional regulation, and the control of mitotic spindle orientation, with implications for development and tissue homeostasis.

2023:4

1. Journal

   Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing is associated with therapeutic response to splicing inhibitor

   Jablonowski Carolyn, Quarni Waise, Singh Shivendra, Tan Haiyan, Bostanthirige Dhanushka Hewa, Jin Hongjian, Fang Jie, Chang Ti-Cheng, Finkelstein David, Cho Ji-Hoon, Hu Dongli, Pagala Vishwajeeth, Sakurada Sadie Miki, Pruett-Miller Shondra M., Wang Ruoning, Murphy Andrew, Freeman Kevin, Peng Junmin, Davidoff Andrew M., Wu Gang, Yang Jun

   2023

   Abstract DOI PMC PMID

   Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that Jumonji Domain Containing 6, Arginine Demethylase and Lysine Hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven neuroblastoma. JMJD6 cooperates with MYC in cellular transformation by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a "molecular glue" that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.

2. Nature Communication

   PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors

   Searcy Madeline B., Larsen Randolph K., Stevens Bradley T., Zhang Yang, Jin Hongjian, Drummond Catherine J., Langdon Casey G., Gadek Katherine E., Vuong Kyna, Reed Kristin B., Garcia Matthew R., Xu Beisi, Kimbrough Darden W., Adkins Grace E., Djekidel Nadhir, Porter Shaina N., Schreiner Patrick A., Pruett-Miller Shondra M., Abraham Brian J., Rehg Jerold E., Hatley Mark E.

   Nature Communications 2023

   Abstract DOI

   Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a FP-RMS mouse model driven by P3F expression and Cdkn2a loss in endothelial cells. Additionally, we show that P3F expression in TP53-null human iPSCs blocks endothelial-directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.

3. Cells

   A Review of Single-Cell RNA-Seq Annotation, Integration, and Cell-Cell Communication

   Cheng Changde, Chen Wenan, Jin Hongjian, Chen Xiang

   Cells 2023

   Abstract DOI

   Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular biology at an unprecedented resolution, enabling the characterization of cellular heterogeneity, identification of rare but significant cell types, and exploration of cell-cell communications and interactions. Its broad applications span both basic and clinical research domains. In this comprehensive review, we survey the current landscape of scRNA-seq analysis methods and tools, focusing on count modeling, cell-type annotation, data integration, including spatial transcriptomics, and the inference of cell-cell communication. We review the challenges encountered in scRNA-seq analysis, including issues of sparsity or low expression, reliability of cell annotation, and assumptions in data integration, and discuss the potential impact of suboptimal clustering and differential expression analysis tools on downstream analyses, particularly in identifying cell subpopulations. Finally, we discuss recent advancements and future directions for enhancing scRNA-seq analysis. Specifically, we highlight the development of novel tools for annotating single-cell data, integrating and interpreting multimodal datasets covering transcriptomics, epigenomics, and proteomics, and inferring cellular communication networks. By elucidating the latest progress and innovation, we provide a comprehensive overview of the rapidly advancing field of scRNA-seq analysis.

4. Nature Communication

   Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma

   Fang Jie, Singh Shivendra, Cheng Changde, Natarajan Sivaraman, Sheppard Heather, Abu-Zaid Ahmed, Durbin Adam D., Lee Ha Won, Wu Qiong, Steele Jacob, Connelly Jon P., Jin Hongjian, Chen Wenan, Fan Yiping, Pruett-Miller Shondra M., Rehg Jerold E., Koo Selene C., Santiago Teresa, Emmons Joseph, Cairo Stefano, Wang Ruoning, Glazer Evan S., Murphy Andrew J., Chen Taosheng, Davidoff Andrew M., Armengol Carolina, Easton John, Chen Xiang, Yang Jun

   Nature Communications 2023

   Abstract DOI

   A lack of relevant genetic models and cell lines hampers our understanding of hepatoblastoma pathogenesis and the development of new therapies for this neoplasm. Here, we report an improved MYC-driven hepatoblastoma-like murine model that recapitulates the pathological features of embryonal type of hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of the human disease. Single-cell RNA-sequencing and spatial transcriptomics identify distinct subpopulations of hepatoblastoma cells. After deriving cell lines from the mouse model, we map cancer dependency genes using CRISPR-Cas9 screening and identify druggable targets shared with human hepatoblastoma (e.g., CDK7, CDK9, PRMT1, PRMT5). Our screen also reveals oncogenes and tumor suppressor genes in hepatoblastoma that engage multiple, druggable cancer signaling pathways. Chemotherapy is critical for human hepatoblastoma treatment. A genetic mapping of doxorubicin response by CRISPR-Cas9 screening identifies modifiers whose loss-of-function synergizes with (e.g., PRKDC) or antagonizes (e.g., apoptosis genes) the effect of chemotherapy. The combination of PRKDC inhibition and doxorubicin-based chemotherapy greatly enhances therapeutic efficacy. These studies provide a set of resources including disease models suitable for identifying and validating potential therapeutic targets in human high-risk hepatoblastoma.

