1
|
Hariharan S, Whitfield BT, Pirozzi CJ, Waitkus MS, Brown MC, Bowie ML, Irvin DM, Roso K, Fuller R, Hostettler J, Dharmaiah S, Gibson EA, Briley A, Mangoli A, Fraley C, Shobande M, Stevenson K, Zhang G, Malgulwar PB, Roberts H, Roskoski M, Spasojevic I, Keir ST, He Y, Castro MG, Huse JT, Ashley DM. Interplay between ATRX and IDH1 mutations governs innate immune responses in diffuse gliomas. Nat Commun 2024; 15:730. [PMID: 38272925 PMCID: PMC10810843 DOI: 10.1038/s41467-024-44932-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
Stimulating the innate immune system has been explored as a therapeutic option for the treatment of gliomas. Inactivating mutations in ATRX, defining molecular alterations in IDH-mutant astrocytomas, have been implicated in dysfunctional immune signaling. However, little is known about the interplay between ATRX loss and IDH mutation on innate immunity. To explore this, we generated ATRX-deficient glioma models in the presence and absence of the IDH1R132H mutation. ATRX-deficient glioma cells are sensitive to dsRNA-based innate immune agonism and exhibit impaired lethality and increased T-cell infiltration in vivo. However, the presence of IDH1R132H dampens baseline expression of key innate immune genes and cytokines in a manner restored by genetic and pharmacological IDH1R132H inhibition. IDH1R132H co-expression does not interfere with the ATRX deficiency-mediated sensitivity to dsRNA. Thus, ATRX loss primes cells for recognition of dsRNA, while IDH1R132H reversibly masks this priming. This work reveals innate immunity as a therapeutic vulnerability of astrocytomas.
Collapse
Affiliation(s)
- Seethalakshmi Hariharan
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Benjamin T Whitfield
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher J Pirozzi
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Matthew S Waitkus
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Michael C Brown
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Michelle L Bowie
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - David M Irvin
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristen Roso
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Rebecca Fuller
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Janell Hostettler
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Sharvari Dharmaiah
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emiley A Gibson
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Aaron Briley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Avani Mangoli
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Casey Fraley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Mariah Shobande
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Kevin Stevenson
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Gao Zhang
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Prit Benny Malgulwar
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hannah Roberts
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Roskoski
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Ivan Spasojevic
- PK/PD Core Laboratory, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine - Oncology, Duke University Medical Center, Durham, NC, USA
| | - Stephen T Keir
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Jason T Huse
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - David M Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA.
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA.
| |
Collapse
|
2
|
Zhu Y, Zhang D, Shukla P, Jung YH, Malgulwar PB, Chagani S, Colic M, Benjamin S, Copland JA, Tan L, Lorenzi PL, Javle M, Huse JT, Roszik J, Hart T, Kwong LN. CRISPR screening identifies BET and mTOR inhibitor synergy in cholangiocarcinoma through serine glycine one carbon. JCI Insight 2024; 9:e174220. [PMID: 38060314 PMCID: PMC10906219 DOI: 10.1172/jci.insight.174220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/05/2023] [Indexed: 01/24/2024] Open
Abstract
Patients with cholangiocarcinoma have poor clinical outcomes due to late diagnoses, poor prognoses, and limited treatment strategies. To identify drug combinations for this disease, we have conducted a genome-wide CRISPR screen anchored on the bromodomain and extraterminal domain (BET) PROTAC degrader ARV825, from which we identified anticancer synergy when combined with genetic ablation of members of the mTOR pathway. This combination effect was validated using multiple pharmacological BET and mTOR inhibitors, accompanied by increased levels of apoptosis and cell cycle arrest. In a xenograft model, combined BET degradation and mTOR inhibition induced tumor regression. Mechanistically, the 2 inhibitor classes converged on H3K27ac-marked epigenetic suppression of the serine glycine one carbon (SGOC) metabolism pathway, including the key enzymes PHGDH and PSAT1. Knockdown of PSAT1 was sufficient to replicate synergy with single-agent inhibition of either BET or mTOR. Our results tie together epigenetic regulation, metabolism, and apoptosis induction as key therapeutic targets for further exploration in this underserved disease.
Collapse
Affiliation(s)
- Yan Zhu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dengyong Zhang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of general surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Pooja Shukla
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Young-Ho Jung
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Prit Benny Malgulwar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sharmeen Chagani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Medina Colic
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah Benjamin
- Department of Natural Sciences, Rice University, Houston, Texas, USA
| | - John A. Copland
- Department of Cancer Biology, Mayo Clinic Jacksonville, Florida, USA
| | - Lin Tan
- Metabolomics Core Facility, Department of Bioinformatics & Computational Biology
| | - Philip L. Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics & Computational Biology
| | | | - Jason T. Huse
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology-Research, Division of Cancer Medicine
- Department of Genomic Medicine, Division of Cancer Medicine, and
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, Division of Cancer Medicine, and
| |
Collapse
|
3
|
Malgulwar PB, Danussi C, Dharmaiah S, Johnson W, Singh A, Rai K, Rao A, Huse JT. Sirtuin 2 inhibition modulates chromatin landscapes genome-wide to induce senescence in ATRX-deficient malignant glioma. Neuro Oncol 2024; 26:55-67. [PMID: 37625115 PMCID: PMC10769000 DOI: 10.1093/neuonc/noad155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Functional inactivation of ATRX characterizes large subgroups of malignant gliomas in adults and children. ATRX deficiency in glioma induces widespread chromatin remodeling, driving transcriptional shifts and oncogenic phenotypes. Effective strategies to therapeutically target these broad epigenomic sequelae remain undeveloped. METHODS We utilized integrated multiomics and the Broad Institute Connectivity Map (CMAP) to identify drug candidates that could potentially revert ATRX-deficient transcriptional changes. We then employed disease-relevant experimental models to evaluate functional phenotypes, coupling these studies with epigenomic profiling to elucidate molecular mechanism(s). RESULTS CMAP analysis and transcriptional/epigenomic profiling implicated the Class III HDAC Sirtuin2 (SIRT2) as a central mediator of ATRX-deficient cellular phenotypes and a driver of unfavorable prognosis in ATRX-deficient glioma. SIRT2 inhibitors reverted Atrx-deficient transcriptional signatures in murine neuroepithelial progenitor cells (mNPCs), impaired cell migration in Atrx/ATRX-deficient mNPCs and human glioma stem cells (GSCs), and increased expression of senescence markers in glioma models. Moreover, SIRT2 inhibition impaired growth and increased senescence in ATRX-deficient GSCs in vivo. These effects were accompanied by genome-wide shifts in enhancer-associated H3K27ac and H4K16ac marks, with the latter in particular demonstrating compelling transcriptional links to SIRT2-dependent phenotypic reversals. Motif analysis of these data identified the transcription factor KLF16 as a mediator of phenotype reversal in Atrx-deficient cells upon SIRT2 inhibition. CONCLUSIONS Our findings indicate that SIRT2 inhibition selectively targets ATRX-deficient gliomas for senescence through global chromatin remodeling, while demonstrating more broadly a viable approach to combat complex epigenetic rewiring in cancer.
