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Floros KV, Fairchild CK, Li J, Zhang K, Roberts JL, Kurupi R, Hu B, Kraskauskiene V, Hosseini N, Shen S, Inge MM, Smith-Fry K, Li L, Sotiriou A, Dalton KM, Jose A, Abdelfadiel EI, Xing Y, Hill RD, Slaughter JM, Shende M, Lorenz MR, Hinojosa MR, Belvin BR, Lai Z, Boikos SA, Stamatouli AM, Lewis JP, Manjili MH, Valerie K, Li R, Banito A, Poklepovic A, Koblinski JE, Siggers T, Dozmorov MG, Jones KB, Radhakrishnan SK, Faber AC. Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in Synovial Sarcoma. bioRxiv 2024:2024.04.25.591023. [PMID: 38712286 PMCID: PMC11071469 DOI: 10.1101/2024.04.25.591023] [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: 05/08/2024]
Abstract
Synovial Sarcoma (SS) is driven by the SS18::SSX fusion oncoprotein. and is ultimately refractory to therapeutic approaches. SS18::SSX alters ATP-dependent chromatin remodeling BAF (mammalian SWI/SNF) complexes, leading to the degradation of canonical (cBAF) complex and amplified presence of an SS18::SSX-containing non-canonical BAF (ncBAF or GBAF) that drives an SS-specific transcription program and tumorigenesis. We demonstrate that SS18::SSX activates the SUMOylation program and SSs are sensitive to the small molecule SAE1/2 inhibitor, TAK-981. Mechanistically, TAK-981 de-SUMOylates the cBAF subunit SMARCE1, stabilizing and restoring cBAF on chromatin, shifting away from SS18::SSX-ncBAF-driven transcription, associated with DNA damage and cell death and resulting in tumor inhibition across both human and mouse SS tumor models. TAK-981 synergized with cytotoxic chemotherapy through increased DNA damage, leading to tumor regression. Targeting the SUMOylation pathway in SS restores cBAF complexes and blocks the SS18::SSX-ncBAF transcriptome, identifying a therapeutic vulnerability in SS, positioning the in-clinic TAK-981 to treat SS.
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Gedik H, Peterson R, Chatzinakos C, Dozmorov MG, Vladimirov V, Riley BP, Bacanu SA. A novel multi-omics mendelian randomization method for gene set enrichment and its application to psychiatric disorders. medRxiv 2024:2024.04.14.24305811. [PMID: 38699366 PMCID: PMC11065030 DOI: 10.1101/2024.04.14.24305811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Genome-wide association studies (GWAS) of psychiatric disorders (PD) yield numerous loci with significant signals, but often do not implicate specific genes. Because GWAS risk loci are enriched in expression/protein/methylation quantitative loci (e/p/mQTL, hereafter xQTL), transcriptome/proteome/methylome-wide association studies (T/P/MWAS, hereafter XWAS) that integrate xQTL and GWAS information, can link GWAS signals to effects on specific genes. To further increase detection power, gene signals are aggregated within relevant gene sets (GS) by performing gene set enrichment (GSE) analyses. Often GSE methods test for enrichment of "signal" genes in curated GS while overlooking their linkage disequilibrium (LD) structure, allowing for the possibility of increased false positive rates. Moreover, no GSE tool uses xQTL information to perform mendelian randomization (MR) analysis. To make causal inference on association between PD and GS, we develop a novel MR GSE (MR-GSE) procedure. First, we generate a "synthetic" GWAS for each MSigDB GS by aggregating summary statistics for x-level (mRNA, protein or DNA methylation (DNAm) levels) from the largest xQTL studies available) of genes in a GS. Second, we use synthetic GS GWAS as exposure in a generalized summary-data-based-MR analysis of complex trait outcomes. We applied MR-GSE to GWAS of nine important PD. When applied to the underpowered opioid use disorder GWAS, none of the four analyses yielded any signals, which suggests a good control of false positive rates. For other PD, MR-GSE greatly increased the detection of GO terms signals (2,594) when compared to the commonly used (non-MR) GSE method (286). Some of the findings might be easier to adapt for treatment, e.g., our analyses suggest modest positive effects for supplementation with certain vitamins and/or omega-3 for schizophrenia, bipolar and major depression disorder patients. Similar to other MR methods, when applying MR-GSE researchers should be mindful of the confounding effects of horizontal pleiotropy on statistical inference.
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Abudahab S, Kronfol MM, Dozmorov MG, Campbell T, Jahr FM, Nguyen J, AlAzzeh O, Al Saeedy DY, Victor A, Lee S, Malay S, Lapato DM, Halquist MS, McRae M, Deshpande LS, Slattum PW, Price ET, McClay JL. Genome-wide analysis of hepatic DNA methylation reveals impact of epigenetic aging on xenobiotic metabolism and transport genes in an aged mouse model. GeroScience 2024:10.1007/s11357-024-01137-9. [PMID: 38558216 DOI: 10.1007/s11357-024-01137-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Hepatic xenobiotic metabolism and transport decline with age, while intact xenobiotic metabolism is associated with longevity. However, few studies have examined the genome-wide impact of epigenetic aging on these processes. We used reduced representation bisulfite sequencing (RRBS) to map DNA methylation changes in liver DNA from mice ages 4 and 24 months. We identified several thousand age-associated differentially methylated sites (a-DMS), many of which overlapped genes encoding Phase I and Phase II drug metabolizing enzymes, in addition to ABC and SLC classes of transporters. Notable genes harboring a-DMS were Cyp1a2, Cyp2d9, and Abcc2 that encode orthologs of the human drug metabolizing enzymes CYP1A2 and CYP2D6, and the multidrug resistance protein 2 (MRP2) transporter. Cyp2d9 hypermethylation with age was significantly associated with reduced gene expression, while Abcc2 expression was unchanged with age. Cyp1a2 lost methylation with age while, counterintuitively, its expression also reduced with age. We hypothesized that age-related dysregulation of the hepatic transcriptional machinery caused down-regulation of genes despite age-related hypomethylation. Bioinformatic analysis of hypomethylated a-DMS in our sample found them to be highly enriched for hepatic nuclear factor 4 alpha (HNF4α) binding sites. HNF4α promotes Cyp1a2 expression and is downregulated with age, which could explain the reduction in Cyp1a2 expression. Overall, our study supports the broad impact of epigenetic aging on xenobiotic metabolism and transport. Future work should evaluate the interplay between hepatic nuclear receptor function and epigenetic aging. These results may have implications for studies of longevity and healthy aging.
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Affiliation(s)
- Sara Abudahab
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Mohamad M Kronfol
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, USA
| | - Thomas Campbell
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA, USA
| | - Fay M Jahr
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Jasmine Nguyen
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Ola AlAzzeh
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Dalia Y Al Saeedy
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Ashley Victor
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Sera Lee
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Shravani Malay
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Matthew S Halquist
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA, USA
| | - MaryPeace McRae
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Laxmikant S Deshpande
- Department of Neurology, Virginia Commonwealth University, Richmond, VA, USA
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Patricia W Slattum
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
- Virginia Center On Aging, Virginia Commonwealth University, Richmond, VA, USA
| | - Elvin T Price
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Joseph L McClay
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA.
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Zheng X, Dozmorov MG, Espinoza L, Bowes MM, Bastacky S, Sawalha AH. Inducible deletion of Ezh2 in CD4+ T cells inhibits kidney T cell infiltration and prevents interstitial nephritis in MRL/ lpr lupus-prone mice. bioRxiv 2024:2024.03.04.583401. [PMID: 38496595 PMCID: PMC10942296 DOI: 10.1101/2024.03.04.583401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Systemic lupus erythematosus is a remitting relapsing autoimmune disease characterized by autoantibody production and multi-organ involvement. T cell epigenetic dysregulation plays an important role in the pathogenesis of lupus. We have previously demonstrated upregulation of the key epigenetic regulator EZH2 in CD4+ T cells isolated from lupus patients. To further investigate the role of EZH2 in the pathogenesis of lupus, we generated a tamoxifen-inducible CD4+ T cell Ezh2 conditional knockout mouse on the MRL/ lpr lupus-prone background. We demonstrate that Ezh2 deletion abrogates lupus-like disease and prevents T cell differentiation. Single-cell analysis suggests impaired T cell function and activation of programed cell death pathways in EZH2-deficient mice. Ezh2 deletion in CD4+ T cells restricts TCR clonal repertoire and prevents kidney-infiltrating effector CD4+ T cell expansion and tubulointerstitial nephritis, which has been linked to end-stage renal disease in patients with lupus nephritis.
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Wall BPG, Nguyen M, Harrell JC, Dozmorov MG. Machine and deep learning methods for predicting 3D genome organization. ArXiv 2024:arXiv:2403.03231v1. [PMID: 38495565 PMCID: PMC10942493] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.
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Affiliation(s)
- Brydon P. G. Wall
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - My Nguyen
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - J. Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Center for Pharmaceutical Engineering, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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6
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Manna D, Reghupaty SC, Camarena MDC, Mendoza RG, Subler MA, Koblinski JE, Martin R, Dozmorov MG, Mukhopadhyay ND, Liu J, Qu X, Das SK, Lai Z, Windle JJ, Fisher PB, Sarkar D. Melanoma differentiation associated gene-9/syndecan binding protein promotes hepatocellular carcinoma. Hepatology 2023; 78:1727-1741. [PMID: 36120720 DOI: 10.1002/hep.32797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUND AND AIMS The oncogene Melanoma differentiation associated gene-9/syndecan binding protein (MDA-9/SDCBP) is overexpressed in many cancers, promoting aggressive, metastatic disease. However, the role of MDA-9 in regulating hepatocellular carcinoma (HCC) has not been well studied. APPROACH AND RESULTS To unravel the function of MDA-9 in HCC, we generated and characterized a transgenic mouse with hepatocyte-specific overexpression of MDA-9 (Alb/MDA-9). Compared with wild-type (WT) littermates, Alb/MDA-9 mice demonstrated significantly higher incidence of N-nitrosodiethylamine/phenobarbital-induced HCC, with marked activation and infiltration of macrophages. RNA sequencing (RNA-seq) in naive WT and Alb/MDA-9 hepatocytes identified activation of signaling pathways associated with invasion, angiogenesis, and inflammation, especially NF-κB and integrin-linked kinase signaling pathways. In nonparenchymal cells purified from naive livers, single-cell RNA-seq showed activation of Kupffer cells and macrophages in Alb/MDA-9 mice versus WT mice. A robust increase in the expression of Secreted phosphoprotein 1 (Spp1/osteopontin) was observed upon overexpression of MDA-9. Inhibition of NF-κB pathway blocked MDA-9-induced Spp1 induction, and knock down of Spp1 resulted in inhibition of MDA-9-induced macrophage migration, as well as angiogenesis. CONCLUSIONS Alb/MDA-9 is a mouse model with MDA-9 overexpression in any tissue type. Our findings unravel an HCC-promoting role of MDA-9 mediated by NF-κB and Spp1 and support the rationale of using MDA-9 inhibitors as a potential treatment for aggressive HCC.
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Affiliation(s)
- Debashri Manna
- Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Saranya Chidambaranathan Reghupaty
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Maria Del Carmen Camarena
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Rachel G Mendoza
- Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Mark A Subler
- Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Jennifer E Koblinski
- Massey Cancer Center , Virginia Commonwealth University , Richmond , Virginia , USA
- Department of Pathology , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Rebecca Martin
- Massey Cancer Center , Virginia Commonwealth University , Richmond , Virginia , USA
- Department of Microbiology and Immunology , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Mikhail G Dozmorov
- Department of Biostatistics , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Nitai D Mukhopadhyay
- Department of Biostatistics , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Jinze Liu
- Department of Biostatistics , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Xufeng Qu
- Massey Cancer Center , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Swadesh K Das
- Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , Virginia , USA
- Massey Cancer Center , Virginia Commonwealth University , Richmond , Virginia , USA
- Virginia Commonwealth University Institute of Molecular Medicine (VIMM) , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute , University of Texas Health Science Center San Antonio , San Antonio , Texas , USA
| | - Jolene J Windle
- Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , Virginia , USA
- Massey Cancer Center , Virginia Commonwealth University , Richmond , Virginia , USA
- Virginia Commonwealth University Institute of Molecular Medicine (VIMM) , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , Virginia , USA
- Massey Cancer Center , Virginia Commonwealth University , Richmond , Virginia , USA
- Virginia Commonwealth University Institute of Molecular Medicine (VIMM) , Virginia Commonwealth University , Richmond , Virginia , USA
| | - Devanand Sarkar
- Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , Virginia , USA
- Massey Cancer Center , Virginia Commonwealth University , Richmond , Virginia , USA
- Virginia Commonwealth University Institute of Molecular Medicine (VIMM) , Virginia Commonwealth University , Richmond , Virginia , USA
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Chougoni KK, Park H, Damle PK, Mason T, Cheng B, Dcona MM, Szomju B, Dozmorov MG, Idowu MO, Grossman SR. Coordinate transcriptional regulation of ErbB2/3 by C-terminal binding protein 2 signals sensitivity to ErbB2 inhibition in pancreatic adenocarcinoma. Oncogenesis 2023; 12:53. [PMID: 37949862 PMCID: PMC10638350 DOI: 10.1038/s41389-023-00498-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
There is a critical need to identify new therapeutic vulnerabilities in pancreatic ductal adenocarcinoma (PDAC). Transcriptional co-regulators C-terminal binding proteins (CtBP) 1 and 2 are highly overexpressed in human PDAC, and CRISPR-based homozygous deletion of Ctbp2 in a mouse PDAC cell line (CKP) dramatically decreased tumor growth, reduced metastasis, and prolonged survival in orthotopic mouse allografts. Transcriptomic profiling of tumors derived from CKP vs. Ctbp2-deleted CKP cells (CKP/KO) revealed significant downregulation of the EGFR-superfamily receptor Erbb3, the heterodimeric signaling partner for both EGFR and ErbB2. Compared with CKP cells, CKP/KO cells also demonstrated reduced Erbb2 expression and did not activate downstream Akt signaling after stimulation of Erbb3 by its ligand neuregulin-1. ErbB3 expression in human PDAC cell lines was similarly dependent on CtBP2 and depletion of ErbB3 in a human PDAC cell line severely attenuated growth, demonstrating the critical role of ErbB3 signaling in maintaining PDAC cell growth. Sensitivity to the ErbB2-targeted tyrosine kinase inhibitor lapatinib, but not the EGFR-targeted agent erlotinib, varied in proportion to the level of ErbB3 expression in mouse and human PDAC cells, suggesting that an ErBb2 inhibitor can effectively leverage CtBP2-driven transcriptional activation of physiologic ErbB2/3 expression and signaling in PDAC cells for therapeutic benefit.
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Affiliation(s)
- Kranthi Kumar Chougoni
- Keck School of Medicine and USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Haemin Park
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Priyadarshan K Damle
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Travis Mason
- Department of Surgery, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Bo Cheng
- Keck School of Medicine and USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Martin M Dcona
- Keck School of Medicine and USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Barbara Szomju
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
- VCU Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Michael O Idowu
- VCU Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Steven R Grossman
- Keck School of Medicine and USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA.
