1
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Alpsoy A, Wu XS, Pal S, Klingbeil O, Kumar P, El Demerdash O, Nalbant B, Vakoc CR. IκBζ is a dual-use coactivator of NF-κB and POU transcription factors. Mol Cell 2024; 84:1149-1157.e7. [PMID: 38309274 PMCID: PMC10960667 DOI: 10.1016/j.molcel.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
OCA-B, OCA-T1, and OCA-T2 belong to a family of coactivators that bind to POU transcription factors (TFs) to regulate gene expression in immune cells. Here, we identify IκBζ (encoded by the NFKBIZ gene) as an additional coactivator of POU TFs. Although originally discovered as an inducible regulator of NF-κB, we show here that IκBζ shares a microhomology with OCA proteins and uses this segment to bind to POU TFs and octamer-motif-containing DNA. Our functional experiments suggest that IκBζ requires its interaction with POU TFs to coactivate immune-related genes. This finding is reinforced by epigenomic analysis of MYD88L265P-mutant lymphoma cells, which revealed colocalization of IκBζ with the POU TF OCT2 and NF-κB:p50 at hundreds of DNA elements harboring octamer and κB motifs. These results suggest that IκBζ is a transcriptional coactivator that can amplify and integrate the output of NF-κB and POU TFs at inducible genes in immune cells.
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Affiliation(s)
- Aktan Alpsoy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sujay Pal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Pramod Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Benan Nalbant
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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2
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Dolfini D, Gnesutta N, Mantovani R. Expression and function of NF-Y subunits in cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189082. [PMID: 38309445 DOI: 10.1016/j.bbcan.2024.189082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/05/2024]
Abstract
NF-Y is a Transcription Factor (TF) targeting the CCAAT box regulatory element. It consists of the NF-YB/NF-YC heterodimer, each containing an Histone Fold Domain (HFD), and the sequence-specific subunit NF-YA. NF-YA expression is associated with cell proliferation and absent in some post-mitotic cells. The review summarizes recent findings impacting on cancer development. The logic of the NF-Y regulome points to pro-growth, oncogenic genes in the cell-cycle, metabolism and transcriptional regulation routes. NF-YA is involved in growth/differentiation decisions upon cell-cycle re-entry after mitosis and it is widely overexpressed in tumors, the HFD subunits in some tumor types or subtypes. Overexpression of NF-Y -mostly NF-YA- is oncogenic and decreases sensitivity to anti-neoplastic drugs. The specific roles of NF-YA and NF-YC isoforms generated by alternative splicing -AS- are discussed, including the prognostic value of their levels, although the specific molecular mechanisms of activity are still to be deciphered.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy.
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3
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Vicario R, Fragkogianni S, Weber L, Lazarov T, Hu Y, Hayashi SY, Craddock BP, Socci ND, Alberdi A, Baako A, Ay O, Ogishi M, Lopez-Rodrigo E, Kappagantula R, Viale A, Iacobuzio-Donahue CA, Zhou T, Ransohoff RM, Chesworth R, Bank NB, Abdel-Wahab O, Boisson B, Elemento O, Casanova JL, Miller WT, Geissmann F. A microglia clonal inflammatory disorder in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577216. [PMID: 38328106 PMCID: PMC10849735 DOI: 10.1101/2024.01.25.577216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer's Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.
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Affiliation(s)
- Rocio Vicario
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Stamatina Fragkogianni
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Leslie Weber
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tomi Lazarov
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Yang Hu
- Department of Physiology and Biophysics, Institute for Compxutational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Samantha Y. Hayashi
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Nicholas D. Socci
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Araitz Alberdi
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ann Baako
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Oyku Ay
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Estibaliz Lopez-Rodrigo
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Rajya Kappagantula
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Agnes Viale
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christine A. Iacobuzio-Donahue
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ting Zhou
- SKI Stem Cell Research Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | | | | | - Omar Abdel-Wahab
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Compxutational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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4
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Sahu S, Poplawska M, Lim SH, Dutta D. CRISPR-based precision medicine for hematologic disorders: Advancements, challenges, and prospects. Life Sci 2023; 333:122165. [PMID: 37832631 DOI: 10.1016/j.lfs.2023.122165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
The development of programmable nucleases to introduce defined alterations in genomic sequences has been a powerful tool for precision medicine. While several nucleases such as zinc-finger nucleases (ZFN), transcriptor activator-like effector nucleases (TALEN), and meganucleases have been explored, the advent of CRISPR/Cas9 technology has revolutionized the field of genome engineering. In addition to disease modeling, the CRISPR/Cas9 technology has contributed to safer and more effective treatment strategies for hematologic diseases and personalized T-cell-based therapies. Here we discuss the applications of the CRISPR technology in the treatment of hematologic diseases, their efficacy, and ongoing clinical trials. We examine the obstacles to their successful use and the approaches investigated to overcome these challenges. Finally, we provide our perspectives to improve this genome editing tool for targeted therapies.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, 1050 Boyles Street, Building 560, Room 32-04, Frederick, MD 21702, USA.
| | - Maria Poplawska
- Department of Medicine (Division of Hematology and Oncology), State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Seah H Lim
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA
| | - Dibyendu Dutta
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA.
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5
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He Z, Zhong Y, Hu H, Li F. ZFP64 Promotes Gallbladder Cancer Progression through Recruiting HDAC1 to Activate NOTCH1 Signaling Pathway. Cancers (Basel) 2023; 15:4508. [PMID: 37760477 PMCID: PMC10527061 DOI: 10.3390/cancers15184508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The lack of meaningful and effective early-stage markers remains the major challenge in the diagnosis of gallbladder cancer (GBC) and a huge barrier to timely treatment. Zinc finger protein 64 (ZFP64), a member of the zinc finger protein family, is considered to be a promising predictor in multiple tumors, but its potential effect in GBC still remains unclear. Here, we identified that ZFP64 was a vital regulatory protein in GBC. We found that ZFP64 expressed higher in GBC gallbladder carcinoma tissues than in normal tissues and was positively correlated with poor prognosis. Furthermore, ZFP64 was responsible for the migration, invasion, proliferation, anti-apoptosis, and epithelial mesenchymal transition (EMT) of GBC cells in vitro and in vivo. Mechanistically, through Co-IP assay, we confirmed that ZFP64 recruits HDAC1 localized to the promoter region of NUMB for deacetylation and therefore inhibits NUMB expression. The downregulation of NUMB enhanced the activation of the Notch1 signaling pathway, which is indispensable for the GBC-promotion effect of ZFP64 on GBC. In conclusion, ZFP64 regulated GBC progression and metastasis through upregulating the Notch1 signaling pathway, and thus ZFP64 is expected to become a new focus for a GBC prognostic marker and targeted therapy.
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Affiliation(s)
- Zhiqiang He
- Department of Biliary Surgery, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Yuhan Zhong
- Laboratory of Liver Transplantation, Key Laboratory of Transplant Engineering and Immunology, National Health Commission (NHC), West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Haijie Hu
- Department of Biliary Surgery, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Fuyu Li
- Department of Biliary Surgery, West China Hospital, Sichuan University, Chengdu 610041, China;
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6
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Sroka MW, Skopelitis D, Vermunt MW, Preall JB, El Demerdash O, de Almeida LMN, Chang K, Utama R, Gryder B, Caligiuri G, Ren D, Nalbant B, Milazzo JP, Tuveson DA, Dobin A, Hiebert SW, Stengel KR, Mantovani R, Khan J, Kohli RM, Shi J, Blobel GA, Vakoc CR. Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma. Proc Natl Acad Sci U S A 2023; 120:e2303859120. [PMID: 37639593 PMCID: PMC10483665 DOI: 10.1073/pnas.2303859120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/11/2023] [Indexed: 08/31/2023] Open
Abstract
Recurrent chromosomal rearrangements found in rhabdomyosarcoma (RMS) produce the PAX3-FOXO1 fusion protein, which is an oncogenic driver and a dependency in this disease. One important function of PAX3-FOXO1 is to arrest myogenic differentiation, which is linked to the ability of RMS cells to gain an unlimited proliferation potential. Here, we developed a phenotypic screening strategy for identifying factors that collaborate with PAX3-FOXO1 to block myo-differentiation in RMS. Unlike most genes evaluated in our screen, we found that loss of any of the three subunits of the Nuclear Factor Y (NF-Y) complex leads to a myo-differentiation phenotype that resembles the effect of inactivating PAX3-FOXO1. While the transcriptomes of NF-Y- and PAX3-FOXO1-deficient RMS cells bear remarkable similarity to one another, we found that these two transcription factors occupy nonoverlapping sites along the genome: NF-Y preferentially occupies promoters, whereas PAX3-FOXO1 primarily binds to distal enhancers. By integrating multiple functional approaches, we map the PAX3 promoter as the point of intersection between these two regulators. We show that NF-Y occupies CCAAT motifs present upstream of PAX3 to function as a transcriptional activator of PAX3-FOXO1 expression in RMS. These findings reveal a critical upstream role of NF-Y in the oncogenic PAX3-FOXO1 pathway, highlighting how a broadly essential transcription factor can perform tumor-specific roles in governing cellular state.