Collapse
Affiliation(s)
- Prit Benny Malgulwar
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Carla Danussi
- Sanofi, Research and Development, Cambridge, Massachusetts, USA
| | - Sharvari Dharmaiah
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - William Johnson
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anand Singh
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kunal Rai
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Arvind Rao
- Departments of Biostatistics, Computational Medicine and Bioinformatics, and Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason T Huse
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
4
|
Hariharan S, Whitfield BT, Pirozzi CJ, Waitkus MS, Brown MC, Bowie ML, Irvin DM, Roso K, Fuller R, Hostettler J, Dharmaiah S, Gibson EA, Briley A, Mangoli A, Fraley C, Shobande M, Stevenson K, Zhang G, Malgulwar PB, Roberts H, Roskoski M, Spasojevic I, Keir ST, He Y, Castro MG, Huse JT, Ashley DM. Interplay between ATRX and IDH1 mutations governs innate immune responses in diffuse gliomas. bioRxiv 2023:2023.04.20.537594. [PMID: 37131619 PMCID: PMC10153255 DOI: 10.1101/2023.04.20.537594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Stimulating the innate immune system has been explored as a therapeutic option for the treatment of gliomas. Inactivating mutations in ATRX , defining molecular alterations in IDH -mutant astrocytomas, have been implicated in dysfunctional immune signaling. However, little is known about the interplay between ATRX loss and IDH mutation on innate immunity. To explore this, we generated ATRX knockout glioma models in the presence and absence of the IDH1 R 132 H mutation. ATRX-deficient glioma cells were sensitive to dsRNA-based innate immune agonism and exhibited impaired lethality and increased T-cell infiltration in vivo . However, the presence of IDH1 R 132 H dampened baseline expression of key innate immune genes and cytokines in a manner restored by genetic and pharmacological IDH1 R132H inhibition. IDH1 R132H co-expression did not interfere with the ATRX KO-mediated sensitivity to dsRNA. Thus, ATRX loss primes cells for recognition of dsRNA, while IDH1 R132H reversibly masks this priming. This work reveals innate immunity as a therapeutic vulnerability of astrocytoma.
Collapse
|
5
|
Malgulwar PB, Danussi C, Dharmaiah S, Johnson WE, Rao A, Huse JT. Sirtuin 2 inhibition modulates chromatin landscapes genome-wide to induce senescence in ATRX-deficient malignant glioma. bioRxiv 2023:2023.01.09.523324. [PMID: 36711727 PMCID: PMC9882017 DOI: 10.1101/2023.01.09.523324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Inactivating mutations in ATRX characterize large subgroups of malignant gliomas in adults and children. ATRX deficiency in glioma induces widespread chromatin remodeling, driving transcriptional shifts and oncogenic phenotypes. Effective strategies to therapeutically target these broad epigenomic sequelae remain undeveloped. We utilized integrated mulit-omics and the Broad Institute Connectivity Map (CMAP) to identify drug candidates that could potentially revert ATRX-deficient transcriptional changes. We then employed disease-relevant experimental models to evaluate functional phenotypes, coupling these studies with epigenomic profiling to elucidate molecular mechanim(s). CMAP analysis and transcriptional/epigenomic profiling implicated the Class III HDAC Sirtuin2 (Sirt2) as a central mediator of ATRX-deficient cellular phenotypes and a driver of unfavorable prognosis in ATRX-deficient glioma. Sirt2 inhibitors reverted Atrx-deficient transcriptional signatures in murine neuroprogenitor cells (mNPCs) and impaired cell migration in Atrx/ATRX-deficient mNPCs and human glioma stem cells (GSCs). While effects on cellular proliferation in these contexts were more modest, markers of senescence significantly increased, suggesting that Sirt2 inhibition promotes terminal differentiation in ATRX-deficient glioma. These phenotypic effects were accompanied by genome-wide shifts in enhancer-associated H3K27ac and H4K16ac marks, with the latter in particular demonstrating compelling transcriptional links to Sirt2-dependent phenotypic reversals. Motif analysis of these data identified the transcription factor KLF16 as a mediator of phenotype reversal in Atrx-deficient cells upon Sirt2 inhibition. Finally, Sirt2 inhibition impaired growth and increased senescence in ATRX-deficient GSCs in vivo . Our findings indicate that Sirt2 inhibition selectively targets ATRX-deficient gliomas through global chromatin remodeling, while demonstrating more broadly a viable approach to combat complex epigenetic rewiring in cancer. One Sentence Summary Our study demonstrates that SIRT2 inhibition promotes senescence in ATRX-deficient glioma model systems through global epigenomic remodeling, impacting key downstream transcriptional profiles.
Collapse
|
6
|
Malgulwar PB, Danussi C, Singh A, Saw AK, Rai K, Huse J. EPCO-23. DYSFUNCTION OF LARGE H3K9ME3 DOMAINS IN ATRX DEFICIENT GLIOMAS INDUCES GENETIC REARRANGEMENTS AND LATENT DEVELOPMENTAL SIGNALING NETWORKS THROUGH SUPER-ENHANCER LANDSCAPES. Neuro Oncol 2022. [PMCID: PMC9660526 DOI: 10.1093/neuonc/noac209.458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Somatic alterations in ATRX (Alpha Thalassemia/Mental Retardation Syndrome X-linked), a member of SWI/SNF family chromatin regulator has been found to be frequently mutated in diffuse gliomas and defines molecular subtypes with aggressive behavior. Mechanistically, ATRX regulates incorporation of histone H3.3 into chromatin sites across the genome, maintains alternative lengthening of telomeres and establishes genomic distribution of polycomb responsive genes. To understand in depth role of ATRX in gliomas, we performed ChIP-seq and/or Cut-and-tag for histone marks that define active transcription, enhancers, repressors, gene bodies and CTCF on Atrx intact and deficient mNPCs (mouse Neural Progenitor Cells). Our integrated analysis reports depletion of H3K9me3 loci’s that coincidently enriched with Atrx binding sites and Lamina-Associated Domains with genes enriched for cell cycle, motility and chromosome organization. This chromatin perturbations at heterochromatin domains was further confirmed in our Hi-C analysis with switching of A-B and B-A compartments, reorganization of TADs with occasional CTCF marks and gain of novel interacting loops that showed gene expression leakage required for gliomagenesis using Capture Hi-C. Notably, we observed aberrant levels of endogenous retroviral elements (ERVs) family members, including upregulation of Line-1 elements in mNPCs and patient derived glioma stem cells (GSCs) and our analysis shows increased copy number variations in ATRX deficient gliomas as a consequence of Line-1 activation in these subsets of tumors. Finally, our integrated omics- analysis demonstrates enrichment of super-enhancers in Atrx deficient background with several putative druggable candidates for clinical benefits. As an example, we show presence of H3K27ac super-enhancer over HOXA locus and targeting pan-HOXA genes using small inhibitor peptides diminished proliferation and migration of mNPCs and GSCs with increased in cell apoptosis with alterations in downstream developmental signaling pathways. To summarize,our data establishes tangible links between Atrx deficiency and multiscale dysregulated cellular phenotype in gliomas with identifying novel targets for therapy.