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Mockenhaupt K, Tyc KM, McQuiston A, Gonsiewski AK, Zarei-Kheirabadi M, Hariprashad A, Biswas DD, Gupta AS, Olex AL, Singh SK, Waters MR, Dupree JL, Dozmorov MG, Kordula T. Yin Yang 1 controls cerebellar astrocyte maturation. Glia 2023; 71:2437-2455. [PMID: 37417428 PMCID: PMC10529878 DOI: 10.1002/glia.24434] [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: 11/22/2022] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/08/2023]
Abstract
Diverse subpopulations of astrocytes tile different brain regions to accommodate local requirements of neurons and associated neuronal circuits. Nevertheless, molecular mechanisms governing astrocyte diversity remain mostly unknown. We explored the role of a zinc finger transcription factor Yin Yang 1 (YY1) that is expressed in astrocytes. We found that specific deletion of YY1 from astrocytes causes severe motor deficits in mice, induces Bergmann gliosis, and results in simultaneous loss of GFAP expression in velate and fibrous cerebellar astrocytes. Single cell RNA-seq analysis showed that YY1 exerts specific effects on gene expression in subpopulations of cerebellar astrocytes. We found that although YY1 is dispensable for the initial stages of astrocyte development, it regulates subtype-specific gene expression during astrocyte maturation. Moreover, YY1 is continuously needed to maintain mature astrocytes in the adult cerebellum. Our findings suggest that YY1 plays critical roles regulating cerebellar astrocyte maturation during development and maintaining a mature phenotype of astrocytes in the adult cerebellum.
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Affiliation(s)
- Karli Mockenhaupt
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Katarzyna M. Tyc
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
- Massey Cancer Center Bioinformatics Shared Resource Core, Virginia Commonwealth University, Richmond, Virginia
| | - Adam McQuiston
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia
| | - Alexandra K. Gonsiewski
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Masoumeh Zarei-Kheirabadi
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Avani Hariprashad
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Debolina D. Biswas
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Angela S. Gupta
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Amy L. Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, Virginia
| | - Sandeep K. Singh
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Michael R. Waters
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Jeff L. Dupree
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia
- Research Service, Central Virginia VA Health Care System, Richmond, Virginia
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
| | - Tomasz Kordula
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
- The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
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Reghupaty SC, Kanwal S, Mendoza RG, Davis E, Li H, Lai Z, Dozmorov MG, Faison MO, Siddiqui RA, Sarkar D. Dysregulation of Type I Interferon (IFN-I) Signaling: A Potential Contributor to Racial Disparity in Hepatocellular Carcinoma (HCC). Cancers (Basel) 2023; 15:4283. [PMID: 37686559 PMCID: PMC10486472 DOI: 10.3390/cancers15174283] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
African-American (AA)/Black hepatocellular carcinoma (HCC) patients have increased incidence and decreased survival rates compared to non-Hispanic (White) patients, the underlying molecular mechanism of which is not clear. Analysis of existing RNA-sequencing (RNA-seq) data in The Cancer Genome Atlas (TCGA) and in-house RNA-sequencing of 14 White and 18 AA/Black HCC patients revealed statistically significant activation of type I interferon (IFN-I) signaling pathway in AA/Black patients. A four-gene signature of IFN-stimulated genes (ISGs) showed increased expression in AA/Black HCC tumors versus White. HCC is a disease of chronic inflammation, and IFN-Is function as pro-inflammatory cytokines. We tested efficacy of ginger extract (GE), a dietary compound known for anti-inflammatory properties, on HCC cell lines derived from White (HepG2), AA/Black (Hep3B and O/20) and Asian (HuH-7) patients. GE exhibited a significantly lower IC50 on Hep3B and O/20 cells than on HepG2 and HuH-7 cells. The GE treatment inhibited the activation of downstream mediators of IFN-I signaling pathways and expression of ISGs in all four HCC cells. Our data suggest that ginger can potentially attenuate IFN-I-mediated signaling pathways in HCC, and cells from AA/Black HCC patients may be more sensitive to ginger. AA/Black HCC patients might benefit from a holistic diet containing ginger.
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Affiliation(s)
| | - Sadia Kanwal
- Food and Nutrition Science Laboratory, College of Agriculture, Virginia State University, Petersburg, VA 23806, USA; (S.K.); (H.L.)
| | - Rachel G. Mendoza
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Eva Davis
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Haiwen Li
- Food and Nutrition Science Laboratory, College of Agriculture, Virginia State University, Petersburg, VA 23806, USA; (S.K.); (H.L.)
| | - Zhao Lai
- Greehey Children’s Cancer Research Institute, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA;
| | - Mikhail G. Dozmorov
- Department of Biostatistics and Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Milton Omar Faison
- Department of Biology, Virginia State University, Petersburg, VA 23806, USA;
| | - Rafat Ali Siddiqui
- Food and Nutrition Science Laboratory, College of Agriculture, Virginia State University, Petersburg, VA 23806, USA; (S.K.); (H.L.)
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Massey Cancer Center, VCU Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, Richmond, VA 23298, USA
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10
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Zheng X, Dozmorov MG, Strohlein CE, Bastacky S, Sawalha AH. Ezh2 Knockout in B Cells Impairs Plasmablast Differentiation and Ameliorates Lupus-like Disease in MRL/lpr Mice. Arthritis Rheumatol 2023; 75:1395-1406. [PMID: 36897808 PMCID: PMC10492897 DOI: 10.1002/art.42492] [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: 07/25/2022] [Revised: 01/25/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023]
Abstract
OBJECTIVES EZH2 regulates B cell development and differentiation. We previously demonstrated increased EZH2 expression in peripheral blood mononuclear cells from lupus patients. The goal of this study was to evaluate the role of EZH2 expression in B cells in the pathogenesis of lupus. METHODS We generated an MRL/lpr mouse with floxed Ezh2, which was crossed with CD19-Cre mice to examine the effect of B cell EZH2 deficiency in MRL/lpr lupus-prone mice. Differentiation of B cells was assessed using flow cytometry. Single-cell RNA sequencing and single-cell B cell receptor sequencing were performed. In vitro B cell culture with an X-box binding protein 1 (XBP1) inhibitor was performed. EZH2 and XBP1 messenger RNA levels in CD19+ B cells isolated from lupus patients and healthy controls were analyzed. RESULTS We show that Ezh2 deletion in B cells significantly decreased autoantibody production and improved glomerulonephritis. B cell development was altered in the bone marrow and spleen of EZH2-deficient mice. Differentiation of germinal center B cells and plasmablasts was impaired. Single-cell RNA sequencing showed that XBP1, a key transcription factor in B cell development, is down-regulated in the absence of EZH2. Inhibiting XBP1 in vitro impairs plasmablast development similar to EZH2 deficiency in mice. Single-cell B cell receptor RNA sequencing revealed defective immunoglobulin class-switch recombination in EZH2-deficient mice. In human lupus B cells, we observed a strong correlation between EZH2 and XBP1 messenger RNA expression levels. CONCLUSION EZH2 overexpression in B cells contributes to disease pathogenesis in lupus.
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Affiliation(s)
- Xiaoqing Zheng
- Department of Pediatrics, Division of Rheumatology, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
| | - Colleen E Strohlein
- Department of Pediatrics, Division of Rheumatology, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sheldon Bastacky
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Amr H Sawalha
- Department of Pediatrics, Division of Rheumatology, Children's Hospital of Pittsburgh, Department of Medicine, Division of Rheumatology and Clinical Immunology, Lupus Center of Excellence, and Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
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11
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Zboril EK, Grible JM, Boyd DC, Hairr NS, Leftwich TJ, Esquivel MF, Duong AK, Turner SA, Ferreira-Gonzalez A, Olex AL, Sartorius CA, Dozmorov MG, Harrell JC. Stratification of Tamoxifen Synergistic Combinations for the Treatment of ER+ Breast Cancer. Cancers (Basel) 2023; 15:3179. [PMID: 37370789 PMCID: PMC10296623 DOI: 10.3390/cancers15123179] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/24/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer alone accounts for the majority of cancer deaths among women, with the most commonly diagnosed subtype being estrogen receptor positive (ER+). Survival has greatly improved for patients with ER+ breast cancer, due in part to the development of antiestrogen compounds, such as tamoxifen. While treatment of the primary disease is often successful, as many as 30% of patients will experience recurrence and metastasis, mainly due to developed endocrine therapy resistance. In this study, we discovered two tamoxifen combination therapies, with simeprevir and VX-680, that reduce the tumor burden in animal models of ER+ breast cancer more than either compound or tamoxifen alone. Additionally, these tamoxifen combinations reduced the expression of HER2, a hallmark of tamoxifen treatment, which can facilitate acquisition of a treatment-resistant phenotype. These combinations could provide clinical benefit by potentiating tamoxifen treatment in ER+ breast cancer.
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Affiliation(s)
- Emily K. Zboril
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jacqueline M. Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - David C. Boyd
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
- Integrative Life Sciences Program, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nicole S. Hairr
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - Tess J. Leftwich
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - Madelyn F. Esquivel
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - Alex K. Duong
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | - Scott A. Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
| | | | - Amy L. Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Carol A. Sartorius
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J. Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA; (E.K.Z.)
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Center for Pharmaceutical Engineering, Virginia Commonwealth University, Richmond, VA 23298, USA
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12
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Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, Harrell JC. Publisher Correction: Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep 2023; 13:7522. [PMID: 37160896 PMCID: PMC10170154 DOI: 10.1038/s41598-023-33284-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| | - Maggie A Marshall
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Narmeen S Rashid
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biology, University of Richmond, Richmond, VA, 23173, USA
| | - Jacqueline M Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Aaron Valentine
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biochemistry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Kavita Murthy
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Abhijit Chakraborty
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Joaquin Reyna
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Daniela Salgado Figueroa
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Laura Hinojosa-Gonzalez
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Erika Da-Inn Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Brittany A Baur
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Ferhat Ay
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Department of Pediatrics, UC San Diego-School of Medicine, La Jolla, CA, 92093, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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13
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Mu W, Davis ES, Lee S, Dozmorov MG, Phanstiel DH, Love MI. bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing. Bioinformatics 2023; 39:btad190. [PMID: 37042725 PMCID: PMC10159650 DOI: 10.1093/bioinformatics/btad190] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/06/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
MOTIVATION Enrichment analysis is a widely utilized technique in genomic analysis that aims to determine if there is a statistically significant association between two sets of genomic features. To conduct this type of hypothesis testing, an appropriate null model is typically required. However, the null distribution that is commonly used can be overly simplistic and may result in inaccurate conclusions. RESULTS bootRanges provides fast functions for generation of block bootstrapped genomic ranges representing the null hypothesis in enrichment analysis. As part of a modular workflow, bootRanges offers greater flexibility for computing various test statistics leveraging other Bioconductor packages. We show that shuffling or permutation schemes may result in overly narrow test statistic null distributions and over-estimation of statistical significance, while creating new range sets with a block bootstrap preserves local genomic correlation structure and generates more reliable null distributions. It can also be used in more complex analyses, such as accessing correlations between cis-regulatory elements (CREs) and genes across cell types or providing optimized thresholds, e.g. log fold change (logFC) from differential analysis. AVAILABILITY AND IMPLEMENTATION bootRanges is freely available in the R/Bioconductor package nullranges hosted at https://bioconductor.org/packages/nullranges.
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Affiliation(s)
- Wancen Mu
- Department of Biostatistics, University of North Carolina, Chapel Hill 27514, United States
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill 27514, United States
| | - Stuart Lee
- Genentech, South San Francisco, Western California 94080, United States
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23284, United States
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill 27514, United States
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill 27514, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill 27514, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill 27514, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill 27514, United States
| | - Michael I Love
- Department of Biostatistics, University of North Carolina, Chapel Hill 27514, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill 27514, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill 27514, United States
- Department of Genetics, University of North Carolina, Chapel Hill 27514, United States
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14
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Davis ES, Mu W, Lee S, Dozmorov MG, Love MI, Phanstiel DH. matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling. Bioinformatics 2023; 39:btad197. [PMID: 37084270 PMCID: PMC10168584 DOI: 10.1093/bioinformatics/btad197] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/01/2023] [Accepted: 03/28/2023] [Indexed: 04/23/2023] Open
Abstract
MOTIVATION Deriving biological insights from genomic data commonly requires comparing attributes of selected genomic loci to a null set of loci. The selection of this null set is non-trivial, as it requires careful consideration of potential covariates, a problem that is exacerbated by the non-uniform distribution of genomic features including genes, enhancers, and transcription factor binding sites. Propensity score-based covariate matching methods allow the selection of null sets from a pool of possible items while controlling for multiple covariates; however, existing packages do not operate on genomic data classes and can be slow for large data sets making them difficult to integrate into genomic workflows. RESULTS To address this, we developed matchRanges, a propensity score-based covariate matching method for the efficient and convenient generation of matched null ranges from a set of background ranges within the Bioconductor framework. AVAILABILITY AND IMPLEMENTATION Package: https://bioconductor.org/packages/nullranges, Code: https://github.com/nullranges, Documentation: https://nullranges.github.io/nullranges.
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Affiliation(s)
- Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Wancen Mu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stuart Lee
- Genentech, South San Francisco, CA, United States
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, United States
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States
| | - Michael I Love
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Genetics & Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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15
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Ogata JD, Mu W, Davis ES, Xue B, Harrell JC, Sheffield NC, Phanstiel DH, Love MI, Dozmorov MG. excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies. Bioinformatics 2023; 39:7126418. [PMID: 37067481 PMCID: PMC10126321 DOI: 10.1093/bioinformatics/btad198] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/16/2023] [Accepted: 04/12/2023] [Indexed: 04/18/2023]
Abstract
SUMMARY Exclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settings. Several labs created exclusion region sets, available primarily through ENCODE and Github. However, the variety of exclusion sets creates uncertainty which sets to use. Furthermore, gap regions (e.g., centromeres, telomeres, short arms) create additional considerations in generating exclusion sets. We generated exclusion sets for the latest human T2T-CHM13 and mouse GRCm39 genomes and systematically assembled and annotated these and other sets in the excluderanges R/Bioconductor data package, also accessible via the BEDbase.org API. The package provides unified access to 82 GenomicRanges objects covering six organisms, multiple genome assemblies and types of exclusion regions. For human hg38 genome assembly, we recommend hg38.Kundaje.GRCh38_unified_blacklist as the most well-curated and annotated, and sets generated by the Blacklist tool for other organisms. AVAILABILITY AND IMPLEMENTATION https://bioconductor.org/packages/excluderanges/. SUPPLEMENTARY INFORMATION Package website: https://dozmorovlab.github.io/excluderanges/.