2022:3

1. Proceedings of the N

   A kinase-independent function of cyclin-dependent kinase 6 promotes outer radial glia expansion and neocortical folding

   Wang Lei, Park Jun Young, Liu Fengming, Olesen Kris M., Hou Shirui, Peng Jamy C., Infield Jordan, Levesque Anna C., Wang Yong-Dong, Jin Hongjian, Fan Yiping, Connelly Patrick J., Pruett-Miller Shondra M., Hu Miaofen G., Hinds Philip W., Han Young-Goo

   Proceedings of the National Academy of Sciences of the United States of America 2022

   Abstract DOI

   The neocortex, the center for higher brain function, first emerged in mammals and has become massively expanded and folded in humans, constituting almost half the volume of the human brain. Primary microcephaly, a developmental disorder in which the brain is smaller than normal at birth, results mainly from there being fewer neurons in the neocortex because of defects in neural progenitor cells (NPCs). Outer radial glia (oRGs), NPCs that are abundant in gyrencephalic species but rare in lissencephalic species, are thought to play key roles in the expansion and folding of the neocortex. However, how oRGs expand, whether they are necessary for neocortical folding, and whether defects in oRGs cause microcephaly remain important questions in the study of brain development, evolution, and disease. Here, we show that oRG expansion in mice, ferrets, and human cerebral organoids requires cyclin-dependent kinase 6 (CDK6), the mutation of which causes primary microcephaly via an unknown mechanism. In a mouse model in which increased Hedgehog signaling expands oRGs and intermediate progenitor cells and induces neocortical folding, CDK6 loss selectively decreased oRGs and abolished neocortical folding. Remarkably, this function of CDK6 in oRG expansion did not require its kinase activity, was not shared by the highly similar CDK4 and CDK2, and was disrupted by the mutation causing microcephaly. Therefore, our results indicate that CDK6 is conserved to promote oRG expansion, that oRGs are necessary for neocortical folding, and that defects in oRG expansion may cause primary microcephaly.

2. Science Translationa

   Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma

   Singh Shivendra, Abu-Zaid Ahmed, Jin Hongjian, Fang Jie, Wu Qiong, Wang Tingting, Feng Helin, Quarni Waise, Shao Ying, Maxham Lily, Abdolvahabi Alireza, Yun Mi-Kyung, Vaithiyalingam Sivaraja, Tan Haiyan, Bowling John, Honnell Victoria, Young Brandon, Guo Yian, Bajpai Richa, Pruett-Miller Shondra M., Grosveld Gerard C., Hatley Mark, Xu Beisi, Fan Yiping, Wu Gang, Chen Eleanor Y., Chen Taosheng, Lewis Peter W., Rankovic Zoran, Li Yimei, Murphy Andrew J., Easton John, Peng Junmin, Chen Xiang, Wang Ruoning, White Stephen W., Davidoff Andrew M., Yang Jun

   Science Translational Medicine 2022

   Abstract DOI

   Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma (RMS) is an aggressive childhood soft tissue sarcoma transformed by the pathognomonic Paired Box 3-Forkhead Box O1 (PAX3-FOXO1) fusion protein, which governs a core regulatory circuitry transcription factor network. Here, we show that the histone lysine demethylase 4B (KDM4B) is a therapeutic vulnerability for PAX3-FOXO1+ RMS. Genetic and pharmacologic inhibition of KDM4B substantially delayed tumor growth. Suppression of KDM4 proteins inhibited the expression of core oncogenic transcription factors and caused epigenetic alterations of PAX3-FOXO1-governed superenhancers. Combining KDM4 inhibition with cytotoxic chemotherapy led to tumor regression in preclinical PAX3-FOXO1+ RMS subcutaneous xenograft models. In summary, we identified a targetable mechanism required for maintenance of the PAX3-FOXO1-related transcription factor network, which may translate to a therapeutic approach for fusion-positive RMS.

3. Neuropathology and A

   The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma/ganglioglioma

   Chiang Jason, Li Xiaoyu, Jin Hongjian, Wu Gang, Lin Tong, Ellison David W.