Collapse
Affiliation(s)
| | | | - Anand Singh
- M.D. Anderson Cancer Center, Houston , Houston, TX , USA
| | - Ajay Kumar Saw
- M.D. Anderson Cancer Center, Houston , Houston, TX , USA
| | - Kunal Rai
- M.D. Anderson Cancer Center, Houston , Houston , USA
| | - Jason Huse
- M.D. Anderson Cancer Center, Houston , Houston, TX , USA
| |
Collapse
|
7
|
Dharmaiah S, Chen B, Malgulwar PB, Tadimeti V, Farooqi A, Huse J. DNAR-11. CHARACTERIZING THE GENOMIC CONSEQUENCES OF G-QUADRUPLEX STABILIZATION IN ATRX-DEFICIENT HIGH-GRADE GLIOMA. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
α-thalassaemia/mental retardation X-linked (ATRX) mutations are a critical molecular marker for high-grade glioma (HGG). These mutations lead to accumulations of abnormal DNA secondary G-quadruplex (G4) structures, thereby inducing replication stress and DNA damage. As G4s arise at GC-rich regions (i.e., pericentromeric and telomeric regions), ATRX-deficiency alters genome-wide accessibility of chromatin and causes transcriptional dysregulation. However, the genomic consequences of this in the context of ATRX-deficiency are poorly understood. Our goal is to target ATRX deficiency through G4 stabilizers, a class of novel small molecule compounds that selectively bind to and stabilize G4s. Using a combination of functional experiments such as cell viability, western blot, flow cytometry, RNA-sequencing (RNA-seq), and immunofluorescence (IF), we evaluated the mechanisms that drive selective lethality upon G4 stabilization. Patient-derived glioma stem cells (GSCs) were treated with either vehicle (DMSO) or varying doses of CX-5461 (G4 stabilizer, Senhwa Biosciences). Excitingly, ATRX-deficient GSCs demonstrate dose-dependent enhanced sensitivity to G4 stabilization, compared to ATRX-intact and vehicle controls. Cell viability assays confirmed the specificity of CX-5461 in comparison to other commercially used G4 stabilizers. G4 stabilization activated p53-independent apoptosis and exhibited G2/M arrest in ATRX-deficient GSCs and, interestingly, upregulated expression of both ATR and ATM pathways, indicating enhanced replication stress and DNA damage, respectively. IF staining confirmed enhanced induction of replication stress and DNA damage markers 53BP1 and gH2AX. Our preliminary findings suggest that ATR and ATM activation leads to Cyclin D1 degradation and inhibition of transcription factor NF-κB, thereby driving apoptosis. In fact, RNA-seq analyses revealed positive enrichment of apoptosis, DNA repair, and NF-κB pathways and negative enrichment of the G2/M checkpoint in ATRX-deficient GSCs treated with CX-5461. Our work defines mechanisms of action and efficacy of a novel therapeutic strategy for pre-clinical ATRX-deficient HGG models, with strong implications for other ATRX-deficient cancers and potential translation into clinical practice.
Collapse
Affiliation(s)
| | - Brandon Chen
- The University of Texas MD Anderson Cancer Center , Houston, TX , USA
| | | | | | | | - Jason Huse
- M.D. Anderson Cancer Center, Houston , Houston, TX , USA
| |
Collapse
|
8
|
Whitfield B, Huse J, Irvin D, Dharmaiah S, Malgulwar PB, Roberts H. IMMU-10. EXPLORING THE IMMUNOLOGIC CONSEQUENCES OF ATRX DEFICIENCY IN GLIOMA. Neuro Oncol 2022. [PMCID: PMC9660435 DOI: 10.1093/neuonc/noac209.508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
ATRX is a key chromatin regulator, which is mutated in large subsets of both adult and pediatric gliomas. Despite being a common mutation, little is known about the biological ramifications of ATRX deficiency. Recently, it has been demonstrated that ATRX deficiency drives increased replication stress, DNA damage, and global epigenetic dysregulation. Despite these advances, little is known about the impact of ATRX deficiency on the tumor microenvironment (TME). In order to explore the impact of ATRX deficiency on the TME we utilized the RCAS/nTVa system to generate a novel murine model of ATRX deficient glioma. Mice bearing allografts of these tumors displayed significantly increased survival relative to the ATRX intact lines. This survival benefit persisted in Nu/nu mice, which lack an adaptive immune system, but not in SCID mice, which lack both adaptive and innate immunity. Bulk RNA sequencing revealed the ATRX deficient tumors displayed increased expression of inflammatory and innate immune gene sets, and western blotting revealed increased phosphorylation of tank binding kinase 1 (TBK1), a key innate immune regulator. Multiplex cytokine analysis of conditioned media also revealed increased expression of inflammatory cytokines such as CCL2, CCL5, and CXCL10 in the supernatant of ATRX deficient cell lines. Taken together, these results indicate that ATRX deficiency can drive innate immune activation, and that this activation can increase survival in vivo. Further exploration is needed to characterize the upstream drivers of TBK1 activation and elucidate alterations to immune cell infiltration in ATRXdeficient tumors.
Collapse
Affiliation(s)
| | - Jason Huse
- M.D. Anderson Cancer Center, Houston , Houston, TX , USA
| | | | | | | | | |
Collapse
|
9
|
Dharmaiah S, Tadimeti V, Malgulwar PB, Alvarez C, Farooqi A, Huse J. CBIO-04. G-QUADRUPLEX STABILIZATION ENHANCES REPLICATION STRESS AND DNA DAMAGE IN ATRX-DEFICIENT HIGH-GRADE GLIOMA. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Loss of function mutations in α-thalassaemia/mental retardation X-linked (ATRX) are a critical molecular hallmark for invariably fatal high-grade glioma (HGG). Mutational inactivation of histone chaperone ATRX leads to accumulations of abnormal DNA secondary structures known as G-quadruplexes (G4s), thereby inducing replication stress and DNA damage. As G4s arise at GC-rich regions (i.e., pericentromeric and telomeric regions), ATRX-deficiency alters genome-wide accessibility of chromatin, leads to transcriptional dysregulation, and induces alternative lengthening of telomeres (ALT). Our goal is to target ATRX deficiency through G4 stabilizers, which represent a class of novel small molecule compounds that selectively bind to and stabilize G4 structures. However, the genomic consequences and efficacy of this therapy for ATRX-deficient HGG are poorly understood. We therefore sought to evaluate the molecular mechanisms that drive selective lethality in patient-derived ATRX-deficient glioma stem cells (GSCs), following G4 stabilization. We found that ATRX-deficient GSCs demonstrate dose-dependent enhanced sensitivity to G4 stabilization, compared to ATRX-intact controls. Cell viability assays confirmed the specificity of our G4 stabilizer in comparison to other commonly used G4 stabilizers. Interestingly, G4 stabilization activated p53-independent apoptosis in ATRX-deficient GSCs. Furthermore, ATRX-deficient GSCs exhibit upregulated expression of both ATR and ATM pathways upon G4 stabilization, indicating enhanced replication stress and DNA damage via double-stranded breaks, respectively. Our preliminary findings suggest that ATR and ATM activation leads to the inhibition of transcription factor NF-κB, which in turn drives apoptosis. Lastly, our data indicate that G4 stabilization perturbs the ALT phenotype in ATRX-deficient GSCs, likely contributing to telomeric dysfunction. Taken together, these findings suggest that G4 stabilizers could synergize with ionizing radiation, the standard of care, as they are both DNA-damaging therapies. Our work defines mechanisms of action and efficacy of a novel therapeutic strategy for ATRX-deficient HGG, with strong implications for other ATRX-deficient cancers.
