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Desai PB, Karve A, Zawit M, Arora P, Dave N, Awosika J, Li N, Fuhrman B, Medvedovic M, Sallans L, Kendler A, DasGupta B, Plas D, Curry R, Zuccarello M, Chaudhary R, Sengupta S, Wise-Draper TM. A Phase 0/1 Pharmacokinetic and Pharmacodynamics and Safety and Tolerability Study of Letrozole in Combination with Standard Therapy in Recurrent High-Grade Gliomas. Clin Cancer Res 2024:741887. [PMID: 38530160 DOI: 10.1158/1078-0432.ccr-23-3341] [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] [Received: 11/18/2023] [Revised: 01/24/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
PURPOSE High grade gliomas (HGGs) carry a poor prognosis, with glioblastoma accounting for almost 50% of primary brain malignancies in the elderly. Unfortunately, despite the use of multiple treatment modalities, the prognosis remains poor in this population. Our pre-clinical studies suggest that the presence of aromatase expression, encoded by CYP19A1, is significantly upregulated in HGGs. Remarkably, we find that letrozole (LTZ), an FDA approved aromatase inhibitor, has marked activity against HGGs. METHODS We conducted a phase 0/I single center clinical trial (NCT03122197) to assess the tumoral availability, pharmacokinetics (PK), safety and tolerability of LTZ in recurrent HGG patients. Planned dose cohorts included 2.5, 5, 10, 12.5, 15, 17.5 and 20 mg of LTZ administered daily pre- and post-surgery or biopsy. Tumor samples were assayed for LTZ content and relevant biomarkers. The Recommended Phase 2 Dose (R2PD) was determined as the dose that resulted in predicted steady state tumoral extracellular fluid (ECF) (Css,ecf) > 2 µM and did not result in ≥ 33% dose limiting adverse events (AEs) assessed using CTCAE v5.0. RESULTS Twenty-one patients were enrolled. Common LTZ related AEs included fatigue, nausea, musculoskeletal, anxiety and dysphoric mood. No DLTs were observed. The 15 mg dose achieved a Css,ecf of 3.6 +/- 0.59 µM. LTZ caused dose-dependent inhibition of estradiol synthesis and modulated DNA damage pathways in tumor tissues as evident using RNA-seq analysis. CONCLUSION Based on safety, brain tumoral PK, and mechanistic data, 15 mg daily is identified as the RP2D for future trials.
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Affiliation(s)
| | | | - Misam Zawit
- University of Cincinnati, Cincinnati, United States
| | | | - Nimita Dave
- University of Cincinnati, Boston, MA, United States
| | - Joy Awosika
- University of Cincinnati Cancer Center, Cincinnati, OH, United States
| | - Ningjing Li
- The University of Texas Health Science Center at Houston, Houston, Texas, United States
| | | | | | | | - Ady Kendler
- University of Cincinnati, Cincinnati, Ohio, United States
| | - Biplab DasGupta
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - David Plas
- University of Cincinnati, Cincinnati, OH, United States
| | | | | | | | - Soma Sengupta
- University of North Carolina Chapel Hill, Chapel Hill, United States
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Kimura E, Mongan M, Xiao B, Christianto A, Wang J, Carreira VS, Bolon B, Zhang X, Burns KA, Biesiada J, Medvedovic M, Puga A, Xia Y. MAP3K1 regulates female reproductive tract development. Dis Model Mech 2024; 17:dmm050669. [PMID: 38501211 PMCID: PMC10985838 DOI: 10.1242/dmm.050669] [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: 12/20/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
Mitogen-activated protein 3 kinase 1 (MAP3K1) has a plethora of cell type-specific functions not yet fully understood. Herein, we describe a role for MAP3K1 in female reproductive tract (FRT) development. MAP3K1 kinase domain-deficient female mice exhibited an imperforate vagina, labor failure and infertility. These defects corresponded with shunted Müllerian ducts (MDs), the embryonic precursors of FRT, that manifested as a contorted caudal vagina and abrogated vaginal-urogenital sinus fusion in neonates. The MAP3K1 kinase domain is required for optimal activation of the Jun-N-terminal kinase (JNK) and cell polarity in the MD epithelium, and for upregulation of WNT signaling in the mesenchyme surrounding the caudal MD. The MAP3K1-deficient epithelial cells and MD epithelium had reduced expression of WNT7B ligands. Correspondingly, conditioned media derived from MAP3K1-competent, but not -deficient, epithelial cells activated a TCF/Lef-luciferase reporter in fibroblasts. These observations indicate that MAP3K1 regulates MD caudal elongation and FRT development, in part through the induction of paracrine factors in the epithelium that trans-activate WNT signaling in the mesenchyme.
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Affiliation(s)
- Eiki Kimura
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Maureen Mongan
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Bo Xiao
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Antonius Christianto
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Jingjing Wang
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Vinicius S. Carreira
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Brad Bolon
- GEMpath Inc., Longmont, CO 80501-1846, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Katherine A. Burns
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Jacek Biesiada
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Alvaro Puga
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
| | - Ying Xia
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
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Bhattacharya D, Barille R, Toukam DK, Gawali VS, Kallay L, Ahmed T, Brown H, Rezvanian S, Karve A, Desai PB, Medvedovic M, Wang K, Ionascu D, Harun N, Wang C, Baschnagel AM, Kritzer JA, Cook JM, Pomeranz Krummel DA, Sengupta S. GABA(A) receptor activation drives GABARAP-Nix mediated autophagy to radiation-sensitize primary and brain-metastatic lung adenocarcinoma tumors. bioRxiv 2023:2023.11.29.569295. [PMID: 38076805 PMCID: PMC10705483 DOI: 10.1101/2023.11.29.569295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
In non-small cell lung cancer (NSCLC) treatment, targeted therapies benefit only a subset of NSCLC, while radiotherapy responses are not durable and toxicity limits therapy. We find that a GABA(A) receptor activator, AM-101, impairs viability and clonogenicity of NSCLC primary and brain metastatic cells. Employing an ex vivo 'chip', AM-101 is as efficacious as the chemotherapeutic docetaxel, which is used with radiotherapy for advanced-stage NSCLC. In vivo , AM-101 potentiates radiation, including conferring a survival benefit to mice bearing NSCLC intracranial tumors. GABA(A) receptor activation stimulates a selective-autophagic response via multimerization of GABA(A) Receptor-Associated Protein (GABARAP), stabilization of mitochondrial receptor Nix, and utilization of ubiquitin-binding protein p62. A targeted-peptide disrupting Nix binding to GABARAP inhibits AM-101 cytotoxicity. This supports a model of GABA(A) receptor activation driving a GABARAP-Nix multimerization axis triggering autophagy. In patients receiving radiotherapy, GABA(A) receptor activation may improve tumor control while allowing radiation dose de-intensification to reduce toxicity. Highlights Activating GABA(A) receptors intrinsic to lung primary and metastatic brain cancer cells triggers a cytotoxic response. GABA(A) receptor activation works as well as chemotherapeutic docetaxel in impairing lung cancer viability ex vivo . GABA(A) receptor activation increases survival of mice bearing lung metastatic brain tumors.A selective-autophagic response is stimulated by GABA(A) receptor activation that includes multimerization of GABARAP and Nix.Employing a new nanomolar affinity peptide that abrogates autophagosome formation inhibits cytotoxicity elicited by GABA(A) receptor activation.
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Ko CI, Biesiada J, Zablon HA, Zhang X, Medvedovic M, Puga A. The aryl hydrocarbon receptor directs the differentiation of murine progenitor blastomeres. Cell Biol Toxicol 2023; 39:1657-1676. [PMID: 36029422 PMCID: PMC10425484 DOI: 10.1007/s10565-022-09755-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/17/2022] [Indexed: 11/02/2022]
Abstract
Key regulatory decisions during cleavage divisions in mammalian embryogenesis determine the fate of preimplantation embryonic cells. Single-cell RNA sequencing of early-stage-2-cell, 4-cell, and 8-cell-blastomeres show that the aryl hydrocarbon receptor (AHR), traditionally considered as an environmental sensor, directs blastomere differentiation. Disruption of AHR functions in Ahr knockout embryos or in embryos from dams exposed to dioxin, the prototypic xenobiotic AHR agonist, significantly impairs blastocyst formation, causing repression and loss of transcriptional heterogeneity of OCT4 and CDX2 and incidence of nonspecific downregulation of pluripotency. Trajectory-the path of differentiation-and gene variability analyses further confirm that deregulation of OCT4 functions and changes of transcriptional heterogeneity resulting from disruption of AHR functions restrict the emergence of differentiating blastomeres in 4-cell embryos. It appears that AHR directs the differentiation of progenitor blastomeres and that disruption of preimplantation AHR functions may significantly perturb embryogenesis leading to long-lasting conditions at the heart of disease in offspring's adulthood.
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Affiliation(s)
- Chia-I Ko
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati, Cincinnati, OH, 45267, USA.
| | - Jacek Biesiada
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati, Cincinnati, OH, 45267, USA
- Center for Biostatistics, 160 Panzeca Way, Cincinnati, OH, 45267, USA
| | - Hesbon A Zablon
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati, Cincinnati, OH, 45267, USA
- Genomics, Epigenomics, and Sequencing Core, 160 Panzeca Way, Cincinnati, OH, 45267, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati, Cincinnati, OH, 45267, USA
- Center for Biostatistics, 160 Panzeca Way, Cincinnati, OH, 45267, USA
| | - Alvaro Puga
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati, Cincinnati, OH, 45267, USA
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Madhuravasal Krishnan J, Kong L, Karns R, Medvedovic M, Sherman KE, Blackard JT. The Synthetic Opioid Fentanyl Increases HIV Replication and Chemokine Co-Receptor Expression in Lymphocyte Cell Lines. Viruses 2023; 15:1027. [PMID: 37113007 PMCID: PMC10145664 DOI: 10.3390/v15041027] [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: 03/28/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND In the United States, the illicit use of synthetic opioids such as fentanyl has led to a serious public health crisis. Synthetic opioids are known to enhance viral replication and to suppress immunologic responses, but their effects on HIV pathogenesis remain unclear. Thus, we examined the impact of fentanyl on HIV-susceptible and HIV-infected cell types. METHODS TZM-bl and HIV-infected lymphocyte cells were incubated with fentanyl at varying concentrations. Expression levels of the CXCR4 and CCR5 chemokine receptors and HIV p24 antigen were quantified with ELISA. HIV proviral DNA was quantified using SYBR RT-PCR. Cell viability was detected with the MTT assay. RNAseq was performed to characterize cellular gene regulation in the presence of fentanyl. RESULTS Fentanyl enhanced expression of both chemokine receptor levels in a dose-dependent manner in HIV-susceptible and infected cell lines. Similarly, fentanyl induced viral expression in HIV-exposed TZM-bl cells and in HIV-infected lymphocyte cell lines. Multiple genes associated with apoptosis, antiviral/interferon response, chemokine signaling, and NFκB signaling were differentially regulated. CONCLUSIONS Synthetic opioid fentanyl impacts HIV replication and chemokine co-receptor expression. Increased virus levels suggest that opioid use may increase the likelihood of transmission and accelerate disease progression.
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Affiliation(s)
- Janani Madhuravasal Krishnan
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (J.M.K.)
| | - Ling Kong
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (J.M.K.)
| | - Rebekah Karns
- Digestive Health Center, Cincinnati Children’s Hospital, Cincinnati, OH 45229, USA
| | - Mario Medvedovic
- Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kenneth E. Sherman
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (J.M.K.)
- Center for Addiction Research, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jason T. Blackard
- Division of Digestive Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (J.M.K.)
- Center for Addiction Research, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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Kimura E, Mongan M, Xiao B, Wang J, Carreira VS, Bolon B, Zhang X, Burns KA, Biesiada J, Medvedovic M, Puga A, Xia Y. The Role of MAP3K1 in the Development of the Female Reproductive Tract. bioRxiv 2023. [PMID: 37131749 PMCID: PMC10153227 DOI: 10.1101/2023.04.20.537715] [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: 05/04/2023]
Abstract
Mitogen-Activated Protein 3 Kinase 1 (MAP3K1) is a dynamic signaling molecule with a plethora of cell-type specific functions, most of which are yet to be understood. Here we describe a role for MAP3K1 in the development of female reproductive tract (FRT). MAP3K1 kinase domain-deficient ( Map3k1 ΔKD ) females exhibit imperforate vagina, labor failure, and infertility. These defects correspond to a shunted Müllerian duct (MD), the principle precursor of the FRT, in embryos, while they manifest as a contorted caudal vagina with abrogated vaginal-urogenital sinus fusion in neonates. In epithelial cells, MAP3K1 acts through JNK and ERK to activate WNT, yet in vivo MAP3K1 is crucial for WNT activity in mesenchyme associated with the caudal MD. Expression of Wnt7b is high in wild type, but low in Map3k1 knockout MD epithelium and MAP3K1-deficient keratinocytes. Correspondingly, conditioned media derived from MAP3K1-competent epithelial cells activate TCF/Lef-luciferase reporter in fibroblasts, suggesting that MAP3K1-induced factors released from epithelial cells trans-activate WNT signaling in fibroblasts. Our results reveal a temporal-spatial and paracrine MAP3K1-WNT crosstalk contributing to MD caudal elongation and FRT development. Highlights MAP3K1 deficient female mice exhibit imperforate vagina and infertilityLoss of MAP3K1 kinase activity impedes Müllerian duct (MD) caudal elongation and fusion with urogenital sinus (UGS) in embryogenesisThe MAP3K1-MAPK pathway up-regulates WNT signaling in epithelial cellsMAP3K1 deficiency down-regulates Wnt7b expression in the MD epithelium and prevents WNT activity in mesenchyme of the caudal MD.