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Affiliation(s)
- Jonathan D Ogata
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Wancen Mu
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bingjie Xue
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23220, USA
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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16
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Del Carmen Camarena M, Komaniecki G, Manna D, Mendoza R, Subler MA, Windle JJ, Dozmorov MG, Lin H, Sarkar D. Abstract 3720: Cysteine palmitoylation of astrocyte elevated gene-1/Metadherin (AEG-1/MTDH) regulates its biological and immunological activity. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3720] [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: 04/07/2023]
Abstract
Abstract
Non-alcoholic steatohepatitis (NASH) is a major risk factor for hepatocellular carcinoma (HCC). Astrocyte elevated gene-1/Metadherin (AEG-1/MTDH) augments steatosis, inflammation, and tumorigenesis, thereby promoting the whole spectrum of this disease process. Targeting AEG-1 is a potential interventional strategy for NASH and HCC. Thus, proper understanding of the regulation of this molecule is essential. We found that AEG-1 is palmitoylated at residue Cysteine75 (Cys75). Mutation of Cys75 to Serine (Ser) completely abolished AEG-1 palmitoylation.Systematic knockdown studies identified zinc finger DHHC-type palmitoyltransferase 6 (ZDHHC6) as the palmitoyltransferase catalyzing the process. To obtain insight into how palmitoylation regulates AEG-1 function, we generated a knock-in mouse by CRISPR/Cas9 in which Cys75 of AEG-1 was mutated to Ser (AEG-1-C75S). No developmental or anatomical abnormality was observed between AEG-1-wild type (AEG-1-WT) and AEG-1-C75S littermates. However, global gene expression analysis by RNA-sequencing unraveled that signaling pathways and upstream regulators, which contribute to cell proliferation, motility, inflammation,angiogenesis, and lipid accumulation, are activated in AEG-1-C75S hepatocytes compared toAEG-1-WT. Feeding these mice with high fat/high sugar diet for 20 weeks showed accumulation of T-regulatory cells and exhausted CD8 T-cells in the livers of AEG-1-C75S mice vs AEG-1-WT, and only in females, suggesting that inhibition of AEG-1 palmitoylation creates an immunosuppressive milieu favoring tumorigenesis. Collectively, these findings suggest that AEG-1-C75S functions as dominant positive, and palmitoylation restricts oncogenic and NASH-promoting functions of AEG-1. Studies are ongoing to unravel the mechanism by which palmitoylation restricts AEG-1 function, and to understand the sex-specific immune-modulatory role of AEG-1 palmitoylation in hepatocarcinogenesis.
Citation Format: Maria Del Carmen Camarena, Garrison Komaniecki, Debashri Manna, Rachel Mendoza, Mark A. Subler, Jolene J. Windle, Mikhail G. Dozmorov, Hening Lin, Devanand Sarkar. Cysteine palmitoylation of astrocyte elevated gene-1/Metadherin (AEG-1/MTDH) regulates its biological and immunological activity. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3720.
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Affiliation(s)
| | | | | | | | | | | | | | - Hening Lin
- 1Virginia Commonwealth University - VCU, Richmond, VA
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17
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Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, Harrell JC. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep 2023; 13:5420. [PMID: 37012431 PMCID: PMC10070455 DOI: 10.1038/s41598-023-32568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2 Mb) interactions, chromatin looping, formation of TAD, chromatin state switching into a more active state, and amplification of ATP-binding cassette transporters. Transcriptome changes suggested the role of long-noncoding RNAs in carboplatin resistance. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of aggressiveness-, metastasis- and other cancer-related pathways. Integrative analysis highlighted increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial energy metabolism. Our results suggest that 3D genome remodeling may be a key mechanism underlying carboplatin resistance.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| | - Maggie A Marshall
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Narmeen S Rashid
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biology, University of Richmond, Richmond, VA, 23173, USA
| | - Jacqueline M Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Aaron Valentine
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biochemistry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Kavita Murthy
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Abhijit Chakraborty
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Joaquin Reyna
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Daniela Salgado Figueroa
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Laura Hinojosa-Gonzalez
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Erika Da-Inn Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Brittany A Baur
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Ferhat Ay
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Department of Pediatrics, UC San Diego-School of Medicine, La Jolla, CA, 92093, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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18
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Boyd DC, Zboril EK, Olex AL, Leftwich TJ, Hairr NS, Byers HA, Valentine AD, Altman JE, Alzubi MA, Grible JM, Turner SA, Ferreira-Gonzalez A, Dozmorov MG, Harrell JC. Discovering Synergistic Compounds with BYL-719 in PI3K Overactivated Basal-like PDXs. Cancers (Basel) 2023; 15:cancers15051582. [PMID: 36900375 PMCID: PMC10001201 DOI: 10.3390/cancers15051582] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Basal-like triple-negative breast cancer (TNBC) tumor cells are difficult to eliminate due to resistance mechanisms that promote survival. While this breast cancer subtype has low PIK3CA mutation rates when compared to estrogen receptor-positive (ER+) breast cancers, most basal-like TNBCs have an overactive PI3K pathway due to gene amplification or high gene expression. BYL-719 is a PIK3CA inhibitor that has been found to have low drug-drug interactions, which increases the likelihood that it could be useful for combinatorial therapy. Alpelisib (BYL-719) with fulvestrant was recently approved for treating ER+ breast cancer patients whose cancer had developed resistance to ER-targeting therapy. In these studies, a set of basal-like patient-derived xenograft (PDX) models was transcriptionally defined with bulk and single-cell RNA-sequencing and clinically actionable mutation profiles defined with Oncomine mutational profiling. This information was overlaid onto therapeutic drug screening results. BYL-719-based, synergistic two-drug combinations were identified with 20 different compounds, including everolimus, afatinib, and dronedarone, which were also found to be effective at minimizing tumor growth. These data support the use of these drug combinations towards cancers with activating PIK3CA mutations/gene amplifications or PTEN deficient/PI3K overactive pathways.
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Affiliation(s)
- David C. Boyd
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
- Integrative Life Sciences Program, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Emily K. Zboril
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Amy L. Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Tess J. Leftwich
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nicole S. Hairr
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Holly A. Byers
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Aaron D. Valentine
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Julia E. Altman
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mohammad A. Alzubi
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
- Integrative Life Sciences Program, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Jacqueline M. Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Scott A. Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | | | - Mikhail G. Dozmorov
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - J. Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Correspondence:
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19
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Weigel C, Maczis MA, Palladino END, Green CD, Maceyka M, Guo C, Wang XY, Dozmorov MG, Milstien S, Spiegel S. Sphingosine Kinase 2 in Stromal Fibroblasts Creates a Hospitable Tumor Microenvironment in Breast Cancer. Cancer Res 2023; 83:553-567. [PMID: 36541910 PMCID: PMC9931683 DOI: 10.1158/0008-5472.can-22-1638] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 05/18/2022] [Revised: 11/08/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Reciprocal interactions between breast cancer cells and the tumor microenvironment (TME) are important for cancer progression and metastasis. We report here that the deletion or inhibition of sphingosine kinase 2 (SphK2), which produces sphingosine-1-phosphate (S1P), markedly suppresses syngeneic breast tumor growth and lung metastasis in mice by creating a hostile microenvironment for tumor growth and invasion. SphK2 deficiency decreased S1P and concomitantly increased ceramides, including C16-ceramide, in stromal fibroblasts. Ceramide accumulation suppressed activation of cancer-associated fibroblasts (CAF) by upregulating stromal p53, which restrained production of tumor-promoting factors to reprogram the TME and to restrict breast cancer establishment. Ablation of p53 in SphK2-deficient fibroblasts reversed these effects, enabled CAF activation and promoted tumor growth and invasion. These data uncovered a novel role of SphK2 in regulating non-cell-autonomous functions of p53 in stromal fibroblasts and their transition to tumor-promoting CAFs, paving the way for the development of a strategy to target the TME and to enhance therapeutic efficacy. SIGNIFICANCE Sphingosine kinase 2 (SphK2) facilitates the activation of stromal fibroblasts to tumor-promoting cancer-associated fibroblasts by suppressing host p53 activity, revealing SphK2 as a potential target to reprogram the TME.
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Affiliation(s)
- Cynthia Weigel
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Melissa A. Maczis
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Elisa N. D. Palladino
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Christopher D. Green
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Michael Maceyka
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Chunqing Guo
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Xiang-Yang Wang
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Mikhail G. Dozmorov
- Departments of Biostatistics and Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Sheldon Milstien
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298
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20
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Komaniecki G, Camarena MDC, Gelsleichter E, Mendoza R, Subler M, Windle JJ, Dozmorov MG, Lai Z, Sarkar D, Lin H. Astrocyte Elevated Gene-1 Cys75 S-Palmitoylation by ZDHHC6 Regulates Its Biological Activity. Biochemistry 2023; 62:543-553. [PMID: 36548985 PMCID: PMC9850907 DOI: 10.1021/acs.biochem.2c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/01/2022] [Indexed: 12/24/2022]
Abstract
Nonalcoholic fatty liver disease is a major risk factor for hepatocellular carcinoma (HCC). Astrocyte elevated gene-1/Metadherin (AEG-1/MTDH) augments lipid accumulation (steatosis), inflammation, and tumorigenesis, thereby promoting the whole spectrum of this disease process. Targeting AEG-1 is a potential interventional strategy for nonalcoholic steatohepatitis (NASH) and HCC. Thus, proper understanding of the regulation of this molecule is essential. We found that AEG-1 is palmitoylated at residue cysteine 75 (Cys75). Mutation of Cys75 to serine (Ser) completely abolished AEG-1 palmitoylation. We identified ZDHHC6 as a palmitoyltransferase catalyzing the process in HEK293T cells. To obtain insight into how palmitoylation regulates AEG-1 function, we generated knock-in mice by CRISPR/Cas9 in which Cys75 of AEG-1 was mutated to Ser (AEG-1-C75S). No developmental or anatomical abnormality was observed between AEG-1-wild type (AEG-1-WT) and AEG-1-C75S littermates. However, global gene expression analysis by RNA-sequencing unraveled that signaling pathways and upstream regulators, which contribute to cell proliferation, motility, inflammation, angiogenesis, and lipid accumulation, were activated in AEG-1-C75S hepatocytes compared to AEG-1-WT. These findings suggest that AEG-1-C75S functions as dominant positive and that palmitoylation restricts oncogenic and NASH-promoting functions of AEG-1. We thus identify a previously unknown regulatory mechanism of AEG-1, which might help design new therapeutic strategies for NASH and HCC.
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Affiliation(s)
- Garrison Komaniecki
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
- C.
Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Maria Del Carmen Camarena
- C.
Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Eric Gelsleichter
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Rachel Mendoza
- Department
of Human and Molecular Genetics, Virginia
Commonwealth University, Richmond, Virginia 23298, United States
| | - Mark Subler
- Department
of Human and Molecular Genetics, Virginia
Commonwealth University, Richmond, Virginia 23298, United States
| | - Jolene J. Windle
- Department
of Human and Molecular Genetics, Virginia
Commonwealth University, Richmond, Virginia 23298, United States
- Massey
Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- VCU
Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Mikhail G. Dozmorov
- Department
of Biostatistics, Virginia Commonwealth
University, Richmond, Virginia 23298, United States
- Department
of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Zhao Lai
- Greehy
Children’s Cancer Research Institute, University of Texas Health
Science Center San Antonio, San Antonio, Texas 78229, United States
| | - Devanand Sarkar
- Department
of Human and Molecular Genetics, Virginia
Commonwealth University, Richmond, Virginia 23298, United States
- Massey
Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- VCU
Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Hening Lin
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
- Howard
Hughes Medical Institute, Department of Chemistry and Chemical Biology,
Cornell University, Ithaca, New York 14853, United States
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21
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Abudahab S, Price ET, Dozmorov MG, Deshpande LS, McClay JL. The Aryl Hydrocarbon Receptor, Epigenetics and the Aging Process. J Nutr Health Aging 2023; 27:291-300. [PMID: 37170437 PMCID: PMC10947811 DOI: 10.1007/s12603-023-1908-1] [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] [Indexed: 05/13/2023]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor, classically associated with the regulation of xenobiotic metabolism in response to environmental toxins. In recent years, transgenic rodent models have implicated AhR in aging and longevity. Moreover, several AhR ligands, such as resveratrol and quercetin, are compounds proven to extend the lifespan of model organisms. In this paper, we first review AhR biology with a focus on aging and highlight several AhR ligands with potential anti-aging properties. We outline how AhR-driven expression of xenobiotic metabolism genes into old age may be a key mechanism through which moderate induction of AhR elicits positive benefits on longevity and healthspan. Furthermore, via integration of publicly available datasets, we show that liver-specific AhR target genes are enriched among genes subject to epigenetic aging. Changes to epigenetic states can profoundly affect transcription factor binding and are a hallmark of the aging process. We suggest that the interplay between AhR and epigenetic aging should be the subject of future research and outline several key gaps in the current literature. Finally, we recommend that a broad range of non-toxic AhR ligands should be investigated for their potential to promote healthspan and longevity.
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Affiliation(s)
- S Abudahab
- Sara Abudahab, Smith Building, 410 North 12th Street, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298-0533, USA.
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22
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Dozmorov MG, Mu W, Davis ES, Lee S, Triche TJ, Phanstiel DH, Love MI. CTCF: an R/bioconductor data package of human and mouse CTCF binding sites. Bioinform Adv 2022; 2:vbac097. [PMID: 36699364 PMCID: PMC9793704 DOI: 10.1093/bioadv/vbac097] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Summary CTCF (CCCTC-binding factor) is an 11-zinc-finger DNA binding protein which regulates much of the eukaryotic genome's 3D structure and function. The diversity of CTCF binding motifs has led to a fragmented landscape of CTCF binding data. We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including the recent Telomere to Telomere and mm39 assemblies. We included selected experimentally determined and predicted CTCF binding sites, such as CTCF-bound cis-regulatory elements from SCREEN ENCODE. We recommend filtering strategies for CTCF binding motifs and demonstrate that liftOver is a viable alternative to convert CTCF coordinates between assemblies. Our comprehensive data resource and usage recommendations can serve to harmonize and strengthen the reproducibility of genomic studies utilizing CTCF binding data. Availability and implementation https://bioconductor.org/packages/CTCF. Companion website: https://dozmorovlab.github.io/CTCF/; Code to reproduce the analyses: https://github.com/dozmorovlab/CTCF.dev. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Wancen Mu
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stuart Lee
- Department of Econometrics and Business Statistics, Monash University, Clayton, NC 3168, Australia,Molecular Medicine Division, Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia
| | - Timothy J Triche
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA,Department of Pediatrics, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA,Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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23
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Rashid NS, Boyd DC, Olex AL, Grible JM, Duong AK, Alzubi MA, Altman JE, Leftwich TJ, Valentine AD, Hairr NS, Zboril EK, Smith TM, Pfefferle AD, Dozmorov MG, Harrell JC. Transcriptomic changes underlying EGFR inhibitor resistance in human and mouse models of basal-like breast cancer. Sci Rep 2022; 12:21248. [PMID: 36482068 PMCID: PMC9731984 DOI: 10.1038/s41598-022-25541-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
The goals of this study were to identify transcriptomic changes that arise in basal-like breast cancer cells during the development of resistance to epidermal growth factor receptor inhibitors (EGFRi) and to identify drugs that are cytotoxic once EGFRi resistance occurs. Human patient-derived xenografts (PDXs) were grown in immunodeficient mice and treated with a set of EGFRi; the EGFRi erlotinib was selected for more expansive in vivo studies. Single-cell RNA sequencing was performed on mammary tumors from the basal-like PDX WHIM2 that was treated with vehicle or erlotinib for 9 weeks. The PDX was then subjected to long-term erlotinib treatment in vivo. Through serial passaging, an erlotinib-resistant subline of WHIM2 was generated. Bulk RNA-sequencing was performed on parental and erlotinib-resistant tumors. In vitro high-throughput drug screening with > 500 clinically used compounds was performed on parental and erlotinib-resistant cells. Previously published bulk gene expression microarray data from MMTV-Wnt1 tumors were contrasted with the WHIM2 PDX data. Erlotinib effectively inhibited WHIM2 tumor growth for approximately 4 weeks. Compared to untreated cells, single-cell RNA sequencing revealed that a greater proportion of erlotinib-treated cells were in the G1 phase of the cell cycle. Comparison of WHIM2 and MMTV-Wnt1 gene expression data revealed a set of 38 overlapping genes that were differentially expressed in the erlotinib-resistant WHIM2 and MMTV-Wnt1 tumors. Comparison of all three data types revealed five genes that were upregulated across all erlotinib-resistant samples: IL19, KLK7, LCN2, SAA1, and SAA2. Of these five genes, LCN2 was most abundantly expressed in triple-negative breast cancers, and its knockdown restored erlotinib sensitivity in vitro. Despite transcriptomic differences, parental and erlotinib-resistant WHIM2 displayed similar responses to the majority of drugs assessed for cytotoxicity in vitro. This study identified transcriptomic changes arising in erlotinib-resistant basal-like breast cancer. These data could be used to identify a biomarker or develop a gene signature predictive of patient response to EGFRi. Future studies should explore the predictive capacity of these gene signatures as well as how LCN2 contributes to the development of EGFRi resistance.