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Affiliation(s)
| | | | - Marit W. Vermunt
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | | | | | | | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Berkley Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH44106
| | | | - Diqiu Ren
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Benan Nalbant
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | | | | | | | - Scott W. Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232
| | - Kristy R. Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY10461
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133Milano, Italy
| | - Javed Khan
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD20892
| | - Rahul M. Kohli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA19104
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Gerd A. Blobel
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
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7
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Santos M, Hwang JW, Bedford MT. CARM1 arginine methyltransferase as a therapeutic target for cancer. J Biol Chem 2023; 299:105124. [PMID: 37536629 PMCID: PMC10474102 DOI: 10.1016/j.jbc.2023.105124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023] Open
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1) is an arginine methyltransferase that posttranslationally modifies proteins that regulate multiple levels of RNA production and processing. Its substrates include histones, transcription factors, coregulators of transcription, and splicing factors. CARM1 is overexpressed in many different cancer types, and often promotes transcription factor programs that are co-opted as drivers of the transformed cell state, a process known as transcription factor addiction. Targeting these oncogenic transcription factor pathways is difficult but could be addressed by removing the activity of the key coactivators on which they rely. CARM1 is ubiquitously expressed, and its KO is less detrimental in embryonic development than deletion of the arginine methyltransferases protein arginine methyltransferase 1 and protein arginine methyltransferase 5, suggesting that therapeutic targeting of CARM1 may be well tolerated. Here, we will summarize the normal in vivo functions of CARM1 that have been gleaned from mouse studies, expand on the transcriptional pathways that are regulated by CARM1, and finally highlight recent studies that have identified oncogenic properties of CARM1 in different biological settings. This review is meant to kindle an interest in the development of human drug therapies targeting CARM1, as there are currently no CARM1 inhibitors available for use in clinical trials.
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Affiliation(s)
- Margarida Santos
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Jee Won Hwang
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark T Bedford
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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8
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Milan TM, Eskenazi APE, de Oliveira LD, da Silva G, Bighetti-Trevisan RL, Freitas GP, de Almeida LO. Interplay between EZH2/β-catenin in stemness of cisplatin-resistant HNSCC and their role as therapeutic targets. Cell Signal 2023:110773. [PMID: 37331417 DOI: 10.1016/j.cellsig.2023.110773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 06/20/2023]
Abstract
The Wnt/β-catenin signaling pathway is associated with the regulation of cancer stem cells, and it can be driven by epigenetic modifications. Here, we aim to identify epigenetic modifications involved in the control of the Wnt/β-catenin signaling and investigate the role of this pathway in the accumulation of cancer stem cells (CSC) and chemoresistance of Head and Neck Squamous Cell Carcinoma (HNSCC). Quantitative-PCR, western blot, shRNA assay, viability assay, flow cytometry assay, spheres formation, xenograft model, and chromatin immunoprecipitation were employed to evaluate the Wnt/β-catenin pathway and EZH2 in wild-type and chemoresistant oral carcinoma cell lines, and in the populations of CSC and non-stem cells. We demonstrated that β-catenin and EZH2 were accumulated in cisplatin-resistant and CSC population. The upstream genes of the Wnt/β-catenin signaling (APC and GSK3β) were decreased, and the downstream gene MMP7 was increased in the chemoresistant cell lines. The inhibition of β-catenin and EZH2 combined effectively decreased the CSC population in vitro and reduced the tumor volume and CSC population in vivo. EZH2 inhibition increased APC and GSK3β, and the Wnt/β-catenin inhibition reduced MMP7 levels. In contrast, EZH2 overexpression decreased APC and GSK3β and increased MMP7. EZH2 and β-catenin inhibitors sensitized chemoresistant cells to cisplatin. EZH2 and H3K27me3 bounded the promoter of APC, leading to its repression. These results suggest that EZH2 regulates β-catenin by inhibiting the upstream gene APC contributing to the accumulation of cancer stem cells and chemoresistance. Moreover, the pharmacological inhibition of the Wnt/β-catenin combined with EZH2 can be an effective strategy for treating HNSCC.
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Affiliation(s)
- Thaís Moré Milan
- Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil; Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
| | - Ana Patrícia Espaladori Eskenazi
- Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
| | - Lucas Dias de Oliveira
- Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Gabriel da Silva
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
| | - Rayana Longo Bighetti-Trevisan
- Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
| | - Gileade Pereira Freitas
- Departament of Oral and Maxillofacial Surgery, School of Dentistry, Federal University of Goiás, Goiás, Brazil.
| | - Luciana Oliveira de Almeida
- Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
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Du X, Wang H, Xu J, Zhang Y, Chen T, Li G. Profiling and integrated analysis of transcriptional addiction gene expression and prognostic value in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:204676. [PMID: 37171044 PMCID: PMC10188332 DOI: 10.18632/aging.204676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/15/2023] [Indexed: 05/13/2023]
Abstract
Transcriptional dysregulation caused by genomic and epigenetic alterations in cancer is called "transcriptional addiction". Transcriptional addiction is an important pathogenic factor of tumor malignancy. Hepatocellular carcinoma (HCC) genomes are highly heterogeneous, with many dysregulated genes. Our study analyzed the possibility that transcriptional addiction-related genes play a significant role in HCC. All data sources for conducting this study were public cancer databases and tissue microarrays. We identified 38 transcriptional addiction genes, and most were differentially expressed genes. Among patients of different groups, there were significant differences in overall survival rates. Both nomogram and risk score were independent predictors of HCC outcomes. Transcriptional addiction gene expression characteristics determine the sensitivity of patients to immunotherapy, cisplatin, and sorafenib. Besides, HDAC2 was identified as an oncogene, and its expression was correlated with patient survival time. Our study conclusively demonstrated that transcriptional addiction is crucial in HCC. We provided biomarkers for predicting the prognosis of HCC patients, which can more precisely guide the patient's treatment.
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Affiliation(s)
- Xiaowei Du
- First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Hao Wang
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Xu
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yufei Zhang
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tingsong Chen
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Gao Li
- Second Department of Oncology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
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10
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Richard Albert J, Kobayashi T, Inoue A, Monteagudo-Sánchez A, Kumamoto S, Takashima T, Miura A, Oikawa M, Miura F, Takada S, Hirabayashi M, Korthauer K, Kurimoto K, Greenberg MVC, Lorincz M, Kobayashi H. Conservation and divergence of canonical and non-canonical imprinting in murids. Genome Biol 2023; 24:48. [PMID: 36918927 PMCID: PMC10012579 DOI: 10.1186/s13059-023-02869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/09/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behavior. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we use low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extraembryonic tissues at allele-specific resolution. RESULTS We identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse reveal that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extraembryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extraembryonic imprinting. Meta-analysis of novel imprinted genes reveals multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the appearance of ZFP57 binding motifs, and the insertion of endogenous retroviral promoters. CONCLUSIONS In summary, we provide an expanded list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.
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Affiliation(s)
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Azusa Inoue
- YCI Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Soichiro Kumamoto
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Asuka Miura
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Mami Oikawa
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Japan
| | - Keegan Korthauer
- Department of Statistics, University of British Columbia, Vancouver, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan
| | | | - Matthew Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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11
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EVI1 drives leukemogenesis through aberrant ERG activation. Blood 2023; 141:453-466. [PMID: 36095844 DOI: 10.1182/blood.2022016592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/10/2022] [Accepted: 08/28/2022] [Indexed: 02/07/2023] Open
Abstract
Chromosomal rearrangements involving the MDS1 and EVI1 complex locus (MECOM) on chromosome 3q26 define an aggressive subtype of acute myeloid leukemia (AML) that is associated with chemotherapy resistance and dismal prognosis. Established treatment regimens commonly fail in these patients, therefore, there is an urgent need for new therapeutic concepts that will require a better understanding of the molecular and cellular functions of the ecotropic viral integration site 1 (EVI1) oncogene. To characterize gene regulatory functions of EVI1 and associated dependencies in AML, we developed experimentally tractable human and murine disease models, investigated the transcriptional consequences of EVI1 withdrawal in vitro and in vivo, and performed the first genome-wide CRISPR screens in EVI1-dependent AML. By integrating conserved transcriptional targets with genetic dependency data, we identified and characterized the ETS transcription factor ERG as a direct transcriptional target of EVI1 that is aberrantly expressed and selectively required in both human and murine EVI1-driven AML. EVI1 controls the expression of ERG and occupies a conserved intragenic enhancer region in AML cell lines and samples from patients with primary AML. Suppression of ERG induces terminal differentiation of EVI1-driven AML cells, whereas ectopic expression of ERG abrogates their dependence on EVI1, indicating that the major oncogenic functions of EVI1 are mediated through aberrant transcriptional activation of ERG. Interfering with this regulatory axis may provide entry points for the development of rational targeted therapies.