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7
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Verma R, Aggarwal P, Bischoff ME, Reigle J, Secic D, Wetzel C, VandenHeuvel K, Biesiada J, Ehmer B, Landero Figueroa JA, Plas DR, Medvedovic M, Meller J, Czyzyk-Krzeska MF. Macrotubule associated protein MAP1LC3C regulates lysosomal exocytosis and induces zinc reprogramming in renal cancer cells. J Biol Chem 2023; 299:104663. [PMID: 37003503 PMCID: PMC10173779 DOI: 10.1016/j.jbc.2023.104663] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Microtubule Associated Protein 1 Light Chain 3 Gamma (MAP1LC3C or LC3C) is a member of the microtubule associated family of proteins that are essential in the formation of autophagosomes and lysosomal degradation of cargo. LC3C has tumor suppressing activity and its expression is dependent on kidney cancer tumor suppressors, such as von Hippel-Lindau protein (VHL) and folliculin (FLCN). Recently We demonstrated that LC3C autophagy is regulated by noncanonical upstream regulatory complexes and targets for degradation postdivision midbody rings associated with cancer cells stemness. Here we show that loss of LC3C leads to peripheral positioning of the lysosomes and lysosomal exocytosis (LE). This process is independent of the autophagic activity of LC3C. Analysis of isogenic cells with low and high LE shows substantial transcriptomic reprogramming with altered expression of Zn-related genes and activity of Polycomb Repressor Complex 2 (PRC2), accompanied by a robust decrease in intracellular Zn. Additionally, metabolomic analysis revealed alterations in amino acid steady-state levels. Cells with augmented LE show increased tumor initiation properties and form aggressive tumors in xenograft models. Immunocytochemistry identified high levels of Lysosomal Associated Membrane Protein 1 (LAMP1) on the plasma membrane of cancer cells in human clear cell renal cell carcinoma (ccRCC) and reduced levels of Zn, suggesting that LE occurs in ccRCC, potentially contributing to the loss of Zn. These data indicate that the reprogramming of lysosomal localization and Zn metabolism with implication for epigenetic remodeling in a subpopulation of tumor propagating cancer cells is an important aspect of tumor suppressing activity of LC3C.
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Affiliation(s)
- Rita Verma
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Parul Aggarwal
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Megan E Bischoff
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - James Reigle
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Dina Secic
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Collin Wetzel
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Katherine VandenHeuvel
- Division of Pathology and Laboratory Medicine, Cincinnati Children Hospital Medical Center, Cincinnati, OH, USA
| | - Jacek Biesiada
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Birgit Ehmer
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Julio A Landero Figueroa
- Agilent Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati College of Arts and Science, Cincinnati, OH 45221, USA; Department of Pharmacology and System Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - David R Plas
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Mario Medvedovic
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jarek Meller
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Department of Electrical Engineering and Computer Science, University of Cincinnati College of Engineering and Applied Sciences, Cincinnati, OH 45221, USA; Department of Pharmacology and System Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Maria F Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Veteran Affairs Medical Center, Department of Veterans Affairs, Cincinnati, OH 45220, USA; Department of Pharmacology and System Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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8
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Galiveti CR, Kuhnell D, Biesiada J, Zhang X, Kelsey KT, Takiar V, Tang AL, Wise‐Draper TM, Medvedovic M, Kasper S, Langevin SM. Small extravesicular microRNA in head and neck squamous cell carcinoma and its potential as a liquid biopsy for early detection. Head Neck 2023; 45:212-224. [PMID: 36271833 PMCID: PMC9742186 DOI: 10.1002/hed.27231] [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: 05/12/2022] [Revised: 09/14/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The objective was to assess secretion of small extracellular vesicular microRNA (exo-miRNA) in head and neck squamous cell carcinoma (HNSCC) according to human papillomavirus (HPV) status, and determine the translational potential as a liquid biopsy for early detection. METHODS This study employed a combination of cell culture and case-control study design using archival pretreatment serum. Small extracellular vesicles (sEV) were isolated from conditioned culture media and human serum samples via differential ultracentrifugation. miRNA-sequencing was performed on each sEV isolate. RESULTS There were clear exo-miRNA profiles that distinguished HNSCC cell lines from nonpathologic oral epithelial control cells. While there was some overlap among profiles across all samples, there were apparent differences in exo-miRNA profiles according to HPV-status. Importantly, differential exo-miRNA profiles were also apparent in serum from early-stage HNSCC cases relative to cancer-free controls. CONCLUSIONS Our findings indicate that exo-miRNA are highly dysregulated in HNSCC and support the potential of exo-miRNA as biomarkers for HNSCC.
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Affiliation(s)
- Chenna R. Galiveti
- Division of Epidemiology, Department of Environmental & Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Damaris Kuhnell
- Division of Epidemiology, Department of Environmental & Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Jacek Biesiada
- Division of Biostatistics and Bioinformatics, Department of Environmental & Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Xiang Zhang
- Division of Environmental Genetics & Molecular Toxicology, Department of Environmental & Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Karl T. Kelsey
- Department of EpidemiologyBrown University School of Public HealthProvidenceRhode IslandUSA
- Department of Pathology & Laboratory Medicine, Alpert Medical SchoolBrown UniversityProvidenceRhode IslandUSA
| | - Vinita Takiar
- Department of Radiation OncologyUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
- Cincinnati VA Medical CenterCincinnatiOhioUSA
- University of Cincinnati Cancer CenterCincinnatiOhioUSA
| | - Alice L. Tang
- University of Cincinnati Cancer CenterCincinnatiOhioUSA
- Department of OtolaryngologyUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Trisha M. Wise‐Draper
- University of Cincinnati Cancer CenterCincinnatiOhioUSA
- Division of Hematology & Oncology, Department of Internal MedicineUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental & Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
- University of Cincinnati Cancer CenterCincinnatiOhioUSA
| | - Susan Kasper
- Division of Environmental Genetics & Molecular Toxicology, Department of Environmental & Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
- University of Cincinnati Cancer CenterCincinnatiOhioUSA
| | - Scott M. Langevin
- Division of Epidemiology, Department of Environmental & Public Health SciencesUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
- University of Cincinnati Cancer CenterCincinnatiOhioUSA
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Behrmann C, Sarma P, Ennis K, Wetzel C, Clark N, Vallabhapurapu S, Reigle J, Meller J, Qi X, Medvedovic M, Sengupta S, Dasgupta B, Plas D. CSIG-16. EXPLOITING A NEGATIVE FEEDBACK LOOP LINKING S6 KINASES AND AXL TO REDUCE PYRIMIDINE BIOSYNTHESIS IN PTEN-DEFICIENT GLIOBLASTOMA. Neuro Oncol 2022. [PMCID: PMC9661136 DOI: 10.1093/neuonc/noac209.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
PTEN inactivation triggers oncodependent signal transduction through the PI3K/Akt signal transduction pathway in glioblastoma (GBM). Targeting the PI3K/Akt pathway to counteract PTEN loss in GBM has been impeded by negative feedback signal transduction networks mediated by the downstream protein kinases S6K1 and S6K2. Here, we show that the receptor tyrosine kinase AXL is a major target of that S6K feedback signaling and that combined inactivation of just S6K1 and AXL is an effective therapeutic strategy for treatment of PTEN-deficient GBM. Chemical-genetic interaction studies in gliomasphere and GBM cell lines revealed critical and independent roles for S6K1 and S6K2 in mediating GBM growth in PTEN-deficient cells. Interestingly, S6K2 exerted a dual role in signal transduction: it sustained GBM growth while also exerting negative feedback control on the upstream receptor tyrosine kinase AXL. Genetic inactivation of S6K2 sensitized PTEN-deficient GBMs to AXL inhibition, indicating that derepressed AXL is required for compensatory signaling upon targeting of the PI3K/Akt pathway. Combining the AXL inhibitor BMS-777607 with S6K1 inhibitor LY-2584702 also prevented compensatory AXL signaling and triggered cytotoxic responses selectively in the PTEN-deficient condition. Importantly, combination inhibition of AXL and S6K1 reduced pyrimidine biosynthesis, a known vulnerability of PTEN-deficient GBMs. The oral inhibitors of S6K1 and AXL were found to be brain-penetrant and effective in reducing GBM growth in several mouse models. These results establish that targeting of AXL can circumvent S6 Kinase dependent feedback to reduce pyrimidine biosynthesis and trigger cytotoxic responses in PTEN-deficient GBMs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati , Cincinnati, OH , USA
| | - Soma Sengupta
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine , Cincinnati, OH , USA
| | | | - David Plas
- University of Cincinnati , Cincinnati , USA
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10
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Bhattacharya D, Barille R, Toukam DK, Gawali V, Kallay L, Ahmed T, Cook J, Karve A, Desai P, Medvedovic M, Krummel DP, Sengupta S. RBIO-02. ACTIVATION OF GABAA RECEPTORS WITH A NON-TOXIC, BRAIN PENETRANT SMALL MOLECULE SENSITIZES LUNG ADENOCARCINOMA PRIMARY AND BRAIN METASTATIC TUMOR CELLS TO RADIATION VIA AUTOPHAGY INDUCTION. Neuro Oncol 2022. [PMCID: PMC9661141 DOI: 10.1093/neuonc/noac209.954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Most advanced-stage non-small cell lung cancer (NSCLC) patients have brain metastases that render a dismal prognosis. Treatment of metastatic brain lesions from NSCLC and other tumor types include radiation as part of a multimodal treatment regimen. Challenges in the application of radiotherapy include overcoming radiation resistance and reducing associated co-morbidities. Non-toxic therapeutics capable of sensitizing tumors to radiation are needed to improve survival and mitigate radiation side-effects. Many CNS and solid systemic tumors express ligand-gated ion channels, which may contribute to tumor growth. Leveraging ion channels is therefore a potential way of diminishing the spread of cancer. We find that NSCLC and its brain metastases express subunits of the type-A GABA-gated chloride channel or GABAA receptor. Importantly, patient-derived NSCLC cells have functional GABAA receptors. We identified a brain penetrant, small molecule activator of GABAA receptors (AMLAL-101), which alone impairs the viability of both primary NSCLC cells and brain metastatic cells. In addition, AMLAL-101 combined with radiation is a highly potent inducer of NSCLC cell death and clonogenic arrest. Using a human ex vivo model of NSCLC-on-chip, we assessed the efficacy and toxicity of AMLAL-101 relative to Docetaxel, an antimicrotubular agent used in treating advanced NSCLC. AMLAL-101 is as potent as Docetaxel but does not exhibit its toxic side effects. AMLAL-101 also potentiates radiation in vivo, significantly reducing lung adenocarcinoma xenograft tumor growth in mice, equivalent to docetaxel plus radiation. Mechanistically, AMLAL-101 activates GABAA receptors in NSCLC and synergizes with radiation by inducing an autophagic response that includes: (i) stabilization of Beclin-1, BNIP3L/NIX, and GABARAP; (ii) ATG7 upregulation; and (iii) utilization of ubiquitin-binding protein p62. Activating GABAA receptors in NSCLC and other tumor types may improve radiation efficacy and mitigate its toxic side effects in treating brain metastases.
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Affiliation(s)
- Debanjan Bhattacharya
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine , Cincinnati, OH , USA
| | - Riccardo Barille
- Department of Biomedical Engineering, University of Cincinnati , Cincinnati , USA
| | - Donatien Kamdem Toukam
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine , Cincinnati, OH , USA
| | - Vaibhavkumar Gawali
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine , Cleveland, OH , USA
| | - Laura Kallay
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine , Cincinnati, OH , USA
| | - Taukir Ahmed
- Department of Chemistry, University of Wisconsin-Milwaukee , Milwaukee, WI , USA
| | - James Cook
- Department of Chemistry, University of Wisconsin-Milwaukee , Milwaukee , USA
| | - Aniruddha Karve
- Division of Pharmaceutical Sciences, University of Cincinnati College of Pharmacy , Cincinnati, OH , USA
| | - Pankaj Desai
- Division of Pharmaceutical Sciences, University of Cincinnati College of Pharmacy , Cincinnati, OH , USA
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati , Cincinnati, OH , USA
| | - Daniel Pomeranz Krummel
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine and Amlal Pharmaceuticals Inc , Cincinnati, OH , USA
| | - Soma Sengupta
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine , Cincinnati, OH , USA
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11
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Crist M, Yaniv B, Palackdharry S, Lehn MA, Medvedovic M, Stone T, Gulati S, Karivedu V, Borchers M, Fuhrman B, Crago A, Curry J, Martinez-Outschoorn U, Takiar V, Wise-Draper TM. Metformin increases natural killer cell functions in head and neck squamous cell carcinoma through CXCL1 inhibition. J Immunother Cancer 2022; 10:jitc-2022-005632. [PMID: 36328378 PMCID: PMC9639146 DOI: 10.1136/jitc-2022-005632] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Metformin slows tumor growth and progression in vitro, and in combination with chemoradiotherapy, resulted in high overall survival in patients with head and neck cancer squamous cell carcinoma (HNSCC) in our phase 1 clinical trial (NCT02325401). Metformin is also postulated to activate an antitumor immune response. Here, we investigate immunologic effects of metformin on natural killer (NK) and natural killer T cells, including results from two phase I open-label studies in patients with HNSCC treated with metformin (NCT02325401, NCT02083692). METHODS Peripheral blood was collected before and after metformin treatment or from newly diagnosed patients with HNSCC. Peripheral immune cell phenotypes were evaluated using flow cytometry, cytokine expression by ELISA and/or IsoLight, and NK cell-mediated cytotoxicity was determined with a flow-based NK cell cytotoxicity assay (NKCA). Patient tumor immune infiltration before and after metformin treatment was analyzed with immunofluorescence. NK cells were treated with either vehicle or metformin and analyzed by RNA sequencing (RNA-seq). NK cells were then treated with inhibitors of significant pathways determined by RNA-seq and analyzed by NKCA, ELISA, and western blot analyses. RESULTS Increased peripheral NK cell activated populations were observed in patients treated with metformin. NK cell tumor infiltration was enhanced in patients with HNSCC treated with metformin preoperatively. Metformin increased antitumorigenic cytokines ex vivo, including significant increases in perforin. Metformin increased HNSCC NK cell cytotoxicity and inhibited the CXCL1 pathway while stimulating the STAT1 pathway within HNSCC NK cells. Exogenous CXCL1 prevented metformin-enhanced NK cell-mediated cytotoxicity. Metformin-mediated NK cell cytotoxicity was found to be AMP-activated protein kinase independent, but dependent on both mechanistic target of rapamycin and pSTAT1. CONCLUSIONS Our data identifies a new role for metformin-mediated immune antitumorigenic function through NK cell-mediated cytotoxicity and downregulation of CXCL1 in HNSCC. These findings will inform future immunomodulating therapies in HNSCC.
