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Ozturk K, Panwala R, Sheen J, Ford K, Jayne N, Portell A, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1. Cell Rep 2024; 43:114436. [PMID: 38968069 PMCID: PMC11345852 DOI: 10.1016/j.celrep.2024.114436] [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: 12/08/2023] [Revised: 05/15/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024] Open
Abstract
Single-gene missense mutations remain challenging to interpret. Here, we deploy scalable functional screening by sequencing (SEUSS), a Perturb-seq method, to generate mutations at protein interfaces of RUNX1 and quantify their effect on activities of downstream cellular programs. We evaluate single-cell RNA profiles of 115 mutations in myelogenous leukemia cells and categorize them into three functionally distinct groups, wild-type (WT)-like, loss-of-function (LoF)-like, and hypomorphic, that we validate in orthogonal assays. LoF-like variants dominate the DNA-binding site and are recurrent in cancer; however, recurrence alone does not predict functional impact. Hypomorphic variants share characteristics with LoF-like but favor protein interactions, promoting gene expression indicative of nerve growth factor (NGF) response and cytokine recruitment of neutrophils. Accessible DNA near differentially expressed genes frequently contains RUNX1-binding motifs. Finally, we reclassify 16 variants of uncertain significance and train a classifier to predict 103 more. Our work demonstrates the potential of targeting protein interactions to better define the landscape of phenotypes reachable by missense mutations.
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Affiliation(s)
- Kivilcim Ozturk
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Jeanna Sheen
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kyle Ford
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Nathan Jayne
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Andrew Portell
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Dong-Er Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Stephan Hutter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Trey Ideker
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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2
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Li T, Liu X, Ruan X, Dong W, Liu Y, Wang P, Liu L, Tiange E, Song J, Pan A, Xue Y. A novel peptide P1-121aa encoded by STK24P1 regulates vasculogenic mimicry via ELF2 phosphorylation in glioblastoma. Exp Neurol 2023; 367:114477. [PMID: 37406957 DOI: 10.1016/j.expneurol.2023.114477] [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: 03/01/2023] [Revised: 05/24/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
Glioblastoma (GBM) is the most common malignant tumor of the central nervous system. Vasculogenic mimicry (VM) is a hematological system composed of tumor cells that exert blood perfusion without relying on vascular endothelial cells. The current poor results of anti-vascular therapy for clinical GBM are associated with the presence of VM; therefore, it is important to investigate VM formation in GBM. Our results demonstrate that STK24P1 encodes P1-121aa with a kinase structural domain, and in vitro kinase assays demonstrated that P1-121aa mediates modification of ELF2 phosphorylation. ChIP and dual luciferase reporter gene assays demonstrated that the transcription factor ELF2 binds to VE-cadherin and the VEGFR2 promoter region, thereby promoting VM formation in glioma cells. P1-121aa, encoded by the pseudogene STK24P1, phosphorylates ELF2 at S107, increasing the stability of the ELF2 protein. ELF2 promotes VEGFR2 and VE-cadherin expression at the transcriptional level, which in turn promotes VM in GBM. This study demonstrates the important roles of STK24P1, P1-121aa, and ELF2 in regulating VM in GBM, which could provide potential targets for GBM treatment.
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Affiliation(s)
- Tianyun Li
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Xiaobai Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - XueLei Ruan
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Weiwei Dong
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yunhui Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Ping Wang
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Libo Liu
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - E Tiange
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Jian Song
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Aini Pan
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yixue Xue
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.
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Ozturk K, Panwala R, Sheen J, Ford K, Payne N, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551876. [PMID: 37577681 PMCID: PMC10418284 DOI: 10.1101/2023.08.03.551876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Understanding the consequences of single amino acid substitutions in cancer driver genes remains an unmet need. Perturb-seq provides a tool to investigate the effects of individual mutations on cellular programs. Here we deploy SEUSS, a Perturb-seq like approach, to generate and assay mutations at physical interfaces of the RUNX1 Runt domain. We measured the impact of 115 mutations on RNA profiles in single myelogenous leukemia cells and used the profiles to categorize mutations into three functionally distinct groups: wild-type (WT)-like, loss-of-function (LOF)-like and hypomorphic. Notably, the largest concentration of functional mutations (non-WT-like) clustered at the DNA binding site and contained many of the more frequently observed mutations in human cancers. Hypomorphic variants shared characteristics with loss of function variants but had gene expression profiles indicative of response to neural growth factor and cytokine recruitment of neutrophils. Additionally, DNA accessibility changes upon perturbations were enriched for RUNX1 binding motifs, particularly near differentially expressed genes. Overall, our work demonstrates the potential of targeting protein interaction interfaces to better define the landscape of prospective phenotypes reachable by amino acid substitutions.
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Scudero OB, Santiago VF, Palmisano G, Simabuco FM, Ventura AM. The respiratory syncytial virus M2-2 protein is targeted for proteasome degradation and inhibits translation and stress granules assembly. PLoS One 2023; 18:e0289100. [PMID: 37490507 PMCID: PMC10368288 DOI: 10.1371/journal.pone.0289100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
The M2-2 protein from the respiratory syncytial virus (RSV) is a 10 kDa protein expressed by the second ORF of the viral gene M2. During infection, M2-2 has been described as the polymerase cofactor responsible for promoting genome replication, which occurs by the induction of changes in interactions between the polymerase and other viral proteins at early stages of infection. Despite its well-explored role in the regulation of the polymerase activity, little has been made to investigate the relationship of M2-2 with cellular proteins. A previous report showed poor recruitment of M2-2 to viral structures, with the protein being mainly localized to the nucleus and cytoplasmic granules. To unravel which other functions M2-2 exerts during infection, we performed proteomic analysis of co-immunoprecipitated cellular partners, identifying enrichment of proteins involved with regulation of translation, protein folding and mRNA splicing. In approaches based on these data, we found that M2-2 expression downregulates eiF2α phosphorylation and inhibits both translation and stress granules assembly. Finally, we also verified that M2-2 is targeted for proteasome degradation, being localized to granules composed of defective ribosomal products at the cytoplasm. These results suggest that besides its functions in the replicative complex, M2-2 may exert additional functions to contribute to successful RSV infection.