   Neuropathology and Applied Neurobiology 2022

   Abstract DOI

   AIMS: Desmoplastic infantile astrocytomas and gangliogliomas (DIA/DIGs) are rare brain tumours of infancy. A distinctive feature of their histopathology is a combination of low-grade and high-grade features. Most DIA/DIGs can be surgically resected and have a good prognosis. However, high-grade features often dominate recurrent tumours, some of which have a poor outcome. In this study, we test the hypothesis that low-grade and high-grade areas in DIA/DIGs have distinct molecular characteristics. METHODS: Tissue samples from microdissected low-grade and high-grade areas in 12 DIA/DIGs were analysed by DNA methylation profiling, whole exome sequencing, RNA sequencing and immunohistochemistry to search for potential differences at multiple molecular levels. RESULTS: Copy number variants among tumours and between the two morphologically distinct areas were infrequent. No recurrent genetic alterations were identified across the tumour series, and high-grade areas did not have additional genetic alterations to explain their distinct morphology or biological behaviour. However, high-grade areas showed relative hypomethylation in genes downstream of the transcription factors SOX9 and LEF1 and evidence of a core SOX9 transcription network alongside activation of the BMP, WNT and MAPK signalling pathways. CONCLUSIONS: This study contributes to our knowledge of molecular genetic alterations in DIA/DIGs, uncovers molecular differences between the two distinct cell populations in these tumours and suggests potential therapeutic targets among the more proliferative cell population in DIA/DIGs.

2021:8

1. Science Advances

   Chromatin architecture at susceptible gene loci in cerebellar Purkinje cells characterizes DNA damage-induced neurodegeneration

   Kwak Young Don, Shaw Timothy I., Downing Susanna M., Tewari Ambika, Jin Hongjian, Li Yang, Dumitrache Lavinia C., Katyal Sachin, Khodakhah Kamran, Russell Helen R., McKinnon Peter J.

   Science Advances 2021

   Abstract DOI

   The pathogenesis of inherited genome instability neurodegenerative syndromes remains largely unknown. Here, we report new disease-relevant murine models of genome instability–driven neurodegeneration involving disabled ATM and APTX that develop debilitating ataxia. We show that neurodegeneration and ataxia result from transcriptional interference in the cerebellum via aberrant messenger RNA splicing. Unexpectedly, these splicing defects were restricted to only Purkinje cells, disrupting the expression of critical homeostatic regulators including ITPR1, GRID2, and CA8. Abundant genotoxic R loops were also found at these Purkinje cell gene loci, further exacerbating DNA damage and transcriptional disruption. Using ATAC-seq to profile global chromatin accessibility in the cerebellum, we found a notably unique chromatin conformation specifically in Purkinje chromatin at the affected gene loci, thereby promoting susceptibility to DNA damage. These data reveal the pathogenic basis of DNA damage in the nervous system and suggest chromatin conformation as a feature in directing genome instability–associated neuropathology.

2. Nature Communication

   KDM6B promotes activation of the oncogenic CDK4/6-pRB-E2F pathway by maintaining enhancer activity in MYCN-amplified neuroblastoma

   D’Oto Alexandra, Fang Jie, Jin Hongjian, Xu Beisi, Singh Shivendra, Mullasseril Anoushka, Jones Victoria, Abu-Zaid Ahmed, Buttlar Xinyu, Cooke Bailey, Hu Dongli, Shohet Jason, Murphy Andrew J., Davidoff Andrew M., Yang Jun

   Nature Communications 2021

   Abstract DOI

   The H3K27me2/me3 histone demethylase KDM6B is essential to neuroblastoma cell survival. However, the mechanism of KDM6B action remains poorly defined. We demonstrate that inhibition of KDM6B activity 1) reduces the chromatin accessibility of E2F target genes and MYCN, 2) selectively leads to an increase of H3K27me3 but a decrease of the enhancer mark H3K4me1 at the CTCF and BORIS binding sites, which may, consequently, disrupt the long-range chromatin interaction of MYCN and E2F target genes, and 3) phenocopies the transcriptome induced by the specific CDK4/6 inhibitor palbociclib. Overexpression of CDK4/6 or Rb1 knockout confers neuroblastoma cell resistance to both palbociclib and the KDM6 inhibitor GSK-J4. These data indicate that KDM6B promotes an oncogenic CDK4/6-pRB-E2F pathway in neuroblastoma cells via H3K27me3-dependent enhancer-promoter interactions, providing a rationale to target KDM6B for high-risk neuroblastoma.