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12
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ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nat Cell Biol 2023; 25:298-308. [PMID: 36658219 PMCID: PMC10101761 DOI: 10.1038/s41556-022-01060-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/24/2022] [Indexed: 01/21/2023]
Abstract
The EWS-FLI1 fusion oncoprotein deregulates transcription to initiate the paediatric cancer Ewing sarcoma. Here we used a domain-focused CRISPR screen to implicate the transcriptional repressor ETV6 as a unique dependency in this tumour. Using biochemical assays and epigenomics, we show that ETV6 competes with EWS-FLI1 for binding to select DNA elements enriched for short GGAA repeat sequences. Upon inactivating ETV6, EWS-FLI1 overtakes and hyper-activates these cis-elements to promote mesenchymal differentiation, with SOX11 being a key downstream target. We show that squelching of ETV6 with a dominant-interfering peptide phenocopies these effects and suppresses Ewing sarcoma growth in vivo. These findings reveal targeting of ETV6 as a strategy for neutralizing the EWS-FLI1 oncoprotein by reprogramming of genomic occupancy.
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13
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Sreekar N, Shrestha S. Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1. Bioinform Biol Insights 2023; 17:11779322231167971. [PMID: 37124129 PMCID: PMC10134125 DOI: 10.1177/11779322231167971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/17/2023] [Indexed: 05/02/2023] Open
Abstract
Eukaryotic non-coding regulatory features contribute significantly to cellular plasticity which on aberration leads to cellular malignancy. Enhancers are cis-regulatory elements that contribute to the development of resistance to endocrine therapy in estrogen receptor (ER)-positive breast cancer leading to poor clinical outcome. ER is vital for therapeutic targets in ER-positive breast cancer. Here, we review and report the different regulatory features present on ER with the objective to delineate potential mechanisms which may contribute to development of resistance. The UCSC Genome Browser, data mining, and bioinformatics tools were used to review enhancers, transcription factors (TFs), histone marks, long non-coding RNAs (lncRNAs), and variants residing in the non-coding region of the ER gene. We report 7 enhancers, 3 of which were rich in TF-binding sites and histone marks in a cell line-specific manner. Furthermore, some enhancers contain estrogen resistance variants and sites for lncRNA. Our review speculates putative models suggesting potential aberrations in gene regulation and expression if these regulatory landscapes and assemblies are altered. This review gives an interesting perspective in designing integrated in vitro studies including non-coding elements to study development of endocrine resistance in ER-positive breast cancer.
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Affiliation(s)
| | - Smeeta Shrestha
- Smeeta Shrestha, Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), 636921, Singapore.
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14
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Sun X, Klingbeil O, Lu B, Wu C, Ballon C, Ouyang M, Wu XS, Jin Y, Hwangbo Y, Huang YH, Somerville TDD, Chang K, Park J, Chung T, Lyons SK, Shi J, Vogel H, Schulder M, Vakoc CR, Mills AA. BRD8 maintains glioblastoma by epigenetic reprogramming of the p53 network. Nature 2023; 613:195-202. [PMID: 36544023 PMCID: PMC10189659 DOI: 10.1038/s41586-022-05551-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/10/2022] [Indexed: 12/24/2022]
Abstract
Inhibition of the tumour suppressive function of p53 (encoded by TP53) is paramount for cancer development in humans. However, p53 remains unmutated in the majority of cases of glioblastoma (GBM)-the most common and deadly adult brain malignancy1,2. Thus, how p53-mediated tumour suppression is countered in TP53 wild-type (TP53WT) GBM is unknown. Here we describe a GBM-specific epigenetic mechanism in which the chromatin regulator bromodomain-containing protein 8 (BRD8) maintains H2AZ occupancy at p53 target loci through the EP400 histone acetyltransferase complex. This mechanism causes a repressive chromatin state that prevents transactivation by p53 and sustains proliferation. Notably, targeting the bromodomain of BRD8 displaces H2AZ, enhances chromatin accessibility and engages p53 transactivation. This in turn enforces cell cycle arrest and tumour suppression in TP53WT GBM. In line with these findings, BRD8 is highly expressed with H2AZ in proliferating single cells of patient-derived GBM, and is inversely correlated with CDKN1A, a canonical p53 target that encodes p21 (refs. 3,4). This work identifies BRD8 as a selective epigenetic vulnerability for a malignancy for which treatment has not improved for decades. Moreover, targeting the bromodomain of BRD8 may be a promising therapeutic strategy for patients with TP53WT GBM.
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Affiliation(s)
- Xueqin Sun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Caizhi Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Carlos Ballon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Meng Ouyang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Genetics Program, Stony Brook University, Stony Brook, NY, USA
| | - Ying Jin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yon Hwangbo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yu-Han Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jung Park
- Department of Neurosurgery, Zucker School of Medicine at Hofstra Northwell, Lake Success, NY, USA
| | - Taemoon Chung
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Scott K Lyons
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Junwei Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Michael Schulder
- Department of Neurosurgery, Zucker School of Medicine at Hofstra Northwell, Lake Success, NY, USA
| | | | - Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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15
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Micro-Slab Coil Design for Hyperpolarized Metabolic Flux Analysis in Multiple Samples. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 10:bioengineering10010014. [PMID: 36671586 PMCID: PMC9854444 DOI: 10.3390/bioengineering10010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Abnormal metabolism is a hallmark of cancer cells. Accumulating evidence suggests that metabolic changes are likely to occur before other cellular responses in cancer cells upon drug treatment. Therefore, the metabolic activity or flux in cancer cells could be a potent biomarker for cancer detection and treatment monitoring. Magnetic resonance (MR)-based sensing technologies have been developed with hyperpolarized molecules for real-time flux analysis, but they still suffer from low sensitivity and throughput. To address this limitation, we have developed an innovative miniaturized MR coil, termed micro-slab MR coil, for simultaneous analysis of metabolic flux in multiple samples. Combining this approach with hyperpolarized probes, we were able to quantify the pyruvate-to-lactate flux in two different leukemic cell lines in a non-destructive manner, simultaneously. Further, we were able to rapidly assess flux changes with drug treatment in a single hyperpolarization experiment. This new multi-sample system has the potential to transform our ability to assess metabolic dynamics at scale.
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16
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Jang JY, Hwang I, Pan H, Yao J, Alinari L, Imada E, Zanettini C, Kluk MJ, Wang Y, Lee Y, Lin HV, Huang X, Di Liberto M, Chen Z, Ballman KV, Cantley LC, Marchionni L, Inghirami G, Elemento O, Baiocchi RA, Chen-Kiang S, Belvedere S, Zheng H, Paik J. A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas. J Clin Invest 2022; 132:160767. [PMID: 36282572 PMCID: PMC9753996 DOI: 10.1172/jci160767] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022] Open
Abstract
Targeting lineage-defined transcriptional dependencies has emerged as an effective therapeutic strategy in cancer treatment. Through screening for molecular vulnerabilities of mantle cell lymphoma (MCL), we identified a set of transcription factors (TFs) including FOXO1, EBF1, PAX5, and IRF4 that are essential for MCL propagation. Integrated chromatin immunoprecipitation and sequencing (ChIP-Seq) with transcriptional network reconstruction analysis revealed FOXO1 as a master regulator that acts upstream in the regulatory TF hierarchy. FOXO1 is both necessary and sufficient to drive MCL lineage commitment through supporting the lineage-specific transcription programs. We further show that FOXO1, but not its close paralog FOXO3, can reprogram myeloid leukemia cells and induce B-lineage gene expression. Finally, we demonstrate that cpd10, a small molecule identified from an enriched FOXO1 inhibitor library, induces a robust cytotoxic response in MCL cells in vitro and suppresses MCL progression in vivo. Our findings establish FOXO1 inhibition as a therapeutic strategy targeting lineage-driven transcriptional addiction in MCL.
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Affiliation(s)
| | - Inah Hwang
- Department of Pathology and Laboratory Medicine and
| | - Heng Pan
- Caryl and Israel Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Eddie Imada
- Department of Pathology and Laboratory Medicine and
| | | | - Michael J. Kluk
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Yizhe Wang
- Department of Pathology and Laboratory Medicine and
| | - Yunkyoung Lee
- Forkhead BioTherapeutics Inc., New York, New York, USA
| | - Hua V. Lin
- Forkhead BioTherapeutics Inc., New York, New York, USA
| | | | - Maurizio Di Liberto
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Zhengming Chen
- Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA.,Division of Biostatistics, Department of Population Health Sciences, and
| | - Karla V. Ballman
- Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA.,Division of Biostatistics, Department of Population Health Sciences, and
| | - Lewis C. Cantley
- Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Robert A. Baiocchi
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Selina Chen-Kiang
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | | | - Hongwu Zheng
- Department of Pathology and Laboratory Medicine and
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
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17
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Integration of CRISPR/Cas9 with artificial intelligence for improved cancer therapeutics. J Transl Med 2022; 20:534. [PMID: 36401282 PMCID: PMC9673220 DOI: 10.1186/s12967-022-03765-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
Abstract
Gene editing has great potential in treating diseases caused by well-characterized molecular alterations. The introduction of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)–based gene-editing tools has substantially improved the precision and efficiency of gene editing. The CRISPR/Cas9 system offers several advantages over the existing gene-editing approaches, such as its ability to target practically any genomic sequence, enabling the rapid development and deployment of novel CRISPR-mediated knock-out/knock-in methods. CRISPR/Cas9 has been widely used to develop cancer models, validate essential genes as druggable targets, study drug-resistance mechanisms, explore gene non-coding areas, and develop biomarkers. CRISPR gene editing can create more-effective chimeric antigen receptor (CAR)-T cells that are durable, cost-effective, and more readily available. However, further research is needed to define the CRISPR/Cas9 system’s pros and cons, establish best practices, and determine social and ethical implications. This review summarizes recent CRISPR/Cas9 developments, particularly in cancer research and immunotherapy, and the potential of CRISPR/Cas9-based screening in developing cancer precision medicine and engineering models for targeted cancer therapy, highlighting the existing challenges and future directions. Lastly, we highlight the role of artificial intelligence in refining the CRISPR system's on-target and off-target effects, a critical factor for the broader application in cancer therapeutics.