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Affiliation(s)
- Orlando Bonito Scudero
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Verônica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernando Moreira Simabuco
- Multidisciplinary Laboratory of Food and Health, School of Applied Sciences, University of Campinas, Limeira, São Paulo, Brazil
- Department of Biochemistry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Armando Morais Ventura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Roy A, Chauhan S, Bhattacharya S, Jakhmola V, Tyagi K, Sachdeva A, Wasai A, Mandal S. Runt-related transcription factors in human carcinogenesis: a friend or foe? J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04769-0. [PMID: 37081242 DOI: 10.1007/s00432-023-04769-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/22/2023]
Abstract
PURPOSE Cancer is one of the deadliest pathologies with more than 19 million new cases and 10 million cancer-related deaths across the globe. Despite development of advanced therapeutic interventions, cancer remains as a fatal pathology due to lack of early prognostic biomarkers, therapy resistance and requires identification of novel drug targets. METHODS Runt-related transcription factors (Runx) family controls several cellular and physiological functions including osteogenesis. Recent literatures from PubMed was mined and the review was written in comprehensive manner RESULTS: Recent literature suggests that aberrant expression of Runx contributes to tumorigenesis of many organs. Conversely, cell- and tissue-specific tumor suppressor roles of Runx are also reported. In this review, we have provided the structural/functional properties of Runx isoforms and its regulation in context of human cancer. Moreover, in an urgent need to discover novel therapeutic interventions against cancer, we comprehensively discussed the reported oncogenic and tumor suppressive roles of Runx isoforms in several tumor types and discussed the discrepancies that may have risen on Runx as a driver of malignant transformation. CONCLUSION Runx may be a novel therapeutic target against a battery of deadly human cancers.
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Affiliation(s)
- Adhiraj Roy
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India.
| | - Shivi Chauhan
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Sujata Bhattacharya
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Vibhuti Jakhmola
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Komal Tyagi
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Abha Sachdeva
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Abdul Wasai
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Supratim Mandal
- Department of Microbiology, University of Kalyani, Kalyani, Nadia, West Bengal, 741235, India
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Gerhardt LM, Koppitch K, van Gestel J, Guo J, Cho S, Wu H, Kirita Y, Humphreys BD, McMahon AP. Lineage Tracing and Single-Nucleus Multiomics Reveal Novel Features of Adaptive and Maladaptive Repair after Acute Kidney Injury. J Am Soc Nephrol 2023; 34:554-571. [PMID: 36735940 PMCID: PMC10103206 DOI: 10.1681/asn.0000000000000057] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/17/2022] [Indexed: 01/22/2023] Open
Abstract
SIGNIFICANCE STATEMENT Understanding the mechanisms underlying adaptive and maladaptive renal repair after AKI and their long-term consequences is critical to kidney health. The authors used lineage tracing of cycling cells and single-nucleus multiomics (profiling transcriptome and chromatin accessibility) after AKI. They demonstrated that AKI triggers a cell-cycle response in most epithelial and nonepithelial kidney cell types. They also showed that maladaptive proinflammatory proximal tubule cells (PTCs) persist until 6 months post-AKI, although they decreased in abundance over time, in part, through cell death. Single-nucleus multiomics of lineage-traced cells revealed regulatory features of adaptive and maladaptive repair. These included activation of cell state-specific transcription factors and cis-regulatory elements, and effects in PTCs even after adaptive repair, weeks after the injury event. BACKGROUND AKI triggers a proliferative response as part of an intrinsic cellular repair program, which can lead to adaptive renal repair, restoring kidney structure and function, or maladaptive repair with the persistence of injured proximal tubule cells (PTCs) and an altered kidney structure. However, the cellular and molecular understanding of these repair programs is limited. METHODS To examine chromatin and transcriptional responses in the same cell upon ischemia-reperfusion injury (IRI), we combined genetic fate mapping of cycling ( Ki67+ ) cells labeled early after IRI with single-nucleus multiomics-profiling transcriptome and chromatin accessibility in the same nucleus-and generated a dataset of 83,315 nuclei. RESULTS AKI triggered a broad cell cycle response preceded by cell type-specific and global transcriptional changes in the nephron, the collecting and vascular systems, and stromal and immune cell types. We observed a heterogeneous population of maladaptive PTCs throughout proximal tubule segments 6 months post-AKI, with a marked loss of maladaptive cells from 4 weeks to 6 months. Gene expression and chromatin accessibility profiling in the same nuclei highlighted differences between adaptive and maladaptive PTCs in the activity of cis-regulatory elements and transcription factors, accompanied by corresponding changes in target gene expression. Adaptive repair was associated with reduced expression of genes encoding transmembrane transport proteins essential to kidney function. CONCLUSIONS Analysis of genome organization and gene activity with single-cell resolution using lineage tracing and single-nucleus multiomics offers new insight into the regulation of renal injury repair. Weeks to months after mild-to-moderate IRI, maladaptive PTCs persist with an aberrant epigenetic landscape, and PTCs exhibit an altered transcriptional profile even following adaptive repair.
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Affiliation(s)
- Louisa M.S. Gerhardt
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Jordi van Gestel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Sam Cho
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
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Deregulated Gene Expression Profiles and Regulatory Networks in Adult and Pediatric RUNX1/RUNX1T1-Positive AML Patients. Cancers (Basel) 2023; 15:cancers15061795. [PMID: 36980682 PMCID: PMC10046396 DOI: 10.3390/cancers15061795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous and complex disease concerning molecular aberrations and prognosis. RUNX1/RUNX1T1 is a fusion oncogene that results from the chromosomal translocation t(8;21) and plays a crucial role in AML. However, its impact on the transcriptomic profile of different age groups of AML patients is not completely understood. Here, we investigated the deregulated gene expression (DEG) profiles in adult and pediatric RUNX1/RUNX1T1-positive AML patients, and compared their functions and regulatory networks. We retrospectively analyzed gene expression data from two independent Gene Expression Omnibus (GEO) datasets (GSE37642 and GSE75461) and computed their differentially expressed genes and upstream regulators, using limma, GEO2Enrichr, and X2K. For validation purposes, we used the TCGA-LAML (adult) and TARGET-AML (pediatric) patient cohorts. We also analyzed the protein–protein interaction (PPI) networks, as well as those composed of transcription factors (TF), intermediate proteins, and kinases foreseen to regulate the top deregulated genes in each group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were further performed for the DEGs in each dataset. We found that the top upregulated genes in (both adult and pediatric) RUNX1/RUNX1T1-positive AML patients are enriched in extracellular matrix organization, the cell projection membrane, filopodium membrane, and supramolecular fiber. Our data corroborate that RUNX1/RUNX1T1 reprograms a large transcriptional network to establish and maintain leukemia via intricate PPI interactions and kinase-driven phosphorylation events.