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Affiliation(s)
- Narmeen S Rashid
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
- Department of Biology, University of Richmond, Richmond, VA, 23173, USA
| | - David C Boyd
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
- Program in Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Amy L Olex
- C. Kenneth and Diane Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Jacqueline M Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Alex K Duong
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Mohammad A Alzubi
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
- Oncology Center-Division of Pediatric Oncology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Julia E Altman
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Tess J Leftwich
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Aaron D Valentine
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Nicole S Hairr
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Emily K Zboril
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Timothy M Smith
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Adam D Pfefferle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Mikhail G Dozmorov
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA.
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23220, USA.
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24
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Chougoni KK, Park H, Damle PK, Dcona MM, Szomju B, Dozmorov MG, Idowu M, Grossman SR. Abstract B073: C-terminal Binding Protein (CtBP): a critical regulator of ErbB2/3 signaling in PDAC. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-b073] [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: 11/17/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains among the most lethal of human cancers with a 5-year survival of ~10%, underscoring the need to identify new therapeutic vulnerabilities. Previously, we reported high expression of transcriptional co-regulators C-terminal binding proteins (CtBP) 1 and 2 in human PDAC, however their precise role in PDAC formation or progression remains unclear. Here we have studied PDAC tumor dependency on CtBPs for growth and metastasis, using an orthotopic syngeneic pancreatic tumor mouse model employing a mouse PDAC cell line (CKP) derived from a pancreatic tumor that formed in a mouse expressing mutated K-Ras in the setting of p53 deletion. CRISPR-based homozygous deletion of Ctbp2 in the parental mouse PDAC cell line (CKP CtBP2 KO) dramatically decreased orthotopic PDAC tumor growth, drastically reduced metastatic potential, and significantly prolonged survival. Interrogating differential gene expression of the orthotopic PDAC tumors from Ctbp2 WT vs Ctbp2 KO cohorts, we identified significant downregulation of the EGFR-superfamily receptor ErbB3 in Ctbp2 KO tumors, and further determined that CtBP2 regulates expression of both the ErbB2 and 3 EGFR superfamily genes in PDAC cells. We therefore hypothesized that CtBP regulation of physiologic ErbB2/3 signaling contributes, in part, to PDAC growth and metastasis. Indeed, we observed that Ctbp2 KO cells exhibited near complete loss of ErbB2/3 expression and exhibited severely attenuated activation of phospho-Akt after neuregulin stimulation of ErbB2/3, and furthermore, human PDAC cells also demonstrated CtBP dependence of ErbB3 expression. Our results suggest that a subset of PDAC tumors are dependent on physiologic ErbB2/3 signaling and could be targeted by pharmacologic inhibitors of ErbB2 and/or ErbB3. Providing proof of concept, the ErbB2-targeted multikinase inhibitor lapatinib effectively killed the ErbB3 expressing CKP PDAC cells, while CKP CtBP2 KO cells, where ErbB3 expression was extinguished, were resistant to lapatinib. Taken together, our data suggests that ErB2/3 targeted therapeutics can effectively target a critical PDAC dependency on physiologic ErbB2/3 signaling which is the result of CtBP’s oncogenic transcriptional program that drives PDAC tumor progression.
Citation Format: Kranthi Kumar Chougoni, Haemin Park, Priyadarshan K. Damle, Martin Michael Dcona, Barbara Szomju, Mikhail G. Dozmorov, Michael Idowu, Steven R. Grossman. C-terminal Binding Protein (CtBP): a critical regulator of ErbB2/3 signaling in PDAC [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B073.
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Affiliation(s)
| | - Haemin Park
- 2Virginia Commonwealth University, Richmond, VA
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25
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Jacob S, Turner TH, Cai J, Floros KV, Yu AK, Coon CM, Khatri R, Alzubi MA, Jakubik CT, Bouck YM, Puchalapalli M, Shende M, Dozmorov MG, Boikos SA, Hu B, Harrell JC, Benes CH, Koblinski JE, Costa C, Faber AC. Genomic screening reveals ubiquitin-like modifier activating enzyme 1 as a potent and druggable target in c-MYC-high triple negative breast cancer models. PNAS Nexus 2022; 1:pgac232. [PMID: 36712364 PMCID: PMC9802478 DOI: 10.1093/pnasnexus/pgac232] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022]
Abstract
Triple negative breast cancer (TNBC) accounts for over 30% of all breast cancer (BC)-related deaths, despite accounting for only 10% to 15% of total BC cases. Targeted therapy development has largely stalled in TNBC, underlined by a lack of traditionally druggable addictions like receptor tyrosine kinases (RTKs). Here, through full genome CRISPR/Cas9 screening of TNBC models, we have uncovered the sensitivity of TNBCs to the depletion of the ubiquitin-like modifier activating enzyme 1 (UBA1). Targeting UBA1 with the first-in-class UBA1 inhibitor TAK-243 induced unresolvable endoplasmic reticulum (ER)-stress and activating transcription factor 4 (ATF4)-mediated upregulation of proapoptotic NOXA, leading to cell death. c-MYC expression correlates with TAK-243 sensitivity and cooperates with TAK-243 to induce a stress response and cell death. Importantly, there was an order of magnitude greater sensitivity of TNBC lines to TAK-243 compared to normal tissue-derived cells. In five patient derived xenograft models (PDXs) of TNBC, TAK-243 therapy led to tumor inhibition or frank tumor regression. Moreover, in an intracardiac metastatic model of TNBC, TAK-243 markedly reduced metastatic burden, indicating UBA1 is a potential new target in TNBC expressing high levels of c-MYC.
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Affiliation(s)
- Sheeba Jacob
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Tia H Turner
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA,Wright Center for Clinical and Translational Research, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Jinyang Cai
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Konstantinos V Floros
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ann K Yu
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Colin M Coon
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Rishabh Khatri
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mohammad A Alzubi
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA,Integrative Life Sciences Program, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Charles T Jakubik
- Center for Cancer Research, Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
| | - Ynes M Bouck
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Madhavi Puchalapalli
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Mayuri Shende
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Sosipatros A Boikos
- Hematology, Oncology and Palliative Care, School of Medicine and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Bin Hu
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA,Wright Center for Clinical and Translational Research, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA,Integrative Life Sciences Program, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Cyril H Benes
- Center for Cancer Research, Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
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Jaster AM, Younkin J, Cuddy T, de la Fuente Revenga M, Poklis JL, Dozmorov MG, González-Maeso J. Differences across sexes on head-twitch behavior and 5-HT 2A receptor signaling in C57BL/6J mice. Neurosci Lett 2022; 788:136836. [PMID: 35963476 PMCID: PMC10114867 DOI: 10.1016/j.neulet.2022.136836] [Citation(s) in RCA: 9] [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] [Received: 06/13/2022] [Revised: 07/27/2022] [Accepted: 08/08/2022] [Indexed: 01/26/2023]
Abstract
Psychedelics, also known as classical hallucinogens, affect processes related to perception, cognition and sensory processing mostly via the serotonin 5-HT2A receptor (5-HT2AR). This class of psychoactive substances, which includes lysergic acid diethylamide (LSD), psilocybin, mescaline and the substituted amphetamine 1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane (DOI), is receiving renewed attention for their potential therapeutic properties as it relates to psychiatric conditions such as depression and substance use disorders. Current studies focused on the potentially clinical effects of psychedelics on human subjects tend to exclude sex as a biological variable. Much of the understanding of psychedelic pharmacology is derived from rodent models, but most of this preclinical research has only focused on male mice. Here we tested the effects of DOI on head-twitch behavior (HTR) - a mouse behavioral proxy of human psychedelic potential - in male and female mice. DOI elicited more HTR in female as compared to male C57BL/6J mice, a sex-specific exacerbated behavior that was not observed in 129S6/SvEv animals. Volinanserin (or M100907) - a 5-HT2AR antagonist - fully prevented DOI-induced HTR in male and female C57BL/6J mice. Accumulation of inositol monophosphate (IP1) in the frontal cortex upon DOI administration showed no sex-related effect in C57BL/6J mice. However, the pharmacokinetic properties of DOI differed among sexes - brain and plasma concentrations of DOI were lower 30 and 60 min after drug administration in female as compared to male C57BL/6J mice. Together, these results suggest strain-dependent and sex-related differences in the behavioral and pharmacokinetic profiles of the 5-HT2AR agonist DOI in C57BL/6J mice, and support the importance of studying sex as a biological variable in preclinical psychedelic research.
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Affiliation(s)
- Alaina M Jaster
- Department of Physiology & Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States; Department of Pharmacology & Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States
| | - Jason Younkin
- Department of Physiology & Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States; Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States
| | - Travis Cuddy
- Department of Physiology & Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States
| | - Mario de la Fuente Revenga
- Department of Physiology & Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States; Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States
| | - Justin L Poklis
- Department of Pharmacology & Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States
| | - Javier González-Maeso
- Department of Physiology & Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, United States.
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Kurupi R, Floros KV, Jacob S, Chawla AT, Cai J, Hu B, Puchalapalli M, Coon CM, Khatri R, Crowther GS, Egan RK, Murchie E, Greninger P, Dalton KM, Ghotra MS, Boikos SA, Koblinski JE, Harada H, Sun Y, Morgan IM, Basu D, Dozmorov MG, Benes CH, Faber AC. Pharmacologic Inhibition of SHP2 Blocks Both PI3K and MEK Signaling in Low-epiregulin HNSCC via GAB1. Cancer Res Commun 2022; 2:1061-1074. [PMID: 36506869 PMCID: PMC9728803 DOI: 10.1158/2767-9764.crc-21-0137] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Preclinical and clinical studies have evidenced that effective targeted therapy treatment against receptor tyrosine kinases (RTKs) in different solid tumor paradigms is predicated on simultaneous inhibition of both the PI3K and MEK intracellular signaling pathways. Indeed, re-activation of either pathway results in resistance to these therapies. Recently, oncogenic phosphatase SHP2 inhibitors have been developed with some now reaching clinical trials. To expand on possible indications for SHP099, we screened over 800 cancer cell lines covering over 25 subsets of cancer. We found HNSCC was the most sensitive adult subtype of cancer to SHP099. We found that, in addition to the MEK pathway, SHP2 inhibition blocks the PI3K pathway in sensitive HNSCC, resulting in downregulation of mTORC signaling and anti-tumor effects across several HNSCC mouse models, including an HPV+ patient-derived xenograft (PDX). Importantly, we found low levels of the RTK ligand epiregulin identified HNSCCs that were sensitive to SHP2 inhibitor, and, adding exogenous epiregulin mitigated SHP099 efficacy. Mechanistically, epiregulin maintained SHP2-GAB1 complexes in the presence of SHP2 inhibition, preventing downregulation of the MEK and PI3K pathways. We demonstrate HNSCCs were highly dependent on GAB1 for their survival and knockdown of GAB1 is sufficient to block the ability of epiregulin to rescue MEK and PI3K signaling. These data connect the sensitivity of HNSCC to SHP2 inhibitors and to a broad reliance on GAB1-SHP2, revealing an important and druggable signaling axis. Overall, SHP2 inhibitors are being heavily developed and may have activity in HNSCCs, and in particular those with low levels of epiregulin.
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Affiliation(s)
- Richard Kurupi
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Konstantinos V Floros
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Sheeba Jacob
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Ayesha T Chawla
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Jinyang Cai
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Bin Hu
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23220
| | - Madhavi Puchalapalli
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23220
| | - Colin M Coon
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Rishabh Khatri
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Giovanna Stein Crowther
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Regina K Egan
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen Murchie
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Krista M Dalton
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Maninderjit S Ghotra
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | | | - Jennifer E Koblinski
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23220
| | - Hisashi Harada
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Yue Sun
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Iain M Morgan
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
| | - Devraj Basu
- Department of Otorhinolaryngology-Head and Neck Surgery, The University of Pennsylvania, Philadelphia, Pennsylvania, U.S.A
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University School of Medicine, Richmond, VA 23220.,Department of Pathology, Virginia Commonwealth University, Richmond, VA, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony C Faber
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia 23298
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Floros KV, Johnson-Berro MO, Kurupi R, Fairchild CK, Dalton K, Hu B, Puchalapalli M, Dozmorov MG, Koblinski JE, Olzmann JA, Cowart LA, Faber AC. Abstract 362: MYCN-amplified neuroblastoma is addicted to iron and vulnerable to ferroptosis. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-362] [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]
Abstract
Abstract
MYCN is amplified in 20% to 25% of neuroblastoma, and MYCN-amplified neuroblastoma contributes to a large percent of pediatric cancer-related deaths. Therapy improvements for this subtype of cancer are a high priority. Ferroptosis is an iron-dependent, oxidative form of cell death that is counteracted mainly by the production of Glutathione Peroxidase 4 (GPX4), a phospholipid hydroperoxidase that is produced through the glutathione pathway. The identification of cancers that may benefit from ferroptosis inducers are just emerging. Here we uncover a MYCN-dependent therapeutic vulnerability in neuroblastoma. Namely, amplified MYCN rewires the cell through expression of key receptors, ultimately enhancing iron influx through increased expression of the iron import transferrin receptor 1 (TFR1). Accumulating iron causes reactive oxygen species (ROS) production, and MYCN-amplified neuroblastomas show enhanced reliance on the system Xc- cystine/glutamate antiporter for ROS detoxification through increased transcription of this receptor. By performing metabolomics, we demonstrate that the transsulfuration pathway is also activated by MYCN. The increased activation of both pathways leads to cysteine accumulation that results in inhibition of lipid peroxidation. Utilizing drugs that target the main components of the glutathione and transsulfuration pathway we sensitize the MYCN neuroblastomas to ferroptotic cell death. These data provide novel insights into how MYCN alters the transcriptome in neuroblastoma to confer growth and survival advantages and simultaneously sheds light on the mechanism of action of ferroptosis inducers with potential application in other types of cancer.