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Affiliation(s)
- McKenzie Crist
- Department of Internal Medicine; Division of Hematology/Oncology, University of Cincinnati, Cincinnati, Ohio, USA
| | - Benyamin Yaniv
- Department of Medicine, UMass Memorial Medical Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Sarah Palackdharry
- University of Cincinnati Cancer Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Maria A Lehn
- Department of Internal Medicine; Division of Hematology/Oncology, University of Cincinnati, Cincinnati, Ohio, USA,Division of Radiation Oncology, University of Cincinnati, Cincinnati, Ohio, USA
| | - Mario Medvedovic
- Department of Environmental Health; Division of Biostatistics and Bioinformatics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Timothy Stone
- Department of Environmental Health; Division of Biostatistics and Bioinformatics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Shuchi Gulati
- Department of Internal Medicine; Division of Hematology/Oncology, University of Cincinnati, Cincinnati, Ohio, USA
| | - Vidhya Karivedu
- Department of Medical Oncology Head and Neck Oncology, The Ohio State University, Columbus, Ohio, USA
| | - Michael Borchers
- Division of Biostatistics and Bioinformatics, University of Cincinnati, Cincinnati, Ohio, USA,Cincinnati VA Medical Center, Cincinnati, Ohio, USA
| | - Bethany Fuhrman
- University of Cincinnati Cancer Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Audrey Crago
- University of Cincinnati Cancer Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Joseph Curry
- Department of Otolaryngology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | | | - Vinita Takiar
- Division of Radiation Oncology, University of Cincinnati, Cincinnati, Ohio, USA,Cincinnati VA Medical Center, Cincinnati, Ohio, USA
| | - Trisha M Wise-Draper
- Department of Internal Medicine; Division of Hematology/Oncology, University of Cincinnati, Cincinnati, Ohio, USA
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12
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Pounders J, Hill EJ, Hooper D, Zhang X, Biesiada J, Kuhnell D, Greenland HL, Esfandiari L, Timmerman E, Foster F, Wang C, Walsh KB, Shatz R, Woo D, Medvedovic M, Langevin S, Sawyer RP. MicroRNA expression within neuronal-derived small extracellular vesicles in frontotemporal degeneration. Medicine (Baltimore) 2022; 101:e30854. [PMID: 36221381 PMCID: PMC9542922 DOI: 10.1097/md.0000000000030854] [Citation(s) in RCA: 4] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA that are powerful regulators of gene expression and can affect the expression of hundreds of genes. miRNAs can be packed in small extracellular vesicles (SEV) and released into the extracellular space by neurons and microglia to act locally as well as pass through the blood-brain barrier and act systemically. We sought to understand the differences in neuronal SEV miRNA expression between frontotemporal dementia (FTD), Alzheimer's disease (AD), and healthy aging. Plasma was obtained from FTD, AD, and healthy aging participants that were matched based on age, sex, and race/ethnicity. Additionally, a subset of participants also provided paired cerebrospinal fluid samples to compare neuronal SEV miRNAs in plasma and cerebrospinal fluid. Neuronal SEV were isolated using differential ultracentrifugation and antibody conjugated Dynabeads® for the neuronal surface marker, L1CAM. RNA sequencing was performed. 12 FTD, 11 with AD, and 10 healthy aging participants were enrolled in the study. In FTD, SEV miRNA-181c was downregulated compared to healthy controls. In AD, miRNA-122 and miRNA-3591 were downregulated compared to those in healthy controls and FTD. Using an FDR <0.2, only miRNA-21-5p was found to have increased expression in the cerebrospinal fluid compared to plasma in a group of AD and FTD participants. SEV miRNA-181c is significantly downregulated in FTD compared to healthy controls and may mediate its effects through microglial-directed neuroinflammation and interaction with TAR DNA-binding protein 43 (TDP-43) based on pathway analysis. Additionally, the FOXO and Hippo pathways may be important mediators of FTD, based on pathway analysis. Lastly, because only one SEV miRNA was differentially expressed between the plasma and cerebrospinal fluid in paired samples, plasma represents an appropriate biofluid for studying neuronal SEV miRNA.
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Affiliation(s)
- Jonathan Pounders
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH, USA
| | - Emily J. Hill
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH, USA
| | - Destiny Hooper
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH, USA
| | - Xiang Zhang
- University of Cincinnati College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA
| | - Jacek Biesiada
- University of Cincinnati College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA
| | - Damaris Kuhnell
- University of Cincinnati College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA
| | - Hannah L. Greenland
- University of Cincinnati College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA
| | - Leyla Esfandiari
- University of Cincinnati, Department of Electrical Engineering and Computer Science, Cincinnati, OH, USA
- University of Cincinnati, Department of Biomedical Engineering, Cincinnati, OH, USA
| | - Emerlee Timmerman
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH, USA
| | - Forrest Foster
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH, USA
| | - Chenran Wang
- University of Cincinnati College of Medicine, Department of Cancer Biology, Cincinnati, OH, USA
| | - Kyle B. Walsh
- University of Cincinnati College of Medicine, Department of Emergency Medicine, Cincinnati, OH, USA
| | - Rhonna Shatz
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH, USA
| | - Daniel Woo
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH, USA
| | - Mario Medvedovic
- University of Cincinnati College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA
| | - Scott Langevin
- University of Cincinnati College of Medicine, Department of Environmental and Public Health Sciences, Cincinnati, OH, USA
| | - Russell P. Sawyer
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH, USA
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13
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Pilarczyk M, Fazel-Najafabadi M, Kouril M, Shamsaei B, Vasiliauskas J, Niu W, Mahi N, Zhang L, Clark NA, Ren Y, White S, Karim R, Xu H, Biesiada J, Bennett MF, Davidson SE, Reichard JF, Roberts K, Stathias V, Koleti A, Vidovic D, Clarke DJB, Schürer SC, Ma'ayan A, Meller J, Medvedovic M. Connecting omics signatures and revealing biological mechanisms with iLINCS. Nat Commun 2022; 13:4678. [PMID: 35945222 PMCID: PMC9362980 DOI: 10.1038/s41467-022-32205-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 11/18/2020] [Accepted: 07/21/2022] [Indexed: 11/21/2022] Open
Abstract
There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Here we present iLINCS ( http://ilincs.org ), an integrative web-based platform for analysis of omics data and signatures of cellular perturbations. The platform facilitates mining and re-analysis of the large collection of omics datasets (>34,000), pre-computed signatures (>200,000), and their connections, as well as the analysis of user-submitted omics signatures of diseases and cellular perturbations. iLINCS analysis workflows integrate vast omics data resources and a range of analytics and interactive visualization tools into a comprehensive platform for analysis of omics signatures. iLINCS user-friendly interfaces enable execution of sophisticated analyses of omics signatures, mechanism of action analysis, and signature-driven drug repositioning. We illustrate the utility of iLINCS with three use cases involving analysis of cancer proteogenomic signatures, COVID 19 transcriptomic signatures and mTOR signaling.
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Affiliation(s)
- Marcin Pilarczyk
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Mehdi Fazel-Najafabadi
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Michal Kouril
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Behrouz Shamsaei
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Juozas Vasiliauskas
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Wen Niu
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Naim Mahi
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Lixia Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Nicholas A Clark
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Yan Ren
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Shana White
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Rashid Karim
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Huan Xu
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Jacek Biesiada
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Mark F Bennett
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Sarah E Davidson
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - John F Reichard
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
| | - Kurt Roberts
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Vasileios Stathias
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL 33136, USA
| | - Amar Koleti
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL 33136, USA
| | - Dusica Vidovic
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL 33136, USA
| | - Daniel J B Clarke
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stephan C Schürer
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine and Center for Computational Science, University of Miami, Miami, FL 33136, USA
| | - Avi Ma'ayan
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jarek Meller
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA
- LINCS Data Coordination and Integration Center (DCIC), New York, USA
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA.
- LINCS Data Coordination and Integration Center (DCIC), Cincinnati, USA.
- LINCS Data Coordination and Integration Center (DCIC), New York, USA.
- LINCS Data Coordination and Integration Center (DCIC), Miami, USA.
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14
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Evangelista JE, Clarke DJB, Xie Z, Lachmann A, Jeon M, Chen K, Jagodnik KM, Jenkins SL, Kuleshov MV, Wojciechowicz ML, Schürer SC, Medvedovic M, Ma'ayan A. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res 2022; 50:W697-W709. [PMID: 35524556 PMCID: PMC9252724 DOI: 10.1093/nar/gkac328] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 02/22/2022] [Revised: 04/04/2022] [Accepted: 04/20/2022] [Indexed: 12/13/2022] Open
Abstract
Millions of transcriptome samples were generated by the Library of Integrated Network-based Cellular Signatures (LINCS) program. When these data are processed into searchable signatures along with signatures extracted from Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus (GEO), connections between drugs, genes, pathways and diseases can be illuminated. SigCom LINCS is a webserver that serves over a million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. SigCom LINCS is built with Signature Commons, a cloud-agnostic skeleton Data Commons with a focus on serving searchable signatures. SigCom LINCS provides a rapid signature similarity search for mimickers and reversers given sets of up and down genes, a gene set, a single gene, or any search term. Additionally, users of SigCom LINCS can perform a metadata search to find and analyze subsets of signatures and find information about genes and drugs. SigCom LINCS is findable, accessible, interoperable, and reusable (FAIR) with metadata linked to standard ontologies and vocabularies. In addition, all the data and signatures within SigCom LINCS are available via a well-documented API. In summary, SigCom LINCS, available at https://maayanlab.cloud/sigcom-lincs, is a rich webserver resource for accelerating drug and target discovery in systems pharmacology.
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Affiliation(s)
- John Erol Evangelista
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Zhuorui Xie
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Minji Jeon
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Kerwin Chen
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Kathleen M Jagodnik
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Sherry L Jenkins
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Maxim V Kuleshov
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Megan L Wojciechowicz
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Stephan C Schürer
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Mario Medvedovic
- Department of Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
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15
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Wise-Draper TM, Gulati S, Palackdharry S, Hinrichs BH, Worden FP, Old MO, Dunlap NE, Kaczmar JM, Patil Y, Riaz MK, Tang A, Mark J, Zender C, Gillenwater AM, Bell D, Kurtzweil N, Mathews M, Allen CL, Mierzwa ML, Casper K, Jandarov R, Medvedovic M, Lee JJ, Harun N, Takiar V, Gillison M. Phase II Clinical Trial of Neoadjuvant and Adjuvant Pembrolizumab in Resectable Local-Regionally Advanced Head and Neck Squamous Cell Carcinoma. Clin Cancer Res 2022; 28:1345-1352. [PMID: 35338369 PMCID: PMC8976828 DOI: 10.1158/1078-0432.ccr-21-3351] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [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: 09/17/2021] [Revised: 12/07/2021] [Accepted: 01/27/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Patients with resected, local-regionally advanced, head and neck squamous cell carcinoma (HNSCC) have a one-year disease-free survival (DFS) rate of 65%-69% despite adjuvant (chemo)radiotherapy. Neoadjuvant PD-1 immune-checkpoint blockade (ICB) has demonstrated clinical activity, but biomarkers of response and effect on survival remain unclear. PATIENTS AND METHODS Eligible patients had resectable squamous cell carcinoma of the oral cavity, larynx, hypopharynx, or oropharynx (p16-negative) and clinical stage T3-T4 and/or two or more nodal metastases or clinical extracapsular nodal extension (ENE). Patients received neoadjuvant pembrolizumab 200 mg 1-3 weeks prior to surgery, were stratified by absence (intermediate-risk) or presence (high-risk) of positive margins and/or ENE, and received adjuvant radiotherapy (60-66 Gy) and concurrent pembrolizumab (every 3 weeks × 6 doses). Patients with high-risk HNSCC also received weekly, concurrent cisplatin (40 mg/m2). Primary outcome was one-year DFS. Secondary endpoints were one-year overall survival (OS) and pathologic response (PR). Safety was evaluated with CTCAE v5.0. RESULTS From February 2016 to October 2020, 92 patients enrolled. The median age was 59 years (range, 27-80), 30% were female, 86% had stage T3-T4, and 69% had ≥N2. At a median follow-up of 28 months, one-year DFS was 97% (95% CI, 71%-90%) in the intermediate-risk group and 66% (95% CI, 55%-84%) in the high-risk group. Patients with a PR had significantly improved one-year DFS relative to patients without response (93% vs. 72%, hazard ratio 0.29; 95% CI, 11%-77%). No new safety signals were identified. CONCLUSIONS Neoadjuvant and adjuvant pembrolizumab increased one-year DFS rate in intermediate-risk, but not high-risk, HNSCC relative to historical control. PR to neoadjuvant ICB is a promising surrogate for DFS.