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Ostwaldt F, Los B, Heyd F. In silico analysis of alternative splicing events implicated in intracellular trafficking during B-lymphocyte differentiation. Front Immunol 2022; 13:1030409. [DOI: 10.3389/fimmu.2022.1030409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
There are multiple regulatory layers that control intracellular trafficking and protein secretion, ranging from transcriptional to posttranslational mechanisms. Finely regulated trafficking and secretion is especially important for lymphocytes during activation and differentiation, as the quantity of secretory cargo increases once the activated cells start to produce and secrete large amounts of cytokines, cytotoxins, or antibodies. However, how the secretory machinery dynamically adapts its efficiency and specificity in general and specifically in lymphocytes remains incompletely understood. Here we present a systematic bioinformatics analysis to address RNA-based mechanisms that control intracellular trafficking and protein secretion during B-lymphocyte activation, and differentiation, with a focus on alternative splicing. Our in silico analyses suggest that alternative splicing has a substantial impact on the dynamic adaptation of intracellular traffic and protein secretion in different B cell subtypes, pointing to another regulatory layer to the control of lymphocyte function during activation and differentiation. Furthermore, we suggest that NERF/ELF2 controls the expression of some COPII-related genes in a cell type-specific manner. In addition, T cells and B cells appear to use different adaptive strategies to adjust their secretory machineries during the generation of effector and memory cells, with antibody secreting B cell specifically increasing the expression of components of the early secretory pathway. Together, our data provide hypotheses how cell type-specific regulation of the trafficking machinery during immune cell activation and differentiation is controlled that can now be tested in wet lab experiments.
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Ager CR, Boda A, Rajapakshe K, Lea ST, Di Francesco ME, Jayaprakash P, Slay RB, Morrow B, Prasad R, Dean MA, Duffy CR, Coarfa C, Jones P, Curran MA. High potency STING agonists engage unique myeloid pathways to reverse pancreatic cancer immune privilege. J Immunother Cancer 2021; 9:jitc-2021-003246. [PMID: 34341132 PMCID: PMC8330562 DOI: 10.1136/jitc-2021-003246] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Intratumoral injection of cyclic dinucleotide (CDN) agonists of the stimulator of interferon genes (STING) pathway engages innate immune activation and priming of adaptive immune effectors to foster local and distal tumor clearance. Despite proven therapeutic efficacy in preclinical models, a thorough understanding of how CDNs reprogram suppressive myeloid stroma in mouse and man is lacking. METHODS Here, we perform deep transcript-level and protein-level profiling of myeloid-derived suppressor cells and M2 macrophages following stimulation with CDNs of ascending potency. Additionally, we leverage orthotopic Kras+/G12DTP53+/R172HPdx1-Cre (KPC) derived models of pancreatic adenocarcinoma (PDAC) to determine the capacity for locally administered CDNs to sensitize PDAC to immune checkpoint blockade. We use bioluminescent in vivo imaging and 30-parameter flow cytometry to profile growth kinetics and remodeling of the tumor stroma post-therapy. RESULTS Highly potent synthetic STING agonists repolarize suppressive myeloid populations of human and murine origin in part through inhibition of Myc signaling, metabolic modulation, and antagonism of cell cycle. Surprisingly, high-potency synthetic agonists engage qualitatively unique pathways as compared with natural CDNs. Consistent with our mechanistic observations, we find that intratumoral injection of the highest activity STING agonist, IACS-8803, into orthotopic pancreatic adenocarcinoma lesions unmasks sensitivity to checkpoint blockade immunotherapy. Dimensionality reduction analyses of high parameter flow cytometry data reveals substantial contributions of both myeloid repolarization and T cell activation underlying the in vivo therapeutic benefit of this approach. CONCLUSIONS This study defines the molecular basis of STING-mediated myeloid reprogramming, revealing previously unappreciated and qualitatively unique pathways engaged by CDNs of ascending potency during functional repolarization. Furthermore, we demonstrate the potential for high potency CDNs to overcome immunotherapy resistance in an orthotopic, multifocal model of PDAC.
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Affiliation(s)
- Casey R Ager
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Immunology Program, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA,Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Akash Boda
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Immunology Program, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Kimal Rajapakshe
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Spencer Thomas Lea
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Immunology Program, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Maria Emilia Di Francesco
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Priyamvada Jayaprakash
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ravaen B Slay
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Brittany Morrow
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Immunology Program, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Rishika Prasad
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Immunology Program, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Meghan A Dean
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Colm R Duffy
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Immunology Program, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Philip Jones
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Curran
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,Immunology Program, University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
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Yang Y, Chen Q, Piao HY, Wang B, Zhu GQ, Chen EB, Xiao K, Zhou ZJ, Shi GM, Shi YH, Wu WZ, Fan J, Zhou J, Dai Z. HNRNPAB-regulated lncRNA-ELF209 inhibits the malignancy of hepatocellular carcinoma. Int J Cancer 2019; 146:169-180. [PMID: 31090062 DOI: 10.1002/ijc.32409] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/20/2019] [Accepted: 05/02/2019] [Indexed: 01/01/2023]
Abstract
Our previous study demonstrated that heterogeneous nuclear ribonucleoprotein AB (HNRNPAB) is a key gene that facilitates metastasis of hepatocellular carcinoma (HCC). However, the molecular mechanisms behind this relationship are not fully understood. In our study, we utilized long-noncoding RNA (lncRNA) microarrays to identify a HNRNPAB-regulated lncRNA named lnc-ELF209. Our findings from chromatin immunoprecipitation assays indicate that HNRNPAB represses lnc-ELF209 transcription by directly binding to its promoter region. We also analyzed clinical samples from HCC patients and cell lines with quantitative real-time polymerase chain reactions, RNA in situ hybridization and immunohistochemistry, and found that there is a negative relationship between HNRNPAB and lnc-ELF209 expression. Up/downregulation assays and rescue assays indicate that lnc-ELF209 inhibits cell migration, invasion and epithelial-mesenchymal transition regulated by HNRNPAB. This suggests a new regulatory mechanism for HNRNPAB-promoted HCC progression. RNA pull-down and LC-MS/MS were used to determine triosephosphate isomerase, heat shock protein 90-beta and vimentin may be involved in the tumor-suppressed function of lnc-ELF209. Furthermore, we found lnc-ELF209 could stabilize TPI protein expression. We also found that lnc-ELF209 overexpression in HCCLM3 cell resulted in a lower rate of lung metastatic, which suggested a less aggressive HCC phenotype. Collectively, these findings offer new insights into the regulatory mechanisms that underlie HNRNPAB cancer-promoting activities and demonstrate that lnc-ELF209 is a HNRNPAB-regulated lncRNA that may play an important role in the inhibition of HCC progression.