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18
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Pingul BY, Huang H, Chen Q, Alikarami F, Zhang Z, Qi J, Bernt KM, Berger SL, Cao Z, Shi J. Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia. iScience 2022; 25:105139. [PMID: 36193052 PMCID: PMC9526175 DOI: 10.1016/j.isci.2022.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 08/05/2022] [Accepted: 09/10/2022] [Indexed: 11/26/2022] Open
Abstract
Transcriptional dysregulation is a prominent feature in leukemia. Here, we systematically surveyed transcription factor (TF) vulnerabilities in leukemia and uncovered TF clusters that exhibit context-specific vulnerabilities within and between different subtypes of leukemia. Among these TF clusters, we demonstrated that acute myeloid leukemia (AML) with high IRF8 expression was addicted to MEF2D. MEF2D and IRF8 form an autoregulatory loop via direct binding to mutual enhancer elements. One important function of this circuit in AML is to sustain PU.1/MEIS1 co-regulated transcriptional outputs via stabilizing PU.1’s chromatin occupancy. We illustrated that AML could acquire dependency on this circuit through various oncogenic mechanisms that results in the activation of their enhancers. In addition to forming a circuit, MEF2D and IRF8 can also separately regulate gene expression, and dual perturbation of these two TFs leads to a more robust inhibition of AML proliferation. Collectively, our results revealed a TF circuit essential for AML survival. MEF2D is a context-specific vulnerability in IRF8hi AML MEF2D and IRF8 form a transcriptional circuit via binding to each other’s enhancers MEF2D-IRF8 circuit supports PU.1’s chromatin occupancy and transcriptional output MEF2D and IRF8 can regulate separate gene expression programs alongside the circuit
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19
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Balinth S, Fisher ML, Hwangbo Y, Wu C, Ballon C, Sun X, Mills AA. EZH2 regulates a SETDB1/ΔNp63α axis via RUNX3 to drive a cancer stem cell phenotype in squamous cell carcinoma. Oncogene 2022; 41:4130-4144. [PMID: 35864175 PMCID: PMC10132824 DOI: 10.1038/s41388-022-02417-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 01/01/2023]
Abstract
Enhancer of zeste homolog 2 (EZH2) and SET domain bifurcated 1 (SETDB1, also known as ESET) are oncogenic methyltransferases implicated in a number of human cancers. These enzymes typically function as epigenetic repressors of target genes by methylating histone H3 K27 and H3-K9 residues, respectively. Here, we show that EZH2 and SETDB1 are essential to proliferation in 3 SCC cell lines, HSC-5, FaDu, and Cal33. Additionally, we find both of these proteins highly expressed in an aggressive stem-like SCC sub-population. Depletion of either EZH2 or SETDB1 disrupts these stem-like cells and their associated phenotypes of spheroid formation, invasion, and tumor growth. We show that SETDB1 regulates this SCC stem cell phenotype through cooperation with ΔNp63α, an oncogenic isoform of the p53-related transcription factor p63. Furthermore, EZH2 is upstream of both SETDB1 and ΔNp63α, activating these targets via repression of the tumor suppressor RUNX3. We show that targeting this pathway with inhibitors of EZH2 results in activation of RUNX3 and repression of both SETDB1 and ΔNp63α, antagonizing the SCC cancer stem cell phenotype. This work highlights a novel pathway that drives an aggressive cancer stem cell phenotype and demonstrates a means of pharmacological intervention.
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Affiliation(s)
- Seamus Balinth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY, USA
| | | | - Yon Hwangbo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Caizhi Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Carlos Ballon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xueqin Sun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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20
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Downregulation of STAT3 in Epstein-Barr Virus-Positive Hodgkin Lymphoma. Biomedicines 2022; 10:biomedicines10071608. [PMID: 35884913 PMCID: PMC9313380 DOI: 10.3390/biomedicines10071608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
STAT3 is a transcription factor which is activated via various signaling transduction pathways or Epstein-Barr virus (EBV) infection and plays an oncogenic role in lymphoid malignancies including Hodgkin lymphoma (HL). The tumor cells of HL are derived from germinal center B-cells and transformed by chromosomal rearrangements, aberrant signal transduction, deregulation of developmental transcription factors, and EBV activity. HL cell lines represent useful models to investigate molecular principles and deduced treatment options of this malignancy. Using cell line L-540, we have recently shown that constitutively activated STAT3 drives aberrant expression of hematopoietic NKL homeobox gene HLX. Here, we analyzed HL cell line AM-HLH which is EBV-positive but, nevertheless, HLX-negative. Consistently, AM-HLH expressed decreased levels of STAT3 proteins which were additionally inactivated and located in the cytoplasm. Combined genomic and expression profiling data revealed several amplified and overexpressed gene candidates involved in opposed regulation of STAT3 and EBV. Corresponding knockdown studies demonstrated that IRF4 and NFATC2 inhibited STAT3 expression. MIR155 (activated by STAT3) and SPIB (repressed by HLX) showed reduced and elevated expression levels in AM-HLH, respectively. However, treatment with IL6 or IL27 activated STAT3, elevated expression of HLX and MIR155, and inhibited IRF4. Taken together, this cell line deals with two conflicting oncogenic drivers, namely, JAK2-STAT3 signaling and EBV infection, but is sensitive to switch after cytokine stimulation. Thus, AM-HLH represents a unique cell line model to study the pathogenic roles of STAT3 and EBV and their therapeutic implications in HL.
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21
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Wei CY, Zhu MX, Zhang PF, Huang XY, Wan JK, Yao XZ, Hu ZT, Chai XQ, Peng R, Yang X, Gao C, Gao J, Wang SW, Zheng YM, Tang Z, Gao Q, Zhou J, Fan JB, Ke AW, Fan J. PKCα/ZFP64/CSF1 axis resets the tumor microenvironment and fuels anti-PD1 resistance in hepatocellular carcinoma. J Hepatol 2022; 77:163-176. [PMID: 35219791 DOI: 10.1016/j.jhep.2022.02.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/28/2022] [Accepted: 02/09/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND & AIMS Despite remarkable advances in treatment, most patients with hepatocellular carcinoma (HCC) respond poorly to anti-programmed cell death 1 (anti-PD1) therapy. A deeper insight into the tolerance mechanism of HCC against this therapy is urgently needed. METHODS We performed next-generation sequencing, multiplex immunofluorescence, and dual-color immunohistochemistry and constructed an orthotopic HCC xenograft tumor model to identify the key gene associated with anti-PD1 tolerance. A spontaneously tumorigenic transgenic mouse model, an in vitro coculture system, mass cytometry, and multiplex immunofluorescence were used to explore the biological function of zinc finger protein 64 (ZFP64) on tumor progression and immune escape. Molecular and biochemical strategies like RNA-sequencing, chromatin immunoprecipitation-sequencing and mass spectrometry were used to gain insight into the underlying mechanisms of ZFP64. RESULTS We showed that ZFP64 is frequently upregulated in tumor tissues from patients with anti-PD1-resistant HCC. Elevated ZFP64 drives anti-PD1 resistance by shifting macrophage polarization toward an alternative activation phenotype (M2) and fostering an inhibitory tumor microenvironment. Mechanistically, we primarily demonstrated that protein kinase C alpha (PKCα) directly phosphorylates ZFP64 at S226, leading to its nuclear translocation and the transcriptional activation of macrophage colony-stimulating factor (CSF1). HCC-derived CSF1 transforms macrophages to the M2 phenotype to drive immune escape and anti-PD1 tolerance. Notably, Gö6976, a protein kinase inhibitor, and lenvatinib, a multi-kinase inhibitor, reset the tumor microenvironment and restore sensitivity to anti-PD1 by blocking the PKCα/ZFP64/CSF1 axis. CONCLUSIONS We propose that the PKCα/ZFP64/CSF1 axis is critical for triggering immune evasion and anti-PD1 tolerance. Inhibiting this axis with Gö6976 or lenvatinib overcomes anti-PD1 resistance in HCC. LAY SUMMARY Despite remarkable treatment progress, most patients with hepatocellular carcinoma respond poorly to anti-PD1 therapy (a type of immunotherapy). A deeper insight into the tolerance mechanisms to this therapy is urgently needed. Herein, we unravel a previously unexplored mechanism linking tumor progression, macrophage polarization, and anti-PD1 resistance, and offer an attractive novel target for anti-PD1 combination therapy, which may benefit patients with hepatocellular carcinoma.