3. Science Advances

   Targeting the spliceosome through RBM39 degradation results in exceptional responses in high-risk neuroblastoma models

   Singh Shivendra, Quarni Waise, Goralski Maria, Wan Shibiao, Jin Hongjian, Velde Lee-Ann, Fang Jie, Wu Qiong, Abu-Zaid Ahmed, Wang Tingting, Singh Ravi, Craft David, Fan Yiping, Confer Thomas, Johnson Melissa, Akers Walter J., Wang Ruoning, Murray Peter J., Thomas Paul G., Nijhawan Deepak, Davidoff Andrew M., Yang Jun

   Science Advances 2021

   Abstract DOI

   Aberrant alternative pre-mRNA splicing plays a critical role in MYC-driven cancers and therefore may represent a therapeutic vulnerability. Here, we show that neuroblastoma, a MYC-driven cancer characterized by splicing dysregulation and spliceosomal dependency, requires the splicing factor RBM39 for survival. Indisulam, a “molecular glue” that selectively recruits RBM39 to the CRL4-DCAF15 E3 ubiquitin ligase for proteasomal degradation, is highly efficacious against neuroblastoma, leading to significant responses in multiple high-risk disease models, without overt toxicity. Genetic depletion or indisulam-mediated degradation of RBM39 induces significant genome-wide splicing anomalies and cell death. Mechanistically, the dependency on RBM39 and high-level expression of DCAF15 determine the exquisite sensitivity of neuroblastoma to indisulam. Our data indicate that targeting the dysregulated spliceosome by precisely inhibiting RBM39, a vulnerability in neuroblastoma, is a valid therapeutic strategy.

4. Nature Communication

   Synthetic essentiality between PTEN and core dependency factor PAX7 dictates rhabdomyosarcoma identity

   Langdon Casey G., Gadek Katherine E., Garcia Matthew R., Evans Myron K., Reed Kristin B., Bush Madeline, Hanna Jason A., Drummond Catherine J., Maguire Matthew C., Leavey Patrick J., Finkelstein David, Jin Hongjian, Schreiner Patrick A., Rehg Jerold E., Hatley Mark E.

   Nature Communications 2021

   Abstract DOI

   PTEN promoter hypermethylation is nearly universal and PTEN copy number loss occurs in ~25% of fusion-negative rhabdomyosarcoma (FN-RMS). Here we show Pten deletion in a mouse model of FN-RMS results in less differentiated tumors more closely resembling human embryonal RMS. PTEN loss activated the PI3K pathway but did not increase mTOR activity. In wild-type tumors, PTEN was expressed in the nucleus suggesting loss of nuclear PTEN functions could account for these phenotypes. Pten deleted tumors had increased expression of transcription factors important in neural and skeletal muscle development including Dbx1 and Pax7. Pax7 deletion completely rescued the effects of Pten loss. Strikingly, these Pten;Pax7 deleted tumors were no longer FN-RMS but displayed smooth muscle differentiation similar to leiomyosarcoma. These data highlight how Pten loss in FN-RMS is connected to a PAX7 lineage-specific transcriptional output that creates a dependency or synthetic essentiality on the transcription factor PAX7 to maintain tumor identity.

5. Journal

   CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes

   Djekidel Mohamed Nadhir, Rosikiewicz Wojciech, Peng Jamy C., Kanneganti Thirumala-Devi, Hui Yawei, Jin Hongjian, Hedges Dale, Schreiner Patrick, Fan Yiping, Wu Gang, Xu Beisi

   2021

   Abstract DOI PMC PMID

   Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans could cause coronavirus disease 2019 (COVID-19). Since its first discovery in Dec 2019, SARS-CoV-2 has become a global pandemic and caused 3.3 million direct/indirect deaths (2021 May). Amongst the scientific community’s response to COVID-19, data sharing has emerged as an essential aspect of the combat against SARS-CoV-2. Despite the ever-growing studies about SARS-CoV-2 and COVID-19, to date, only a few databases were curated to enable access to gene expression data. Furthermore, these databases curated only a small set of data and do not provide easy access for investigators without computational skills to perform analyses. To fill this gap and advance open-access to the growing gene expression data on this deadly virus, we collected about 1,500 human bulk RNA-seq datasets from publicly available resources, developed a database and visualization tool, named CovidExpress (https://stjudecab.github.io/covidexpress). This open access database will allow research investigators to examine the gene expression in various tissues, cell lines, and their response to SARS-CoV-2 under different experimental conditions, accelerating the understanding of the etiology of this disease to inform the drug and vaccine development. Our integrative analysis of this big dataset highlights a set of commonly regulated genes in SARS-CoV-2 infected lung and Rhinovirus infected nasal tissues, including OASL that were under-studied in COVID-19 related reports. Our results also suggested a potential FURIN positive feedback loop that might explain the evolutional advantage of SARS-CoV-2.

6. Nature Communication

   Retinoblastoma from human stem cell-derived retinal organoids

   Norrie Jackie L., Nityanandam Anjana, Lai Karen, Chen Xiang, Wilson Matthew, Stewart Elizabeth, Griffiths Lyra, Jin Hongjian, Wu Gang, Orr Brent, Tran Quynh, Allen Sariah, Reilly Colleen, Zhou Xin, Zhang Jiakun, Newman Kyle, Johnson Dianna, Brennan Rachel, Dyer Michael A.