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Affiliation(s)
- Yi Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Qing Chen
- Department of General Surgery, Zhongshan Hospital (South), Fudan University, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hai-Yan Piao
- Medical Oncology Department of Gastrointestinal cancer, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Er-Bao Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Kun Xiao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Zheng-Jun Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Guo-Ming Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Ying-Hong Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Wei-Zhong Wu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
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11
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RUNX family: Oncogenes or tumor suppressors (Review). Oncol Rep 2019; 42:3-19. [PMID: 31059069 PMCID: PMC6549079 DOI: 10.3892/or.2019.7149] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Runt-related transcription factor (RUNX) proteins belong to a transcription factors family known as master regulators of important embryonic developmental programs. In the last decade, the whole family has been implicated in the regulation of different oncogenic processes and signaling pathways associated with cancer. Furthermore, a suppressor tumor function has been also reported, suggesting the RUNX family serves key role in all different types of cancer. In this review, the known biological characteristics, specific regulatory abilities and experimental evidence of RUNX proteins will be analyzed to demonstrate their oncogenic potential and tumor suppressor abilities during oncogenic processes, suggesting their importance as biomarkers of cancer. Additionally, the importance of continuing with the molecular studies of RUNX proteins' and its dual functions in cancer will be underlined in order to apply it in the future development of specific diagnostic methods and therapies against different types of cancer.
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12
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ChIP-on-chip analysis of thyroid hormone-regulated genes and their physiological significance. Oncotarget 2017; 7:22448-59. [PMID: 26968954 PMCID: PMC5008372 DOI: 10.18632/oncotarget.7988] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/23/2016] [Indexed: 01/04/2023] Open
Abstract
Triiodothyronine (T3) and its receptor (TR) modulate several physiological processes, including cell development, proliferation, differentiation and metabolism. The regulatory mechanism of T3/TR involves binding to the thyroid hormone response element (TRE) within the target gene promoter. However, the number of target genes directly regulated by TRα1 and the specific pathways of TR-regulated target genes remain largely unknown. Here, we expressed TRα1 in a HepG2 cell line and used chromatin immunoprecipitation coupled with microarray to determine the genes that are directly regulated by TRα1 and also involved in cell metabolism and proliferation. Our analysis identified E74-like factor 2 (ELF2), a transcription factor associated with tumor growth, as a direct target downregulated by T3/TR. Overexpression of ELF2 enhanced tumor cell proliferation, and conversely, its knockdown suppressed tumor growth. Additionally, ELF2 restored the proliferative ability of hepatoma cells inhibited by T3/TR. Our findings collectively support a potential role of T3/TR in tumor growth inhibition through regulation of ELF2.
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13
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Rosewick N, Durkin K, Artesi M, Marçais A, Hahaut V, Griebel P, Arsic N, Avettand-Fenoel V, Burny A, Charlier C, Hermine O, Georges M, Van den Broeke A. Cis-perturbation of cancer drivers by the HTLV-1/BLV proviruses is an early determinant of leukemogenesis. Nat Commun 2017; 8:15264. [PMID: 28534499 PMCID: PMC5457497 DOI: 10.1038/ncomms15264] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
Human T-cell leukaemia virus type-1 (HTLV-1) and bovine leukaemia virus (BLV) infect T- and B-lymphocytes, respectively, provoking a polyclonal expansion that will evolve into an aggressive monoclonal leukaemia in ∼5% of individuals following a protracted latency period. It is generally assumed that early oncogenic changes are largely dependent on virus-encoded products, especially TAX and HBZ, while progression to acute leukaemia/lymphoma involves somatic mutations, yet that both are independent of proviral integration site that has been found to be very variable between tumours. Here, we show that HTLV-1/BLV proviruses are integrated near cancer drivers which they affect either by provirus-dependent transcription termination or as a result of viral antisense RNA-dependent cis-perturbation. The same pattern is observed at polyclonal non-malignant stages, indicating that provirus-dependent host gene perturbation contributes to the initial selection of the multiple clones characterizing the asymptomatic stage, requiring additional alterations in the clone that will evolve into full-blown leukaemia/lymphoma. Human T-cell leukaemia virus type-1 and bovine leukaemia virus infect T and B lymphocytes and lead to aggressive leukaemia. Here, the authors show these proviruses integrate near cancer drivers perturbing transcription termination or antisense RNA-dependent interaction, suggesting post-transcriptional mechanisms in some cases.