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Affiliation(s)
- Chuan-Yuan Wei
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China; Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Meng-Xuan Zhu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Peng-Fei Zhang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Xiao-Yong Huang
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Jin-Kai Wan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Xiu-Zhong Yao
- Department of Radiology, Zhongshan Hospital of Fudan University, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, P. R. China
| | - Ze-Tao Hu
- Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, 200433, P. R. China
| | - Xiao-Qiang Chai
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Rui Peng
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Xuan Yang
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Chao Gao
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Jian Gao
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Si-Wei Wang
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Yi-Min Zheng
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Zheng Tang
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Jia-Bin Fan
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China.
| | - Ai-Wu Ke
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China.
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China.
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22
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Qiu G, Deng Y. ZFP64 transcriptionally activates PD-1 and CTLA-4 and plays an oncogenic role in esophageal cancer. Biochem Biophys Res Commun 2022; 622:72-78. [DOI: 10.1016/j.bbrc.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/05/2022] [Indexed: 11/02/2022]
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23
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Harada T, Heshmati Y, Kalfon J, Perez MW, Xavier Ferrucio J, Ewers J, Hubbell Engler B, Kossenkov A, Ellegast JM, Yi JS, Bowker A, Zhu Q, Eagle K, Liu T, Kai Y, Dempster JM, Kugener G, Wickramasinghe J, Herbert ZT, Li CH, Vrabič Koren J, Weinstock DM, Paralkar VR, Nabet B, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia. Genes Dev 2022; 36:368-389. [PMID: 35301220 PMCID: PMC8973843 DOI: 10.1101/gad.349284.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 12/12/2022]
Abstract
In this study, Harada et al. identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. This study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes. Acute myeloid leukemia with KMT2A (MLL) rearrangements is characterized by specific patterns of gene expression and enhancer architecture, implying unique core transcriptional regulatory circuitry. Here, we identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. Rapid transcription factor degradation followed by measurements of genome-wide transcription rates and superresolution microscopy revealed that MEF2D and IRF8 form a distinct core regulatory module with a narrow direct transcriptional program that includes activation of the key oncogenes MYC, HOXA9, and BCL2. Our study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes.
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Affiliation(s)
- Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yaser Heshmati
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jérémie Kalfon
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Monika W Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Juliana Xavier Ferrucio
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jazmin Ewers
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Benjamin Hubbell Engler
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | | | - Jana M Ellegast
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joanna S Yi
- Baylor College of Medicine, Houston, Texas 77030, USA
| | - Allyson Bowker
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Qian Zhu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Ken Eagle Consulting, Houston, Texas 77494, USA
| | - Tianxin Liu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yan Kai
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Joshua M Dempster
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Guillaume Kugener
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Zachary T Herbert
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | | | - David M Weinstock
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Vikram R Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Charles Y Lin
- Baylor College of Medicine, Houston, Texas 77030, USA
| | - Neekesh V Dharia
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02215, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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24
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Wei Y, Huang YH, Skopelitis DS, Iyer SV, Costa AS, Yang Z, Kramer M, Adelman ER, Klingbeil O, Demerdash OE, Polyanskaya SA, Chang K, Goodwin S, Hodges E, McCombie WR, Figueroa ME, Vakoc CR. SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia. Cancer Discov 2022; 12:450-467. [PMID: 34531253 PMCID: PMC8831445 DOI: 10.1158/2159-8290.cd-20-1849] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 06/25/2021] [Accepted: 09/13/2021] [Indexed: 01/09/2023]
Abstract
An enhanced requirement for nutrients is a hallmark property of cancer cells. Here, we optimized an in vivo genetic screening strategy in acute myeloid leukemia (AML), which led to the identification of the myo-inositol transporter SLC5A3 as a dependency in this disease. We demonstrate that SLC5A3 is essential to support a myo-inositol auxotrophy in AML. The commonality among SLC5A3-dependent AML lines is the transcriptional silencing of ISYNA1, which encodes the rate-limiting enzyme for myo-inositol biosynthesis, inositol-3-phosphate synthase 1. We use gain- and loss-of-function experiments to reveal a synthetic lethal genetic interaction between ISYNA1 and SLC5A3 in AML, which function redundantly to sustain intracellular myo-inositol. Transcriptional silencing and DNA hypermethylation of ISYNA1 occur in a recurrent manner in human AML patient samples, in association with IDH1/IDH2 and CEBPA mutations. Our findings reveal myo-inositol as a nutrient dependency in AML caused by the aberrant silencing of a biosynthetic enzyme. SIGNIFICANCE: We show how epigenetic silencing can provoke a nutrient dependency in AML by exploiting a synthetic lethality relationship between biosynthesis and transport of myo-inositol. Blocking the function of this solute carrier may have therapeutic potential in an epigenetically defined subset of AML.This article is highlighted in the In This Issue feature, p. 275.
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Affiliation(s)
- Yiliang Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Yu-Han Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | | | - Shruti V. Iyer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.,Stony Brook University, Stony Brook, New York
| | - Ana S.H. Costa
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Zhaolin Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Emmalee R. Adelman
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | | | - Sofya A. Polyanskaya
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.,School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Emily Hodges
- Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Maria E. Figueroa
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida
| | - Christopher R. Vakoc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.,Corresponding Author: Christopher R. Vakoc, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724. Phone: 516-367-5030; E-mail:
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25
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Lin S, Larrue C, Scheidegger NK, Seong BKA, Dharia NV, Kuljanin M, Wechsler CS, Kugener G, Robichaud AL, Conway AS, Mashaka T, Mouche S, Adane B, Ryan JA, Mancias JD, Younger ST, Piccioni F, Lee LH, Wunderlich M, Letai A, Tamburini J, Stegmaier K. An In Vivo CRISPR Screening Platform for Prioritizing Therapeutic Targets in AML. Cancer Discov 2022; 12:432-449. [PMID: 34531254 PMCID: PMC8831447 DOI: 10.1158/2159-8290.cd-20-1851] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/26/2021] [Accepted: 09/13/2021] [Indexed: 02/02/2023]
Abstract
CRISPR-Cas9-based genetic screens have successfully identified cell type-dependent liabilities in cancer, including acute myeloid leukemia (AML), a devastating hematologic malignancy with poor overall survival. Because most of these screens have been performed in vitro using established cell lines, evaluating the physiologic relevance of these targets is critical. We have established a CRISPR screening approach using orthotopic xenograft models to validate and prioritize AML-enriched dependencies in vivo, including in CRISPR-competent AML patient-derived xenograft (PDX) models tractable for genome editing. Our integrated pipeline has revealed several targets with translational value, including SLC5A3 as a metabolic vulnerability for AML addicted to exogenous myo-inositol and MARCH5 as a critical guardian to prevent apoptosis in AML. MARCH5 repression enhanced the efficacy of BCL2 inhibitors such as venetoclax, further highlighting the clinical potential of targeting MARCH5 in AML. Our study provides a valuable strategy for discovery and prioritization of new candidate AML therapeutic targets. SIGNIFICANCE: There is an unmet need to improve the clinical outcome of AML. We developed an integrated in vivo screening approach to prioritize and validate AML dependencies with high translational potential. We identified SLC5A3 as a metabolic vulnerability and MARCH5 as a critical apoptosis regulator in AML, both of which represent novel therapeutic opportunities.This article is highlighted in the In This Issue feature, p. 275.
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Affiliation(s)
- Shan Lin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Clément Larrue
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Nastassja K. Scheidegger
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Bo Kyung A. Seong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Neekesh V. Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Miljan Kuljanin
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Caroline S. Wechsler
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts
| | | | - Amanda L. Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts
| | - Amy Saur Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts
| | - Thelma Mashaka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sarah Mouche
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Biniam Adane
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jeremy A. Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joseph D. Mancias
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott T. Younger
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Lynn H. Lee
- Division of Oncology, Cancer and Blood Disease Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Anthony Letai
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jérôme Tamburini
- Translational Research Centre in Onco-hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Corresponding Author: Kimberly Stegmaier, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215. Phone: 617-632-4438; E-mail:
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26
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Zhu M, Zhang P, Yu S, Tang C, Wang Y, Shen Z, Chen W, Liu T, Cui Y. Targeting ZFP64/GAL-1 axis promotes therapeutic effect of nab-paclitaxel and reverses immunosuppressive microenvironment in gastric cancer. J Exp Clin Cancer Res 2022; 41:14. [PMID: 34996504 PMCID: PMC8740411 DOI: 10.1186/s13046-021-02224-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/13/2021] [Indexed: 01/03/2023] Open
Abstract
Background Chemoresistance is a main obstacle in gastric cancer (GC) treatment, but its molecular mechanism still needs to be elucidated. Here, we aim to reveal the underlying mechanisms of nanoparticle albumin-bound paclitaxel (nab-paclitaxel) resistance in GC. Methods We performed RNA sequencing (RNA-seq) on samples from patients who were resistant or sensitive to nab-paclitaxel, and identified Zinc Finger Protein 64 (ZFP64) as critical for nab-paclitaxel resistance in GC. CCK8, flow cytometry, TUNEL staining, sphere formation assays were performed to investigate the effects of ZFP64 in vitro, while subcutaneous tumor formation models were established in nude mice or humanized mice to evaluate the biological roles of ZFP64 in vivo. Chromatin immunoprecipitation sequencing (CHIP-seq) and double-luciferase reporter gene assay were conducted to reveal the underlying mechanism of ZFP64. Results ZFP64 overexpression was linked with aggressive phenotypes, nab-paclitaxel resistance and served as an independent prognostic factor in GC. As a transcription factor, ZFP64 directly binds to Galectin-1 (GAL-1) promoter and promoted GAL-1 transcription, thus inducing stem-cell like phenotypes and immunosuppressive microenvironment in GC. Importantly, compared to treatment with nab-paclitaxel alone, nab-paclitaxel plus GAL-1 blockade significantly enhanced the anti-tumor effect in mouse models, particularly in humanized mice. Conclusions Our data support a pivotal role for ZFP64 in GC progression by simultaneously promoting cellular chemotherapy resistance and tumor immunosuppression. Treatment with the combination of nab-paclitaxel and a GAL-1 inhibitor might benefit a subgroup of GC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02224-x.