   Nature Communications 2021

   Abstract DOI

   Retinoblastoma is a childhood cancer of the developing retina that initiates with biallelic inactivation of the RB1 gene. Children with germline mutations in RB1 have a high likelihood of developing retinoblastoma and other malignancies later in life. Genetically engineered mouse models of retinoblastoma share some similarities with human retinoblastoma but there are differences in their cellular differentiation. To develop a laboratory model of human retinoblastoma formation, we make induced pluripotent stem cells (iPSCs) from 15 participants with germline RB1 mutations. Each of the stem cell lines is validated, characterized and then differentiated into retina using a 3-dimensional organoid culture system. After 45 days in culture, the retinal organoids are dissociated and injected into the vitreous of eyes of immunocompromised mice to support retinoblastoma tumor growth. Retinoblastomas formed from retinal organoids made from patient-derived iPSCs have molecular, cellular and genomic features indistinguishable from human retinoblastomas. This model of human cancer based on patient-derived iPSCs with germline cancer predisposing mutations provides valuable insights into the cellular origins of this debilitating childhood disease as well as the mechanism of tumorigenesis following RB1 gene inactivation.

7. iScience

   17-DMAG dually inhibits Hsp90 and histone lysine demethylases in alveolar rhabdomyosarcoma

   Singh Shivendra, Abu-Zaid Ahmed, Lin Wenwei, Low Jonathan, Abdolvahabi Alireza, Jin Hongjian, Wu Qiong, Cooke Bailey, Fang Jie, Bowling John, Vaithiyalingam Sivaraja, Currier Duane, Yun Mi-Kyung, Fernando Dinesh M., Maier Julie, Tillman Heather, Bulsara Purva, Lu Zhaohua, Das Sourav, Shelat Anang, Li Zhenmei, Young Brandon, Lee Richard, Rankovic Zoran, Murphy Andrew J., White Stephen W., Davidoff Andrew M., Chen Taosheng, Yang Jun

   iScience 2021

   Abstract DOI

   Histone lysine demethylases (KDMs) play critical roles in oncogenesis and therefore may be effective targets for anticancer therapy. Using a time-resolved fluorescence resonance energy transfer demethylation screen assay, in combination with multiple orthogonal validation approaches, we identified geldanamycin and its analog 17-DMAG as KDM inhibitors. In addition, we found that these Hsp90 inhibitors increase degradation of the alveolar rhabdomyosarcoma (aRMS) driver oncoprotein PAX3-FOXO1 and induce the repressive epigenetic mark H3K9me3 and H3K36me3 at genomic loci of PAX3-FOXO1 targets. We found that as monotherapy 17-DMAG significantly inhibits expression of PAX3-FOXO1 target genes and multiple oncogenic pathways, induces a muscle differentiation signature, delays tumor growth and extends survival in aRMS xenograft mouse models. The combination of 17-DMAG with conventional chemotherapy significantly enhances therapeutic efficacy, indicating that targeting KDM in combination with chemotherapy may serve as a therapeutic approach to PAX3-FOXO1-positive aRMS.

8. Neuro-Oncology Advan

   A genetic mouse model with postnatal Nf1 and p53 loss recapitulates the histology and transcriptome of human malignant peripheral nerve sheath tumor

   Inoue Akira, Janke Laura J., Gudenas Brian L., Jin Hongjian, Fan Yiping, Paré Joshua, Clay Michael R., Northcott Paul A., Hirbe Angela C., Cao Xinwei

   Neuro-Oncology Advances 2021

   Abstract DOI

   BACKGROUND: Malignant peripheral nerve sheath tumors (MPNST) are aggressive sarcomas. Somatic inactivation of NF1 and cooperating tumor suppressors, including CDKN2A/B, PRC2, and p53, is found in most MPNST. Inactivation of LATS1/2 of the Hippo pathway was recently shown to cause tumors resembling MPNST histologically, although Hippo pathway mutations are rarely found in MPNST. Because existing genetically engineered mouse (GEM) models of MPNST do not recapitulate some of the key genetic features of human MPNST, we aimed to establish a GEM-MPNST model that recapitulated the human disease genetically, histologically, and molecularly. METHODS: We combined 2 genetically modified alleles, an Nf1;Trp53 cis-conditional allele and an inducible Plp-CreER allele (NP-Plp), to model the somatic, possibly postnatal, mutational events in human MPNST. We also generated conditional Lats1;Lats2 knockout mice. We performed histopathologic analyses of mouse MPNST models and transcriptomic comparison of mouse models and human nerve sheath tumors. RESULTS: Postnatal Nf1;Trp53 cis-deletion resulted in GEM-MPNST that were histologically more similar to human MPNST than the widely used germline Nf1;Trp53 cis-heterozygous (NPcis) model and showed partial loss of H3K27me3. At the transcriptome level, Nf1;p53-driven GEM-MPNST were distinct from Lats-driven GEM-MPNST and resembled human MPNST more closely than do Lats-driven tumors. CONCLUSIONS: The NP-Plp model recapitulates human MPNST genetically, histologically, and molecularly.