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Affiliation(s)
- Nicolas Rosewick
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Keith Durkin
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Maria Artesi
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Ambroise Marçais
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, 149-161 rue de Sèvres, Paris 75010, France
| | - Vincent Hahaut
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Philip Griebel
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Canada S7N 5E3
| | - Natasa Arsic
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Canada S7N 5E3
| | - Véronique Avettand-Fenoel
- Laboratoire de Virologie, AP-HP, Hôpital Necker-Enfants Malades, Université Paris Descartes, Sorbonne Paris Cité, EA7327, 149 rue de Sèvres, Paris 75010, France
| | - Arsène Burny
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, Brussels 1000, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Olivier Hermine
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, 149-161 rue de Sèvres, Paris 75010, France.,INSERM U1163-ERL8254, Institut Imagine, 24 B Boulevard du Montparnasse, Paris 75010, France
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Anne Van den Broeke
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium.,Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, Brussels 1000, Belgium
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14
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Guan FHX, Bailey CG, Metierre C, O'Young P, Gao D, Khoo TL, Holst J, Rasko JEJ. The antiproliferative ELF2 isoform, ELF2B, induces apoptosis in vitro and perturbs early lymphocytic development in vivo. J Hematol Oncol 2017; 10:75. [PMID: 28351373 PMCID: PMC5371273 DOI: 10.1186/s13045-017-0446-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/20/2017] [Indexed: 01/08/2023] Open
Abstract
Background ELF2 (E74-like factor 2) also known as NERF (new Ets-related factor), a member of the Ets family of transcription factors, regulates genes important in B and T cell development, cell cycle progression, and angiogenesis. Conserved ELF2 isoforms, ELF2A, and ELF2B, arising from alternative promoter usage can exert opposing effects on target gene expression. ELF2A activates, whilst ELF2B represses, gene expression, and the balance of expression between these isoforms may be important in maintaining normal cellular function. Methods We compared the function of ELF2 isoforms ELF2A and ELF2B with other ELF subfamily proteins ELF1 and ELF4 in primary and cancer cell lines using proliferation, colony-forming, cell cycle, and apoptosis assays. We further examined the role of ELF2 isoforms in haemopoietic development using a Rag1-/-murine bone marrow reconstitution model. Results ELF2B overexpression significantly reduced cell proliferation and clonogenic capacity, minimally disrupted cell cycle kinetics, and induced apoptosis. In contrast, ELF2A overexpression only marginally reduced clonogenic capacity with little effect on proliferation, cell cycle progression, or apoptosis. Deletion of the N-terminal 19 amino acids unique to ELF2B abrogated the antiproliferative and proapoptotic functions of ELF2B thereby confirming its crucial role. Mice expressing Elf2a or Elf2b in haemopoietic cells variously displayed perturbations in the pre-B cell stage and multiple stages of T cell development. Mature B cells, T cells, and myeloid cells in steady state were unaffected, suggesting that the main role of ELF2 is restricted to the early development of B and T cells and that compensatory mechanisms exist. No differences in B and T cell development were observed between ELF2 isoforms. Conclusions We conclude that ELF2 isoforms are important regulators of cellular proliferation, cell cycle progression, and apoptosis. In respect to this, ELF2B acts in a dominant negative fashion compared to ELF2A and as a putative tumour suppressor gene. Given that these cellular processes are critical during haemopoiesis, we propose that the regulatory interplay between ELF2 isoforms contributes substantially to early B and T cell development. Electronic supplementary material The online version of this article (doi:10.1186/s13045-017-0446-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fiona H X Guan
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Cynthia Metierre
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Patrick O'Young
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Dadi Gao
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Teh Liane Khoo
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jeff Holst
- Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia.,Origins of Cancer Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia. .,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia. .,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia.
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15
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Williams MJ, Klockars A, Eriksson A, Voisin S, Dnyansagar R, Wiemerslage L, Kasagiannis A, Akram M, Kheder S, Ambrosi V, Hallqvist E, Fredriksson R, Schiöth HB. The Drosophila ETV5 Homologue Ets96B: Molecular Link between Obesity and Bipolar Disorder. PLoS Genet 2016; 12:e1006104. [PMID: 27280443 PMCID: PMC4900636 DOI: 10.1371/journal.pgen.1006104] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 05/13/2016] [Indexed: 12/24/2022] Open
Abstract
Several reports suggest obesity and bipolar disorder (BD) share some physiological and behavioural similarities. For instance, obese individuals are more impulsive and have heightened reward responsiveness, phenotypes associated with BD, while bipolar patients become obese at a higher rate and earlier age than people without BD; however, the molecular mechanisms of such an association remain obscure. Here we demonstrate, using whole transcriptome analysis, that Drosophila Ets96B, homologue of obesity-linked gene ETV5, regulates cellular systems associated with obesity and BD. Consistent with a role in obesity and BD, loss of nervous system Ets96B during development increases triacylglyceride concentration, while inducing a heightened startle-response, as well as increasing hyperactivity and reducing sleep. Of notable interest, mouse Etv5 and Drosophila Ets96B are expressed in dopaminergic-rich regions, and loss of Ets96B specifically in dopaminergic neurons recapitulates the metabolic and behavioural phenotypes. Moreover, our data indicate Ets96B inhibits dopaminergic-specific neuroprotective systems. Additionally, we reveal that multiple SNPs in human ETV5 link to body mass index (BMI) and BD, providing further evidence for ETV5 as an important and novel molecular intermediate between obesity and BD. We identify a novel molecular link between obesity and bipolar disorder. The Drosophila ETV5 homologue Ets96B regulates the expression of cellular systems with links to obesity and behaviour, including the expression of a conserved endoplasmic reticulum molecular chaperone complex known to be neuroprotective. Finally, a connection between the obesity-linked gene ETV5 and bipolar disorder emphasizes a functional relationship between obesity and BD at the molecular level. The World Health Organization suggests obesity is a major cause of poor health and is becoming the leading public health concern. Likewise, mood-based disorders, such as bipolar disorder, are one of the top ten causes of disability worldwide. There is evidence that obesity and bipolar disorder may be linked and that obesity may exacerbate bipolar disorder symptoms. For the first time, our work evidences a molecular-link between obesity and bipolar disorder. In humans the obesity-linked gene ETV5 was also associated with bipolar disorder. Using the model organism Drosophila melanogaster (the fruit fly) we show that the ETV5 homologue Ets96B regulates a series of genes known to be neuroprotective and inhibiting the expression of Ets96 in dopaminergic neurons induces phenotypes linked to obesity and bipolar disorder, including increased lipid storage, increased anxiety and reduced sleep. Our work will help to further the understanding of how these to disorders may interact.