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Affiliation(s)
- Mengxuan Zhu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Center of Evidence-based Medicine, Fudan University, Shanghai, China
| | - Pengfei Zhang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Center of Evidence-based Medicine, Fudan University, Shanghai, China
| | - Shan Yu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Cheng Tang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yan Wang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhenbin Shen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Weidong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,Center of Evidence-based Medicine, Fudan University, Shanghai, China.
| | - Yuehong Cui
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,Center of Evidence-based Medicine, Fudan University, Shanghai, China.
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27
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Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung T, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, Mathelier A. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res 2022; 50:D165-D173. [PMID: 34850907 PMCID: PMC8728201 DOI: 10.1093/nar/gkab1113] [Citation(s) in RCA: 792] [Impact Index Per Article: 396.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022] Open
Abstract
JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.
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Affiliation(s)
- Jaime A Castro-Mondragon
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Rafael Riudavets-Puig
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Ieva Rauluseviciute
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Jeremy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Paul Boddie
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Aziz Khan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305, USA
| | - Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Tiffany Y Leung
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Alejandro Aguirre
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | | | - Daniel Schmelter
- UCSC Genome Browser, University of California Santa Cruz, Santa Cruz, CA95060, USA
| | - Damir Baranasic
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | | | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK2200 Copenhagen N, Denmark
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
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28
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Malouf C, Antunes ETB, O'Dwyer M, Jakobczyk H, Sahm F, Landua SL, Anderson RA, Soufi A, Halsey C, Ottersbach K. miR-130b and miR-128a are essential lineage-specific codrivers of t(4;11) MLL-AF4 acute leukemia. Blood 2021; 138:2066-2092. [PMID: 34111240 DOI: 10.1182/blood.2020006610] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/28/2021] [Indexed: 11/20/2022] Open
Abstract
t(4;11) MLL-AF4 acute leukemia is one of the most aggressive malignancies in the infant and pediatric population, yet we have little information on the molecular mechanisms responsible for disease progression. This impairs the development of therapeutic regimens that can address the aggressive phenotype and lineage plasticity of MLL-AF4-driven leukemogenesis. This study highlights novel mechanisms of disease development by focusing on 2 microRNAs (miRNAs) upregulated in leukemic blasts from primary patient samples: miR-130b and miR-128a. We show that miR-130b and miR-128a are downstream targets of MLL-AF4 and can individually drive the transition from a pre-leukemic stage to an acute leukemia in an entirely murine Mll-AF4 in vivo model. They are also required to maintain the disease phenotype. Interestingly, miR-130b overexpression led to a mixed/B-cell precursor (BCP)/myeloid leukemia, propagated by the lymphoid-primed multipotent progenitor (LMPP) population, whereas miR-128a overexpression resulted in a pro-B acute lymphoblastic leukemia (ALL), maintained by a highly expanded Il7r+c-Kit+ blast population. Molecular and phenotypic changes induced by these two miRNAs fully recapitulate the human disease, including central nervous system infiltration and activation of an MLL-AF4 expression signature. Furthermore, we identified 2 downstream targets of these miRNAs, NR2F6 and SGMS1, which in extensive validation studies are confirmed as novel tumor suppressors of MLL-AF4+ leukemia. Our integrative approach thus provides a platform for the identification of essential co-drivers of MLL-rearranged leukemias, in which the preleukemia to leukemia transition and lineage plasticity can be dissected and new therapeutic approaches can be tested.
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Affiliation(s)
| | | | | | | | | | | | - Richard A Anderson
- Medical Research Council (MRC) Centre for Reproductive Health, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom; and
| | | | - Christina Halsey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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29
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Transcription factor MEF2D is required for the maintenance of MLL-rearranged acute myeloid leukemia. Blood Adv 2021; 5:4727-4740. [PMID: 34597364 PMCID: PMC8759131 DOI: 10.1182/bloodadvances.2021004469] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022] Open
Abstract
MEF2D is highly expressed in MLL-rearranged AML and required for leukemia development in vitro and in vivo. MEF2D suppresses CEBPE-mediated myeloid differentiation in AML.
Acute myeloid leukemia (AML) with MLL-rearrangement (MLL-r) comprises ∼10% of all AML cases and portends poor outcomes. Much remains uncovered on how MLL-r AML drives leukemia development while preventing cells from normal myeloid differentiation. Here, we identified that transcription factor MEF2D is a super-enhancer-associated, highly expressed gene in MLL-r AML. Knockout of MEF2D profoundly impaired leukemia growth, induced myeloid differentiation, and delayed oncogenic progression in vivo. Mechanistically, MEF2D loss led to robust activation of a CEBPE-centered myeloid differentiation program in AML cells. Chromatin profiling revealed that MEF2D binds to and suppresses the chromatin accessibility of CEBPE cis-regulatory regions. In human acute leukemia samples, MEF2D expression showed a strong negative correlation with the expression of CEBPE. Depletion of CEBPE partially rescued the cell growth defect and myeloid cell differentiation induced by the loss of MEF2D. Lastly, we show that MEF2D is positively regulated by HOXA9, and downregulation of MEF2D is an important mechanism for DOT1L inhibitor-induced antileukemia effects. Collectively, our findings suggest that MEF2D plays a critical role in human MLL-r AML and uncover the MEF2D-CEBPE axis as a crucial transcriptional mechanism regulating leukemia cell self-renewal and differentiation block.
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30
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Zhao GN, Tian ZW, Tian T, Zhu ZP, Zhao WJ, Tian H, Cheng X, Hu FJ, Hu ML, Tian S, Ding T, Chen S, Ji YX, Zhang P, Zhang XJ, She ZG, Yuan Y, Chen W, Bai L, Li H. TMBIM1 is an inhibitor of adipogenesis and its depletion promotes adipocyte hyperplasia and improves obesity-related metabolic disease. Cell Metab 2021; 33:1640-1654.e8. [PMID: 34107313 DOI: 10.1016/j.cmet.2021.05.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/12/2021] [Accepted: 05/13/2021] [Indexed: 01/09/2023]
Abstract
Obesity is characterized by the excessive accumulation of the white adipose tissue (WAT), but healthy expansion of WAT via adipocyte hyperplasia can offset the negative metabolic effects of obesity. Thus, identification of novel adipogenesis regulators that promote hyperplasia may lead to effective therapies for obesity-induced metabolic disorders. Using transcriptomic approaches, we identified transmembrane BAX inhibitor motif-containing 1 (TMBIM1) as an inhibitor of adipogenesis. Gain or loss of function of TMBIM1 in preadipocytes inhibited or promoted adipogenesis, respectively. In vivo, in response to caloric excess, adipocyte precursor (AP)-specific Tmbim1 knockout (KO) mice displayed WAT hyperplasia and improved systemic metabolic health, while overexpression of Tmbim1 in transgenic mice showed the opposite effects. Moreover, mature adipocyte-specific Tmbim1 KO did not affect WAT cellularity or nutrient homeostasis. Mechanistically, TMBIM1 binds to and promotes the autoubiquitination and degradation of NEDD4, which is an E3 ligase that stabilizes PPARγ. Our data show that TMBIM1 is a potent repressor of adipogenesis and a potential therapeutic target for obesity-related metabolic disease.
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Affiliation(s)
- Guang-Nian Zhao
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China
| | - Zheng-Wei Tian
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China
| | - Tian Tian
- Institute of Model Animal, Wuhan University, Wuhan, China; Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhi-Peng Zhu
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China
| | - Wen-Jie Zhao
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China
| | - Han Tian
- Institute of Model Animal, Wuhan University, Wuhan, China
| | - Xu Cheng
- Institute of Model Animal, Wuhan University, Wuhan, China; Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Feng-Jiao Hu
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China
| | - Man-Li Hu
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China
| | - Song Tian
- Institute of Model Animal, Wuhan University, Wuhan, China
| | - Ting Ding
- Department of Endocrinology, Huanggang Central Hospital, Huanggang, China; Huanggang Institute of Translational Medicine, Huanggang, China
| | - Siping Chen
- Department of Endocrinology, Huanggang Central Hospital, Huanggang, China; Huanggang Institute of Translational Medicine, Huanggang, China
| | - Yan-Xiao Ji
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China
| | - Peng Zhang
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China
| | - Xiao-Jing Zhang
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China
| | - Zhi-Gang She
- Institute of Model Animal, Wuhan University, Wuhan, China; Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yufeng Yuan
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China; Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, China.
| | - Wenping Chen
- Department of Endocrinology, Huanggang Central Hospital, Huanggang, China; Huanggang Institute of Translational Medicine, Huanggang, China.
| | - Lan Bai
- Institute of Model Animal, Wuhan University, Wuhan, China; Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Hongliang Li
- Medical Science Research Center, Zhongnan Hospital, School of Basic Medical Sciences, Wuhan University, Wuhan, China; Institute of Model Animal, Wuhan University, Wuhan, China; Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China; Huanggang Institute of Translational Medicine, Huanggang, China.