Citation Format: Konstantinos V. Floros, Mia O. Johnson-Berro, Richard Kurupi, Carter K. Fairchild, Krista Dalton, Bin Hu, Madhavi Puchalapalli, Mikhail G. Dozmorov, Jennifer E. Koblinski, James A. Olzmann, Lauren A. Cowart, Anthony C. Faber. MYCN-amplified neuroblastoma is addicted to iron and vulnerable to ferroptosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 362.
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Manna D, Reghupaty SC, Mendoza RG, Camarena MD, Subler MA, Koblinski J, Martin R, Dozmorov MG, Das SK, Windle JJ, Fisher PB, Sarkar D. Abstract 920: Melanoma differentiation associated gene-9/syndecan binding protein (mda-9/sdcbp): A positive regulator of hepatocellular carcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-920] [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]
Abstract
Abstract
Background: Hepatocellular carcinoma (HCC) is a major clinical challenge because of increasing rates of incidence and mortality, and high resistance to standard radio- and chemotherapy. Identification of novel molecules regulating HCC facilitates development of targeted therapies having a lasting impact on HCC patient survival. The oncogene MDA-9/SDCBP promotes tumorigenesis and metastasis in many cancers. In The Cancer Genome Atlas (TCGA), 8% of HCC patients show amplification of MDA-9 gene. However, the role of MDA-9 in regulating HCC has not been well-studied.
Objective: To unravel the function of MDA-9 in HCC using a transgenic mouse model with hepatocyte-specific overexpression of MDA-9 (Alb/MDA-9).
Study design: Alb/MDA-9 mice were generated in B6/CBA background by using the mouse albumin promoter/enhancer element to drive human MDA-9 expression. N-nitrosodiethylamine (DEN)/phenobarbital (PB) was used for induction of HCC. Tumor immune profile was analyzed by Opal multiplex staining and flow cytometry. RNA-sequencing (RNA-seq) was performed to analyze MDA-9-mediated gene regulation.
Results: At 18 months of age, none of the WT mice developed liver tumor, while one male and one female Alb/MDA-9 mice (n = 11) developed one isolated tumor each, suggesting that MDA-9 may not be a strong driver oncogene, rather it might promote HCC progression once tumor is initiated. Indeed, at 32 weeks after induction of HCC using DEN/PB, tumor burden in the livers of Alb/MDA-9 mice was significantly higher compared to WT. These tumors showed loss of hepatic architecture and hepatocyte ballooning, features of HCC. Increased staining for the proliferation marker PCNA, HCC markers AFP and cytokeratin, and angiogenesis marker CD31 in tumor sections, and significantly increased levels of serum liver enzymes, AST and ALT, were observed in Alb/MDA-9 mice vs WT. Macrophage-mediated inflammation plays a central role in HCC. Compared to WT, Alb/MDA-9 tumors showed marked infiltration of CD11b+ myeloid cells, FoxP3+ T regulatory cells and F4/80+ macrophages. RNA-seq in naïve WT and Alb/MDA-9 hepatocytes identified activation of signaling pathways associated with invasion, angiogenesis and inflammation.
Conclusions: MDA-9 overexpression in hepatocytes promotes HCC by stimulating inflammation, angiogenesis and immune modulation. Studies are ongoing to obtain in-depth understanding of the molecular mechanisms by which MDA-9 exerts these pleiotropic effects. This study was supported by NIH/NCI Grant 1R01CA244993-01 (DS and PBF).
Citation Format: Debashri Manna, Saranya Chidambaranathan Reghupaty, Rachel Gredler Mendoza, Maria Del Camarena, Mark A. Subler, Jennifer Koblinski, Rebecca Martin, Mikhail G. Dozmorov, Swadesh K. Das, Jolene J. Windle, Paul B. Fisher, Devanand Sarkar. Melanoma differentiation associated gene-9/syndecan binding protein (mda-9/sdcbp): A positive regulator of hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 920.
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Rajesh Y, Reghupaty SC, Mendoza RG, Manna D, Banerjee I, Subler MA, Weldon K, Lai Z, Giashuddin S, Fisher PB, Sanyal AJ, Martin RK, Dozmorov MG, Windle JJ, Sarkar D. Dissecting the Balance Between Metabolic and Oncogenic Functions of Astrocyte-Elevated Gene-1/Metadherin. Hepatol Commun 2022; 6:561-575. [PMID: 34741448 PMCID: PMC8870024 DOI: 10.1002/hep4.1834] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/18/2021] [Accepted: 10/02/2021] [Indexed: 12/02/2022] Open
Abstract
Obesity is an enormous global health problem, and obesity-induced nonalcoholic steatohepatitis (NASH) is contributing to a rising incidence and mortality for hepatocellular carcinoma (HCC). Increase in de novo lipogenesis and decrease in fatty acid β-oxidation (FAO) underlie hepatic lipid accumulation in NASH. Astrocyte-elevated gene-1/metadherin (AEG-1) overexpression contributes to both NASH and HCC. AEG-1 harbors an LXXLL motif through which it blocks activation of peroxisome proliferator activated receptor α (PPARα), a key regulator of FAO. To better understand the role of LXXLL motif in mediating AEG-1 function, using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, we generated a mouse model (AEG-1-L24K/L25H) in which the LXXLL motif in AEG-1 was mutated to LXXKH. We observed increased activation of PPARα in AEG-1-L24K/L25H livers providing partial protection from high-fat diet-induced steatosis. Interestingly, even with equal gene dosage levels, compared with AEG-1-wild-type livers, AEG-1-L24K/L25H livers exhibited increase in levels of lipogenic enzymes, mitogenic activity and inflammation, which are attributes observed when AEG-1 is overexpressed. These findings indicate that while LXXLL motif favors steatotic activity of AEG-1, it keeps in check inflammatory and oncogenic functions, thus maintaining a homeostasis in AEG-1 function. AEG-1 is being increasingly appreciated as a viable target for ameliorating NASH and NASH-HCC, and as such, in-depth understanding of the functions and molecular attributes of this molecule is essential. Conclusion: The present study unravels the unique role of the LXXLL motif in mediating the balance between the metabolic and oncogenic functions of AEG-1.
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Affiliation(s)
- Yetirajam Rajesh
- Department of Human and Molecular GeneticsVirginia Commonwealth UniversityRichmondVAUSA
| | | | - Rachel G Mendoza
- Department of Human and Molecular GeneticsVirginia Commonwealth UniversityRichmondVAUSA
| | - Debashri Manna
- Department of Human and Molecular GeneticsVirginia Commonwealth UniversityRichmondVAUSA
| | - Indranil Banerjee
- Department of Human and Molecular GeneticsVirginia Commonwealth UniversityRichmondVAUSA
| | - Mark A Subler
- Department of Human and Molecular GeneticsVirginia Commonwealth UniversityRichmondVAUSA
| | - Korri Weldon
- Greehey Children's Cancer Research InstituteUniversity of Texas Health Science Center San AntonioSan AntonioTXUSA
| | - Zhao Lai
- Greehey Children's Cancer Research InstituteUniversity of Texas Health Science Center San AntonioSan AntonioTXUSA
| | - Shah Giashuddin
- Department of Pathology and Laboratory MedicineNew York Presbyterian Health System at Weill Cornell Medical CollegeNew YorkNYUSA
| | - Paul B Fisher
- Department of Human and Molecular GeneticsVirginia Commonwealth UniversityRichmondVAUSA.,Massey Cancer CenterVirginia Commonwealth UniversityRichmondVAUSA.,VCU Institute of Molecular MedicineVirginia Commonwealth UniversityRichmondVAUSA
| | - Arun J Sanyal
- Department of Internal MedicineVirginia Commonwealth UniversityRichmondVAUSA
| | - Rebecca K Martin
- Department of Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Mikhail G Dozmorov
- Department of BiostatisticsVirginia Commonwealth UniversityRichmondVAUSA
| | - Jolene J Windle
- Department of Human and Molecular GeneticsVirginia Commonwealth UniversityRichmondVAUSA.,Massey Cancer CenterVirginia Commonwealth UniversityRichmondVAUSA
| | - Devanand Sarkar
- Department of Human and Molecular GeneticsVirginia Commonwealth UniversityRichmondVAUSA.,Massey Cancer CenterVirginia Commonwealth UniversityRichmondVAUSA.,VCU Institute of Molecular MedicineVirginia Commonwealth UniversityRichmondVAUSA
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31
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Grible JM, Leftwich T, Olex AL, Duong AK, Hairr N, Rashid NS, Smith TM, Signaevskaia L, Boyd DC, Dozmorov MG, Harrell JC. Abstract P3-09-06: Targeting tumor subpopulations based on single-cell transcriptomics. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p3-09-06] [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]
Abstract
Abstract
Breast cancers that are hormone receptor negative, such that they do not express the estrogen receptor (ER), progesterone receptor (PR), or human epidermal growth factor receptor 2 (HER2), are known as triple-negative breast cancer (TNBC), and are predominantly of the basal-like subtype. These tumors aggressively metastasize, have limited effective therapeutic options, and are prevalent in patients of African descent. In these studies, we utilized a racially diverse set of 21 breast cancer patient-derived xenografts (PDXs) and 6 cell lines to identify new therapeutic combinations that may exhibit increased efficacy for patients based on ancestral heritage. Tumor subpopulation abundance was measured by single-cell RNA-sequencing (scRNAseq) a set of 13 PDXs, including some that had been subjected to long term carboplatin treatment or endocrine therapy in vivo. We identified two to four major cell types per PDX and sought to integrate this information with cytotoxic high throughput screens (HTS) of 516 clinically actionable agents. Among several interesting and overlapping findings from these multiscale models, BIRC5 (Survivin) was identified as a readily actionable target in the proliferative component of all TNBC models assayed. Analysis of public datasets found that BIRC5 expression in TNBC patient tumors was significantly correlated with reduced metastasis-free survival. In vitro and in vivo studies from our group and others found that YM155, which targets Survivin, was highly cytotoxic towards breast cancer cells. YM155 has been previously safely administered in Phase I/II clinical trials. To uncover putative dependency pathways that may be exploited to prevent acquired resistance to BIRC5 (Survivin) inhibition, we performed synergistic HTS assays whereby the efficacy of our 516 therapeutic library was assessed in the presence versus absence of YM155. Those drugs which were found to be more highly effective when given in combination with YM155 were then selected for ongoing in vitro and in vivo applications. Grant ID: 1R01CA246182-01A1 (NIH/NCI), CCR19608826 (Susan G. Komen Foundation), VCU School of Medicine VETAR, the Jeffress Trust, UL1TR002649 (CTSA/NCATS)
Citation Format: Jacqueline M Grible, Tess Leftwich, Amy L Olex, Alex K Duong, Nicole Hairr, Narmeen S Rashid, Timothy M Smith, Lia Signaevskaia, David C Boyd, Mikhail G Dozmorov, Joshua C Harrell. Targeting tumor subpopulations based on single-cell transcriptomics [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-09-06.
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Affiliation(s)
| | | | - Amy L Olex
- Virginia Commonwealth University, Richmond, VA
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32
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Floros KV, Chawla AT, Johnson-Berro MO, Khatri R, Stamatouli AM, Boikos SA, Dozmorov MG, Cowart LA, Faber AC. MYCN upregulates the transsulfuration pathway to suppress the ferroptotic vulnerability in MYCN-amplified neuroblastoma. Cell Stress 2022; 6:21-29. [PMID: 35174317 PMCID: PMC8802432 DOI: 10.15698/cst2022.02.264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Ferroptosis is an iron-dependent, oxidative form of cell death that is countered mainly by glutathione peroxidase 4 (GPX4) and the production of glutathione (GSH), which is formed from cysteine. The identification of the cancers that may benefit from pharmacological ferroptotic induction is just emerging. We recently demonstrated that inducing ferroptosis genetically or pharmacologically in MYCN-amplified neuroblastoma (NB) is a novel and effective way to kill these cells. MYCN increases iron metabolism and subsequent hydroxyl radicals through increased expression of the transferrin receptor 1 (TfR1) and low levels of the ferroportin receptor. To counter increased hydroxyl radicals, MYCN binds to the promoter of SLC3A2 (solute carrier family 3 member 2). SLC3A2 is a subunit of system Xc-, which is the cysteine-glutamate antiporter that exports glutamate and imports cystine. Cystine is converted to cysteine intracellularly. Here, we investigated other ways MYCN may increase cysteine levels. By performing metabolomics in a syngeneic NB cell line either expressing MYCN or GFP, we demonstrate that the transsulfuration pathway is activated by MYCN. Furthermore, we demonstrate that MYCN-amplified NB cell lines and tumors have higher levels of cystathionine beta-synthase (CBS), the rate-limiting enzyme in transsulfuration, which leads to higher levels of the thioether cystathionine (R-S-(2-amino-2-carboxyethyl)-l-homocysteine). In addition, MYCN-amplified NB tumors have high levels of methylthioadenosine phosphorylase (MTAP), an enzyme that helps salvage methionine following polyamine metabolism. MYCN directly binds to the promoter of MTAP. We propose that MYCN orchestrates both enhanced cystine uptake and enhanced activity of the transsulfuration pathway to counteract increased reactive oxygen species (ROS) from iron-induced Fenton reactions, ultimately contributing to a ferroptosis vulnerability in MYCN-amplified neuroblastoma.
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Affiliation(s)
- Konstantinos V. Floros
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Ayesha T. Chawla
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Mia O. Johnson-Berro
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Rishabh Khatri
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Angeliki M. Stamatouli
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Sosipatros A. Boikos
- Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University and Massey Cancer Center, Richmond, VA, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - L. Ashley Cowart
- Department of Biochemistry and Molecular Biology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
- Hunter Holmes McGuire Veteran’s Affairs Medical Center, Richmond, VA, USA
- * Corresponding Author: Dr. L. Ashley Cowart, VCU School of Medicine and Massey Cancer Center, Sanger Hall Room 2-016, 1101 E. Marshall St. Richmond, VA 23298, Phone: 804-827-7910; E-mail:
| | - Anthony C. Faber
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
- * Corresponding Author: Dr. L. Ashley Cowart, VCU School of Medicine and Massey Cancer Center, Sanger Hall Room 2-016, 1101 E. Marshall St. Richmond, VA 23298, Phone: 804-827-7910; E-mail:
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Green CD, Dozmorov MG, Spiegel S. Analysis of Liver Responses to Non-alcoholic Steatohepatitis by mRNA-Sequencing. Methods Mol Biol 2022; 2455:163-179. [PMID: 35212994 PMCID: PMC9210455 DOI: 10.1007/978-1-0716-2128-8_14] [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] [Indexed: 06/14/2023]
Abstract
Non-alcoholic steatohepatitis (NASH) is a major cause of chronic liver disease that can ultimately lead to cirrhosis and hepatocellular carcinoma. Although NASH is associated with excessive liver lipid accumulation, hepatocyte injury, inflammation, and fibrosis, its etiology remains incompletely understood. These can be characterized by determining transcriptional changes in specific genes previously found to be involved in these processes. As an inherently multifaceted disease, studies of NASH often require unbiased examination of major genes and pathways to identify the mechanisms involved in this disorder. To address this need, quantitative approaches such as mRNA-sequencing have been developed for the global assessment of gene expression. Here, we describe a protocol for bulk mRNA-sequencing that can be utilized for both liver samples and specific cell types isolated from the liver. This approach provides an important resource to further understand the molecular changes that occur during the development of NASH that can be utilized to design better therapeutic treatments.