Collapse
Affiliation(s)
| | | | | | | | | | - Jason Huse
- MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
10
|
Malgulwar PB, Danussi C, Singh A, Kannan K, Rai K, Huse J. EPCO-08. ATRX DEFICIENCY INDUCES DYSFUNCTIONAL HETEROCHROMATIN ARCHITECTURE IN GLIOMAS AND ESTABLISHES DISEASE-DEFINING TRANSCRIPTIONAL NETWORKS. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Loss of ATRX (Alpha Thalassemia/Mental Retardation Syndrome X, a member of SWI/SNF family chromatin regulator is altered in diffuse gliomas and defines molecular subtypes with aggressive behavior. Mechanistically, ATRX regulates incorporation of histone H3.3 into chromatin sites across the genome, maintains alternative lengthening of telomeres and establishes genomic distribution of polycomb responsive genes. We have recently reported Atrx deficiency induces glioma oncogenic features via widespread alterations in chromatin accessibility using mouse Neural Progenitor Cells (mNPCs- Tp53 -/-,Atrx -/-). Surprisingly, Atrx was found to be associated with transcription start site and enhancer regions, suggesting their strong association with epigenome architecture. In this background, we have recently performed ChIP-seq for histone marks that define active transcription, enhancers, repressors and gene bodies and Cohesion molecules on Atrx intact and deficient mNPCs. Our integrated analysis reports depletion of H3K9me3 loci’s with enrichment of H3K27me3 marks that coincidently enriched with Atrx binding sites and Lamina-Associated Domains (LADs). GSEA confirmed that the genes corresponding to “newly formed LADs” in mNPC-to-astrocyte differentiation are significantly enriched for genes down-regulated in Atrx deficient mNPCs and belongs to Gene Ontology categories such as cell cycle, chromosome organization and DNA damage. Alternatively, genes corresponding to decreased LAD association are enriched for up-regulated genes in Atrx deficient mNPCs and for regulation of differentiation, adhesion and cell death. Additionally, whole-genome bisulphite sequencing further demonstrated loss of methylation marks at H3K9me3 sites in Atrx deficient mNPCs, suggesting perturbations of heterochromatin regions leading to activation of canonical signals that define glioma phenotype and disease-state. To summarize, our data establishes tangible links between Atrx deficiency and dysregulated chromatin and heterochromatin architecture in gliomas and suggests the role of Atrx in establishing global chromatin features and transcriptional networks. Further, our data unravel novel therapeutic molecules/pathways for engineering potential.
Collapse
Affiliation(s)
| | - Carla Danussi
- MD Anderson Cancer Center, Houston, Houston, TX, USA
| | - Anand Singh
- MD Anderson Cancer Center, Houston, Houston, TX, USA
| | | | - Kunal Rai
- MD Anderson Cancer Center, Houston, Houston, TX, USA
| | - Jason Huse
- MD Anderson Cancer Center, Houston, Houston, TX, USA
| |
Collapse
|
11
|
Fukumura K, Malgulwar PB, Fischer G, Hu X, Zhang X, Yu D, Debeb B, Davies M, Huse J. BSCI-07. Multiomics characterization of brain metastases in multiple histologies identifies enrichment of oxidative phosphorylation as a promising therapeutic target. Neurooncol Adv 2021. [PMCID: PMC8351303 DOI: 10.1093/noajnl/vdab071.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Purpose Brain metastasis (BM) is a lethal complication from systematic malignant tumors, and the incidence is approximately 10–30% of patients with advanced cancer. Extensive genomic analyses with large sample sets and the following functional studies revealed clinically relevant characteristics for BMs. However, these studies have not identified specific abnormalities driving BM in multiple tumor histologies yet. To identify molecular pathogenesis and promising therapeutic targets shared across multiple histologies of BMs, we performed multiomics molecular profiling, along with functional studies using in vitro and in vivo BM models. Methods Frozen tissues of patient-matched BMs and primary tumors (or extracranial metastases) from breast cancer (N= 14), lung cancer (N = 14) and renal cell carcinomas (N = 7) patients were carried out whole-exome sequencing, mRNA-Seq and reverse-phase protein array. Paired parental and brain metastatic derivatives of MDA-MB-231 and BT474 were examined to assess findings from the multiomics datasets. SCID/beige mice were inoculated with MDA-IBC3 cells via tail vein injection and administered an oxidative phosphorylation (OXPHOS) inhibitor by oral gavage daily for 96 days. Results The multiomics molecular profiling identified enrichment of OXPHOS shared across the histologies of BMs. Brain metastatic derivative cell lines also demonstrated enhanced oxidative metabolism, along with the sensitivity to an OXPHOS inhibitor. Moreover, in vivo studies revealed that OXPHOS inhibition significantly impaired the formation of BM, and fresh brain metastatic derivatives from the murine BM model exhibited the higher oxidative metabolism and sensitivity to the OXPHOS inhibitor as with the prior in vitro studies. Conclusions Our multiomics characterization of BMs demonstrates heightened oxidative metabolism shared across the multiple histologies, and the OXPHOS inhibition affects more effectively for brain metastatic derivatives rather than the parentals. Further investigation focusing on metabolic abnormalities in BM will likely develop promising therapeutic strategies against BMs.
Collapse
Affiliation(s)
| | | | - Grant Fischer
- The University of Texas MD Anderson Cancer Center, TX, USA
| | - Xiaoding Hu
- The University of Texas MD Anderson Cancer Center, TX, USA
| | | | - Dihua Yu
- The University of Texas MD Anderson Cancer Center, TX, USA
| | - Bisrat Debeb
- The University of Texas MD Anderson Cancer Center, TX, USA
| | - Michael Davies
- The University of Texas MD Anderson Cancer Center, TX, USA
| | - Jason Huse
- The University of Texas MD Anderson Cancer Center, TX, USA
| |
Collapse
|
12
|
Fukumura K, Malgulwar PB, Fischer GM, Hu X, Mao X, Song X, Hernandez SD, Zhang XHF, Zhang J, Parra ER, Yu D, Debeb BG, Davies MA, Huse JT. Multi-omic molecular profiling reveals potentially targetable abnormalities shared across multiple histologies of brain metastasis. Acta Neuropathol 2021; 141:303-321. [PMID: 33394124 DOI: 10.1007/s00401-020-02256-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/28/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022]
Abstract
The deadly complication of brain metastasis (BM) is largely confined to a relatively narrow cross-section of systemic malignancies, suggesting a fundamental role for biological mechanisms shared across commonly brain metastatic tumor types. To identify and characterize such mechanisms, we performed genomic, transcriptional, and proteomic profiling using whole-exome sequencing, mRNA-seq, and reverse-phase protein array analysis in a cohort of the lung, breast, and renal cell carcinomas consisting of BM and patient-matched primary or extracranial metastatic tissues. While no specific genomic alterations were associated with BM, correlations with impaired cellular immunity, upregulated oxidative phosphorylation (OXPHOS), and canonical oncogenic signaling pathways including phosphoinositide 3-kinase (PI3K) signaling, were apparent across multiple tumor histologies. Multiplexed immunofluorescence analysis confirmed significant T cell depletion in BM, indicative of a fundamentally altered immune microenvironment. Moreover, functional studies using in vitro and in vivo modeling demonstrated heightened oxidative metabolism in BM along with sensitivity to OXPHOS inhibition in murine BM models and brain metastatic derivatives relative to isogenic parentals. These findings demonstrate that pathophysiological rewiring of oncogenic signaling, cellular metabolism, and immune microenvironment broadly characterizes BM. Further clarification of this biology will likely reveal promising targets for therapeutic development against BM arising from a broad variety of systemic cancers.