2020:3

1. Nature Immunology

   Beta cell-specific CD8+ T cells maintain stem cell memory-associated epigenetic programs during type 1 diabetes

   Abdelsamed Hossam A., Zebley Caitlin C., Nguyen Hai, Rutishauser Rachel L., Fan Yiping, Ghoneim Hazem E., Crawford Jeremy Chase, Alfei Francesca, Alli Shanta, Ribeiro Susan Pereira, Castellaw Ashley H., McGargill Maureen A., Jin Hongjian, Boi Shannon K., Speake Cate, Serti Elisavet, Turka Laurence A., Busch Michael E., Stone Mars, Deeks Steven G., Sekaly Rafick-Pierre, Zehn Dietmar, James Eddie A., Nepom Gerald T., Youngblood Ben

   Nature Immunology 2020

   Abstract DOI

   The pool of beta cell-specific CD8+ T cells in type 1 diabetes (T1D) sustains an autoreactive potential despite having access to a constant source of antigen. To investigate the long-lived nature of these cells, we established a DNA methylation-based T cell ’multipotency index’ and found that beta cell-specific CD8+ T cells retained a stem-like epigenetic multipotency score. Single-cell assay for transposase-accessible chromatin using sequencing confirmed the coexistence of naive and effector-associated epigenetic programs in individual beta cell-specific CD8+ T cells. Assessment of beta cell-specific CD8+ T cell anatomical distribution and the establishment of stem-associated epigenetic programs revealed that self-reactive CD8+ T cells isolated from murine lymphoid tissue retained developmentally plastic phenotypic and epigenetic profiles relative to the same cells isolated from the pancreas. Collectively, these data provide new insight into the longevity of beta cell-specific CD8+ T cell responses and document the use of this methylation-based multipotency index for investigating human and mouse CD8+ T cell differentiation.

2. eLife

   The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth

   Mondal Baisakhi, Jin Hongjian, Kallappagoudar Satish, Sedkov Yurii, Martinez Tanner, Sentmanat Monica F., Poet Greg J., Li Chunliang, Fan Yiping, Pruett-Miller Shondra M., Herz Hans-Martin

   eLife 2020

   Abstract DOI

   The mitotic deacetylase complex (MiDAC) is a recently identified histone deacetylase (HDAC) complex. While other HDAC complexes have been implicated in neurogenesis, the physiological role of MiDAC remains unknown. Here, we show that MiDAC constitutes an important regulator of neural differentiation. We demonstrate that MiDAC functions as a modulator of a neurodevelopmental gene expression program and binds to important regulators of neurite outgrowth. MiDAC upregulates gene expression of pro-neural genes such as those encoding the secreted ligands SLIT3 and NETRIN1 (NTN1) by a mechanism suggestive of H4K20ac removal on promoters and enhancers. Conversely, MiDAC inhibits gene expression by reducing H3K27ac on promoter-proximal and -distal elements of negative regulators of neurogenesis. Furthermore, loss of MiDAC results in neurite outgrowth defects that can be rescued by supplementation with SLIT3 and/or NTN1. These findings indicate a crucial role for MiDAC in regulating the ligands of the SLIT3 and NTN1 signaling axes to ensure the proper integrity of neurite development.

3. Bioinformatics

   ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in

   Jin Hongjian, Kasper Lawryn H., Larson Jon D., Wu Gang, Baker Suzanne J., Zhang Jinghui, Fan Yiping

   Bioinformatics 2020

   Abstract DOI

   MOTIVATION: The traditional reads per million normalization method is inappropriate for the evaluation of ChIP-seq data when treatments or mutations have global effects. Changes in global levels of histone modifications can be detected with exogenous reference spike-in controls. However, most ChIP-seq studies overlook the normalization that must be corrected with spike-in. A method that retrospectively renormalizes datasets without spike-in is lacking. RESULTS: ChIPseqSpikeInFree is a novel ChIP-seq normalization method to effectively determine scaling factors for samples across various conditions and treatments, which does not rely on exogenous spike-in chromatin or peak detection to reveal global changes in histone modification occupancy. Application of ChIPseqSpikeInFree on five datasets demonstrates that this in silico approach reveals a similar magnitude of global changes as the spike-in method does. AVAILABILITY AND IMPLEMENTATION: St. Jude Cloud (https://pecan.stjude.cloud/permalink/spikefree) and St. Jude Github ( https://github.com/stjude/ChIPseqSpikeInFree). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