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Affiliation(s)
- Michael J. Williams
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Anica Klockars
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Anders Eriksson
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Sarah Voisin
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Rohit Dnyansagar
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Lyle Wiemerslage
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Anna Kasagiannis
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Mehwish Akram
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Sania Kheder
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Valerie Ambrosi
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Emilie Hallqvist
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Robert Fredriksson
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B. Schiöth
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
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16
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Novel transcription factor variants through RNA-sequencing: the importance of being "alternative". Int J Mol Sci 2015; 16:1755-71. [PMID: 25590302 PMCID: PMC4307332 DOI: 10.3390/ijms16011755] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 12/26/2014] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing is a pervasive mechanism of RNA maturation in higher eukaryotes, which increases proteomic diversity and biological complexity. It has a key regulatory role in several physiological and pathological states. The diffusion of Next Generation Sequencing, particularly of RNA-Sequencing, has exponentially empowered the identification of novel transcripts revealing that more than 95% of human genes undergo alternative splicing. The highest rate of alternative splicing occurs in transcription factors encoding genes, mostly in Krüppel-associated box domains of zinc finger proteins. Since these molecules are responsible for gene expression, alternative splicing is a crucial mechanism to "regulate the regulators". Indeed, different transcription factors isoforms may have different or even opposite functions. In this work, through a targeted re-analysis of our previously published RNA-Sequencing datasets, we identified nine novel transcripts in seven transcription factors genes. In silico analysis, combined with RT-PCR, cloning and Sanger sequencing, allowed us to experimentally validate these new variants. Through computational approaches we also predicted their novel structural and functional properties. Our findings indicate that alternative splicing is a major determinant of transcription factor diversity, confirming that accurate analysis of RNA-Sequencing data can reliably lead to the identification of novel transcripts, with potentially new functions.
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17
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Bledsoe KL, McGee-Lawrence ME, Camilleri ET, Wang X, Riester SM, van Wijnen AJ, Oliveira AM, Westendorf JJ. RUNX3 facilitates growth of Ewing sarcoma cells. J Cell Physiol 2014; 229:2049-56. [PMID: 24812032 DOI: 10.1002/jcp.24663] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/06/2014] [Indexed: 01/01/2023]
Abstract
Ewing sarcoma is an aggressive pediatric small round cell tumor that predominantly occurs in bone. Approximately 85% of Ewing sarcomas harbor the EWS/FLI fusion protein, which arises from a chromosomal translocation, t(11:22)(q24:q12). EWS/FLI interacts with numerous lineage-essential transcription factors to maintain mesenchymal progenitors in an undifferentiated state. We previously showed that EWS/FLI binds the osteogenic transcription factor RUNX2 and prevents osteoblast differentiation. In this study, we investigated the role of another Runt-domain protein, RUNX3, in Ewing sarcoma. RUNX3 participates in mesenchymal-derived bone formation and is a context dependent tumor suppressor and oncogene. RUNX3 was detected in all Ewing sarcoma cells examined, whereas RUNX2 was detected in only 73% of specimens. Like RUNX2, RUNX3 binds to EWS/FLI via its Runt domain. EWS/FLI prevented RUNX3 from activating the transcription of a RUNX-responsive reporter, p6OSE2. Stable suppression of RUNX3 expression in the Ewing sarcoma cell line A673 delayed colony growth in anchorage independent soft agar assays and reversed expression of EWS/FLI-responsive genes. These results demonstrate an important role for RUNX3 in Ewing sarcoma.
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18
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Reiner G, Dreher F, Drungowski M, Hoeltig D, Bertsch N, Selke M, Willems H, Gerlach GF, Probst I, Tuemmler B, Waldmann KH, Herwig R. Pathway deregulation and expression QTLs in response to Actinobacillus pleuropneumoniae infection in swine. Mamm Genome 2014; 25:600-17. [DOI: 10.1007/s00335-014-9536-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/10/2014] [Indexed: 11/27/2022]
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19
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Abstract
The t(12;21) chromosomal translocation, targeting the gene encoding the RUNX1 transcription factor, is observed in 25% of pediatric acute lymphoblastic leukemia (ALL) and is an initiating event in the disease. To elucidate the mechanism by which RUNX1 disruption initiates leukemogenesis, we investigated its normal role in murine B-cell development. This study revealed 2 critical functions of Runx1: (1) to promote survival and development of progenitors specified to the B-cell lineage, a function that can be substituted by ectopic Bcl2 expression, and (2) to enable the developmental transition through the pre-B stage triggered by the pre-B-cell antigen receptor (pre-BCR). Gene expression analysis and genomewide Runx1 occupancy studies support the hypothesis that Runx1 reinforces the transcription factor network governing early B-cell survival and development and specifically regulates genes encoding members of the Lyn kinase subfamily (key integrators of interleukin-7 and pre-BCR signaling) and the stage-specific transcription factors SpiB and Aiolos (critical downstream effectors of pre-BCR signaling). Interrogation of expression databases of 257 ALL samples demonstrated the specific down-regulation of the SPIB and IKZF3 genes (the latter encoding AIOLOS) in t(12;21) ALL, providing novel insight into the mechanism by which the translocation blocks B-cell development and promotes leukemia.
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20
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Chuang LSH, Ito K, Ito Y. RUNX family: Regulation and diversification of roles through interacting proteins. Int J Cancer 2012. [PMID: 23180629 DOI: 10.1002/ijc.27964] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Runt-related transcription factors (RUNX) belong to an ancient family of metazoan genes involved in developmental processes. Through multiple protein-interacting partners, RUNX proteins have been implicated in diverse signaling pathways and cellular processes. The frequent inactivation of RUNX genes in cancer indicates crucial roles for RUNX in tumor suppression. This review discusses the abilities of RUNX proteins, in particular RUNX3, to integrate oncogenic signals or environmental cues and to initiate appropriate tumor suppressive responses.