Collapse
Affiliation(s)
- Kazutaka Fukumura
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Prit Benny Malgulwar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Grant M Fischer
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaoding Hu
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xizeng Mao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sharia D Hernandez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dihua Yu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Bisrat G Debeb
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Michael A Davies
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jason T Huse
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| |
Collapse
|
13
|
Kapoor M, Das S, Biswas A, Malgulwar PB, Devi NK, Seth S, Bhargava B, Rao VR. D190Y mutation in C-terminal tail region of TNNI3 gene causing severe form of restrictive cardiomyopathy with mild hypertrophy in an Indian patient. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
14
|
Fukumura K, Malgulwar PB, Fischer G, Hu XD, Debeb BG, Yu D, Davies M, Huse J. EXTH-06. INTEGRATED MOLECULAR PROFILING REVEALS TARGETABLE MOLECULAR ABNORMALITIES SHARED ACROSS MULTIPLE HISTOLOGIES OF BRAIN METASTASIS. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Brain metastases (BMs) occur in approximately 20–40% of patients with advanced cancer, and the estimated prevalence of new BMs in United States is between 200,000–300,000 per year. While the incidence of BM has increased over the past decades due to improvements in brain tumor detection technology, the prognosis is still very poor with the median overall survival times from weeks to few months. Therefore, identification of the precise molecular landscape and therapeutic targets for BMs is absolutely essential in tangible improvement of patient management. Here, we performed integrated genomic, transcriptional, and proteomic profiling in a cohort of lung, breast, and renal cell carcinomas consisting of both BMs and patient-matched primary or extracranial metastatic tissues to identify shared cellular and molecular factors driving BMs across distinct primary tumor histologies. Although the comprehensive analysis identified the unique genomic, transcriptional and proteomic landscapes according to the different histopathologies, elevated PI3K/AKT and RAS/MAPK signaling was observed as a generalizable feature across the entire specimen cohort, along with relative immunosuppression and metabolic upregulation of the electron transport chain (ETC). Interestingly, immunosuppression via T cell depletion was significantly associated with unfavorable prognosis of patients with BMs, and ETC inhibition as the prospective therapeutic target for BM patients was demonstrated using in vitro and in vivo disease models. Taken together, our findings suggest that abnormalities involving oncogenic signaling, metabolism, and the immune microenvironment are shared across multiple histologies of BMs, and may be amenable to therapeutic targeting.
Collapse
Affiliation(s)
- Kazutaka Fukumura
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Prit Benny Malgulwar
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Grant Fischer
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiao Ding Hu
- Department of Breast Medical Oncology-Rsch, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bisrat Godefay Debeb
- Department of Breast Medical Oncology-Rsch, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dihua Yu
- Department of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Huse
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
15
|
Nambirajan A, Malgulwar PB, Sharma A, Boorgula MT, Doddamani R, Singh M, Suri V, Sarkar C, Sharma MC. Clinicopathological evaluation of PD-L1 expression and cytotoxic T-lymphocyte infiltrates across intracranial molecular subgroups of ependymomas: are these tumors potential candidates for immune check-point blockade? Brain Tumor Pathol 2019; 36:152-161. [PMID: 31388782 DOI: 10.1007/s10014-019-00350-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/25/2019] [Indexed: 02/02/2023]
Abstract
Immune check-point blockade (ICB) targeting programmed cell death ligand-1 (PD-L1)/programmed death-1 (PD-1) axis has created paradigm shift in cancer treatment. 'ST-RELA' and 'PF-A' molecular subgroups of ependymomas (EPN) show poor outcomes. We aimed to understand the potential candidature of EPNs for ICB. Supratentorial (ST) Grade II/III EPNs were classified into ST-RELA, ST-YAP, and ST-not otherwise specified (NOS), based on RELA/YAP1 fusion transcripts and/or L1CAM and p65 protein expression. Posterior fossa (PF) EPNs were classified into PF-A and PF-B based on H3K27me3 expression. Immunohistochemistry for PD-L1 and CD8 was performed. RelA protein enrichment at PDL1 promoter site was analysed by chromatin immunoprecipitation-qPCR (ChIP-qPCR). Eighty-three intracranial EPNs were studied. Median tumor infiltrating CD8 + cytotoxic T-lymphocyte (CTL) density was 6/mm2, and was higher in ST-EPNs (median 10/mm2) as compared to PF-EPNs (median 3/mm2). PD-L1 expression was noted in 17/83 (20%) EPNs, including 12/31 ST-RELA and rare ST-NOS (2/12), PF-A (2/25) and PF-B (1/13) EPNs. Twelve EPNs (14%) showed high CTL density and concurrent PD-L1 positivity, of which majority (10/12) were ST-RELA EPNs. Enrichment of RelA protein was seen at PDL1 promoter. Increased CTL densities and upregulation of PD-L1 in ST-RELA ependymomas suggests potential candidature for immunotherapy.
Collapse
Affiliation(s)
- Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Agrima Sharma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Meher Thej Boorgula
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ramesh Doddamani
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Manmohan Singh
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| |
Collapse
|
16
|
Malgulwar PB, Sharma V, Tomar AS, Verma C, Nambirajan A, Singh M, Suri V, Sarkar C, Sharma MC. Transcriptional co-expression regulatory network analysis for Snail and Slug identifies IL1R1, an inflammatory cytokine receptor, to be preferentially expressed in ST-EPN- RELA and PF-EPN-A molecular subgroups of intracranial ependymomas. Oncotarget 2018; 9:35480-35492. [PMID: 30464804 PMCID: PMC6231457 DOI: 10.18632/oncotarget.26211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/08/2018] [Indexed: 12/14/2022] Open
Abstract
Recent molecular subgrouping of ependymomas (EPN) by DNA methylation profiling has identified ST-EPN-RELA and PF-EPN-A subgroups to be associated with poor outcome. Snail/Slug are cardinal epithelial-to-mesenchymal transcription factors (EMT-TFs) and are overexpressed in several CNS tumors, including EPNs. A systematic analysis of gene-sets/modules co-expressed with Snail and Slug genes using published expression microarray dataset (GSE27279)identified 634 genes for Snail with enriched TGF-β, PPAR and PI3K signaling pathways, and 757 genes for Slug with enriched focal adhesion, ECM-receptor interaction and regulation of actin cytoskeleton related pathways. Of 37 genes commonly expressed with both Snail and Slug, IL1R1, a cytokine receptor of interleukin-1 receptor family, was positively correlated with Snail (r=0.43) and Slug (r=0.51), preferentially expressed in ST-EPN-RELA and PF-EPN-A molecular groups, and enriched for pathways related to inflammation, angiogenesis and glycolysis. IL1R1 expression was fairly specific to EPNs among various CNS tumors analyzed. It also showed significant positive correlation with EMT, stemness and MDSC (myeloid derived suppressor cell) markers. Our study reports IL1R1 as a poor prognostic marker associated with EMT-like phenotype and stemness in EPNs. Our findings emphasize the need to further examine and validate IL1R1 as a novel therapeutic target in aggressive subsets of intracranial EPNs.
Collapse
Affiliation(s)
- Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Vikas Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Ashutosh Singh Tomar
- Center for Cellular and Molecular Biology-Council of Scientific and Industrial Research (CCMB-CSIR), Hyderabad, Telangana-500007, India
| | - Chaitenya Verma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Manmohan Singh
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| |
Collapse
|
17
|
Malgulwar PB, Nambirajan A, Pathak P, Rajeshwari M, Suri V, Sarkar C, Singh M, Sharma MC. Epithelial-to-mesenchymal transition-related transcription factors are up-regulated in ependymomas and correlate with a poor prognosis. Hum Pathol 2018; 82:149-157. [PMID: 30067950 DOI: 10.1016/j.humpath.2018.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 06/01/2018] [Accepted: 07/21/2018] [Indexed: 12/13/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) plays an important role in invasion and metastasis of various cancers including gliomas. EMT has also been linked to cancer stem cells and resistance to chemotherapy. An initial in-silico data mining in a published ependymoma (EPN) patient series (GSE21687) revealed up-regulation of EMT transcription factors in tumor samples. Furthermore, quantitative real-time polymerase chain reaction-based gene expression analysis of EMT transcription factors in 96 EPNs showed significant up-regulation of SNAI1, SNAI2, ZEB1, and TWIST1 as compared with normal brain, associated with up-regulation of CDH2/N-cadherin and down-regulation of CDH1/E-cadherin. Although this was observed in varying degrees in all clinicopathological-molecular subgroups of EPNs, it was most evident in supratentorial EPNs harboring fusions of RELA (v-rel avian reticuloendotheliosis viral oncogene homolog A) gene and in posterior fossa EPNs. Immunohistochemistry performed in 60 of the above cases corroborated with gene expression patterns, and immunopositivity for Snail, Slug, Zeb1, and Twist1 was observed in 80%, 80%, 81%, and 63% of all EPNs. Immunopositivity for N-cadherin and E-cadherin was observed in 76.6% and 2% of the cases, respectively. Univariate Cox regression analysis showed that low expression of CDH1/E-cadherin (P = .002) and high expression levels of CDH2/N-cadherin (P < .001), SNAI1/Snail (P = .023), SNAI2/Slug (P < .001), and ZEB1 (P < .001) were associated with shorter progression-free survival. Here, we report for the first time the existence of EMT-like phenotype in EPNs. These factors could represent new prognostic and therapeutic targets in EPN.