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Affiliation(s)
| | - Shuchi Gulati
- Division of Hematology/Oncology, University of Cincinnati, Cincinnati, Ohio
| | | | | | | | - Matthew O Old
- Department of Otolaryngology, Ohio State University, Columbus, Ohio
| | - Neal E Dunlap
- Department of Radiation Oncology, University of Louisville, Louisville, Kentucky
| | - John M Kaczmar
- Division of Hematology/Oncology, Medical University of South Carolina, Charleston, South Carolina
| | - Yash Patil
- Department of Otolaryngology, University of Cincinnati, Cincinnati, Ohio
| | | | - Alice Tang
- Department of Otolaryngology, University of Cincinnati, Cincinnati, Ohio
| | - Jonathan Mark
- Department of Otolaryngology, Eastern Virginia Medical School, Norfolk, Virginia
| | - Chad Zender
- Department of Otolaryngology, University of Cincinnati, Cincinnati, Ohio
| | | | - Diana Bell
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Maria Mathews
- University of Cincinnati Cancer Center, Cincinnati, Ohio
| | - Casey L Allen
- University of Cincinnati Cancer Center, Cincinnati, Ohio
| | - Michelle L Mierzwa
- Department of Radiation Oncology, University of Michigan Cancer Center, Ann Arbor, Michigan
| | - Keith Casper
- Department of Otolaryngology, University of Michigan Cancer Center, Ann Arbor, Michigan
| | - Roman Jandarov
- Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio
| | - J Jack Lee
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nusrat Harun
- Division of Biostatistics and Epidemiology, Cincinnati Children's Medical Center, Cincinnati, Ohio
| | - Vinita Takiar
- Department of Radiation Oncology, University of Cincinnati and Cincinnati VA Medical Center, Cincinnati, Ohio
| | - Maura Gillison
- The University of Texas MD Anderson Cancer Center, Houston, Texas
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16
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Sawyer RP, Hill EJ, Yokoyama J, Medvedovic M, Ren Y, Zhang X, Choubey D, Shatz RS, Miller B, Woo D. Differences in peripheral immune system gene expression in frontotemporal degeneration. Medicine (Baltimore) 2022; 101:e28645. [PMID: 35060553 PMCID: PMC8772666 DOI: 10.1097/md.0000000000028645] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/28/2021] [Accepted: 01/03/2022] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT The peripheral immune system has a key pathophysiologic role in Frontotemporal degeneration (FTD). We sought a comprehensive transcriptome-wide evaluation of gene expression alterations unique to the peripheral immune system in FTD compared to healthy controls and amyotrophic lateral sclerosis.Nineteen subjects with FTD with 19 matched healthy controls and 9 subjects with amyotrophic lateral sclerosis underwent isolation of peripheral blood mononuclear cells (PBMCs) which then underwent bulk ribonucleic acid sequencing.There was increased expression in genes associated with CD19+ B-cells, CD4+ T-cells, and CD8+ T-cells in FTD participants compared to healthy controls. In contrast, there was decreased expression in CD33+ myeloid cells, CD14+ monocytes, BDCA4+ dendritic cells, and CD56+ natural killer cells in FTD and healthy controls. Additionally, there was decreased expression is seen in associated with 2 molecular processes: autophagy with phagosomes and lysosomes, and protein processing/export. Significantly downregulated in PBMCs of FTD subjects were genes involved in antigen processing and presentation as well as lysosomal lumen formation compared to healthy control PBMCs.Our findings that the immune signature based on gene expression in PBMCs of FTD participants favors adaptive immune cells compared to innate immune cells. And decreased expression in genes associated with phagosomes and lysosomes in PBMCs of FTD participants compared to healthy controls.
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Affiliation(s)
- Russell P. Sawyer
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH
| | - Emily J. Hill
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH
| | - Jennifer Yokoyama
- Department of Neurology, University of California, San Francisco, CA
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH
| | - Yan Ren
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH
| | - Xiang Zhang
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH
| | - Divaker Choubey
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH
| | - Rhonna S. Shatz
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH
| | - Bruce Miller
- Department of Neurology, University of California, San Francisco, CA
| | - Daniel Woo
- University of Cincinnati College of Medicine, Department of Neurology and Rehabilitation Medicine, Cincinnati, OH
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17
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Reigle J, Secic D, Biesiada J, Wetzel C, Shamsaei B, Chu J, Zang Y, Zhang X, Talbot NJ, Bischoff ME, Zhang Y, Thakar CV, Gaitonde K, Sidana A, Bui H, Cunningham JT, Zhang Q, Schmidt LS, Linehan WM, Medvedovic M, Plas DR, Figueroa JAL, Meller J, Czyzyk-Krzeska MF. Tobacco smoking induces metabolic reprogramming of renal cell carcinoma. J Clin Invest 2021; 131:140522. [PMID: 32970633 DOI: 10.1172/jci140522] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUNDClear cell renal cell carcinoma (ccRCC) is the most common histologically defined renal cancer. However, it is not a uniform disease and includes several genetic subtypes with different prognoses. ccRCC is also characterized by distinctive metabolic reprogramming. Tobacco smoking (TS) is an established risk factor for ccRCC, with unknown effects on tumor pathobiology.METHODSWe investigated the landscape of ccRCCs and paired normal kidney tissues using integrated transcriptomic, metabolomic, and metallomic approaches in a cohort of white males who were long-term current smokers (LTS) or were never smokers (NS).RESULTSAll 3 Omics domains consistently identified a distinct metabolic subtype of ccRCCs in LTS, characterized by activation of oxidative phosphorylation (OXPHOS) coupled with reprogramming of the malate-aspartate shuttle and metabolism of aspartate, glutamate, glutamine, and histidine. Cadmium, copper, and inorganic arsenic accumulated in LTS tumors, showing redistribution among intracellular pools, including relocation of copper into the cytochrome c oxidase complex. A gene expression signature based on the LTS metabolic subtype provided prognostic stratification of The Cancer Genome Atlas ccRCC tumors that was independent of genomic alterations.CONCLUSIONThe work identified the TS-related metabolic subtype of ccRCC with vulnerabilities that can be exploited for precision medicine approaches targeting metabolic pathways. The results provided rationale for the development of metabolic biomarkers with diagnostic and prognostic applications using evaluation of OXPHOS status. The metallomic analysis revealed the role of disrupted metal homeostasis in ccRCC, highlighting the importance of studying effects of metals from e-cigarettes and environmental exposures.FUNDINGDepartment of Defense, Veteran Administration, NIH, ACS, and University of Cincinnati Cancer Institute.
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Affiliation(s)
- James Reigle
- Department of Cancer Biology and.,Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Dina Secic
- Department of Cancer Biology and.,Agilent Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati College of Arts and Science, Cincinnati, Ohio, USA
| | - Jacek Biesiada
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Collin Wetzel
- Department of Cancer Biology and.,Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati College of Arts and Science, Cincinnati, Ohio, USA
| | - Behrouz Shamsaei
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Yuanwei Zang
- Department of Cancer Biology and.,Department of Urology, Qilu Hospital, Shandong University, Jinan, China
| | - Xiang Zhang
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental and Public Health Sciences, and
| | | | | | - Yongzhen Zhang
- Department of Cancer Biology and.,Department of Urology, Qilu Hospital, Shandong University, Jinan, China
| | - Charuhas V Thakar
- Division of Nephrology, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Cincinnati Veteran Affairs Medical Center, Department of Veterans Affairs, Cincinnati, Ohio, USA
| | - Krishnanath Gaitonde
- Division of Nephrology, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Urology, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Abhinav Sidana
- Division of Urology, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Hai Bui
- Cincinnati Veteran Affairs Medical Center, Department of Veterans Affairs, Cincinnati, Ohio, USA
| | | | - Qing Zhang
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, North Carolina, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Mario Medvedovic
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Julio A Landero Figueroa
- Agilent Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati College of Arts and Science, Cincinnati, Ohio, USA.,Department of Pharmacology and System Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jarek Meller
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Department of Pharmacology and System Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Department of Electrical Engineering and Computer Science, University of Cincinnati College of Engineering and Applied Sciences, Cincinnati, Ohio, USA
| | - Maria F Czyzyk-Krzeska
- Department of Cancer Biology and.,Cincinnati Veteran Affairs Medical Center, Department of Veterans Affairs, Cincinnati, Ohio, USA.,Department of Pharmacology and System Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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18
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Al Mahi N, Zhang EY, Sherman S, Yu JJ, Medvedovic M. Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling. Int J Mol Sci 2021; 22:ijms22094371. [PMID: 33922083 PMCID: PMC8122562 DOI: 10.3390/ijms22094371] [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] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
In the connectivity map (CMap) approach to drug repositioning and development, transcriptional signature of disease is constructed by differential gene expression analysis between the diseased tissue or cells and the control. The negative correlation between the transcriptional disease signature and the transcriptional signature of the drug, or a bioactive compound, is assumed to indicate its ability to “reverse” the disease process. A major limitation of traditional CMaP analysis is the use of signatures derived from bulk disease tissues. Since the key driver pathways are most likely dysregulated in only a subset of cells, the “averaged” transcriptional signatures resulting from bulk analysis lack the resolution to effectively identify effective therapeutic agents. The use of single-cell RNA-seq (scRNA-seq) transcriptomic assay facilitates construction of disease signatures that are specific to individual cell types, but methods for using scRNA-seq data in the context of CMaP analysis are lacking. Lymphangioleiomyomatosis (LAM) mutations in TSC1 or TSC2 genes result in the activation of the mTOR complex 1 (mTORC1). The mTORC1 inhibitor Sirolimus is the only FDA-approved drug to treat LAM. Novel therapies for LAM are urgently needed as the disease recurs with discontinuation of the treatment and some patients are insensitive to the drug. We developed methods for constructing disease transcriptional signatures and CMaP analysis using scRNA-seq profiling and applied them in the analysis of scRNA-seq data of lung tissue from naïve and sirolimus-treated LAM patients. New methods successfully implicated mTORC1 inhibitors, including Sirolimus, as capable of reverting the LAM transcriptional signatures. The CMaP analysis mimicking standard bulk-tissue approach failed to detect any connection between the LAM signature and mTORC1 signaling. This indicates that the precise signature derived from scRNA-seq data using our methods is the crucial difference between the success and the failure to identify effective therapeutic treatments in CMaP analysis.
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Affiliation(s)
- Naim Al Mahi
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- AbbVie Inc., North Chicago, IL 60064, USA
| | - Erik Y. Zhang
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (E.Y.Z.); (J.J.Y.)
| | | | - Jane J. Yu
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (E.Y.Z.); (J.J.Y.)
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Correspondence:
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19
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Ren Y, Sivaganesan S, Clark NA, Zhang L, Biesiada J, Niu W, Plas DR, Medvedovic M. Predicting mechanism of action of cellular perturbations with pathway activity signatures. Bioinformatics 2021; 36:4781-4788. [PMID: 32653926 DOI: 10.1093/bioinformatics/btaa590] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/15/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Misregulation of signaling pathway activity is etiologic for many human diseases, and modulating activity of signaling pathways is often the preferred therapeutic strategy. Understanding the mechanism of action (MOA) of bioactive chemicals in terms of targeted signaling pathways is the essential first step in evaluating their therapeutic potential. Changes in signaling pathway activity are often not reflected in changes in expression of pathway genes which makes MOA inferences from transcriptional signatures (TSeses) a difficult problem. RESULTS We developed a new computational method for implicating pathway targets of bioactive chemicals and other cellular perturbations by integrated analysis of pathway network topology, the Library of Integrated Network-based Cellular Signature TSes of genetic perturbations of pathway genes and the TS of the perturbation. Our methodology accurately predicts signaling pathways targeted by the perturbation when current pathway analysis approaches utilizing only the TS of the perturbation fail. AVAILABILITY AND IMPLEMENTATION Open source R package paslincs is available at https://github.com/uc-bd2k/paslincs. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yan Ren
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - Siva Sivaganesan
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, OH 45221-0025, USA
| | - Nicholas A Clark
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - Lixia Zhang
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - Jacek Biesiada
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - Wen Niu
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
| | - David R Plas
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0521, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
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20
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VonHandorf A, Zablon HA, Biesiada J, Zhang X, Medvedovic M, Puga A. Hexavalent chromium promotes differential binding of CTCF to its cognate sites in Euchromatin. Epigenetics 2021; 16:1361-1376. [PMID: 33319643 DOI: 10.1080/15592294.2020.1864168] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Hexavalent chromium compounds are well-established respiratory carcinogens to which humans are commonly exposed in industrial and occupational settings. In addition, natural and anthropogenic sources of these compounds contribute to the exposure of global populations through multiple routes, including dermal, ingestion and inhalation that elevate the risk of cancer by largely unresolved mechanisms. Cr(VI) has genotoxic properties that include ternary adduct formation with DNA, increases in DNA damage, mostly by double-strand break formation, and altered transcriptional responses. Our previous work using ATAC-seq showed that CTCF motifs were enriched in Cr(VI)-dependent differentially accessible chromatin, suggesting that CTCF, a key transcription factor responsible for the regulation of the transcriptome, might be a chromium target. To test this hypothesis, we investigated the effect of Cr(VI) treatment on the binding of CTCF to its cognate sites and ensuing changes in transcription-related histone modifications. Differentially bound CTCF sites were enriched by Cr(VI) treatment within transcription-related regions, specifically transcription start sites and upstream genic regions. Functional annotation of the affected genes highlighted biological processes previously associated with Cr(VI) exposure. Notably, we found that differentially bound CTCF sites proximal to the promoters of this subset of genes were frequently associated with the active histone marks H3K27ac, H3K4me3, and H3K36me3, in agreement with the concept that Cr(VI) targets CTCF in euchromatic regions of the genome. Our results support the conclusion that Cr(VI) treatment promotes the differential binding of CTCF to its cognate sites in genes near transcription-active boundaries, targeting these genes for dysregulation.
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Affiliation(s)
- Andrew VonHandorf
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Hesbon A Zablon
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jacek Biesiada
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Alvaro Puga
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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21
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Schulert GS, Pickering AV, Do T, Dhakal S, Fall N, Schnell D, Medvedovic M, Salomonis N, Thornton S, Grom AA. Monocyte and bone marrow macrophage transcriptional phenotypes in systemic juvenile idiopathic arthritis reveal TRIM8 as a mediator of IFN-γ hyper-responsiveness and risk for macrophage activation syndrome. Ann Rheum Dis 2020; 80:617-625. [PMID: 33277241 DOI: 10.1136/annrheumdis-2020-217470] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVES Systemic juvenile idiopathic arthritis (SJIA) confers high risk for macrophage activation syndrome (MAS), a life-threatening cytokine storm driven by interferon (IFN)-γ. SJIA monocytes display IFN-γ hyper-responsiveness, but the molecular basis of this remains unclear. The objective of this study is to identify circulating monocyte and bone marrow macrophage (BMM) polarisation phenotypes in SJIA including molecular features contributing to IFN response. METHODS Bulk RNA-seq was performed on peripheral blood monocytes (n=26 SJIA patients) and single cell (sc) RNA-seq was performed on BMM (n=1). Cultured macrophages were used to define consequences of tripartite motif containing 8 (TRIM8) knockdown on IFN-γ signalling. RESULTS Bulk RNA-seq of SJIA monocytes revealed marked transcriptional changes in patients with elevated ferritin levels. We identified substantial overlap with multiple polarisation states but little evidence of IFN-induced signature. Interestingly, among the most highly upregulated genes was TRIM8, a positive regulator of IFN-γ signalling. In contrast to PBMC from SJIA patients without MAS, scRNA-seq of BMM from a patient with SJIA and MAS identified distinct subpopulations of BMM with altered transcriptomes, including upregulated IFN-γ response pathways. These BMM also showed significantly increased expression of TRIM8. In vitro knockdown of TRIM8 in macrophages significantly reduced IFN-γ responsiveness. CONCLUSIONS Macrophages with an 'IFN-γ response' phenotype and TRIM8 overexpression were expanded in the bone marrow from an MAS patient. TRIM8 is also upregulated in SJIA monocytes, and augments macrophage IFN-γ response in vitro, providing both a candidate molecular mechanism and potential therapeutic target for monocyte hyper-responsiveness to IFNγ in cytokine storms including MAS.