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Affiliation(s)
- Christopher D Green
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, USA.
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Sarah Spiegel
- School of Medicine and Massey Cancer Center, Richmond, VA, USA
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Kronfol MM, Abudahab S, Dozmorov MG, Jahr FM, Halquist MS, McRae M, Wijesinghe DS, Price ET, Slattum PW, McClay JL. Histone acetylation at the sulfotransferase 1a1 gene is associated with its hepatic expression in normal aging. Pharmacogenet Genomics 2021; 31:207-214. [PMID: 34320608 PMCID: PMC8490294 DOI: 10.1097/fpc.0000000000000443] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Phase II drug metabolism is poorly studied in advanced age and older adults may exhibit significant variability in their expression of phase II enzymes. We hypothesized that age-related changes to epigenetic regulation of genes involved in phase II drug metabolism may contribute to these effects. METHODS We examined published epigenome-wide studies of human blood and identified the SULT1A1 and UGT1A6 genes as the top loci showing epigenetic changes with age. To assess possible functional alterations with age in the liver, we assayed DNA methylation (5mC) and histone acetylation changes around the mouse homologs Sult1a1 and Ugt1a6 in liver tissue from mice aged 4-32 months. RESULTS Our sample shows a significant loss of 5mC at Sult1a1 (β = -1.08, 95% CI [-1.8, -0.2], SE = 0.38, P = 0.011), mirroring the loss of 5mC with age observed in human blood DNA at the same locus. We also detected increased histone 3 lysine 9 acetylation (H3K9ac) with age at Sult1a1 (β = 0.11, 95% CI [0.002, 0.22], SE = 0.05, P = 0.04), but no change to histone 3 lysine 27 acetylation (H3K27ac). Sult1a1 gene expression is significantly positively associated with H3K9ac levels, accounting for 23% of the variation in expression. We did not detect any significant effects at Ugt1a6. CONCLUSIONS Sult1a1 expression is under epigenetic influence in normal aging and this influence is more pronounced for H3K9ac than DNA methylation or H3K27ac in this study. More generally, our findings support the relevance of epigenetics in regulating key drug-metabolizing pathways. In the future, epigenetic biomarkers could prove useful to inform dosing in older adults.
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Affiliation(s)
- Mohamad M. Kronfol
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Sara Abudahab
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Mikhail G. Dozmorov
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia
| | - Fay M. Jahr
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Matthew S. Halquist
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - MaryPeace McRae
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Dayanjan S. Wijesinghe
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Elvin T. Price
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
- Geriatric Pharmacotherapy Program, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
- Institute for Inclusion, Inquiry and Innovation: Health and Wellness in Aging Populations Core, Virginia Commonwealth University, Richmond, Virginia
| | - Patricia W. Slattum
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
- Geriatric Pharmacotherapy Program, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
- Institute for Inclusion, Inquiry and Innovation: Health and Wellness in Aging Populations Core, Virginia Commonwealth University, Richmond, Virginia
| | - Joseph L. McClay
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
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Hampton JD, Peterson EJ, Katner SJ, Turner TH, Alzubi MA, Harrell JC, Dozmorov MG, Turner JBM, Gigliotti PJ, Kraskauskiene V, Shende M, Idowu MO, Puchallapalli M, Hu B, Litovchick L, Katsuta E, Takabe K, Farrell NP, Koblinski JE. Exploitation of sulfated glycosaminoglycan status for precision medicine of Triplatin in triple-negative breast cancer. Mol Cancer Ther 2021; 21:271-281. [PMID: 34815360 DOI: 10.1158/1535-7163.mct-20-0969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 10/06/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022]
Abstract
Triple-negative breast cancer (TNBC) is a subtype of breast cancer lacking targetable biomarkers. TNBC is known to be most aggressive, and when metastatic is often drug resistant and uncurable. Biomarkers predicting response to therapy improve treatment decisions and allow personalized approaches for TNBC patients. This study explores sulfated glycosaminoglycan (sGAG) levels as a predictor of TNBC response to platinum therapy. sGAG levels were quantified in three distinct TNBC tumor models including cell line-derived, patient-derived xenograft (PDX) tumors, and isogenic models deficient in sGAG biosynthesis. The in vivo antitumor efficacy of Triplatin, a sGAG-directed platinum agent, was compared in these models to the clinical platinum agent, carboplatin. We determined that >40% of TNBC PDX tissue microarray samples have high levels of sGAGs. The in vivo accumulation of Triplatin in tumors as well as antitumor efficacy of Triplatin positively correlated with sGAG levels on tumor cells, whereas carboplatin followed the opposite trend. In carboplatin-resistant tumor models expressing high levels of sGAGs, Triplatin decreased primary tumor growth, reduced lung metastases, and inhibited metastatic growth in lungs, liver, and ovaries. sGAG levels served as a predictor of Triplatin sensitivity in TNBC. Triplatin may be particularly beneficial in treating patients with chemotherapy-resistant tumors who have evidence of residual disease after standard neoadjuvant chemotherapy. More effective neoadjuvant and adjuvant treatment will likely improve clinical outcome of TNBC.
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Affiliation(s)
| | | | - Samantha J Katner
- Biochemistry, Chemistry, and Geology, Minnesota State University, Mankato
| | | | | | | | | | | | | | | | | | - Michael O Idowu
- Pathology, Virginia Commonwealth University Massey Cancer Center
| | | | - Bin Hu
- Department of Pathology, Virginia Commonwealth University
| | | | | | - Kazuaki Takabe
- Surgical Oncology, Roswell Park Comprehensive Cancer Center
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Stilianoudakis SC, Marshall MA, Dozmorov MG. preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution. Bioinformatics 2021; 38:621-630. [PMID: 34741515 PMCID: PMC8756196 DOI: 10.1093/bioinformatics/btab743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/07/2021] [Accepted: 11/02/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Chromosome conformation capture technologies (Hi-C) revealed extensive DNA folding into discrete 3D domains, such as Topologically Associating Domains and chromatin loops. The correct binding of CTCF and cohesin at domain boundaries is integral in maintaining the proper structure and function of these 3D domains. 3D domains have been mapped at the resolutions of 1 kilobase and above. However, it has not been possible to define their boundaries at the resolution of boundary-forming proteins. RESULTS To predict domain boundaries at base-pair resolution, we developed preciseTAD, an optimized transfer learning framework trained on high-resolution genome annotation data. In contrast to current TAD/loop callers, preciseTAD-predicted boundaries are strongly supported by experimental evidence. Importantly, this approach can accurately delineate boundaries in cells without Hi-C data. preciseTAD provides a powerful framework to improve our understanding of how genomic regulators are shaping the 3D structure of the genome at base-pair resolution. AVAILABILITY AND IMPLEMENTATION preciseTAD is an R/Bioconductor package available at https://bioconductor.org/packages/preciseTAD/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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37
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Rashid NS, Hairr NS, Murray G, Olex AL, Leftwich TJ, Grible JM, Reed J, Dozmorov MG, Harrell JC. Identification of nuclear export inhibitor-based combination therapies in preclinical models of triple-negative breast cancer. Transl Oncol 2021; 14:101235. [PMID: 34628286 PMCID: PMC8512760 DOI: 10.1016/j.tranon.2021.101235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/30/2021] [Revised: 09/12/2021] [Accepted: 10/01/2021] [Indexed: 12/19/2022] Open
Abstract
High-throughput drug screening reveals promising therapeutic candidates for TNBC. KPT-330, an XPO1 inhibitor, and GSK2126458 exhibit synergism in preclinical models of TNBC. XPO1 is overexpressed in basal-like breast tumors. XPO1 expression is associated with PIK3CA, MTOR, and MKI67 expression at the single-cell level. XPO1 overexpression in basal-like patients is associated with greater rates of metastases.
An estimated 284,000 Americans will be diagnosed with breast cancer in 2021. Of these individuals, 15–20% have basal-like triple-negative breast cancer (TNBC), which is known to be highly metastatic. Chemotherapy is standard of care for TNBC patients, but chemoresistance is a common clinical problem. There is currently a lack of alternative, targeted treatment strategies for TNBC; this study sought to identify novel therapeutic combinations to treat basal-like TNBCs. For these studies, four human basal-like TNBC cell lines were utilized to determine the cytotoxicity profile of 1363 clinically-used drugs. Ten promising therapeutic candidates were identified, and synergism studies were performed in vitro. Two drug combinations that included KPT-330, an XPO1 inhibitor, were synergistic in all four cell lines. In vivo testing of four basal-like patient-derived xenografts (PDX) identified one combination, KPT-330 and GSK2126458 (a PI3K/mTOR inhibitor), that decreased tumor burden in mice significantly more than monotherapy with either single agent. Bulk and single-cell RNA-sequencing, immunohistochemistry, and analysis of published genomic datasets found that XPO1 was abundantly expressed in human basal-like TNBC cell lines, PDXs, and patient tumor samples. Within basal-like PDXs, XPO1 overexpression was associated with increased proliferation at the cellular level. Within patient datasets, XPO1 overexpression was correlated with greater rates of metastasis in patients with basal-like tumors. These studies identify a promising potential new combination therapy for patients with basal-like breast cancer.
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Affiliation(s)
- Narmeen S Rashid
- Department of Pathology, School of Medicine, Virginia Commonwealth University, 1101 East Marshall St, Office 4-007, P.O. Box 980662, Richmond, VA 23298-0662, USA; Department of Biology, University of Richmond, Richmond, VA USA
| | - Nicole S Hairr
- Department of Pathology, School of Medicine, Virginia Commonwealth University, 1101 East Marshall St, Office 4-007, P.O. Box 980662, Richmond, VA 23298-0662, USA
| | - Graeme Murray
- C. Kenneth and Diane Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA USA
| | - Amy L Olex
- C. Kenneth and Diane Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA USA
| | - Tess J Leftwich
- Department of Pathology, School of Medicine, Virginia Commonwealth University, 1101 East Marshall St, Office 4-007, P.O. Box 980662, Richmond, VA 23298-0662, USA
| | - Jacqueline M Grible
- Department of Pathology, School of Medicine, Virginia Commonwealth University, 1101 East Marshall St, Office 4-007, P.O. Box 980662, Richmond, VA 23298-0662, USA
| | - Jason Reed
- C. Kenneth and Diane Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA USA; Department of Physics, Virginia Commonwealth University, Richmond, VA USA
| | - Mikhail G Dozmorov
- Department of Pathology, School of Medicine, Virginia Commonwealth University, 1101 East Marshall St, Office 4-007, P.O. Box 980662, Richmond, VA 23298-0662, USA; Department of Biostatistics, Virginia Commonwealth University, Richmond, VA USA
| | - J Chuck Harrell
- Department of Pathology, School of Medicine, Virginia Commonwealth University, 1101 East Marshall St, Office 4-007, P.O. Box 980662, Richmond, VA 23298-0662, USA; C. Kenneth and Diane Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA USA.
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38
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Heisey DAR, Jacob S, Lochmann TL, Kurupi R, Ghotra MS, Calbert ML, Shende M, Maves YK, Koblinski JE, Dozmorov MG, Boikos SA, Benes CH, Faber AC. Pharmaceutical Interference of the EWS-FLI1-driven Transcriptome By Cotargeting H3K27ac and RNA Polymerase Activity in Ewing Sarcoma. Mol Cancer Ther 2021; 20:1868-1879. [PMID: 34315769 DOI: 10.1158/1535-7163.mct-20-0489] [Citation(s) in RCA: 6] [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: 06/12/2020] [Revised: 12/23/2020] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
The EWSR1-FLI1 t(11;22)(q24;q12) translocation is the hallmark genomic alteration of Ewing sarcoma, a malignancy of the bone and surrounding tissue, predominantly affecting children and adolescents. Although significant progress has been made for the treatment of localized disease, patients with metastasis or who relapse after chemotherapy have less than a 30% five-year survival rate. EWS-FLI1 is currently not clinically druggable, driving the need for more effective targeted therapies. Treatment with the H3K27 demethylase inhibitor, GSK-J4, leads to an increase in H3K27me and a decrease in H3K27ac, a significant event in Ewing sarcoma because H3K27ac associates strongly with EWS-FLI1 binding at enhancers and promoters and subsequent activity of EWS-FLI1 target genes. We were able to identify targets of EWS-FLI1 tumorigenesis directly inhibited by GSK-J4. GSK-J4 disruption of EWS-FLI1-driven transcription was toxic to Ewing sarcoma cells and slowed tumor growth in patient-derived xenografts (PDX) of Ewing sarcoma. Responses were markedly exacerbated by cotreatment with a disruptor of RNA polymerase II activity, the CDK7 inhibitor THZ1. This combination together suppressed EWS-FLI1 target genes and viability of ex vivo PDX Ewing sarcoma cells in a synergistic manner. In PDX models of Ewing Sarcoma, the combination shrank tumors. We present a new therapeutic strategy to treat Ewing sarcoma by decreasing H3K27ac at EWS-FLI1-driven transcripts, exacerbated by blocking phosphorylation of the C-terminal domain of RNA polymerase II to further hinder the EWS-FLI1-driven transcriptome.
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Affiliation(s)
- Daniel A R Heisey
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Sheeba Jacob
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Timothy L Lochmann
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Richard Kurupi
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Maninderjit S Ghotra
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Marissa L Calbert
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia
| | - Mayuri Shende
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | | | | | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
| | - Sosipatros A Boikos
- Hematology, Oncology and Palliative Care, School of Medicine and Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia.
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Anthony C Faber
- VCU Philips Institute, School of Dentistry and Massey Cancer Center; Richmond, Virginia.