Collapse
Affiliation(s)
- Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Madhu Rajeshwari
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Manmohan Singh
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India.
| |
Collapse
|
18
|
Nambirajan A, Suri V, Kedia S, Goyal K, Malgulwar PB, Khanna G, Panda PK, Gulati S, Garg A, Sharma MC. Paediatric diffuse leptomeningeal tumor with glial and neuronal differentiation harbouring chromosome 1p/19q co-deletion and H3.3 K27M mutation: unusual molecular profile and its therapeutic implications. Brain Tumor Pathol 2018; 35:186-191. [PMID: 30030640 DOI: 10.1007/s10014-018-0325-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 06/23/2018] [Indexed: 12/24/2022]
Abstract
Diffuse leptomeningeal glioneuronal tumor (DL-GNT) is a newly introduced tumor entity of uncertain prognosis characterised by a primary diffuse leptomeningeal growth pattern, oligodendroglial-like morphology and dual glial/neuronal differentiation. Predominantly occurring in children, these tumors present as chronic meningitis and mimic infectious/inflammatory diseases. They are surgically challenging tumors with a high incidence of delayed morbidity and mortality despite low-grade histology. Their molecular genetic profile is not fully elucidated and few reports have identified chromosome 1p and 19q deletions, and BRAF alterations. We present a rare instance of a DL-GNT in a 13-year-old female who presented with slowly progressive and sequential neurological deficits over a 12-month duration. Imaging showed leptomeningeal thickening and spinal lesions. Biopsy from the spinal mass showed histomorphological features characteristic of DL-GNT. Further molecular analysis revealed 1p and 19q co-deletion and H3K27M mutation, while no mutation were identified in IDH, TERT, or BRAF genes. Patient died 4 months after diagnosis. Only one previous case of DL-GNT has been reported to harbour H3K27M mutation. Although H3K27M mutations have been described in rare examples of low-grade glial and glioneuronal tumors, whether DL-GNTs with H3K27M represent a rare growth pattern of the aggressive H3K27M-mutant diffuse midline gliomas needs further clarification.
Collapse
Affiliation(s)
- Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sweta Kedia
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Keshav Goyal
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Gaurav Khanna
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Prateek Kumar Panda
- Departments of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sheffali Gulati
- Departments of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ajay Garg
- Departments of Neuroradiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| |
Collapse
|
19
|
Malgulwar PB, Nambirajan A, Pathak P, Faruq M, Rajeshwari M, Singh M, Suri V, Sarkar C, Sharma MC. C11orf95-RELA fusions and upregulated NF-KB signalling characterise a subset of aggressive supratentorial ependymomas that express L1CAM and nestin. J Neurooncol 2018; 138:29-39. [PMID: 29354850 DOI: 10.1007/s11060-018-2767-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/14/2018] [Indexed: 12/16/2022]
Abstract
Ependymomas (EPN) show site specific genetic alterations and a recent DNA methylation profiling study identified nine molecular subgroups. C11orf95-RELA and YAP1 fusions characterise the RELA and YAP1 molecular subgroups, respectively, of supratentorial (ST)-EPNs. Current guidelines recommend molecular subgrouping over histological grade for accurate prognostication. Clinicopathological features of ST-EPNs in correlation with C11orf95-RELA and YAP1 fusions have been assessed in only few studies. We aimed to study these fusions in EPNs, and identify diagnostic and prognostic markers. qRT-PCR and Sanger Sequencing for the detection of C11orf95-RELA, YAP1-MAMLD1 and YAP1-FAM118B fusion transcripts, gene expression analysis for NFKB1, and immunohistochemistry for p53, MIB-1, nestin, VEGF, and L1CAM were performed. 88 EPNs (10-Grade I and 78-Grade II/III) from all sites were included. RELA fusions were unique to Grade II/III ST-EPNs, detected in 81.4% (22/27) and 18.5% (5/27) of pediatric and adult ST-EPNs respectively. ST-EPNs harbouring RELA fusions showed frequent grade III histology (81.5%), clear cell morphology (70.3%), upregulated NFKB1 expression, MIB-1 labelling indices (LI) ≥ 10% (77.8%), and immunopositivity for nestin (95.7%), VEGF (72%), L1CAM (79%), and p53 (64%). Presence of RELA fusions, L1CAM immunopositivity and MIB-1 LI ≥ 10% associated with poor outcome. L1CAM showed 81% concordance with RELA fusions. YAP1-MAMLD1 fusion was identified in a single RELA fusion negative adult anaplastic ST-EPN. RELA fusions are frequent in ST-EPNs and associate with poor outcome. L1CAM is a surrogate immunohistochemical marker. RELA fusion positive ST-EPNs strongly express nestin indicating increased stemness. Further evaluation of the interactions between NFKB and stem cell pathways is warranted.
Collapse
Affiliation(s)
- Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology-Council of Scientific and Industrial Research (IGIB-CSIR), New Delhi, India
| | - Madhu Rajeshwari
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Manmohan Singh
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| |
Collapse
|
20
|
Agrawal R, Garg A, Benny Malgulwar P, Sharma V, Sarkar C, Kulshreshtha R. p53 and miR-210 regulated NeuroD2, a neuronal basic helix-loop-helix transcription factor, is downregulated in glioblastoma patients and functions as a tumor suppressor under hypoxic microenvironment. Int J Cancer 2017; 142:1817-1828. [DOI: 10.1002/ijc.31209] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 10/27/2017] [Accepted: 11/29/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Rahul Agrawal
- Department of Biochemical Engineering and Biotechnology; Indian Institute of Technology Delhi; New Delhi India
| | - Ankita Garg
- Department of Biochemical Engineering and Biotechnology; Indian Institute of Technology Delhi; New Delhi India
| | - Prit Benny Malgulwar
- Department of Pathology; All India Institute of Medical Sciences; New Delhi India
| | - Vikas Sharma
- Department of Biochemical Engineering and Biotechnology; Indian Institute of Technology Delhi; New Delhi India
| | - Chitra Sarkar
- Department of Pathology; All India Institute of Medical Sciences; New Delhi India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology; Indian Institute of Technology Delhi; New Delhi India
| |
Collapse
|
21
|
Ahmad F, Patrick S, Sheikh T, Sharma V, Pathak P, Malgulwar PB, Kumar A, Joshi SD, Sarkar C, Sen E. Telomerase reverse transcriptase (TERT) - enhancer of zeste homolog 2 (EZH2) network regulates lipid metabolism and DNA damage responses in glioblastoma. J Neurochem 2017; 143:671-683. [PMID: 28833137 DOI: 10.1111/jnc.14152] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/29/2017] [Accepted: 08/11/2017] [Indexed: 12/27/2022]
Abstract
Elevated expression of enhancer of zeste homolog 2 (EZH2), a histone H3K27 methyltransferase, was observed in gliomas harboring telomerase reverse transcriptase (TERT) promoter mutations. Given the known involvement of TERT and EZH2 in glioma progression, the correlation between the two and subsequently its involvement in metabolic programming was investigated. Inhibition of human telomerase reverse transcriptase either pharmacologically or through genetic manipulation not only decreased EZH2 expression, but also (i) abrogated FASN levels, (ii) decreased de novo fatty acid accumulation, and (iii) increased ataxia-telangiectasia-mutated (ATM) phosphorylation levels. Conversely, diminished TERT and FASN levels upon siRNA-mediated EZH2 knockdown indicated a positive correlation between TERT and EZH2. Interestingly, ATM kinase inhibitor rescued TERT inhibition-mediated decrease in FASN and EZH2 levels. Importantly, TERT promoter mutant tumors exhibited greater microsatellite instability, heightened FASN levels and lipid accumulation. Coherent with in vitro findings, pharmacological inhibition of TERT by costunolide decreased lipid accumulation and elevated ATM expression in heterotypic xenograft glioma mouse model. By bringing TERT-EZH2 network at the forefront as driver of dysregulated metabolism, our findings highlight the non-canonical but distinct role of TERT in metabolic reprogramming and DNA damage responses in glioblastoma.