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31
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ZMYND8-regulated IRF8 transcription axis is an acute myeloid leukemia dependency. Mol Cell 2021; 81:3604-3622.e10. [PMID: 34358447 DOI: 10.1016/j.molcel.2021.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023]
Abstract
The transformed state in acute leukemia requires gene regulatory programs involving transcription factors and chromatin modulators. Here, we uncover an IRF8-MEF2D transcriptional circuit as an acute myeloid leukemia (AML)-biased dependency. We discover and characterize the mechanism by which the chromatin "reader" ZMYND8 directly activates IRF8 in parallel with the MYC proto-oncogene through their lineage-specific enhancers. ZMYND8 is essential for AML proliferation in vitro and in vivo and associates with MYC and IRF8 enhancer elements that we define in cell lines and in patient samples. ZMYND8 occupancy at IRF8 and MYC enhancers requires BRD4, a transcription coactivator also necessary for AML proliferation. We show that ZMYND8 binds to the ET domain of BRD4 via its chromatin reader cassette, which in turn is required for proper chromatin occupancy and maintenance of leukemic growth in vivo. Our results rationalize ZMYND8 as a potential therapeutic target for modulating essential transcriptional programs in AML.
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32
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ZNF410 represses fetal globin by singular control of CHD4. Nat Genet 2021; 53:719-728. [PMID: 33859416 PMCID: PMC8180380 DOI: 10.1038/s41588-021-00843-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/10/2021] [Indexed: 02/02/2023]
Abstract
Known fetal hemoglobin (HbF) silencers have potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here, through transcription factor (TF) CRISPR screening, we identify zinc-finger protein (ZNF) 410 as an HbF repressor. ZNF410 does not bind directly to the genes encoding γ-globins, but rather its chromatin occupancy is concentrated solely at CHD4, encoding the NuRD nucleosome remodeler, which is itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for the effects of ZNF410 on fetal globin repression. Knockout of ZNF410 or its mouse homolog Zfp410 reduces CHD4 levels by 60%, enough to substantially de-repress HbF while eluding cellular or organismal toxicity. These studies suggest a potential target for HbF induction for β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved TF with singular devotion to regulation of a chromatin subcomplex.
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33
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Camolotto SA, Belova VK, Torre-Healy L, Vahrenkamp JM, Berrett KC, Conway H, Shea J, Stubben C, Moffitt R, Gertz J, Snyder EL. Reciprocal regulation of pancreatic ductal adenocarcinoma growth and molecular subtype by HNF4α and SIX1/4. Gut 2021; 70:900-914. [PMID: 32826305 PMCID: PMC7945295 DOI: 10.1136/gutjnl-2020-321316] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/17/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with a 5-year survival of less than 5%. Transcriptomic analysis has identified two clinically relevant molecular subtypes of PDAC: classical and basal-like. The classical subtype is characterised by a more favourable prognosis and better response to chemotherapy than the basal-like subtype. The classical subtype also expresses higher levels of lineage specifiers that regulate endodermal differentiation, including the nuclear receptor hepatocyte nuclear factor 4 α (HNF4α). The objective of this study is to evaluate the role of HNF4α, SIX4 and SIX1 in regulating the growth and molecular subtype of PDAC. DESIGN We manipulate the expression of HNF4α, SIX4 and SIX1 in multiple in vitro and in vivo PDAC models. We determine the consequences of manipulating these genes on PDAC growth, differentiation and molecular subtype using functional assays, gene expression analysis and cross-species comparisons with human datasets. RESULTS We show that HNF4α restrains tumour growth and drives tumour cells toward an epithelial identity. Gene expression analysis of murine models and human tumours shows that HNF4α activates expression of genes associated with the classical subtype. HNF4α also directly represses SIX4 and SIX1, two mesodermal/neuronal lineage specifiers expressed in the basal-like subtype. Finally, SIX4 and SIX1 drive proliferation and regulate differentiation in HNF4α-negative PDAC. CONCLUSION Our data show that HNF4α regulates the growth and molecular subtype of PDAC by multiple mechanisms, including activation of the classical gene expression programme and repression of SIX4 and SIX1, which may represent novel dependencies of the basal-like subtype.
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Affiliation(s)
- Soledad A Camolotto
- Department of Pathology, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Veronika K Belova
- Department of Pathology, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Luke Torre-Healy
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Kristofer C Berrett
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Hannah Conway
- HCI Clinical Trials Operations, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Jill Shea
- Department of Surgery, University of Utah, Salt Lake City, Utah, USA
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Richard Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
| | - Eric L Snyder
- Department of Pathology, Huntsman Cancer Institute, University of Utah Health, Salt Lake City, Utah, USA
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34
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Takao S, Forbes L, Uni M, Cheng S, Pineda JMB, Tarumoto Y, Cifani P, Minuesa G, Chen C, Kharas MG, Bradley RK, Vakoc CR, Koche RP, Kentsis A. Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia. eLife 2021; 10:65905. [PMID: 33527899 PMCID: PMC7886351 DOI: 10.7554/elife.65905] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
Dysregulated gene expression contributes to most prevalent features in human cancers. Here, we show that most subtypes of acute myeloid leukemia (AML) depend on the aberrant assembly of MYB transcriptional co-activator complex. By rapid and selective peptidomimetic interference with the binding of CBP/P300 to MYB, but not CREB or MLL1, we find that the leukemic functions of MYB are mediated by CBP/P300 co-activation of a distinct set of transcription factor complexes. These MYB complexes assemble aberrantly with LYL1, E2A, C/EBP family members, LMO2, and SATB1. They are organized convergently in genetically diverse subtypes of AML and are at least in part associated with inappropriate transcription factor co-expression. Peptidomimetic remodeling of oncogenic MYB complexes is accompanied by specific proteolysis and dynamic redistribution of CBP/P300 with alternative transcription factors such as RUNX1 to induce myeloid differentiation and apoptosis. Thus, aberrant assembly and sequestration of MYB:CBP/P300 complexes provide a unifying mechanism of oncogenic gene expression in AML. This work establishes a compelling strategy for their pharmacologic reprogramming and therapeutic targeting for diverse leukemias and possibly other human cancers caused by dysregulated gene control.
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Affiliation(s)
- Sumiko Takao
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Lauren Forbes
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Masahiro Uni
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Shuyuan Cheng
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Medical Scientist Training Program, University of Washington, Seattle, United States.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| | - Yusuke Tarumoto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States
| | - Gerard Minuesa
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States
| | - Celine Chen
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States
| | - Michael G Kharas
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
| | | | - Richard P Koche
- Center for Epigenetics Research, Sloan Kettering Institute, New York, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, United States.,Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, United States.,Departments of Pharmacology and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
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35
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Chou HC, Bhalla K, Demerdesh OE, Klingbeil O, Hanington K, Aganezov S, Andrews P, Alsudani H, Chang K, Vakoc CR, Schatz MC, McCombie WR, Stillman B. The human origin recognition complex is essential for pre-RC assembly, mitosis, and maintenance of nuclear structure. eLife 2021; 10:61797. [PMID: 33522487 PMCID: PMC7877914 DOI: 10.7554/elife.61797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/30/2021] [Indexed: 12/23/2022] Open
Abstract
The origin recognition complex (ORC) cooperates with CDC6, MCM2-7, and CDT1 to form pre-RC complexes at origins of DNA replication. Here, using tiling-sgRNA CRISPR screens, we report that each subunit of ORC and CDC6 is essential in human cells. Using an auxin-inducible degradation system, we created stable cell lines capable of ablating ORC2 rapidly, revealing multiple cell division cycle phenotypes. The primary defects in the absence of ORC2 were cells encountering difficulty in initiating DNA replication or progressing through the cell division cycle due to reduced MCM2-7 loading onto chromatin in G1 phase. The nuclei of ORC2-deficient cells were also large, with decompacted heterochromatin. Some ORC2-deficient cells that completed DNA replication entered into, but never exited mitosis. ORC1 knockout cells also demonstrated extremely slow cell proliferation and abnormal cell and nuclear morphology. Thus, ORC proteins and CDC6 are indispensable for normal cellular proliferation and contribute to nuclear organization.