2019:3

1. Acta Neuropathologic

   Correction to: H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo

   Silveira André B., Kasper Lawryn H., Fan Yiping, Jin Hongjian, Wu Gang, Shaw Timothy I., Zhu Xiaoyan, Larson Jon D., Easton John, Shao Ying, Yergeau Donald A., Rosencrance Celeste, Boggs Kristy, Rusch Michael C., Ding Liang, Zhang Junyuan, Finkelstein David, Noyes Rachel M., Russell Brent L., Xu Beisi, Broniscer Alberto, Wetmore Cynthia, Pounds Stanley B., Ellison David W., Zhang Jinghui, Baker Suzanne J.

   Acta Neuropathologica 2019

   Abstract DOI

   The original article can be found online.

2. JCI insight

   The E3 ligase Hrd1 stabilizes Tregs by antagonizing inflammatory cytokine-induced ER stress response

   Xu Yuanming, Melo-Cardenas Johanna, Zhang Yana, Gau Isabella, Wei Juncheng, Montauti Elena, Zhang Yusi, Gao Beixue, Jin Hongjian, Sun Zhaolin, Lee Sang-Myeong, Fang Deyu

   JCI insight 2019

   Abstract DOI

   Treg differentiation, maintenance, and function are controlled by the transcription factor FoxP3, which can be destabilized under inflammatory or other pathological conditions. Tregs can be destabilized under inflammatory or other pathological conditions, but the underlying mechanisms are not fully defined. Herein, we show that inflammatory cytokines induce ER stress response, which destabilizes Tregs by suppressing FoxP3 expression, suggesting a critical role of the ER stress response in maintaining Treg stability. Indeed, genetic deletion of Hrd1, an E3 ligase critical in suppressing the ER stress response, leads to elevated expression of ER stress-responsive genes in Treg and largely diminishes Treg suppressive functions under inflammatory condition. Mice with Treg-specific ablation of Hrd1 displayed massive multiorgan lymphocyte infiltration, body weight loss, and the development of severe small intestine inflammation with aging. At the molecular level, the deletion of Hrd1 led to the activation of both the ER stress sensor IRE1α and its downstream MAPK p38. Pharmacological suppression of IRE1α kinase, but not its endoribonuclease activity, diminished the elevated p38 activation and fully rescued the stability of Hrd1-null Tregs. Taken together, our studies reveal ER stress response as a previously unappreciated mechanism underlying Treg instability and that Hrd1 is crucial for maintaining Treg stability and functions through suppressing the IRE1α-mediated ER stress response.

3. Cancer Cell

   Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression

   Larson Jon D., Kasper Lawryn H., Paugh Barbara S., Jin Hongjian, Wu Gang, Kwon Chang-Hyuk, Fan Yiping, Shaw Timothy I., Silveira André B., Qu Chunxu, Xu Raymond, Zhu Xiaoyan, Zhang Junyuan, Russell Helen R., Peters Jennifer L., Finkelstein David, Xu Beisi, Lin Tong, Tinkle Christopher L., Patay Zoltan, Onar-Thomas Arzu, Pounds Stanley B., McKinnon Peter J., Ellison David W., Zhang Jinghui, Baker Suzanne J.

   Cancer Cell 2019

   Abstract DOI

   Diffuse intrinsic pontine gliomas (DIPGs) are incurable childhood brainstem tumors with frequent histone H3 K27M mutations and recurrent alterations in PDGFRA and TP53. We generated genetically engineered inducible mice and showed that H3.3 K27M enhanced neural stem cell self-renewal while preserving regional identity. Neonatal induction of H3.3 K27M cooperated with activating platelet-derived growth factor receptor α (PDGFRα) mutant and Trp53 loss to accelerate development of diffuse brainstem gliomas that recapitulated human DIPG gene expression signatures and showed global changes in H3K27 posttranslational modifications, but relatively restricted gene expression changes. Genes upregulated in H3.3 K27M tumors were enriched for those associated with neural development where H3K27me3 loss released the poised state of apparently bivalent promoters, whereas downregulated genes were enriched for those encoding homeodomain transcription factors.

2017:1

1. Oncogene

   FOXA1 inhibits prostate cancer neuroendocrine differentiation

   Kim J., Jin H., Zhao J. C., Yang Y. A., Li Y., Yang X., Dong X., Yu J.