Collapse
Affiliation(s)
- Fahim Ahmad
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
| | - Shruti Patrick
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
| | - Touseef Sheikh
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
| | - Vikas Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Anupam Kumar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Shanker Datt Joshi
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Ellora Sen
- Division of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, India
| |
Collapse
|
22
|
Sharma V, Malgulwar PB, Purkait S, Patil V, Pathak P, Agrawal R, Kulshreshtha R, Mallick S, Julka PK, Suri A, Sharma BS, Suri V, Sharma MC, Sarkar C. Genome-wide ChIP-seq analysis of EZH2-mediated H3K27me3 target gene profile highlights differences between low- and high-grade astrocytic tumors. Carcinogenesis 2017; 38:152-161. [PMID: 27993893 DOI: 10.1093/carcin/bgw126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/30/2016] [Indexed: 01/19/2023] Open
Abstract
Enhancer of zeste homolog-2(EZH2) is a key epigenetic regulator that functions as oncogene and also known for inducing altered trimethylation of histone at lysine-27 (H3K27me3) mark in various tumors. However, H3K27me3 targets and their precise relationship with gene expression are largely unknown in astrocytic tumors. In this study, we checked EZH2 messenger RNA and protein expression in 90 astrocytic tumors of different grades using quantitative PCR and immunohistochemistry, respectively. Further, genome-wide ChIP-seq analysis for H3K27me3 modification was also performed on 11 glioblastomas (GBMs) and 2 diffuse astrocytoma (DA) samples. Our results showed EZH2 to be highly overexpressed in astrocytic tumors with a significant positive correlation with grade. Interestingly, ChIP-seq mapping revealed distinct differences in genes and pathways targeted by these H3K27me3 modifications between GBM versus DA. Neuroactive ligand receptor pathway was found most enriched in GBM (P = 9.4 × 10-25), whereas DA were found to be enriched in metabolic pathways. Also, GBM showed a higher enrichment of H3K27me3 targets reported in embryonic stem cells and glioma stem cells as compared with DAs. Our results show majority of these H3K27me3 target genes were downregulated, not only due to H3K27me3 modification but also due to concomitant DNA methylation. Further, H3K27me3 modification-associated gene silencing was not restricted to promoter but also present in gene body and transcription start site regions. To the best of our knowledge, this is the first high-resolution genome-wide mapping of H3K27me3 modification in adult astrocytic primary tissue samples of human, highlighting the differences between grades. Interestingly, we identified SLC25A23 as important target of H3K27me3 modification, which was downregulated in GBM and its low expression was associated with poor prognosis in GBMs.
Collapse
Affiliation(s)
- Vikas Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Suvendu Purkait
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vikas Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rahul Agrawal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | | | | | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Bhawani Shankar Sharma
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| |
Collapse
|
23
|
Malgulwar PB, Pathak P, Singh M, Kale SS, Suri V, Sarkar C, Sharma MC. Downregulation of SMARCB1/INI1 expression in pediatric chordomas correlates with upregulation of miR-671-5p and miR-193a-5p expressions. Brain Tumor Pathol 2017; 34:155-159. [PMID: 28825187 DOI: 10.1007/s10014-017-0295-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/01/2017] [Indexed: 12/31/2022]
Abstract
Loss of SMARCB1/INI1 expression is considered to be a hallmark for childhood chordomas (CCs). Although mutation/loss of 22q has strongly established the loss of SMARCB1/INI1 in cancers, the cause in CCs remains elusive. Recent studies suggest role of miRNAs in regulation of SMARCB1/INI1 expressions. We examined 5 reported/target predicted miRNAs to SMARCB1/INI1 in SMARCB1/INI1 immunonegative and immunopositive cases, and found upregulation of miR-671-5p and miR-193a-5p in SMARCB1/INI1-immunonegative cases. Notably, these two miRNAs were significantly predicted to target TGF-β signaling, suggestive of dysregulation of developmental and osteoblast regulation pathway in CCs. Overall, we suggest miR-671-5p- and miR-193a-5p-mediated epigenetic mode of SMARCB1/INI1 loss and downregulated TGF-β pathway in CCs.
Collapse
Affiliation(s)
- Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Manmohan Singh
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Shashank Sharad Kale
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| |
Collapse
|
24
|
Malgulwar PB, Nambirajan A, Pathak P, Faruq M, Suri V, Sarkar C, Jagdevan A, Sharma BS, Sharma MC. Study of β-catenin and BRAF alterations in adamantinomatous and papillary craniopharyngiomas: mutation analysis with immunohistochemical correlation in 54 cases. J Neurooncol 2017; 133:487-495. [DOI: 10.1007/s11060-017-2465-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 05/06/2017] [Indexed: 01/03/2023]
|
25
|
Agrawal R, Dale TP, Al-Zubaidi MA, Benny Malgulwar P, Forsyth NR, Kulshreshtha R. Pluripotent and Multipotent Stem Cells Display Distinct Hypoxic miRNA Expression Profiles. PLoS One 2016; 11:e0164976. [PMID: 27783707 PMCID: PMC5081191 DOI: 10.1371/journal.pone.0164976] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 10/04/2016] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs are reported to have a crucial role in the regulation of self-renewal and differentiation of stem cells. Hypoxia has been identified as a key biophysical element of the stem cell culture milieu however, the link between hypoxia and miRNA expression in stem cells remains poorly understood. We therefore explored miRNA expression in hypoxic human embryonic and mesenchymal stem cells (hESCs and hMSCs). A total of 50 and 76 miRNAs were differentially regulated by hypoxia (2% O2) in hESCs and hMSCs, respectively, with a negligible overlap of only three miRNAs. We found coordinate regulation of precursor and mature miRNAs under hypoxia suggesting their regulation mainly at transcriptional level. Hypoxia response elements were located upstream of 97% of upregulated hypoxia regulated miRNAs (HRMs) suggesting hypoxia-inducible-factor (HIF) driven transcription. HIF binding to the candidate cis-elements of specific miRNAs under hypoxia was confirmed by Chromatin immunoprecipitation coupled with qPCR. Role analysis of a subset of upregulated HRMs identified linkage to reported inhibition of differentiation while a downregulated subset of HRMs had a putative role in the promotion of differentiation. MiRNA-target prediction correlation with published hypoxic hESC and hMSC gene expression profiles revealed HRM target genes enriched in the cytokine:cytokine receptor, HIF signalling and pathways in cancer. Overall, our study reveals, novel and distinct hypoxia-driven miRNA signatures in hESCs and hMSCs with the potential for application in optimised culture and differentiation models for both therapeutic application and improved understanding of stem cell biology.