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Affiliation(s)
- Grant S Schulert
- Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA .,Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Thuy Do
- Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sanjeev Dhakal
- Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ndate Fall
- Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Daniel Schnell
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mario Medvedovic
- Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Nathan Salomonis
- Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sherry Thornton
- Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Alexei A Grom
- Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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22
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Leung YK, Biesiada J, Govindarajah V, Ying J, Kendler A, Medvedovic M, Ho SM. Low-Dose Bisphenol A in a Rat Model of Endometrial Cancer: A CLARITY-BPA Study. Environ Health Perspect 2020; 128:127005. [PMID: 33296240 PMCID: PMC7725436 DOI: 10.1289/ehp6875] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bisphenol A (BPA) is known to be biologically active in experimental models even at low levels of exposure. However, its impact on endometrial cancer remains unclear. OBJECTIVES This study aimed to investigate whether lifelong exposure to different doses of BPA induced uterine abnormalities and molecular changes in a rat model. METHODS Sprague-Dawley rats were exposed to 5 doses of BPA [0, 25, 250, 2,500, or 25,000 μ g / kg body weight (BW)/d] or 2 doses of 17 α - ethynylestradiol (EE2) (0.05 and 0.5 μ g / kg BW/d) starting from gestational day 6 up to 1 y old according to the CLARITY-BPA consortium protocol. The BW, uterus weight, and histopathology end points of the uteri were analyzed at postnatal (PND) day 21, 90, and 365. Estrous cycling status was evaluated in PND90 and PND365 rats. Transcriptomic analyses of estrus stage uteri were conducted on PND365 rats. RESULTS Based on the analysis of the combined effects of all testing outcomes (including immunohistological, morphological, and estrous cycle data) in a semiblinded fashion, using statistical models, 25 μ g / kg BW/d BPA [BPA(25)], or 250 μ g / kg BW/d BPA [BPA(250)] exerted effects similar to that of EE2 at 0.5 μ g / kg BW/d in 1-y-old rats. Transcriptome analyses of estrus stage uteri revealed a set of 710 genes shared only between the BPA(25) and BPA(250) groups, with 115 of them predicted to be regulated by estradiol and 57 associated with female cancers. An interesting finding is that the expression of 476 human orthologous genes in this rat BPA signature robustly predicted the overall survival (p = 1.68 × 10 - 5 , hazard ratio = 2.62 ) of endometrial cancer patients. DISCUSSION Lifelong exposure of rats to low-dose BPA at 25 and 250 μ g / kg BW/d altered the estrous cycle and uterine pathology with similarity to EE2. The exposure also disrupted a unique low-dose BPA-gene signature with predictive value for survival outcomes in patients with endometrial cancer. https://doi.org/10.1289/EHP6875.
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Affiliation(s)
- Yuet-Kin Leung
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA
- Center for Environmental Genetics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Jacek Biesiada
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA
- Center for Environmental Genetics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Vinothini Govindarajah
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Jun Ying
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA
- Center for Environmental Genetics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Ady Kendler
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA
- Center for Environmental Genetics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Shuk-Mei Ho
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, Ohio, USA
- Center for Environmental Genetics, University of Cincinnati, Cincinnati, Ohio, USA
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23
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de Gannes M, Ko CI, Zhang X, Biesiada J, Niu L, Koch SE, Medvedovic M, Rubinstein J, Puga A. Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes That Govern Cardiomyocyte Maturation. Toxicol Sci 2020; 178:325-337. [PMID: 33017471 DOI: 10.1093/toxsci/kfaa153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Congenital heart disease (CHD), the leading birth defect worldwide, has a largely unknown etiology, likely to result from complex interactions between genetic and environmental factors during heart development, at a time when the heart adapts to diverse physiological and pathophysiological conditions. Crucial among these is the regulation of cardiomyocyte development and postnatal maturation, governed by dynamic changes in DNA methylation. Previous work from our laboratory has shown that exposure to the environmental toxicant tetrachlorodibenzo-p-dioxin (TCDD) disrupts several molecular networks responsible for heart development and function. To test the hypothesis that the disruption caused by TCDD in the heart results from changes in DNA methylation and gene expression patterns of cardiomyocytes, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under control of the cardiomyocyte-specific Nkx2-5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte-specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 111 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue toward the elucidation of the complex interactions between genetic and epigenetic mechanisms after developmental TCDD exposure that may contribute to CHD.
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Affiliation(s)
- Matthew de Gannes
- Department of Environmental Health and Center for Environmental Genetics
| | - Chia-I Ko
- Department of Environmental Health and Center for Environmental Genetics
| | - Xiang Zhang
- Department of Environmental Health and Center for Environmental Genetics
| | - Jacek Biesiada
- Department of Environmental Health and Center for Environmental Genetics
| | - Liang Niu
- Department of Environmental Health and Center for Environmental Genetics
| | - Sheryl E Koch
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - Mario Medvedovic
- Department of Environmental Health and Center for Environmental Genetics
| | - Jack Rubinstein
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - Alvaro Puga
- Department of Environmental Health and Center for Environmental Genetics
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24
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Pomeranz Krummel DA, Nasti TH, Kaluzova M, Kallay L, Bhattacharya D, Melms JC, Izar B, Xu M, Burnham A, Ahmed T, Li G, Lawson D, Kowalski J, Cao Y, Switchenko JM, Ionascu D, Cook JM, Medvedovic M, Jenkins A, Khan MK, Sengupta S. Melanoma Cell Intrinsic GABA A Receptor Enhancement Potentiates Radiation and Immune Checkpoint Inhibitor Response by Promoting Direct and T Cell-Mediated Antitumor Activity. Int J Radiat Oncol Biol Phys 2020; 109:1040-1053. [PMID: 33289666 DOI: 10.1016/j.ijrobp.2020.10.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE Most patients with metastatic melanoma show variable responses to radiation therapy and do not benefit from immune checkpoint inhibitors. Improved strategies for combination therapy that leverage potential benefits from radiation therapy and immune checkpoint inhibitors are critical. METHODS AND MATERIALS We analyzed metastatic melanoma tumors in the TCGA cohort for expression of genes coding for subunits of type A γ-aminobutyric acid (GABA) receptor (GABAAR), a chloride ion channel and major inhibitory neurotransmitter receptor. Electrophysiology was used to determine whether melanoma cells possess intrinsic GABAAR activity. Melanoma cell viability studies were conducted to test whether enhancing GABAAR mediated chloride transport using benzodiazepine-impaired viability. A syngeneic melanoma mouse model was used to assay the effect of benzodiazepine on tumor volume and its ability to potentiate radiation therapy or immunotherapy. Treated tumors were analyzed for changes in gene expression by RNA sequencing and presence of tumor-infiltrating lymphocytes by flow cytometry. RESULTS Genes coding for subunits of GABAARs express functional GABAARs in melanoma cells. By enhancing GABAAR-mediated anion transport, benzodiazepines depolarize melanoma cells and impair their viability. In vivo, benzodiazepine alone reduces tumor growth and potentiates radiation therapy and α-PD-L1 antitumor activity. The combination of benzodiazepine, radiation therapy, and α-PD-L1 results in near complete regression of treated tumors and a potent abscopal effect, mediated by increased infiltration of polyfunctional CD8+ T cells. Treated tumors show expression of cytokine-cytokine receptor interactions and overrepresentation of p53 signaling. CONCLUSIONS This study identifies an antitumor strategy combining radiation and/or an immune checkpoint inhibitor with modulation of GABAARs in melanoma using benzodiazepine.
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Affiliation(s)
- Daniel A Pomeranz Krummel
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Tahseen H Nasti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
| | | | - Laura Kallay
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Debanjan Bhattacharya
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Johannes C Melms
- Columbia Center for Translational Immunology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Benjamin Izar
- Columbia Center for Translational Immunology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Maxwell Xu
- Johns Hopkins University, Baltimore, Maryland
| | - Andre Burnham
- Emory University School of Medicine, Atlanta, Georgia
| | - Taukir Ahmed
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Guanguan Li
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - David Lawson
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Jeanne Kowalski
- Department of Oncology, LIVESTRONG Cancer Institutes, Dell Medical School, University of Texas, Austin, Texas
| | - Yichun Cao
- Biostatistics Shared Resource, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Jeffrey M Switchenko
- Biostatistics Shared Resource, Winship Cancer Institute of Emory University, Atlanta, Georgia; Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Dan Ionascu
- Department of Radiation Oncology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - James M Cook
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Andrew Jenkins
- Departments of Anesthesiology, Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia
| | - Mohammad K Khan
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Soma Sengupta
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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25
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Shamsaei B, Chojnacki S, Pilarczyk M, Najafabadi M, Niu W, Chen C, Ross K, Matlock A, Muhlich J, Chutipongtanate S, Zheng J, Turner J, Vidović D, Jaffe J, MacCoss M, Wu C, Pillai A, Ma'ayan A, Schürer S, Kouril M, Medvedovic M, Meller J. piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res 2020; 48:W85-W93. [PMID: 32469073 PMCID: PMC7319557 DOI: 10.1093/nar/gkaa436] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 03/25/2020] [Revised: 04/29/2020] [Accepted: 05/27/2020] [Indexed: 02/03/2023] Open
Abstract
Rapid progress in proteomics and large-scale profiling of biological systems at the protein level necessitates the continued development of efficient computational tools for the analysis and interpretation of proteomics data. Here, we present the piNET server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. The primary input for the server consists of a set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Several interconnected workflows can be used to generate: (i) interactive graphs and tables providing comprehensive annotation and mapping between peptides and proteins with PTM sites; (ii) high resolution and interactive visualization for enzyme-substrate networks, including kinases and their phospho-peptide targets; (iii) mapping and visualization of LINCS signature connectivity for chemical inhibitors or genetic knockdown of enzymes upstream of their target PTM sites. piNET has been built using a modular Spring-Boot JAVA platform as a fast, versatile and easy to use tool. The Apache Lucene indexing is used for fast mapping of peptides into UniProt entries for the human, mouse and other commonly used model organism proteomes. PTM-centric network analyses combine PhosphoSitePlus, iPTMnet and SIGNOR databases of validated enzyme-substrate relationships, for kinase networks augmented by DeepPhos predictions and sequence-based mapping of PhosphoSitePlus consensus motifs. Concordant LINCS signatures are mapped using iLINCS. For each workflow, a RESTful API counterpart can be used to generate the results programmatically in the json format. The server is available at http://pinet-server.org, and it is free and open to all users without login requirement.
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Affiliation(s)
- Behrouz Shamsaei
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA
| | - Szymon Chojnacki
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA
| | - Marcin Pilarczyk
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA
| | - Mehdi Najafabadi
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA
| | - Wen Niu
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA
| | - Chuming Chen
- Center for Bioinformatics & Computational Biology; University of Delaware, USA
| | - Karen Ross
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, USA
| | - Andrea Matlock
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, USA
| | - Jeremy Muhlich
- Department of Systems Biology, Harvard Medical School, USA
| | - Somchai Chutipongtanate
- Department of Cancer Biology, University of Cincinnati College of Medicine, USA.,Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Jie Zheng
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, USA
| | - John Turner
- Department of Pharmacology, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Center for Computational Science, University of Miami, Miami, USA
| | - Dušica Vidović
- Department of Pharmacology, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Center for Computational Science, University of Miami, Miami, USA
| | - Jake Jaffe
- Broad Institute of MIT and Harvard & Inzen Therapeutics, USA
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington, USA
| | - Cathy Wu
- Center for Bioinformatics & Computational Biology; University of Delaware, USA.,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, USA
| | - Ajay Pillai
- Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Avi Ma'ayan
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, USA
| | - Stephan Schürer
- Department of Pharmacology, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Center for Computational Science, University of Miami, Miami, USA
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA.,Department of Biomedical Informatics, University of Cincinnati College of Medicine, USA
| | - Jarek Meller
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, USA.,Department of Electrical Engineering and Computer Science, University of Cincinnati, USA
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26
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Sengupta S, Nasti T, Kaluzova M, Kallay L, Melms J, Izar B, Xu M, Bhattacharya D, Burnham A, Li G, Ahmed T, Lawson D, Kowalski J, Cook J, Medvedovic M, Jenkins A, Khan M, Pomeranz Krummel D. 20. MELANOMA CELL INTRINSIC GABAA RECEPTOR ENHANCEMENT POTENTIATES RADIATION AND IMMUNE CHECKPOINT INHIBITOR RESPONSE BY PROMOTING DIRECT AND T CELL-MEDIATED ANTI-TUMOR ACTIVITY. Neurooncol Adv 2020. [PMCID: PMC7401396 DOI: 10.1093/noajnl/vdaa073.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Most metastatic melanoma patients exhibit poor and variable response to radiotherapy and targeted therapies, including immune checkpoint inhibitors. There is a need for therapeutics that can potentiate existing treatments to positively impact clinical outcomes of metastatic melanoma patients. We reanalyzed melanoma TCGA transcriptomes and identified, as linked to previously defined molecular subgroups, enhanced expression of genes coding for subunits of the Type A GABA receptor (GABAAR), a chloride ion channel and major inhibitory neurotransmitter receptor. Using whole-cell patch clamp electrophysiology, we find that melanoma cells possess GABAARs that control membrane permeability to anions. Select benzodiazepines, by enhancing GABAAR mediated anion transport, depolarize melanoma cell mitochondrial membrane potential and impair cell viability in vitro. Using a syngeneic melanoma mouse model, we find that a benzodiazepine promotes reduction in tumor volume when administered alone and potentiated radiation or immune checkpoint inhibitor α-PD-L1. When a benzodiazepine is combined with concurrent α-PD-L1 and a sub-lethal radiation dose, there is near complete loss of tumor, beyond what is observed for benzodiazepine with radiation or α-PD-L1. Mechanistically, benzodiazepine with radiation or α-PD-L1 results in ipsilateral and an abscopal tumor volume reduction commensurate with enhanced infiltration into the tumor milieu of polyfunctional CD8 T-cells. There is also an increased expression of genes with roles in the cytokine-cytokine receptor and p53 signaling pathways. This study provides evidence for melanoma cell GABAARs as a therapeutic vulnerability with benzodiazepines promoting both direct and immune-mediated anti-tumor activity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - James Cook
- University of Wisconsin, Milwaukee, WI, USA
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27
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Stathias V, Turner J, Koleti A, Vidovic D, Cooper D, Fazel-Najafabadi M, Pilarczyk M, Terryn R, Chung C, Umeano A, Clarke DJB, Lachmann A, Evangelista JE, Ma’ayan A, Medvedovic M, Schürer SC. LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic Acids Res 2020; 48:D431-D439. [PMID: 31701147 PMCID: PMC7145650 DOI: 10.1093/nar/gkz1023] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/17/2019] [Accepted: 11/04/2019] [Indexed: 12/21/2022] Open
Abstract
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal of generating a large-scale and comprehensive catalogue of perturbation-response signatures by utilizing a diverse collection of perturbations across many model systems and assay types. The LINCS Data Portal (LDP) has been the primary access point for the compendium of LINCS data and has been widely utilized. Here, we report the first major update of LDP (http://lincsportal.ccs.miami.edu/signatures) with substantial changes in the data architecture and APIs, a completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. The cornerstone of this update has been the decision to reprocess all high-level LINCS datasets and make them accessible at the data point level enabling users to directly access and download any subset of signatures across the entire library independent from the originating source, project or assay. Access to the individual signatures also enables the newly implemented signature search functionality, which utilizes the iLINCS platform to identify conditions that mimic or reverse gene set queries. A newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.