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39
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Gurley JM, Gmyrek GB, McClellan ME, Hargis EA, Hauck SM, Dozmorov MG, Wren JD, Carr DJJ, Elliott MH. Neuroretinal-Derived Caveolin-1 Promotes Endotoxin-Induced Inflammation in the Murine Retina. Invest Ophthalmol Vis Sci 2021; 61:19. [PMID: 33079993 PMCID: PMC7585394 DOI: 10.1167/iovs.61.12.19] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose The immune-privileged environment and complex organization of retinal tissue support the retina's essential role in visual function, yet confound inquiries into cell-specific inflammatory effects that lead to dysfunction and degeneration. Caveolin-1 (Cav1) is an integral membrane protein expressed in several retinal cell types and is implicated in immune regulation. However, whether Cav1 promotes or inhibits inflammatory processes in the retina (as well as in other tissues) remains unclear. Previously, we showed that global-Cav1 depletion resulted in reduced retinal inflammatory cytokine production but paradoxically elevated retinal immune cell infiltration. We hypothesized that these disparate responses are the result of differential cell-specific Cav1 functions in the retina. Methods We used Cre/lox technology to deplete Cav1 specifically in the neural retinal (NR) compartment to clarify the role NR-specific Cav1 (NR-Cav1) in the retinal immune response to intravitreal inflammatory challenge induced by activation of Toll-like receptor-4 (TLR4). We used multiplex protein suspension array and flow cytometry to evaluate innate immune activation. Additionally, we used bioinformatics assessment of differentially expressed membrane-associated proteins to infer relationships between NR-Cav1 and immune response pathways. Results NR-Cav1 depletion, which primarily affects Müller glia Cav1 expression, significantly altered immune response pathway regulators, decreased retinal inflammatory cytokine production, and reduced retinal immune cell infiltration in response to LPS-stimulated inflammatory induction. Conclusions Cav1 expression in the NR compartment promotes the innate TLR4-mediated retinal tissue immune response. Additionally, we have identified novel potential immune modulators differentially expressed with NR-Cav1 depletion. This study further clarifies the role of NR-Cav1 in retinal inflammation.
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Affiliation(s)
- Jami M Gurley
- Department of Ophthalmology/Dean McGee Eye Institute, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, United States
| | - Grzegorz B Gmyrek
- Department of Ophthalmology/Dean McGee Eye Institute, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, United States
| | - Mark E McClellan
- Department of Ophthalmology/Dean McGee Eye Institute, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, United States
| | - Elizabeth A Hargis
- Department of Ophthalmology/Dean McGee Eye Institute, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, United States
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University (VCU), Richmond, Virginia, United States
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, United States
| | - Daniel J J Carr
- Department of Ophthalmology/Dean McGee Eye Institute, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, United States.,Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, United States
| | - Michael H Elliott
- Department of Ophthalmology/Dean McGee Eye Institute, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, United States
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40
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Fuemmeler BF, Dozmorov MG, Do EK, Zhang J(J, Grenier C, Huang Z, Maguire RL, Kollins SH, Hoyo C, Murphy SK. DNA Methylation in Babies Born to Nonsmoking Mothers Exposed to Secondhand Smoke during Pregnancy: An Epigenome-Wide Association Study. Environ Health Perspect 2021; 129:57010. [PMID: 34009014 PMCID: PMC8132610 DOI: 10.1289/ehp8099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/09/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Maternal smoking during pregnancy is related to altered DNA methylation in infant umbilical cord blood. The extent to which low levels of smoke exposure among nonsmoking pregnant women relates to offspring DNA methylation is unknown. OBJECTIVE This study sought to evaluate relationships between maternal prenatal plasma cotinine levels and DNA methylation in umbilical cord blood in newborns using the Infinium HumanMethylation 450K BeadChip. METHODS Participants from the Newborn Epigenetics Study cohort who reported not smoking during pregnancy had verified low levels of cotinine from maternal prenatal plasma (0 ng / mL to < 4 ng / mL ), and offspring epigenetic data from umbilical cord blood were included in this study (n = 79 ). Multivariable linear regression models were fit to the data, controlling for cell proportions, age, race, education, and parity. Estimates represent changes in response to any 1 -ng / mL unit increase in exposure. RESULTS Multivariable linear regression models yielded 29,049 CpGs that were differentially methylated in relation to increases in cotinine at a 5% false discovery rate. Top CpGs were within or near genes involved in neuronal functioning (PRKG1, DLGAP2, BSG), carcinogenesis (FHIT, HSPC157) and inflammation (AGER). Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggest cotinine was related to methylation of gene pathways controlling neuronal signaling, metabolic regulation, cell signaling and regulation, and cancer. Further, enhancers associated with transcription start sites were enriched in altered CpGs. Using an independent sample from the same study population (n = 115 ), bisulfite pyrosequencing was performed with infant cord blood DNA for two genes within our top 20 hits (AGER and PRKG1). Results from pyrosequencing replicated epigenome results for PRKG1 (cg17079497, estimate = - 1.09 , standard error ( SE ) = 0.45 , p = 0.018 ) but not for AGER (cg09199225; estimate = - 0.16 , SE = 0.21 , p = 0.44 ). DISCUSSION Secondhand smoke exposure among nonsmoking women may alter DNA methylation in regions involved in development, carcinogenesis, and neuronal functioning. These novel findings suggest that even low levels of smoke exposure during pregnancy may be sufficient to alter DNA methylation in distinct sites of mixed umbilical cord blood leukocytes in pathways that are known to be altered in cord blood from pregnant active smokers. https://doi.org/10.1289/EHP8099.
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Affiliation(s)
- Bernard F. Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, Virginia, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Elizabeth K. Do
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, Virginia, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Junfeng (Jim) Zhang
- Nicholas School of the Environment and Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Rachel L. Maguire
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biological Sciences, Center for Human Health and the Environment North Carolina State University, Raleigh, North Carolina, USA
| | - Scott H. Kollins
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment North Carolina State University, Raleigh, North Carolina, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
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41
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Dozmorov MG, Tyc KM, Sheffield NC, Boyd DC, Olex AL, Reed J, Harrell JC. Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines. Gigascience 2021; 10:6242846. [PMID: 33880552 DOI: 10.1093/gigascience/giab022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/18/2020] [Revised: 01/14/2021] [Accepted: 03/09/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Sequencing of patient-derived xenograft (PDX) mouse models allows investigation of the molecular mechanisms of human tumor samples engrafted in a mouse host. Thus, both human and mouse genetic material is sequenced. Several methods have been developed to remove mouse sequencing reads from RNA-seq or exome sequencing PDX data and improve the downstream signal. However, for more recent chromatin conformation capture technologies (Hi-C), the effect of mouse reads remains undefined. RESULTS We evaluated the effect of mouse read removal on the quality of Hi-C data using in silico created PDX Hi-C data with 10% and 30% mouse reads. Additionally, we generated 2 experimental PDX Hi-C datasets using different library preparation strategies. We evaluated 3 alignment strategies (Direct, Xenome, Combined) and 3 pipelines (Juicer, HiC-Pro, HiCExplorer) on Hi-C data quality. CONCLUSIONS Removal of mouse reads had little-to-no effect on data quality as compared with the results obtained with the Direct alignment strategy. Juicer extracted more valid chromatin interactions for Hi-C matrices, regardless of the mouse read removal strategy. However, the pipeline effect was minimal, while the library preparation strategy had the largest effect on all quality metrics. Together, our study presents comprehensive guidelines on PDX Hi-C data processing.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA.,Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Katarzyna M Tyc
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA.,Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - David C Boyd
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA.,Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jason Reed
- Virginia Commonwealth University, Massey Cancer Center, Richmond, VA, 23298, USA.,Department of Physics, Virginia Commonwealth University, Richmond, VA 23220, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA
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42
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Bekhbat M, Mukhara D, Dozmorov MG, Stansfield JC, Benusa SD, Hyer MM, Rowson SA, Kelly SD, Qin Z, Dupree JL, Tharp GK, Tansey MG, Neigh GN. Adolescent stress sensitizes the adult neuroimmune transcriptome and leads to sex-specific microglial and behavioral phenotypes. Neuropsychopharmacology 2021; 46:949-958. [PMID: 33558677 PMCID: PMC8115118 DOI: 10.1038/s41386-021-00970-2] [Citation(s) in RCA: 17] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 01/30/2023]
Abstract
Adolescent exposure to chronic stress, a risk factor for mood disorders in adulthood, sensitizes the neuroinflammatory response to a subsequent immune challenge. We previously showed that chronic adolescent stress (CAS) in rats led to distinct patterns of neuroimmune priming in adult male and female rats. However, sex differences in the neuroimmune consequences of CAS and their underlying mechanisms are not fully understood. Here we hypothesized that biological sex would dictate differential induction of inflammation-related transcriptomic pathways and immune cell involvement (microglia activation and leukocyte presence) in the hippocampus of male and female rats with a history of CAS. Adolescent rats underwent CAS (six restraint and six social defeat episodes during postnatal days 38-49), and behavioral assessments were conducted in adolescence and adulthood. Neuroimmune measures were obtained following vehicle or a systemic lipopolysaccharide (LPS) challenge in adulthood. CAS led to increased time in the corners of the open field in adolescence. In males, CAS also increased social avoidance. As adults, CAS rats displayed an exaggerated enrichment of the nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) pathway and chemokine induction following LPS challenge, and increased number of perivascular CD45+ cells in the hippocampus. However, CAS females, but not males, showed exaggerated glucocorticoid receptor (GR) pathway enrichment and increased microglial complexity. These results provide further insight to the mechanisms by which peripheral immune events may influence neuroimmune responses differentially among males and females and further demonstrate the importance of adolescent stress in shaping adult responses.
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Affiliation(s)
- Mandakh Bekhbat
- grid.189967.80000 0001 0941 6502Department of Physiology, Emory University, Atlanta, GA 30322 USA
| | - Deepika Mukhara
- grid.224260.00000 0004 0458 8737Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA 23298 USA
| | - Mikhail G. Dozmorov
- grid.417264.20000 0001 2194 2791Center for Clinical and Translational Research, Virginia Commonwealth University Medical Center, Richmond, VA 23298 USA
| | - John C. Stansfield
- grid.417264.20000 0001 2194 2791Center for Clinical and Translational Research, Virginia Commonwealth University Medical Center, Richmond, VA 23298 USA
| | - Savannah D. Benusa
- grid.224260.00000 0004 0458 8737Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA 23298 USA
| | - Molly M. Hyer
- grid.224260.00000 0004 0458 8737Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA 23298 USA
| | - Sydney A. Rowson
- grid.189967.80000 0001 0941 6502Department of Physiology, Emory University, Atlanta, GA 30322 USA
| | - Sean D. Kelly
- grid.189967.80000 0001 0941 6502Department of Physiology, Emory University, Atlanta, GA 30322 USA
| | - Zhaohui Qin
- grid.189967.80000 0001 0941 6502Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA USA
| | - Jeffrey L. Dupree
- grid.224260.00000 0004 0458 8737Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA 23298 USA
| | - Gregory K. Tharp
- grid.189967.80000 0001 0941 6502Division of Developmental & Cognitive Neuroscience, Yerkes National Primate Research Center, Atlanta, GA 30322 USA
| | - Malú G. Tansey
- grid.189967.80000 0001 0941 6502Department of Physiology, Emory University, Atlanta, GA 30322 USA
| | - Gretchen N. Neigh
- grid.189967.80000 0001 0941 6502Department of Physiology, Emory University, Atlanta, GA 30322 USA ,grid.224260.00000 0004 0458 8737Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA 23298 USA ,grid.189967.80000 0001 0941 6502Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA 30322 USA
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Iness AN, Rubinsak L, Meas SJ, Chaoul J, Sayeed S, Pillappa R, Temkin SM, Dozmorov MG, Litovchick L. Oncogenic B-Myb Is Associated With Deregulation of the DREAM-Mediated Cell Cycle Gene Expression Program in High Grade Serous Ovarian Carcinoma Clinical Tumor Samples. Front Oncol 2021; 11:637193. [PMID: 33747961 PMCID: PMC7969987 DOI: 10.3389/fonc.2021.637193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/02/2020] [Accepted: 02/08/2021] [Indexed: 12/21/2022] Open
Abstract
Cell cycle control drives cancer progression and treatment response in high grade serous ovarian carcinoma (HGSOC). MYBL2 (encoding B-Myb), an oncogene with prognostic significance in several cancers, is highly expressed in most HGSOC cases; however, the clinical significance of B-Myb in this disease has not been well-characterized. B-Myb is associated with cell proliferation through formation of the MMB (Myb and MuvB core) protein complex required for transcription of mitotic genes. High B-Myb expression disrupts the formation of another transcriptional cell cycle regulatory complex involving the MuvB core, DREAM (DP, RB-like, E2F, and MuvB), in human cell lines. DREAM coordinates cell cycle dependent gene expression by repressing over 800 cell cycle genes in G0/G1. Here, we take a bioinformatics approach to further evaluate the effect of B-Myb expression on DREAM target genes in HGSOC and validate our cellular model with clinical specimens. We show that MYBL2 is highly expressed in HGSOC and correlates with expression of DREAM and MMB target genes in both The Cancer Genome Atlas (TCGA) as well as independent analyses of HGSOC primary tumors (N = 52). High B-Myb expression was also associated with poor overall survival in the TCGA cohort and analysis by a DREAM target gene expression signature yielded a negative impact on survival. Together, our data support the conclusion that high expression of MYBL2 is associated with deregulation of DREAM/MMB-mediated cell cycle gene expression programs in HGSOC and may serve as a prognostic factor independent of its cell cycle role. This provides rationale for further, larger scale studies aimed to determine the clinical predictive value of the B-Myb gene expression signature for treatment response as well as patient outcomes.
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Affiliation(s)
- Audra N Iness
- Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Lisa Rubinsak
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, United States
| | - Steven J Meas
- School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Jessica Chaoul
- School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Sadia Sayeed
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States.,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Raghavendra Pillappa
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States
| | - Sarah M Temkin
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, United States
| | - Mikhail G Dozmorov
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States.,Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, United States.,Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States
| | - Larisa Litovchick
- Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States.,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
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44
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James CD, Saini S, Sesay F, Ko K, Felthousen-Rusbasan J, Iness AN, Nulton T, Windle B, Dozmorov MG, Morgan IM, Litovchick L. Restoring the DREAM Complex Inhibits the Proliferation of High-Risk HPV Positive Human Cells. Cancers (Basel) 2021; 13:cancers13030489. [PMID: 33513914 PMCID: PMC7866234 DOI: 10.3390/cancers13030489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Human papillomaviruses are responsible for around 5% of all cancers, and to date there are no anti-viral therapeutics available for treating these cancers. In this report we demonstrate that in HPV positive cells the transcriptional repressor DREAM complex is disrupted by E7 proteins, with a resulting increase in expression of DREAM target genes. Expression of a mutant DREAM component, LIN52 S20C, competes with E7 and partially rescues DREAM complex formation. This restoration attenuates the growth of HPV positive cells, including HPV positive cervical cancer cell lines. We propose that restoration of the DREAM complex in HPV positive cancers is a novel therapeutic approach that could be adapted to aid in the treatment of these cancers. Abstract High-risk (HR) human papillomaviruses are known causative agents in 5% of human cancers including cervical, ano-genital and head and neck carcinomas. In part, HR-HPV causes cancer by targeting host-cell tumor suppressors including retinoblastoma protein (pRb) and RB-like proteins p107 and p130. HR-HPV E7 uses a LxCxE motif to bind RB proteins, impairing their ability to control cell-cycle dependent transcription. E7 disrupts DREAM (Dimerization partner, RB-like, E2F and MuvB), a transcriptional repressor complex that can include p130 or p107, but not pRb, which regulates genes required for cell cycle progression. However, it is not known whether disruption of DREAM plays a significant role in HPV-driven tumorigenesis. In the DREAM complex, LIN52 is an adaptor that binds directly to p130 via an E7-like LxSxE motif. Replacement of the LxSxE sequence in LIN52 with LxCxE (LIN52-S20C) increases p130 binding and partially restores DREAM assembly in HPV-positive keratinocytes and human cervical cancer cells, inhibiting proliferation. Our findings demonstrate that disruption of the DREAM complex by E7 is an important process promoting cellular proliferation by HR-HPV. Restoration of the DREAM complex in HR-HPV positive cells may therefore have therapeutic benefits in HR-HPV positive cancers.