Collapse
Affiliation(s)
- Rahul Agrawal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India-110016
| | - Tina P. Dale
- Guy Hilton Research Centre, Institute of Science and Technology in Medicine, University of Keele, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, United Kingdom
| | - Mohammed A. Al-Zubaidi
- Guy Hilton Research Centre, Institute of Science and Technology in Medicine, University of Keele, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, United Kingdom
- College of Pharmacy, Al-Mustansiriyah University, Baghdad, Iraq
| | - Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India-110029
| | - Nicholas R. Forsyth
- Guy Hilton Research Centre, Institute of Science and Technology in Medicine, University of Keele, Thornburrow Drive, Hartshill, Stoke-on-Trent, Staffordshire, ST4 7QB, United Kingdom
- * E-mail: , (RK); (NRF)
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India-110016
- * E-mail: , (RK); (NRF)
| |
Collapse
|
26
|
Malgulwar PB, Pathak P, Desiraju BK, Nambirajan A, Sarkar C, Suri V, Singh M, Sharma MC. EPN-13EPITHELIAL-TO-MESENCHYMAL TRANSITIONS IN CHILDHOOD EPENDYMOMAS MECHANISTICALLY LINKS ONCOGENIC C11orf95-RELA FUSION DRIVEN ACTIVATION OF SNAI1/SNAIL. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now070.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
27
|
Nambirajan A, Malgulwar PB, Pathak P, Faruq M, Rajeshwari M, Gupta RK, Suri V, Sarkar C, Singh M, Sharma MC. EPN-03C11orf95-RELA FUSION POSITIVE PEDIATRIC SUPRATENTORIAL EPENDYMOMAS ARE AN AGGRESSIVE SUBSET WITH INCREASED EXPRESSION OF STEM CELL MARKER NESTIN AND VASCULAR ENDOTHELIAL DERIVED GROWTH FACTOR. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now070.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
28
|
Nambirajan A, Malgulwar PB, Sharma MC, Singh A, Pathak P, Satyarthee GD, Garg A. C11orf95-RELAfusion present in a primary intracranial extra-axial ependymoma: Report of a case with literature review. Neuropathology 2016; 36:490-495. [DOI: 10.1111/neup.12299] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/15/2016] [Accepted: 02/15/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Aruna Nambirajan
- Department of Pathology; All India Institute of Medical Sciences; New Delhi India
| | - Prit Benny Malgulwar
- Department of Pathology; All India Institute of Medical Sciences; New Delhi India
| | - Mehar C. Sharma
- Department of Pathology; All India Institute of Medical Sciences; New Delhi India
| | - Anutosh Singh
- Neurosurgery; All India Institute of Medical Sciences; New Delhi India
| | - Pankaj Pathak
- Department of Pathology; All India Institute of Medical Sciences; New Delhi India
| | | | - Ajay Garg
- Neuroradiology; All India Institute of Medical Sciences; New Delhi India
| |
Collapse
|
29
|
Sharma V, Purkait S, Takkar S, Malgulwar PB, Kumar A, Pathak P, Suri V, Sharma MC, Suri A, Kale SS, Kulshreshtha R, Sarkar C. Analysis of EZH2: micro-RNA network in low and high grade astrocytic tumors. Brain Tumor Pathol 2016; 33:117-28. [PMID: 26746204 DOI: 10.1007/s10014-015-0245-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/10/2015] [Indexed: 12/25/2022]
Abstract
Enhancer of Zeste homologue2 (EZH2) is an epigenetic regulator that functions as oncogene in astrocytic tumors, however, EZH2 regulation remains little studied. In this study, we measured EZH2 levels in low (Gr-II,DA) and high grade (Gr-IV,GBM) astrocytic tumors and found significant increased EZH2 transcript level with grade(median DA-8.5, GBM-28.9).However, a different trend was reflected in protein levels, with GBMs showing high EZH2 LI(median-26.5) compared to DA (median 0.3). This difference in correlation of EZH2 protein and RNA levels suggested post-transcriptional regulation of EZH2, likely mediated by miRNAs. We selected eleven miRNAs that strongly predicted to target EZH2 and measured their expression. Three miRNAs (miR-26a-5p,miR27a-3p and miR-498) showed significant correlation with EZH2 protein, suggesting them as regulators of EZH2, however miR-26a-5p levels decreased with grade. ChIP analyses revealed H3K27me3 modifications in miR-26a promoter suggesting feedback loop between EZH2 and miR26a. We further measured six downstream miRNA targets of EZH2 and found significant downregulation of four (miR-181a/b and 200b/c) in GBM. Interestingly, EZH2 associated miRNAs were predicted to target 25 genes in glioma-pathway, suggesting their role in tumor formation or progression. Collectively, our work suggests EZH2 and its miRNA interactors may serve as promising biomarkers for progression of astrocytic tumors and may offer novel therapeutic strategies.
Collapse
Affiliation(s)
- Vikas Sharma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Suvendu Purkait
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sonam Takkar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Anupam Kumar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Mehar C Sharma
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Shashank Sharad Kale
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| |
Collapse
|
30
|
Yadav R, Sharma MC, Malgulwar PB, Pathak P, Sigamani E, Suri V, Sarkar C, Kumar A, Singh M, Sharma BS, Garg A, Bakhshi S, Faruq M. Prognostic value of MIB-1, p53, epidermal growth factor receptor, and INI1 in childhood chordomas. Neuro Oncol 2013; 16:372-81. [PMID: 24305715 DOI: 10.1093/neuonc/not228] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Chordomas are slow-growing tumors and most commonly involve the sacrum and clivus. Multiple recurrences are frequent. Childhood chordomas are rare and often show exceptionally aggressive behavior, resulting in short survival and a high incidence of metastatic spread. OBJECTIVE This study examined the histologic features and immunohistochemical profile of pediatric chordomas and compared them with their adult counterparts. METHODS Nine pediatric and 13 adult cases were included in the study. Childhood chordomas were classified into conventional, atypical, and poorly differentiated types. Immunohistochemistry was performed for cytokeratin, epithelial membrane antigen, vimentin, S100, brachyury, p53, INI1, epidermal growth factor receptor (EGFR), and CD117. Cytogenetic analyses were performed in a subset of tumors for SMARCB1/INI1 locus on 22q chromosome by fluorescent in situ hybridization (FISH) and analysis of the SMARCB1/INI1 gene sequence. RESULTS All tumors showed expression of cytokeratin, epithelial membrane antigen, S100, vimentin, brachyury, and EGFR. Atypical morphology, p53 expression, higher MIB-1 labelling index (LI), and INI1 loss were more frequently seen in pediatric chordomas as compared with adults. None of the tumors showed CD117 expression. No point mutation in the SMARCB1/INI1 gene was noted in the tumors examined; however, 4 pediatric and 1 adult chordoma showed loss of this locus on FISH analysis. CONCLUSIONS A subset of pediatric chordomas with atypical histomorphologic features needs to be identified, as they behave in an aggressive manner and require adjuvant therapy. Pediatric chordomas more frequently show p53 expression, INI1 loss, and higher MIB-1 LI as compared with adults, whereas EGFR expression is common to both.
Collapse
Affiliation(s)
- Rajni Yadav
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (R.Y., M.C.S., P.B.M., P.P., E.S., V.S. C.S.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.J., M.S., B.S.S.); Department of Neuroradiology, All India Institute of Medical Sciences, New Delhi, India (A.G.); Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India (S.B.)
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|