   Oncogene 2017

   Abstract DOI

   Neuroendocrine prostate cancer (NEPC) has increasingly become a clinical challenge. The mechanisms by which neuroendocrine (NE) cells arises from prostate adenocarcinoma cells are poorly understood. FOXA1 is a transcription factor of the forkhead family that is required for prostate epithelial differentiation. In this study, we demonstrated that FOXA1 loss drives NE differentiation, demarcated by phenotypical changes and NEPC marker expressions. Mechanistically, this is mediated by FOXA1 binding to the promoter of interleukin 8 (IL-8), a chemokine previously shown elevated in NEPC, to directly inhibit its expression. Further, IL-8 upregulation activates the MAPK/ERK pathway, leading to ERK phosphorylation and enolase 2 (ENO2) expression. IL-8 knockdown or ERK inhibition, on the other hand, abolished FOXA1 loss-induced NE differentiation. Analysis of xenograft mouse models confirmed FOXA1 loss in NEPC tumors relative to its adenocarcinoma counterparts. Importantly, FOXA1 is downregulated in human NEPC tumors compared to primary and castration-resistant prostate cancers, and its expression is negatively correlated with that of ENO2. These findings indicate that FOXA1 transcriptionally suppresses IL-8, the expression of which would otherwise stimulate the MAPK/ERK pathway to promote NE differentiation of prostate cancer cells. Our data strongly suggest that FOXA1 loss may play a significant role in enabling prostate cancer progression to NEPC, whereas IL-8 and MAPK/ERK pathways may be promising targets for therapeutic intervention.

2016:2

1. Oncotarget

   Identification and validation of regulatory SNPs that modulate transcription factor chromatin binding and gene expression in prostate cancer

   Jin Hong-Jian, Jung Segun, DebRoy Auditi R., Davuluri Ramana V.

   Oncotarget 2016

   Abstract DOI

   Prostate cancer (PCa) is the second most common solid tumor for cancer related deaths in American men. Genome wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with the increased risk of PCa. Because most of the susceptibility SNPs are located in noncoding regions, little is known about their functional mechanisms. We hypothesize that functional SNPs reside in cell type-specific regulatory elements that mediate the binding of critical transcription factors (TFs), which in turn result in changes in target gene expression. Using PCa-specific functional genomics data, here we identify 38 regulatory candidate SNPs and their target genes in PCa. Through risk analysis by incorporating gene expression and clinical data, we identify 6 target genes (ZG16B, ANKRD5, RERE, FAM96B, NAALADL2 and GTPBP10) as significant predictors of PCa biochemical recurrence. In addition, 5 SNPs (rs2659051, rs10936845, rs9925556, rs6057110 and rs2742624) are selected for experimental validation using Chromatin immunoprecipitation (ChIP), dual-luciferase reporter assay in LNCaP cells, showing allele-specific enhancer activity. Furthermore, we delete the rs2742624-containing region using CRISPR/Cas9 genome editing and observe the drastic downregulation of its target gene UPK3A. Taken together, our results illustrate that this new methodology can be applied to identify regulatory SNPs and their target genes that likely impact PCa risk. We suggest that similar studies can be performed to characterize regulatory variants in other diseases.

2. Oncogene

   FOXA1 acts upstream of GATA2 and AR in hormonal regulation of gene expression

   Zhao J. C., Fong K.-W., Jin H.-J., Yang Y. A., Kim J., Yu J.

   Oncogene 2016

   Abstract DOI

   Hormonal regulation of gene expression by androgen receptor (AR) is tightly controlled by many transcriptional cofactors, including pioneer factors FOXA1 and GATA2, which, however, exhibit distinct expression patterns and functional roles in prostate cancer. Here, we examined how FOXA1, GATA2 and AR crosstalk and regulate hormone-dependent gene expression in prostate cancer cells. Chromatin immunoprecipitation sequencing analysis revealed that FOXA1 reprograms both AR and GATA2 cistrome by preferably recruiting them to FKHD-containing genomic sites. By contrast, GATA2 is unable to shift AR or FOXA1 to GATA motifs. Rather, GATA2 co-occupancy enhances AR and FOXA1 binding to nearby ARE and FKHD sites, respectively. Similarly, AR increases, but not reprograms, GATA2 and FOXA1 cistromes. Concordantly, GATA2 and AR strongly enhance the transcriptional program of each other, whereas FOXA1 regulates GATA2- and AR-mediated gene expression in a context-dependent manner due to its reprogramming effects. Taken together, our data delineated for the first time the distinct mechanisms by which GATA2 and FOXA1 regulate AR cistrome and suggest that FOXA1 acts upstream of GATA2 and AR in determining hormone-dependent gene expression in prostate cancer.