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21
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Molteni C, Cazzaniga G, Condorelli D, Fortuna C, Biondi A, Musumarra G. Successful Application of OPLS-DA for the Discrimination of Wild-Type and Mutated Cells in Acute Lymphoblastic Leukemia. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200860195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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22
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Laitem C, Leprivier G, Choul-Li S, Begue A, Monte D, Larsimont D, Dumont P, Duterque-Coquillaud M, Aumercier M. Ets-1 p27: a novel Ets-1 isoform with dominant-negative effects on the transcriptional properties and the subcellular localization of Ets-1 p51. Oncogene 2009; 28:2087-99. [PMID: 19377509 DOI: 10.1038/onc.2009.72] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The transcription factor Ets-1 is implicated in various physiological processes and invasive pathologies. We identified a novel variant of ets-1, ets-1Delta(III-VI), resulting from the alternative splicing of exons III to VI. This variant encodes a 27 kDa isoform, named Ets-1 p27. Ets-1 p27 lacks the threonine-38 residue, the Pointed domain and the transactivation domain, all of which are required for the transactivation of Ets-1 target genes. Both inhibitory domains surrounding the DNA-binding domain are conserved, suggesting that Ets-1 p27, like the full-length Ets-1 p51 isoform, is autoinhibited for DNA binding. We showed that Ets-1 p27 binds DNA in the same way as Ets-1 p51 does and that it acts both at a transcriptional and a subcellular localization level, thereby constituting a dual-acting dominant negative of Ets-1 p51. Ets-1 p27 blocks Ets-1 p51-mediated transactivation of target genes and induces the translocation of Ets-1 p51 from the nucleus to the cytoplasm. Furthermore, Ets-1 p27 overexpression represses the tumor properties of MDA-MB-231 mammary carcinoma cells in correlation with the known implication of Ets-1 in various cellular mechanisms. Thus the dual-acting dominant-negative function of Ets-1 p27 gives to the Ets-1 p27/Ets-1 p51 ratio a determining effect on cell fate.
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Affiliation(s)
- C Laitem
- CNRS Unité Mixte de Recherche 8161, Institut de Biologie de Lille, Institut Pasteur de Lille, Universités de Lille 1 and Lille 2, IFR 142, Lille, France
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23
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Hanington PC, Tam J, Katzenback BA, Hitchen SJ, Barreda DR, Belosevic M. Development of macrophages of cyprinid fish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2009; 33:411-429. [PMID: 19063916 DOI: 10.1016/j.dci.2008.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 11/11/2008] [Accepted: 11/14/2008] [Indexed: 05/27/2023]
Abstract
The innate immune responses of early vertebrates, such as bony fishes, play a central role in host defence against infectious diseases and one of the most important effector cells of innate immunity are macrophages. In order for macrophages to be effective in host defence they must be present at all times in the tissues of their host and importantly, the host must be capable of rapidly increasing macrophage numbers during times of need. Hematopoiesis is a process of formation and development of mature blood cells, including macrophages. Hematopoiesis is controlled by soluble factors known as cytokines, that influence changes in transcription factors within the target cells, resulting in cell fate changes and the final development of specific effector cells. The processes involved in macrophage development have been largely derived from mammalian model organisms. However, recent advancements have been made in the understanding of macrophage development in bony fish, a group of organisms that rely heavily on their innate immune defences. Our understanding of the growth factors involved in teleost macrophage development, as well as the receptors and regulatory mechanisms in place to control them has increased substantially. Furthermore, model organisms such as the zebrafish have emerged as important instruments in furthering our understanding of the transcriptional control of cell development in fish as well as in mammals. This review highlights the recent advancements in our understanding of teleost macrophage development. We focused on the growth factors identified to be important in the regulation of macrophage development from a progenitor cell into a functional macrophage and discuss the important transcription factors that have been identified to function in teleost hematopoiesis. We also describe the findings of in vivo studies that have reinforced observations made in vitro and have greatly improved the relevance and importance of using teleost fish as model organisms for studying developmental processes.
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Qiu Y, Morii E, Zhang B, Tomita Y, Aozasa K. E74-like factor 2 transactivates valosin-containing protein gene, a gene involved in cancer growth. Exp Mol Pathol 2008; 84:226-9. [DOI: 10.1016/j.yexmp.2008.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 03/02/2008] [Accepted: 04/22/2008] [Indexed: 10/22/2022]
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Kowarz E, Burmeister T, Lo Nigro L, Jansen MWJC, Delabesse E, Klingebiel T, Dingermann T, Meyer C, Marschalek R. Complex MLL rearrangements in t(4;11) leukemia patients with absent AF4 · MLL fusion allele. Leukemia 2007; 21:1232-8. [PMID: 17410185 DOI: 10.1038/sj.leu.2404686] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The human mixed lineage leukemia (MLL) gene is frequently involved in genetic rearrangements with more than 55 different translocation partner genes, all associated with acute leukemia. Reciprocal chromosomal translocations generate two MLL fusion alleles, where 5'- and 3'-portions of MLL are fused to gene segments of given fusion partners. In case of t(4;11) patients, about 80% of all patients exhibit both reciprocal fusion alleles, MLL.AF4 and AF4.MLL, respectively. By contrast, 20% of all t(4;11) patients seem to encode only the MLL.AF4 fusion allele. Here, we analyzed these 'MLL.AF4(+)/AF4.MLL(-)' patients at the genomic DNA level to unravel their genetic situation. Cryptic translocations and three-way translocations were found in this group of t(4;11) patients. Reciprocal MLL fusions with novel translocation partner genes, for example NF-KB1 and RABGAP1L, were identified and actively transcribed in leukemic cells. In other patients, the reciprocal 3'-MLL gene segment was fused out-of-frame to PBX1, ELF2, DSCAML1 and FXYD6. The latter rearrangements caused haploinsufficiency of genes that are normally expressed in hematopoietic cells. Finally, patients were identified that encode only solitary 3'-MLL gene segments on the reciprocal allele. Based on these data, we propose that all t(4;11) patients exhibit reciprocal MLL alleles, but due to the individual recombination events, provide different pathological disease mechanisms.