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Affiliation(s)
- Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, USA
- Center for Computational Science, University of Miami, USA
- BD2K-LINCS Data Coordination and Integration Center, USA
| | - John Turner
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, USA
- BD2K-LINCS Data Coordination and Integration Center, USA
| | - Amar Koleti
- Center for Computational Science, University of Miami, USA
- BD2K-LINCS Data Coordination and Integration Center, USA
| | - Dusica Vidovic
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, USA
- BD2K-LINCS Data Coordination and Integration Center, USA
| | - Daniel Cooper
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, USA
- BD2K-LINCS Data Coordination and Integration Center, USA
| | - Mehdi Fazel-Najafabadi
- BD2K-LINCS Data Coordination and Integration Center, USA
- Laboratory for Statistical Genomics and Systems Biology, Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, USA
| | - Marcin Pilarczyk
- BD2K-LINCS Data Coordination and Integration Center, USA
- Laboratory for Statistical Genomics and Systems Biology, Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, USA
| | - Raymond Terryn
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, USA
| | - Caty Chung
- BD2K-LINCS Data Coordination and Integration Center, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, USA
| | - Afoma Umeano
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, USA
| | - Daniel J B Clarke
- BD2K-LINCS Data Coordination and Integration Center, USA
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Alexander Lachmann
- BD2K-LINCS Data Coordination and Integration Center, USA
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, USA
| | - John Erol Evangelista
- BD2K-LINCS Data Coordination and Integration Center, USA
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Avi Ma’ayan
- BD2K-LINCS Data Coordination and Integration Center, USA
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Mario Medvedovic
- BD2K-LINCS Data Coordination and Integration Center, USA
- Laboratory for Statistical Genomics and Systems Biology, Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, USA
- Center for Computational Science, University of Miami, USA
- BD2K-LINCS Data Coordination and Integration Center, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, USA
- To whom correspondence should be addressed. Tel: +1 305 243 6552;
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28
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Langevin SM, Kuhnell D, Biesiada J, Zhang X, Medvedovic M, Talaska GG, Burns KA, Kasper S. Comparability of the small RNA secretome across human biofluids concomitantly collected from healthy adults. PLoS One 2020; 15:e0229976. [PMID: 32275679 PMCID: PMC7147728 DOI: 10.1371/journal.pone.0229976] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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] [Received: 10/28/2019] [Accepted: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
Small extracellular vesicles (sEV) are nano-sized (40–150 nm), membrane-encapsulated vesicles that are released by essentially all cells into the extracellular space and function as intercellular signaling vectors through the horizontal transfer of biologic molecules, including microRNA (miRNA) and other small non-coding RNA (ncRNA), that can alter the phenotype of recipient cells. sEV are present in essentially all extracellular biofluids, including serum, urine and saliva, and offer a new avenue for discovery and development of novel biomarkers of various disease states and exposures. The objective of this study was to systematically interrogate similarities and differences between sEV ncRNA derived from saliva, serum and urine, as well as cell-free small ncRNA (cf-ncRNA) from serum. Saliva, urine and serum were concomitantly collected from 4 healthy donors to mitigate potential bias that can stem from interpersonal and temporal variability. sEV were isolated from each respective biofluid, along with cf-RNA from serum. sEV were isolated from the respective biofluids via differential ultracentrifugation with a 30% sucrose cushion to minimize protein contamination. Small RNA-sequencing was performed on each sample, and cluster analysis was performed based on ncRNA profiles. While some similarities existed in terms of sEV ncRNA cargo across biofluids, there are also notable differences in ncRNA class and ncRNA secretion, with sEV in each biofluid bearing a unique ncRNA profile, including major differences in composition by ncRNA class. We conclude that sEV ncRNA cargo varies according to biofluid, so thus should be carefully selected and interpreted when designing or contrasting translational or epidemiological studies.
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Affiliation(s)
- Scott M Langevin
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America.,Cincinnati Cancer Center, Cincinnati, OH, United States of America
| | - Damaris Kuhnell
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
| | - Jacek Biesiada
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
| | - Xiang Zhang
- Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
| | - Mario Medvedovic
- Cincinnati Cancer Center, Cincinnati, OH, United States of America.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
| | - Glenn G Talaska
- Division of Environmental & Industrial Hygiene, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
| | - Katherine A Burns
- Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
| | - Susan Kasper
- Cincinnati Cancer Center, Cincinnati, OH, United States of America.,Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
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29
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Thorman AW, Reigle J, Chutipongtanate S, Shamsaei B, Pilarczyk M, Fazel-Najafabadi M, Adamczak R, Kouril M, Medvedovic M, Meller J. Connectivity Enhanced Structure Activity Relationship (ceSAR): A Novel Approach to Increase Accuracy and Speed of Virtual Drug Discovery. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.05660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jarek Meller
- University of Cincinnati
- Cincinnati Children's Hospital and Medical Center
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30
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Jodele S, Medvedovic M, Luebbering N, Chen J, Dandoy CE, Laskin BL, Davies SM. Interferon-complement loop in transplant-associated thrombotic microangiopathy. Blood Adv 2020; 4:1166-1177. [PMID: 32208488 PMCID: PMC7094010 DOI: 10.1182/bloodadvances.2020001515] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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: 01/17/2020] [Accepted: 02/26/2020] [Indexed: 12/16/2022] Open
Abstract
Transplant-associated thrombotic microangiopathy (TA-TMA) is an important cause of morbidity and mortality after hematopoietic stem cell transplantation (HSCT). The complement inhibitor eculizumab improves TA-TMA, but not all patients respond to therapy, prompting a search for additional targetable pathways of endothelial injury. TA-TMA is relatively common after HSCT and can serve as a model to study mechanisms of tissue injury in other thrombotic microangiopathies. In this work, we performed transcriptome analyses of peripheral blood mononuclear cells collected before HSCT, at onset of TA-TMA, and after resolution of TA-TMA in children with and without TA-TMA after HSCT. We observed significant upregulation of the classical, alternative, and lectin complement pathways during active TA-TMA. Essentially all upregulated genes and pathways returned to baseline expression levels at resolution of TA-TMA after eculizumab therapy, supporting the clinical practice of discontinuing complement blockade after resolution of TA-TMA. Further analysis of the global transcriptional regulatory network showed a notable interferon signature associated with TA-TMA with increased STAT1 and STAT2 signaling that resolved after complement blockade. In summary, we observed activation of multiple complement pathways in TA-TMA, in contrast to atypical hemolytic uremic syndrome (aHUS), where complement activation occurs largely via the alternative pathway. Our data also suggest a key relationship between increased interferon signaling, complement activation, and TA-TMA. We propose a model of an "interferon-complement loop" that can perpetuate endothelial injury and thrombotic microangiopathy. These findings open opportunities to study novel complement blockers and combined anti-complement and anti-interferon therapies in patients with TA-TMA and other microangiopathies like aHUS and lupus-associated TMAs.
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Affiliation(s)
- Sonata Jodele
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Disease Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH; and
| | - Nathan Luebbering
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Disease Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Jenny Chen
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH; and
| | - Christopher E Dandoy
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Disease Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Benjamin L Laskin
- Division of Nephrology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stella M Davies
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Disease Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
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31
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Stefely JA, Zhang Y, Freiberger EC, Kwiecien NW, Thomas HE, Davis AM, Lowry ND, Vincent CE, Shishkova E, Clark NA, Medvedovic M, Coon JJ, Pagliarini DJ, Mercer CA. Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy. Autophagy 2020; 16:2219-2237. [PMID: 31971854 DOI: 10.1080/15548627.2020.1719746] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Macroautophagy/autophagy is suppressed by MTOR (mechanistic target of rapamycin kinase) and is an anticancer target under active investigation. Yet, MTOR-regulated autophagy remains incompletely mapped. We used proteomic profiling to identify proteins in the MTOR-autophagy axis. Wild-type (WT) mouse cell lines and cell lines lacking individual autophagy genes (Atg5 or Ulk1/Ulk2) were treated with an MTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling revealed an elevation of known autophagy proteins and candidates for new autophagy components, including CALCOCO1 (calcium binding and coiled-coil domain protein 1). We show that CALCOCO1 physically interacts with MAP1LC3C, a key protein in the machinery of autophagy. Genetic deletion of CALCOCO1 disrupted autophagy of the endoplasmic reticulum (reticulophagy). Together, these results reveal a role for CALCOCO1 in MTOR-regulated selective autophagy. More generally, the resource generated by this work provides a foundation for establishing links between the MTOR-autophagy axis and proteins not previously linked to this pathway. Abbreviations: ATG: autophagy-related; CALCOCO1: calcium binding and coiled-coil domain protein 1; CALCOCO2/NDP52: calcium binding and coiled-coil domain protein 2; CLIR: MAP1LC3C-interacting region; CQ: chloroquine; KO: knockout; LIR: MAP1LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MLN: MLN0128 ATP-competitive MTOR kinase inhibitor; MTOR: mechanistic target of rapamycin kinase; reticulophagy: selective autophagy of the endoplasmic reticulum; TAX1BP1/CALCOCO3: TAX1 binding protein 1; ULK: unc 51-like autophagy activating kinase; WT: wild-type.
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Affiliation(s)
- Jonathan A Stefely
- Morgridge Institute for Research , Madison, WI, USA.,Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, WI, USA.,Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Yu Zhang
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Elyse C Freiberger
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Nicholas W Kwiecien
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Hala Elnakat Thomas
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Alexander M Davis
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Nathaniel D Lowry
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Catherine E Vincent
- Genome Center of Wisconsin , Madison, WI, USA.,Department of Chemistry, Hartwick College , Oneonta, NY, USA
| | | | - Nicholas A Clark
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Joshua J Coon
- Morgridge Institute for Research , Madison, WI, USA.,Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA
| | - David J Pagliarini
- Morgridge Institute for Research , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Carol A Mercer
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
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Abstract
BACKGROUND N6-Methyladenosine (m6A) methylation is the most prevalent internal posttranscriptional modification on mammalian mRNA. The role of m6A mRNA methylation in the heart is not known. METHODS To determine the role of m6A methylation in the heart, we isolated primary cardiomyocytes and performed m6A immunoprecipitation followed by RNA sequencing. We then generated genetic tools to modulate m6A levels in cardiomyocytes by manipulating the levels of the m6A RNA methylase methyltransferase-like 3 (METTL3) both in culture and in vivo. We generated cardiac-restricted gain- and loss-of-function mouse models to allow assessment of the METTL3-m6A pathway in cardiac homeostasis and function. RESULTS We measured the level of m6A methylation on cardiomyocyte mRNA, and found a significant increase in response to hypertrophic stimulation, suggesting a potential role for m6A methylation in the development of cardiomyocyte hypertrophy. Analysis of m6A methylation showed significant enrichment in genes that regulate kinases and intracellular signaling pathways. Inhibition of METTL3 completely abrogated the ability of cardiomyocytes to undergo hypertrophy when stimulated to grow, whereas increased expression of the m6A RNA methylase METTL3 was sufficient to promote cardiomyocyte hypertrophy both in vitro and in vivo. Finally, cardiac-specific METTL3 knockout mice exhibit morphological and functional signs of heart failure with aging and stress, showing the necessity of RNA methylation for the maintenance of cardiac homeostasis. CONCLUSIONS Our study identified METTL3-mediated methylation of mRNA on N6-adenosines as a dynamic modification that is enhanced in response to hypertrophic stimuli and is necessary for a normal hypertrophic response in cardiomyocytes. Enhanced m6A RNA methylation results in compensated cardiac hypertrophy, whereas diminished m6A drives eccentric cardiomyocyte remodeling and dysfunction, highlighting the critical importance of this novel stress-response mechanism in the heart for maintaining normal cardiac function.
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Affiliation(s)
- Lisa E Dorn
- Department of Physiology and Cell Biology (L.E.D., F.A.), Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus
| | - Lior Lasman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel (L.L., J.H.H.)
| | - Jing Chen
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, OH (J.C., M.M.)
| | - Xianyao Xu
- Department of Biomedical Engineering (X.X., T.J.H.), Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus
| | - Thomas J Hund
- Department of Biomedical Engineering (X.X., T.J.H.), Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, OH (J.C., M.M.)