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Affiliation(s)
- Claire D. James
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
| | - Siddharth Saini
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
| | - Fatmata Sesay
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
| | - Kevin Ko
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
| | - Jessica Felthousen-Rusbasan
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
| | - Audra N. Iness
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
| | - Tara Nulton
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
| | - Brad Windle
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
- Massey Cancer Center, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA;
- Department of Pathology, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
| | - Iain M. Morgan
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (C.D.J.); (K.K.); (T.N.); (B.W.)
- Massey Cancer Center, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
- Correspondence: (I.M.M.); (L.L.)
| | - Larisa Litovchick
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA; (S.S.); (F.S.); (J.F.-R.); (A.N.I.)
- Massey Cancer Center, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
- Correspondence: (I.M.M.); (L.L.)
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Floros KV, Cai J, Jacob S, Kurupi R, Fairchild CK, Shende M, Coon CM, Powell KM, Belvin BR, Hu B, Puchalapalli M, Ramamoorthy S, Swift K, Lewis JP, Dozmorov MG, Glod J, Koblinski JE, Boikos SA, Faber AC. MYCN-Amplified Neuroblastoma Is Addicted to Iron and Vulnerable to Inhibition of the System Xc-/Glutathione Axis. Cancer Res 2021; 81:1896-1908. [PMID: 33483374 DOI: 10.1158/0008-5472.can-20-1641] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 12/02/2020] [Accepted: 01/13/2021] [Indexed: 11/16/2022]
Abstract
MYCN is amplified in 20% to 25% of neuroblastoma, and MYCN-amplified neuroblastoma contributes to a large percent of pediatric cancer-related deaths. Therapy improvements for this subtype of cancer are a high priority. Here we uncover a MYCN-dependent therapeutic vulnerability in neuroblastoma. Namely, amplified MYCN rewires the cell through expression of key receptors, ultimately enhancing iron influx through increased expression of the iron import transferrin receptor 1. Accumulating iron causes reactive oxygen species (ROS) production, and MYCN-amplified neuroblastomas show enhanced reliance on the system Xc- cystine/glutamate antiporter for ROS detoxification through increased transcription of this receptor. This dependence creates a marked vulnerability to targeting the system Xc-/glutathione (GSH) pathway with ferroptosis inducers. This reliance can be exploited through therapy with FDA-approved rheumatoid arthritis drugs sulfasalazine (SAS) and auranofin: in MYCN-amplified, patient-derived xenograft models, both therapies blocked growth and induced ferroptosis. SAS and auranofin activity was largely mitigated by the ferroptosis inhibitor ferrostatin-1, antioxidants like N-acetyl-L-cysteine, or by the iron scavenger deferoxamine (DFO). DFO reduced auranofin-induced ROS, further linking increased iron capture in MYCN-amplified neuroblastoma to a therapeutic vulnerability to ROS-inducing drugs. These data uncover an oncogene vulnerability to ferroptosis caused by increased iron accumulation and subsequent reliance on the system Xc-/GSH pathway. SIGNIFICANCE: This study shows how MYCN increases intracellular iron levels and subsequent GSH pathway activity and demonstrates the antitumor activity of FDA-approved SAS and auranofin in patient-derived xenograft models of MYCN-amplified neuroblastoma.
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Affiliation(s)
- Konstantinos V Floros
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia
| | - JinYang Cai
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia
| | - Sheeba Jacob
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia
| | - Richard Kurupi
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia
| | - Carter K Fairchild
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia
| | - Mayuri Shende
- Department of Pathology, Virginia Commonwealth University and Massey Cancer Center, Richmond, Virginia
| | - Colin M Coon
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia
| | - Krista M Powell
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia
| | - Benjamin R Belvin
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia
- Department of Biochemistry, Virginia Commonwealth University, Richmond, Virginia
| | - Bin Hu
- Department of Pathology, Virginia Commonwealth University and Massey Cancer Center, Richmond, Virginia
| | - Madhavi Puchalapalli
- Department of Pathology, Virginia Commonwealth University and Massey Cancer Center, Richmond, Virginia
| | - Sivapriya Ramamoorthy
- Discovery and Translational Sciences, Metabolon Inc., Research Triangle Park, North Carolina
| | - Kimberly Swift
- Discovery and Translational Sciences, Metabolon Inc., Research Triangle Park, North Carolina
| | - Janina P Lewis
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia
- Department of Biochemistry, Virginia Commonwealth University, Richmond, Virginia
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
| | - John Glod
- National Cancer Institute Pediatric Oncology Branch, Bethesda, Maryland
| | - Jennifer E Koblinski
- Department of Pathology, Virginia Commonwealth University and Massey Cancer Center, Richmond, Virginia
| | - Sosipatros A Boikos
- Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University and Massey Cancer Center, Richmond, Virginia
| | - Anthony C Faber
- School of Dentistry, VCU Philips Institute and Massey Cancer Center, Richmond, Virginia.
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46
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Cresswell KG, Stansfield JC, Dozmorov MG. Correction to: SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering. BMC Bioinformatics 2020; 21:373. [PMID: 32854628 PMCID: PMC7453525 DOI: 10.1186/s12859-020-03710-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Clark NM, Martinez LM, Murdock S, deLigio JT, Olex AL, Effi C, Dozmorov MG, Bos PD. Regulatory T Cells Support Breast Cancer Progression by Opposing IFN-γ-Dependent Functional Reprogramming of Myeloid Cells. Cell Rep 2020; 33:108482. [PMID: 33296659 DOI: 10.1016/j.celrep.2020.108482] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 12/11/2019] [Revised: 06/30/2020] [Accepted: 11/13/2020] [Indexed: 12/21/2022] Open
Abstract
Regulatory T (Treg) cell infiltration of solid tumors often correlates with poor prognosis, but their tumor-suppressive function lacks mechanistic understanding. Through a combination of transgenic mice, cell fate mapping, adoptive transfer, and co-injection strategies, we demonstrate that Treg cell ablation-dependent anti-tumor effects in murine breast cancer require intratumoral recruitment of CCR2+ inflammatory monocytes, which primarily differentiate into tumor-associated macrophages (TAMs), and lead to reprogramming of their function in an IFN-γ-dependent manner. Furthermore, transcriptomic signatures from murine TAMs in Treg cell-ablated conditions correlate with increased overall survival in human breast cancer. Our studies highlight the strong myeloid dependency of breast cancer and provide the basis for the development of therapeutic strategies based on manipulation of the IFN-γ signaling pathway in monocytes.
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Affiliation(s)
- Nicholas M Clark
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; Integrative Life Sciences Graduate Program, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Leandro M Martinez
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Steven Murdock
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - James T deLigio
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Comfort Effi
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA; Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Paula D Bos
- Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
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48
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Dozmorov MG, Cresswell KG, Bacanu SA, Craver C, Reimers M, Kendler KS. A method for estimating coherence of molecular mechanisms in major human disease and traits. BMC Bioinformatics 2020; 21:473. [PMID: 33087046 PMCID: PMC7579960 DOI: 10.1186/s12859-020-03821-x] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/15/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Phenotypes such as height and intelligence, are thought to be a product of the collective effects of multiple phenotype-associated genes and interactions among their protein products. High/low degree of interactions is suggestive of coherent/random molecular mechanisms, respectively. Comparing the degree of interactions may help to better understand the coherence of phenotype-specific molecular mechanisms and the potential for therapeutic intervention. However, direct comparison of the degree of interactions is difficult due to different sizes and configurations of phenotype-associated gene networks. METHODS We introduce a metric for measuring coherence of molecular-interaction networks as a slope of internal versus external distributions of the degree of interactions. The internal degree distribution is defined by interaction counts within a phenotype-specific gene network, while the external degree distribution counts interactions with other genes in the whole protein-protein interaction (PPI) network. We present a novel method for normalizing the coherence estimates, making them directly comparable. RESULTS Using STRING and BioGrid PPI databases, we compared the coherence of 116 phenotype-associated gene sets from GWAScatalog against size-matched KEGG pathways (the reference for high coherence) and random networks (the lower limit of coherence). We observed a range of coherence estimates for each category of phenotypes. Metabolic traits and diseases were the most coherent, while psychiatric disorders and intelligence-related traits were the least coherent. We demonstrate that coherence and modularity measures capture distinct network properties. CONCLUSIONS We present a general-purpose method for estimating and comparing the coherence of molecular-interaction gene networks that accounts for the network size and shape differences. Our results highlight gaps in our current knowledge of genetics and molecular mechanisms of complex phenotypes and suggest priorities for future GWASs.
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Affiliation(s)
- Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA USA
| | - Kellen G. Cresswell
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavior Genetics and the Department of Psychiatry, Virginia Commonwealth University, Richmond, VA USA
| | - Carl Craver
- Philosophy-Neuroscience-Psychology Program, Washington University in St. Louis, St. Louis, MO USA
| | - Mark Reimers
- Department Physiology, Michigan State University, East Lansing, MI USA
- Department Biomedical Engineering, Michigan State University, East Lansing, MI USA
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavior Genetics and the Department of Psychiatry, Virginia Commonwealth University, Richmond, VA USA
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49
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Cresswell KG, Stansfield JC, Dozmorov MG. SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering. BMC Bioinformatics 2020; 21:319. [PMID: 32689928 PMCID: PMC7372752 DOI: 10.1186/s12859-020-03652-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 12/19/2019] [Accepted: 07/10/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The three-dimensional (3D) structure of the genome plays a crucial role in gene expression regulation. Chromatin conformation capture technologies (Hi-C) have revealed that the genome is organized in a hierarchy of topologically associated domains (TADs), sub-TADs, and chromatin loops. Identifying such hierarchical structures is a critical step in understanding genome regulation. Existing tools for TAD calling are frequently sensitive to biases in Hi-C data, depend on tunable parameters, and are computationally inefficient. METHODS To address these challenges, we developed a novel sliding window-based spectral clustering framework that uses gaps between consecutive eigenvectors for TAD boundary identification. RESULTS Our method, implemented in an R package, SpectralTAD, detects hierarchical, biologically relevant TADs, has automatic parameter selection, is robust to sequencing depth, resolution, and sparsity of Hi-C data. SpectralTAD outperforms four state-of-the-art TAD callers in simulated and experimental settings. We demonstrate that TAD boundaries shared among multiple levels of the TAD hierarchy were more enriched in classical boundary marks and more conserved across cell lines and tissues. In contrast, boundaries of TADs that cannot be split into sub-TADs showed less enrichment and conservation, suggesting their more dynamic role in genome regulation. CONCLUSION SpectralTAD is available on Bioconductor, http://bioconductor.org/packages/SpectralTAD/ .
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Affiliation(s)
- Kellen G Cresswell
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - John C Stansfield
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA.
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50
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Joachims ML, Leehan KM, Dozmorov MG, Georgescu C, Pan Z, Lawrence C, Marlin MC, Macwana S, Rasmussen A, Radfar L, Lewis DM, Stone DU, Grundahl K, Scofield RH, Lessard CJ, Wren JD, Thompson LF, Guthridge JM, Sivils KL, Moore JS, Farris AD. Sjögren's Syndrome Minor Salivary Gland CD4 + Memory T Cells Associate with Glandular Disease Features and have a Germinal Center T Follicular Helper Transcriptional Profile. J Clin Med 2020; 9:jcm9072164. [PMID: 32650575 PMCID: PMC7408878 DOI: 10.3390/jcm9072164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/25/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Abstract
To assess the types of salivary gland (SG) T cells contributing to Sjögren's syndrome (SS), we evaluated SG T cell subtypes for association with disease features and compared the SG CD4+ memory T cell transcriptomes of subjects with either primary SS (pSS) or non-SS sicca (nSS). SG biopsies were evaluated for proportions and absolute numbers of CD4+ and CD8+ T cells. SG memory CD4+ T cells were evaluated for gene expression by microarray. Differentially-expressed genes were identified, and gene set enrichment and pathways analyses were performed. CD4+CD45RA- T cells were increased in pSS compared to nSS subjects (33.2% vs. 22.2%, p < 0.0001), while CD8+CD45RA- T cells were decreased (38.5% vs. 46.0%, p = 0.0014). SG fibrosis positively correlated with numbers of memory T cells. Proportions of SG CD4+CD45RA- T cells correlated with focus score (r = 0.43, p < 0.0001), corneal damage (r = 0.43, p < 0.0001), and serum Ro antibodies (r = 0.40, p < 0.0001). Differentially-expressed genes in CD4+CD45RA- cells indicated a T follicular helper (Tfh) profile, increased homing and increased cellular interactions. Predicted upstream drivers of the Tfh signature included TCR, TNF, TGF-β1, IL-4, and IL-21. In conclusion, the proportions and numbers of SG memory CD4+ T cells associate with key SS features, consistent with a central role in disease pathogenesis.
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Affiliation(s)
- Michelle L. Joachims
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Kerry M. Leehan
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Mikhail G. Dozmorov
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Constantin Georgescu
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Zijian Pan
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Christina Lawrence
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - M. Caleb Marlin
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Susan Macwana
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Astrid Rasmussen
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Lida Radfar
- College of Dentistry, University of Oklahoma Health Sciences Center, 1201 N Stonewall Avenue, Oklahoma City, OK 73117, USA; (L.R.); (D.M.L.)
| | - David M. Lewis
- College of Dentistry, University of Oklahoma Health Sciences Center, 1201 N Stonewall Avenue, Oklahoma City, OK 73117, USA; (L.R.); (D.M.L.)
| | - Donald U. Stone
- Dean McGee Eye Institute, University of Oklahoma Health Sciences Center, 608 Stanton L. Young Boulevard, Oklahoma City, OK 73104, USA;
| | - Kiely Grundahl
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - R. Hal Scofield
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
- Department of Medicine, University of Oklahoma Health Sciences Center, 1100 N Lindsay Avenue, Oklahoma City, OK 73104, USA
- Department of Veteran’s Affairs Medical Center, 931 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Christopher J. Lessard
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Jonathan D. Wren
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Linda F. Thompson
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Joel M. Guthridge
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Kathy L. Sivils
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - Jacen S. Moore
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
| | - A. Darise Farris
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Oklahoma City, OK 73104, USA; (M.L.J.); (K.M.L.); (M.G.D.); (C.G.); (Z.P.); (C.L.); (M.C.M.); (S.M.); (A.R.); (K.G.); (R.H.S.); (C.J.L.); (J.D.W.); (L.F.T.); (J.M.G.); (K.L.S.); (J.S.M.)
- Correspondence: ; Tel.: +1-405-271-7389
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