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Affiliation(s)
- E Kowarz
- Institute of Pharmaceutical Biology, ZAFES, DCAL, JWG-University Frankfurt, Biocenter, Frankfurt, Main, Germany
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Zhang B, Tomita Y, Qiu Y, He J, Morii E, Noguchi S, Aozasa K. E74-like factor 2 regulates valosin-containing protein expression. Biochem Biophys Res Commun 2007; 356:536-41. [PMID: 17368566 DOI: 10.1016/j.bbrc.2007.02.160] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
Enhanced expression of valosin-containing protein (VCP) correlates with invasion and metastasis of cancers. To clarify the transcription mechanism of VCP, human and mouse genomic sequence was compared, revealing a 260 bp DNA sequence in the 5'-flanking region of VCP gene to be highly conserved between the two, in which binding motif of E74-like factor 2/new Ets-related factor (ELF2/NERF) was identified. Chromatin immunoprecipitation assay showed binding of ELF2/NERF to the 5'-flanking region of VCP gene. Knock-down of ELF2/NERF by siRNA decreased expression level of VCP. Viability of cells under tumor necrosis factor-alpha treatment significantly reduced in ELF2/NERF-knock-down breast cancer cell line. Immunohistochemical analysis on clinical breast cancer specimens showed a correlation of nuclear ELF2/NERF expression with VCP expression and proliferative activity of cells shown by Ki-67 immunohistochemistry. These findings indicate that ELF2/NERF promotes VCP transcription and that ELF2/NERF-VCP pathway might be important for cell survival and proliferation under cytokine stress.
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Affiliation(s)
- Binglin Zhang
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
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Finco TS, Justice-Healy GE, Patel SJ, Hamilton VE. Regulation of the human LAT gene by the Elf-1 transcription factor. BMC Mol Biol 2006; 7:4. [PMID: 16464244 PMCID: PMC1382244 DOI: 10.1186/1471-2199-7-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Accepted: 02/07/2006] [Indexed: 12/01/2022] Open
Abstract
Background The LAT gene encodes an intracellular adaptor protein that links cell-surface receptor engagement to numerous downstream signalling events, and thereby plays an integral role in the function of cell types that express the gene, including T cells, mast cells, natural killer cells, and platelets. To date, the mechanisms responsible for the transcriptional regulation of this gene have not been investigated. Results In this study we have mapped the transcriptional start sites for the human LAT gene and localized the 5' and 3' boundaries of the proximal promoter. We find that the promoter contains both positive and negative regulatory regions, and that two binding sites for the Ets family of transcription factors have a strong, positive effect on gene expression. Each site binds the Ets family member Elf-1, and overexpression of Elf-1 augments LAT promoter activity. The promoter also contains a Runx binding site adjacent to one of the Ets sites. This site, which is shown to bind Runx-1, has an inhibitory effect on gene expression. Finally, data is also presented indicating that the identified promoter may regulate cell-type specific expression. Conclusion Collectively, these results provide the first insights into the transcriptional regulation of the LAT gene, including the discovery that the Ets transcription factor Elf-1 may play a central role in its expression.
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Affiliation(s)
- Timothy S Finco
- Department of Biology, Agnes Scott College, Decatur, GA 30030, USA
| | | | - Shivani J Patel
- Department of Biology, Agnes Scott College, Decatur, GA 30030, USA
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Rainis L, Toki T, Pimanda JE, Rosenthal E, Machol K, Strehl S, Göttgens B, Ito E, Izraeli S. The proto-oncogene ERG in megakaryoblastic leukemias. Cancer Res 2005; 65:7596-602. [PMID: 16140924 DOI: 10.1158/0008-5472.can-05-0147] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aneuploidy is one of the hallmarks of cancer. Acquired additions of chromosome 21 are a common finding in leukemias, suggesting a contributory role to leukemogenesis. About 10% of patients with a germ line trisomy 21 (Down syndrome) are born with transient megakaryoblastic leukemia. We and others have shown acquired mutations in the X chromosome gene GATA1 in all these cases. The gene or genes on chromosome 21 whose overexpression promote the megakaryoblastic phenotype are presently unknown. We propose that ERG, an Ets transcription factor situated on chromosome 21, is one such candidate. We show that ERG is expressed in hematopoietic stem cells, megakaryoblastic cell lines, and in primary leukemic cells from Down syndrome patients. ERG expression is induced upon megakaryocytic differentiation of the erythroleukemia cell lines K562 and UT-7, and forced expression of ERG in K562 cells induces erythroid to megakaryoblastic phenotypic switch. We also show that ERG activates the gpIb megakaryocytic promoter and binds the gpIIb promoter in vivo. Furthermore, both ERG and ETS2 bind in vivo the hematopoietic enhancer of SCL/TAL1, a key regulator of hematopoietic stem cell and megakaryocytic development. We propose that trisomy 21 facilitates the occurrence of megakaryoblastic leukemias through a shift toward the megakaryoblastic lineage caused by the excess expression of ERG, and possibly by other chromosome 21 genes, such as RUNX1 and ETS2, in hematopoietic progenitor cells, coupled with a differentiation arrest caused by the acquisition of mutations in GATA1.
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MESH Headings
- Base Sequence
- Basic Helix-Loop-Helix Transcription Factors
- Cell Lineage
- Chromosomes, Human, Pair 21/genetics
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Erythroid-Specific DNA-Binding Factors
- GATA1 Transcription Factor
- HeLa Cells
- Hematopoietic Stem Cells/metabolism
- Humans
- K562 Cells
- Leukemia, Erythroblastic, Acute/genetics
- Leukemia, Erythroblastic, Acute/pathology
- Leukemia, Megakaryoblastic, Acute/genetics
- Leukemia, Megakaryoblastic, Acute/metabolism
- Leukemia, Megakaryoblastic, Acute/pathology
- Molecular Sequence Data
- Oncogene Proteins/biosynthesis
- Oncogene Proteins/genetics
- Promoter Regions, Genetic
- Proto-Oncogene Mas
- Proto-Oncogene Proteins/metabolism
- T-Cell Acute Lymphocytic Leukemia Protein 1
- Trans-Activators/biosynthesis
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcriptional Regulator ERG
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Affiliation(s)
- Liat Rainis
- Department of Pediatric Hematology-Oncology, Safra Children's Hospital and Hematology Institute, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
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