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel (L.L., J.H.H.)
| | - Jop H van Berlo
- Cardiovascular Division, Lillehei Heart Institute and Stem Cell Institute, University of Minnesota, Minneapolis (J.H.v.B.)
| | - Federica Accornero
- Department of Physiology and Cell Biology (L.E.D., F.A.), Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus
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33
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Koleti A, Terryn R, Stathias V, Chung C, Cooper DJ, Turner JP, Vidovic D, Forlin M, Kelley TT, D'Urso A, Allen BK, Torre D, Jagodnik KM, Wang L, Jenkins SL, Mader C, Niu W, Fazel M, Mahi N, Pilarczyk M, Clark N, Shamsaei B, Meller J, Vasiliauskas J, Reichard J, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC. Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. Nucleic Acids Res 2019; 46:D558-D566. [PMID: 29140462 PMCID: PMC5753343 DOI: 10.1093/nar/gkx1063] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [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: 08/15/2017] [Accepted: 10/19/2017] [Indexed: 11/21/2022] Open
Abstract
The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content.
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Affiliation(s)
- Amar Koleti
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA
| | - Raymond Terryn
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA
| | - Vasileios Stathias
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA.,Department of Human Genetics and Genomics, Miller School of Medicine, University of Miami, FL, USA
| | - Caty Chung
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA
| | - Daniel J Cooper
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA
| | - John P Turner
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA
| | - Dušica Vidovic
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA
| | - Michele Forlin
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA
| | - Tanya T Kelley
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA
| | - Alessandro D'Urso
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA
| | - Bryce K Allen
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA
| | - Denis Torre
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathleen M Jagodnik
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lily Wang
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sherry L Jenkins
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christopher Mader
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA
| | - Wen Niu
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Mehdi Fazel
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Naim Mahi
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Marcin Pilarczyk
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Nicholas Clark
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Behrouz Shamsaei
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Jarek Meller
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Juozas Vasiliauskas
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - John Reichard
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Mario Medvedovic
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Avi Ma'ayan
- BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ajay Pillai
- Division of Genome Sciences, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephan C Schürer
- Center for Computational Science, University of Miami, FL, USA.,BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA
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34
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Langevin SM, Kuhnell D, Niu L, Biesiada J, Leung YK, Deka R, Chen A, Medvedovic M, Kelsey KT, Kasper S, Zhang X. Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma. Epigenomics 2019; 11:987-1002. [PMID: 31215230 DOI: 10.2217/epi-2018-0172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: The goal of this study was to comprehensively interrogate and map DNA methylation across 16 CpG-dense regions previously associated with oral and pharyngeal squamous cell carcinoma (OPSCC). Materials & methods: Targeted multiplex bisulfite amplicon sequencing was performed on four OPSCC cell lines and primary non-neoplastic oral epithelial cells. Real-time quantitative polymerase chain reaction (RT-qPCR) was performed for a subset of associated genes. Results: There was clear differential methylation between one or more OPSCC cell lines and control cells for the majority of CpG-dense regions. Conclusion: Targeted multiplex bisulfite amplicon sequencing allowed us to efficiently map methylation across the entire region of interest with a high degree of sensitivity and helps shed light on novel differentially methylated regions that may have value as biomarkers of OPSCC.
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Affiliation(s)
- Scott M Langevin
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.,Cincinnati Cancer Center, Cincinnati, OH 45267, USA
| | - Damaris Kuhnell
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Liang Niu
- Division of Biostatistics & Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jacek Biesiada
- Division of Biostatistics & Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yuet-Kin Leung
- Cincinnati Cancer Center, Cincinnati, OH 45267, USA.,Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Ranjan Deka
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Aimin Chen
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Mario Medvedovic
- Cincinnati Cancer Center, Cincinnati, OH 45267, USA.,Division of Biostatistics & Bioinformatics, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912, USA.,Department of Pathology & Laboratory Medicine, Alpert Medical School, Brown University, Providence, RI 02912, USA
| | - Susan Kasper
- Cincinnati Cancer Center, Cincinnati, OH 45267, USA.,Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiang Zhang
- Cincinnati Cancer Center, Cincinnati, OH 45267, USA.,Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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35
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Abstract
The vast amount of RNA-seq data deposited in Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) is still a grossly underutilized resource for biomedical research. To remove technical roadblocks for reusing these data, we have developed a web-application GREIN (GEO RNA-seq Experiments Interactive Navigator) which provides user-friendly interfaces to manipulate and analyze GEO RNA-seq data. GREIN is powered by the back-end computational pipeline for uniform processing of RNA-seq data and the large number (>6,500) of already processed datasets. The front-end user interfaces provide a wealth of user-analytics options including sub-setting and downloading processed data, interactive visualization, statistical power analyses, construction of differential gene expression signatures and their comprehensive functional characterization, and connectivity analysis with LINCS L1000 data. The combination of the massive amount of back-end data and front-end analytics options driven by user-friendly interfaces makes GREIN a unique open-source resource for re-using GEO RNA-seq data. GREIN is accessible at: https://shiny.ilincs.org/grein , the source code at: https://github.com/uc-bd2k/grein , and the Docker container at: https://hub.docker.com/r/ucbd2k/grein .
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Affiliation(s)
- Naim Al Mahi
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, 3223 Eden Avenue, Cincinnati, OH, 45220, USA
| | - Mehdi Fazel Najafabadi
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, 3223 Eden Avenue, Cincinnati, OH, 45220, USA
| | - Marcin Pilarczyk
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, 3223 Eden Avenue, Cincinnati, OH, 45220, USA
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, 3223 Eden Avenue, Cincinnati, OH, 45220, USA.
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36
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Huang W, Medvedovic M, Zhang J, Niu L. ChIAPoP: a new tool for ChIA-PET data analysis. Nucleic Acids Res 2019; 47:e37. [PMID: 30753588 PMCID: PMC6468250 DOI: 10.1093/nar/gkz062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/19/2018] [Accepted: 01/24/2019] [Indexed: 01/05/2023] Open
Abstract
Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a popular assay method for studying genome-wide chromatin interactions mediated by a protein of interest. The main goal of ChIA-PET data analysis is to detect interactions between DNA regions. Here, we propose a new method and the associated data analysis pipeline, ChIAPoP, to detect chromatin interactions from ChIA-PET data. We compared ChIAPoP with other popular methods, including a hypergeometric model (used in ChIA-PET tool), MICC (used in ChIA-PET2), ChiaSig and mango. The results showed that ChIA-PoP performed better than or at least as well as these top existing methods in detecting true chromatin interactions. ChIAPoP is freely available to the public at https://github.com/wh90999/ChIAPoP.
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Affiliation(s)
- Weichun Huang
- National Exposure Research Laboratory, Environmental Protection Agency, Research Triangle Park, NC 27709, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Jingwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Niu
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
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37
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Moret N, Clark NA, Hafner M, Wang Y, Lounkine E, Medvedovic M, Wang J, Gray N, Jenkins J, Sorger PK. Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. Cell Chem Biol 2019; 26:765-777.e3. [PMID: 30956147 DOI: 10.1016/j.chembiol.2019.02.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 07/11/2018] [Revised: 11/28/2018] [Accepted: 02/26/2019] [Indexed: 12/15/2022]
Abstract
Libraries of well-annotated small molecules have many uses in chemical genetics, drug discovery, and therapeutic repurposing. Multiple libraries are available, but few data-driven approaches exist to compare them and design new libraries. We describe an approach to scoring and creating libraries based on binding selectivity, target coverage, and induced cellular phenotypes as well as chemical structure, stage of clinical development, and user preference. The approach, available via the online tool http://www.smallmoleculesuite.org, assembles sets of compounds with the lowest possible off-target overlap. Analysis of six kinase inhibitor libraries using our approach reveals dramatic differences among them and led us to design a new LSP-OptimalKinase library that outperforms existing collections in target coverage and compact size. We also describe a mechanism of action library that optimally covers 1,852 targets in the liganded genome. Our tools facilitate creation, analysis, and updates of both private and public compound collections.
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Affiliation(s)
- Nienke Moret
- HMS LINCS and Druggable Genome Centers, Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Warren Alpert 444, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas A Clark
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Marc Hafner
- HMS LINCS and Druggable Genome Centers, Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Warren Alpert 444, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yuan Wang
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Eugen Lounkine
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 360 Longwood Avenue, Longwood Center 2209, Boston, MA 02115, USA
| | - Nathanael Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 360 Longwood Avenue, Longwood Center 2209, Boston, MA 02115, USA
| | - Jeremy Jenkins
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Peter K Sorger
- HMS LINCS and Druggable Genome Centers, Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Warren Alpert 444, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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38
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Chakrabarti J, Steele N, Holokai L, Broda T, Biesiada J, Pitstick A, Mayhew C, Medvedovic M, Wells J, Zavros Y. Induction of CD44 Variant Isoforms is an Early Epithelial Response to
Helicobacter pylori
Infection. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.869.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Nina Steele
- Cell & Dev BiologyUniversity of MichiganAnn ArborMI
| | - Loryn Holokai
- Mol Gen & BiochemUniversity of CincinnatiCincinnatiOH
| | | | - Jacek Biesiada
- Environmental ScienceUniversity of CincinnatiCincinnatiOH
| | | | | | | | | | - Yana Zavros
- Pharmacology & Systems PhysiologyUniversity of CincinnatiCincinnatiOH
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Langevin SM, Kuhnell D, Orr-Asman MA, Biesiada J, Zhang X, Medvedovic M, Thomas HE. Balancing yield, purity and practicality: a modified differential ultracentrifugation protocol for efficient isolation of small extracellular vesicles from human serum. RNA Biol 2019; 16:5-12. [PMID: 30604646 DOI: 10.1080/15476286.2018.1564465] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ultracentrifugation remains the gold standard for isolation of small extracellular vesicles (sEV), particularly for cancer applications. The objective of this study was to determine if a widely used ultracentrifugation protocol for isolation of serum sEV could be modified to reduce the number of ultracentrifugation cycles and increase efficiency, while maintaining equal or better sample purity and yield. Serum was obtained from two healthy subjects. sEVs were isolated from 1 mL aliquots using three different ultracentrifugation protocols. Co-isolation of RNA carrier protein was assessed by performing Western blots for ApoA-I, ApoB, and Ago2. Small RNA-sequencing was performed on the sEV isolates, and differential detection of small ncRNA was compared across isolation protocols. Reduction from three- to two-ultracentrifuge cycles with no sucrose cushion resulted in a much higher sEV yield but also had the highest levels of lipoprotein and Ago2 contamination. However, the two-ultracentrifugation cycle protocol that incorporated a 30% sucrose cushion into the first cycle resulted in slightly higher sEV yields with lower levels of protein contamination compared to the lengthier three-ultracentrifugation cycle approach, therefore presenting a more efficient alternative approach for isolation of serum sEVs. It was also notable that there were some differences in sEV ncRNA cargo according to protocol, although it was less than expected given the differences in co-isolated RNA carrier proteins. Our results suggest that use of the modified serum sEV isolation protocol with two ultracentrifugation cycles and incorporating a 30% sucrose cushion offers a more efficient approach in terms of efficiency and purity.
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Affiliation(s)
- Scott M Langevin
- a Division of Epidemiology, Department of Environmental Health , University of Cincinnati College of Medicine , Cincinnati , OH , USA.,b Cincinnati Cancer Center , Cincinnati , OH , USA
| | - Damaris Kuhnell
- a Division of Epidemiology, Department of Environmental Health , University of Cincinnati College of Medicine , Cincinnati , OH , USA
| | - Melissa A Orr-Asman
- c Division of Hematology/Oncology, Department of Internal Medicine , University of Cincinnati College of Medicine , Cincinnati , OH , USA
| | - Jacek Biesiada
- d Division of Biostatistics & Bioinformatics, Department of Environmental Health , University of Cincinnati College of Medicine , Cincinnati , OH , USA
| | - Xiang Zhang
- b Cincinnati Cancer Center , Cincinnati , OH , USA.,e Division of Environmental Genetics & Molecular Toxicology, Department of Environmental Health , University of Cincinnati College of Medicine , Cincinnati , OH , USA
| | - Mario Medvedovic
- b Cincinnati Cancer Center , Cincinnati , OH , USA.,d Division of Biostatistics & Bioinformatics, Department of Environmental Health , University of Cincinnati College of Medicine , Cincinnati , OH , USA
| | - Hala Elnakat Thomas
- b Cincinnati Cancer Center , Cincinnati , OH , USA.,c Division of Hematology/Oncology, Department of Internal Medicine , University of Cincinnati College of Medicine , Cincinnati , OH , USA
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Lounder DT, Khandelwal P, Gloude NJ, Dandoy CE, Jodele S, Medvedovic M, Denson LA, Lane A, Lake K, Litts B, Wilkey A, Davies SM. Interleukin-22 levels are increased in gastrointestinal graft- versus-host disease in children. Haematologica 2018; 103:e480-e482. [PMID: 29773594 PMCID: PMC6165817 DOI: 10.3324/haematol.2017.174771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Dana T Lounder
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Pooja Khandelwal
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Nicholas J Gloude
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Christopher E Dandoy
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Sonata Jodele
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, OH, USA
| | - Lee A Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Adam Lane
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Kelly Lake
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Bridget Litts
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Alyss Wilkey
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Stella M Davies
- Division of Bone Marrow Transplant and Immune Deficiency, Cincinnati Children's Hospital Medical Center, OH, USA
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Vairamani K, Prasad V, Wang Y, Huang W, Chen Y, Medvedovic M, Lorenz JN, Shull GE. NBCe1 Na +-HCO3 - cotransporter ablation causes reduced apoptosis following cardiac ischemia-reperfusion injury in vivo. World J Cardiol 2018; 10:97-109. [PMID: 30344957 PMCID: PMC6189072 DOI: 10.4330/wjc.v10.i9.97] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/05/2018] [Accepted: 07/16/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the hypothesis that cardiomyocyte-specific loss of the electrogenic NBCe1 Na+-HCO3- cotransporter is cardioprotective during in vivo ischemia-reperfusion (IR) injury.