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Affiliation(s)
- Hsiang-Chen Chou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.,Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, United States
| | - Kuhulika Bhalla
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Sergey Aganezov
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Habeeb Alsudani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Michael C Schatz
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
| | | | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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36
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Lan X, Ren R, Feng R, Ly LC, Lan Y, Zhang Z, Aboreden N, Qin K, Horton JR, Grevet JD, Mayuranathan T, Abdulmalik O, Keller CA, Giardine B, Hardison RC, Crossley M, Weiss MJ, Cheng X, Shi J, Blobel GA. ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression. Mol Cell 2020; 81:239-254.e8. [PMID: 33301730 DOI: 10.1016/j.molcel.2020.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Abstract
Metazoan transcription factors typically regulate large numbers of genes. Here we identify via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA-binding protein that in human erythroid cells directly activates only a single gene, the NuRD component CHD4. Specificity is conveyed by two highly evolutionarily conserved clusters of ZNF410 binding sites near the CHD4 gene with no counterparts elsewhere in the genome. Loss of ZNF410 in adult-type human erythroid cell culture systems and xenotransplantation settings diminishes CHD4 levels and derepresses the fetal hemoglobin genes. While previously known to be silenced by CHD4, the fetal globin genes are exposed here as among the most sensitive to reduced CHD4 levels.. In vitro DNA binding assays and crystallographic studies reveal the ZNF410-DNA binding mode. ZNF410 is a remarkably selective transcriptional activator in erythroid cells, and its perturbation might offer new opportunities for treatment of hemoglobinopathies.
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Affiliation(s)
- Xianjiang Lan
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lana C Ly
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, NSW 2052, Australia
| | - Yemin Lan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicholas Aboreden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kunhua Qin
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeremy D Grevet
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, NSW 2052, Australia
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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37
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Zhang H, Zhang Y, Zhou X, Wright S, Hyle J, Zhao L, An J, Zhao X, Shao Y, Xu B, Lee HM, Chen T, Zhou Y, Chen X, Lu R, Li C. Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen. eLife 2020; 9:e57858. [PMID: 33001025 PMCID: PMC7599066 DOI: 10.7554/elife.57858] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/30/2020] [Indexed: 12/26/2022] Open
Abstract
Aberrant HOXA9 expression is a hallmark of most aggressive acute leukemias, notably those with KMT2A (MLL) gene rearrangements. HOXA9 overexpression not only predicts poor diagnosis and outcome but also plays a critical role in leukemia transformation and maintenance. However, our current understanding of HOXA9 regulation in leukemia is limited, hindering development of therapeutic strategies. Here, we generated the HOXA9-mCherry knock-in reporter cell lines to dissect HOXA9 regulation. By utilizing the reporter and CRISPR/Cas9 screens, we identified transcription factors controlling HOXA9 expression, including a novel regulator, USF2, whose depletion significantly down-regulated HOXA9 expression and impaired MLLr leukemia cell proliferation. Ectopic expression of Hoxa9 rescued impaired leukemia cell proliferation upon USF2 loss. Cut and Run analysis revealed the direct occupancy of USF2 at HOXA9 promoter in MLLr leukemia cells. Collectively, the HOXA9 reporter facilitated the functional interrogation of the HOXA9 regulome and has advanced our understanding of the molecular regulation network in HOXA9-driven leukemia.
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Affiliation(s)
- Hao Zhang
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research HospitalMemphisUnited States
- Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children’s Research HospitalMemphisUnited States
| | - Xinyue Zhou
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children’s Research HospitalMemphisUnited States
- Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children’s Research HospitalMemphisUnited States
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children’s Research HospitalMemphisUnited States
- Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children’s Research HospitalMemphisUnited States
| | - Lianzhong Zhao
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Jie An
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children’s Research HospitalMemphisUnited States
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Hyeong-Min Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research HospitalMemphisUnited States
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research HospitalMemphisUnited States
| | - Yang Zhou
- Department of Biomedical Engineering School of Engineering, University of Alabama at BirminghamBirminghamUnited States
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Rui Lu
- Division of Hematology/Oncology, University of Alabama at BirminghamBirminghamUnited States
- O’Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research HospitalMemphisUnited States
- Cancer Biology Program/Comprehensive Cancer Center, St. Jude Children’s Research HospitalMemphisUnited States
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38
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Liu Q, Garcia M, Wang S, Chen CW. Therapeutic Target Discovery Using High-Throughput Genetic Screens in Acute Myeloid Leukemia. Cells 2020; 9:cells9081888. [PMID: 32806592 PMCID: PMC7465943 DOI: 10.3390/cells9081888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
The development of high-throughput gene manipulating tools such as short hairpin RNA (shRNA) and CRISPR/Cas9 libraries has enabled robust characterization of novel functional genes contributing to the pathological states of the diseases. In acute myeloid leukemia (AML), these genetic screen approaches have been used to identify effector genes with previously unknown roles in AML. These AML-related genes centralize alongside the cellular pathways mediating epigenetics, signaling transduction, transcriptional regulation, and energy metabolism. The shRNA/CRISPR genetic screens also realized an array of candidate genes amenable to pharmaceutical targeting. This review aims to summarize genes, mechanisms, and potential therapeutic strategies found via high-throughput genetic screens in AML. We also discuss the potential of these findings to instruct novel AML therapies for combating drug resistance in this genetically heterogeneous disease.
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Affiliation(s)
- Qiao Liu
- Fujian Provincial Key Laboratory on Hematology, Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou 350108, China; (Q.L.); (S.W.)
- Union Clinical Medical College, Fujian Medical University, Fuzhou 350108, China
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
| | - Michelle Garcia
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
- Pomona College, Claremont, CA 91711, USA
| | - Shaoyuan Wang
- Fujian Provincial Key Laboratory on Hematology, Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou 350108, China; (Q.L.); (S.W.)
- Union Clinical Medical College, Fujian Medical University, Fuzhou 350108, China
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
- Correspondence:
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Shiroma Y, Takahashi RU, Yamamoto Y, Tahara H. Targeting DNA binding proteins for cancer therapy. Cancer Sci 2020; 111:1058-1064. [PMID: 32073717 PMCID: PMC7156841 DOI: 10.1111/cas.14355] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
Dysregulation or mutation of DNA binding proteins such as transcription factors (TFs) is associated with the onset and progression of various types of disease, including cancer. Alteration of TF activity occurs in numerous cancer tissues due to gene amplification, deletion, and point mutations, and epigenetic modification. Although cancer‐associated TFs are promising targets for cancer therapy, development of drugs targeting these TFs has historically been difficult due to the lack of high‐throughput screening methods. Recent advances in technology for identification and selective inhibition of DNA binding proteins enable cancer researchers to develop novel therapeutics targeting cancer‐associated TFs. In the present review, we summarize known cancer‐associated TFs according to cancer type and introduce recently developed high‐throughput approaches to identify selective inhibitors of cancer‐associated TFs.
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Affiliation(s)
- Yoshitomo Shiroma
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ryou-U Takahashi
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yuki Yamamoto
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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Molecular mechanisms for stemness maintenance of acute myeloid leukemia stem cells. BLOOD SCIENCE 2019; 1:77-83. [PMID: 35402786 PMCID: PMC8975089 DOI: 10.1097/bs9.0000000000000020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/17/2019] [Indexed: 11/26/2022] Open
Abstract
Human acute myeloid leukemia (AML) is a fatal hematologic malignancy characterized with accumulation of myeloid blasts and differentiation arrest. The development of AML is associated with a serial of genetic and epigenetic alterations mainly occurred in hematopoietic stem and progenitor cells (HSPCs), which change HSPC state at the molecular and cellular levels and transform them into leukemia stem cells (LSCs). LSCs play critical roles in leukemia initiation, progression, and relapse, and need to be eradicated to achieve a cure in clinic. Key to successfully targeting LSCs is to fully understand the unique cellular and molecular mechanisms for maintaining their stemness. Here, we discuss LSCs in AML with a focus on identification of unique biological features of these stem cells to decipher the molecular mechanisms of LSC maintenance.
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Hamdan FH, Johnsen SA. Perturbing Enhancer Activity in Cancer Therapy. Cancers (Basel) 2019; 11:cancers11050634. [PMID: 31067678 PMCID: PMC6563029 DOI: 10.3390/cancers11050634] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/26/2019] [Accepted: 05/05/2019] [Indexed: 02/07/2023] Open
Abstract
Tight regulation of gene transcription is essential for normal development, tissue homeostasis, and disease-free survival. Enhancers are distal regulatory elements in the genome that provide specificity to gene expression programs and are frequently misregulated in cancer. Recent studies examined various enhancer-driven malignant dependencies and identified different approaches to specifically target these programs. In this review, we describe numerous features that make enhancers good transcriptional targets in cancer therapy and discuss different approaches to overcome enhancer perturbation. Interestingly, a number of approved therapeutic agents, such as cyclosporine, steroid hormones, and thiazolidinediones, actually function by affecting enhancer landscapes by directly targeting very specific transcription factor programs. More recently, a broader approach to targeting deregulated enhancer programs has been achieved via Bromodomain and Extraterminal (BET) inhibition or perturbation of transcription-related cyclin-dependent kinases (CDK). One challenge to enhancer-targeted therapy is proper patient stratification. We suggest that monitoring of enhancer RNA (eRNA) expression may serve as a unique biomarker of enhancer activity that can help to predict and monitor responsiveness to enhancer-targeted therapies. A more thorough investigation of cancer-specific enhancers and the underlying mechanisms of deregulation will pave the road for an effective utilization of enhancer modulators in a precision oncology approach to cancer treatment.
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Affiliation(s)
- Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Steven A Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
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