METHODS An NBCe1 (Slc4a4 gene) conditional knockout mouse (KO) model was prepared by gene targeting. Cardiovascular performance of wildtype (WT) and cardiac-specific NBCe1 KO mice was analyzed by intraventricular pressure measurements, and changes in cardiac gene expression were determined by RNA Seq analysis. Response to in vivo IR injury was analyzed after 30 min occlusion of the left anterior descending artery followed by 3 h of reperfusion.
RESULTS Loss of NBCe1 in cardiac myocytes did not impair cardiac contractility or relaxation under basal conditions or in response to β-adrenergic stimulation, and caused only limited changes in gene expression patterns, such as those for electrical excitability. However, following ischemia and reperfusion, KO heart sections exhibited significantly fewer apoptotic nuclei than WT sections.
CONCLUSION These studies indicate that cardiac-specific loss of NBCe1 does not impair cardiovascular performance, causes only minimal changes in gene expression patterns, and protects against IR injury in vivo .
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Affiliation(s)
- Kanimozhi Vairamani
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3026, United States
| | - Vikram Prasad
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229-3039, United States
| | - Yigang Wang
- Department of Pathology, University of Cincinnati, College of Medicine, Cincinnati, OH 45267-0529, United States
| | - Wei Huang
- Department of Pathology, University of Cincinnati, College of Medicine, Cincinnati, OH 45267-0529, United States
| | - Yinhua Chen
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3039, United States
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati, College of Medicine, Cincinnati, OH 45267-0056, United States
| | - John N Lorenz
- Department of Pharmacology and Systems Physiology, University of Cincinnati, College of Medicine, Cincinnati, OH 45267-0575, United States
| | - Gary E Shull
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, College of Medicine, Cincinnati, OH 45267-0524, United States
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Steele NG, Chakrabarti J, Wang J, Biesiada J, Holokai L, Chang J, Nowacki LM, Hawkins J, Mahe M, Sundaram N, Shroyer N, Medvedovic M, Helmrath M, Ahmad S, Zavros Y. An Organoid-Based Preclinical Model of Human Gastric Cancer. Cell Mol Gastroenterol Hepatol 2018; 7:161-184. [PMID: 30522949 PMCID: PMC6279812 DOI: 10.1016/j.jcmgh.2018.09.008] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 09/10/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Our goal was to develop an initial study for the proof of concept whereby gastric cancer organoids are used as an approach to predict the tumor response in individual patients. METHODS Organoids were derived from resected gastric cancer tumors (huTGOs) or normal stomach tissue collected from sleeve gastrectomies (huFGOs). Organoid cultures were treated with standard-of-care chemotherapeutic drugs corresponding to patient treatment: epirubicin, oxaliplatin, and 5-fluorouracil. Organoid response to chemotherapeutic treatment was correlated with the tumor response in each patient from whom the huTGOs were derived. HuTGOs were orthotopically transplanted into the gastric mucosa of NOD scid gamma mice. RESULTS Whereas huFGOs exhibited a half maximal inhibitory concentration that was similar among organoid lines, divergent responses and varying half maximal inhibitory concentration values among the huTGO lines were observed in response to chemotherapeutic drugs. HuTGOs that were sensitive to treatment were derived from a patient with a near complete tumor response to chemotherapy. However, organoids resistant to treatment were derived from patients who exhibited no response to chemotherapy. Orthotropic transplantation of organoids resulted in the engraftment and development of human adenocarcinoma. RNA sequencing revealed that huTGOs closely resembled the patient's native tumor tissue and not commonly used gastric cancer cell lines and cell lines derived from the organoid cultures. CONCLUSIONS The treatment of patient-derived organoids alongside patients from whom cultures were derived will ultimately test their usefulness to predict individual therapy response and patient outcome.
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Affiliation(s)
- Nina G. Steele
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Jayati Chakrabarti
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, Ohio
| | - Jiang Wang
- Department of Pathology and Lab Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jacek Biesiada
- Department of Environmental Health, Division of Biostatistics and Bioinformatics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Loryn Holokai
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, Ohio
| | - Julie Chang
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio
| | - Lauren M. Nowacki
- Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas
| | - Jennifer Hawkins
- Department of Pediatric Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Maxime Mahe
- Department of Pediatric Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Nambirajan Sundaram
- Department of Pediatric Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Noah Shroyer
- Department of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas
| | - Mario Medvedovic
- Department of Environmental Health, Division of Biostatistics and Bioinformatics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Michael Helmrath
- Department of Pediatric Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Syed Ahmad
- Department of Surgery, University of Cincinnati Cancer Institute, Cincinnati, Ohio
| | - Yana Zavros
- Department of Pathology and Lab Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio,Correspondence Address correspondence to: Yana Zavros, PhD, University of Cincinnati College of Medicine, Department of Pharmacology and Systems Physiology, 231 Albert B. Sabin Way, Room 4255 MSB, Cincinnati, Ohio 45267-0576. fax: (513) 558-3756.
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Leung YK, Ouyang B, Niu L, Xie C, Ying J, Medvedovic M, Chen A, Weihe P, Valvi D, Grandjean P, Ho SM. Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort. Epigenetics 2018; 13:290-300. [PMID: 29560787 DOI: 10.1080/15592294.2018.1445901] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Faroe islanders consume marine foods contaminated with methylmercury (MeHg), polychlorinated biphenyls (PCBs), and other toxicants associated with chronic disease risks. Differential DNA methylation at specific CpG sites in cord blood may serve as a surrogate biomarker of health impacts from chemical exposures. We aimed to identify key environmental chemicals in cord blood associated with DNA methylation changes in a population with elevated exposure to chemical mixtures. We studied 72 participants of a Faroese birth cohort recruited between 1986 and 1987 and followed until adulthood. The cord blood DNA methylome was profiled using Infinium HumanMethylation450 BeadChips. We determined the associations of CpG site changes with concentrations of MeHg, major PCBs, other organochlorine compounds [hexachlorobenzene (HCB), p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE) and p,p'-dichlorodiphenyltrichloroethane], and perfluoroalkyl substances. In a combined sex analysis, among the 16 chemicals studied, PCB congener 105 (CB-105) exposure was associated with the majority of differentially methylated CpG sites (214 out of a total of 250). In female-only analysis, only 73 CB-105 associated CpG sites were detected, 44 of which were mapped to genes in the ELAV1-associated cancer network. In males-only, methylation changes were seen for perfluorooctane sulfonate, HCB, and p,p'-DDE in 10,598, 1,238, and 1,473 CpG sites, respectively, 15% of which were enriched in cytobands of the X-chromosome associated with neurological disorders. In this multiple-pollutant and genome-wide study, we identified key epigenetic toxicants. The significant enrichment of specific X-chromosome sites in males implies potential sex-specific epigenome responses to prenatal chemical exposures.
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Affiliation(s)
- Yuet-Kin Leung
- a Division of Environmental Genetics and Molecular Toxicology.,e Center of Environmental Genetics.,f Cincinnati Cancer Center , University of Cincinnati Medical Center , Cincinnati , USA
| | - Bin Ouyang
- a Division of Environmental Genetics and Molecular Toxicology.,e Center of Environmental Genetics
| | - Liang Niu
- b Biostatistics & Bioinformatics.,e Center of Environmental Genetics
| | - Changchun Xie
- b Biostatistics & Bioinformatics.,e Center of Environmental Genetics
| | - Jun Ying
- b Biostatistics & Bioinformatics.,c Public Health Science and
| | - Mario Medvedovic
- b Biostatistics & Bioinformatics.,e Center of Environmental Genetics.,f Cincinnati Cancer Center , University of Cincinnati Medical Center , Cincinnati , USA
| | - Aimin Chen
- d Epidemiology Department of Environmental Health.,e Center of Environmental Genetics
| | - Pal Weihe
- h Department of Occupational Medicine and Public Health , Faroese Hospital System , Torshavn , Faroe Islands
| | - Damaskini Valvi
- i Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , USA
| | - Philippe Grandjean
- i Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , USA.,j Department of Environmental Medicine , University of Southern Denmark , Odense , Denmark
| | - Shuk-Mei Ho
- a Division of Environmental Genetics and Molecular Toxicology.,e Center of Environmental Genetics.,f Cincinnati Cancer Center , University of Cincinnati Medical Center , Cincinnati , USA.,g Cincinnati Veteran Affairs Medical Center , Cincinnati , USA
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VonHandorf A, Sánchez-Martín FJ, Biesiada J, Zhang H, Zhang X, Medvedovic M, Puga A. Chromium disrupts chromatin organization and CTCF access to its cognate sites in promoters of differentially expressed genes. Epigenetics 2018; 13:363-375. [PMID: 29561703 PMCID: PMC6140807 DOI: 10.1080/15592294.2018.1454243] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 12/15/2017] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 01/22/2023] Open
Abstract
Hexavalent chromium compounds are well-established respiratory carcinogens used in industrial processes. While inhalation exposure constitutes an occupational risk affecting mostly chromium workers, environmental exposure from drinking water is a widespread gastrointestinal cancer risk, affecting millions of people throughout the world. Cr(VI) is genotoxic, forming protein-Cr-DNA adducts and silencing tumor suppressor genes, but its mechanism of action at the molecular level is poorly understood. Our prior work using FAIRE showed that Cr(VI) disrupted the binding of transcription factors CTCF and AP-1 to their cognate chromatin sites. Here, we used two complementary approaches to test the hypothesis that chromium perturbs chromatin organization and dynamics. DANPOS2 analyses of MNase-seq data identified several chromatin alterations induced by Cr(VI) affecting nucleosome architecture, including occupancy changes at specific genome locations; position shifts of 10 nucleotides or more; and changes in position amplitude or fuzziness. ATAC-seq analysis revealed that Cr(VI) disrupted the accessibility of chromatin regions enriched for CTCF and AP-1 binding motifs, with a significant co-occurrence of binding sites for both factors in the same region. Cr(VI)-enriched CTCF sites were confirmed by ChIP-seq and found to correlate with evolutionarily conserved sites occupied by CTCF in vivo, as determined by comparison with ENCODE-validated CTCF datasets from mouse liver. In addition, more than 30% of the Cr(VI)-enriched CTCF sites were located in promoters of genes differentially expressed from chromium treatment. Our results support the conclusion that Cr(VI) exposure promotes broad changes in chromatin accessibility and suggest that the subsequent effects on transcription regulation may result from disruption of CTCF binding and nucleosome spacing, implicating transcription regulatory mechanisms as primary Cr(VI) targets.
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Affiliation(s)
- Andrew VonHandorf
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United State
| | - Francisco Javier Sánchez-Martín
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United State
| | - Jacek Biesiada
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United State
| | - Hongxia Zhang
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United State
| | - Xiang Zhang
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United State
| | - Mario Medvedovic
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United State
| | - Alvaro Puga
- Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United State
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Mierzwa M, Biesiada J, Zhang X, Kuhnell D, Redmond K, Huth B, Takiar V, Wise-Draper T, Sadraei N, Tang A, Mark J, Casper K, Medvedovic M, Langevin S. Whole-Exome Sequencing of Aggressive Cutaneous Head and Neck Squamous Cell Carcinoma. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2017.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Haque SU, Niu L, Kuhnell D, Hendershot J, Biesiada J, Niu W, Hagan MC, Kelsey KT, Casper KA, Wise-Draper TM, Medvedovic M, Langevin SM. Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma. Head Neck 2018; 40:1555-1564. [PMID: 29575229 DOI: 10.1002/hed.25136] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 05/24/2017] [Revised: 11/30/2017] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Long non-coding RNA (lncRNA) has emerged as a new avenue of interest due to its various biological functions in cancer. Abnormal expression of lncRNA has been reported in other malignancies but has been understudied in head and neck squamous cell carcinoma (HNSCC). METHODS The lncRNA expression was interrogated via quantitative real-time polymerase chain reaction (qRT-PCR) array for 19 human papillomavirus (HPV)-negative HNSCC tumor-normal pairs. The Cancer Genome Atlas (TCGA) was used to validate these results. The association between differentially expressed lncRNA and survival outcomes was analyzed. RESULTS Differential expression was validated for 5 lncRNA (SPRY4-IT1, HEIH, LUCAT1, LINC00152, and HAND2-AS1). There was also an inverse association between MEG3 expression (not significantly differentially expressed in TCGA tumors but highly variable expression) and 3-year recurrence-free survival (RFS). CONCLUSION We identified and validated differential expression of 5 lncRNA in HPV-negative HNSCC. Low MEG3 expression was associated with favorable 3-year RFS, although the significance of this finding remains unclear.
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Affiliation(s)
- Sulsal-Ul Haque
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Liang Niu
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Damaris Kuhnell
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jacob Hendershot
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jacek Biesiada
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Wen Niu
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Matthew C Hagan
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Keith A Casper
- Department of Otolaryngology, University of Michigan, Ann Arbor, Michigan
| | - Trisha M Wise-Draper
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati College of Medicine, Cincinnati, Ohio.,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
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Abdel-Hameed EA, Rouster SD, Boyce CL, Zhang X, Biesiada J, Medvedovic M, Sherman KE. Ultra-Deep Genomic Sequencing of HCV NS5A Resistance-Associated Substitutions in HCV/HIV Coinfected Patients. Dig Dis Sci 2018; 63:645-652. [PMID: 29330726 DOI: 10.1007/s10620-017-4895-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/18/2017] [Indexed: 12/09/2022]
Abstract
BACKGROUND AND AIMS The prevalence of naturally occurring HCV-NS5A resistance-associated substitutions (RAS) to DAA drugs might affect the response to treatment in HCV/HIV coinfected subjects. There are limited data on the frequency of HCV-NS5A naturally occurring drug-RAS at baseline in HCV/HIV coinfected patients when ultra-deep sequencing methodologies are applied. METHODS HCV-NS5A-RAS were evaluated among 25 subjects in each group. Patients were matched by age, gender, and hepatic fibrosis stage category to control for selection bias. RESULTS Within subtype 1a, RAS were observed in 28% of HCV monoinfected and 48% of HCV/HIV coinfected subjects. More patients in the HCV/HIV coinfected group had clinically relevant mutations to DAA directed at NS5A. CONCLUSION While the clinical significance of this observation may be limited in highly drug adherent populations, some HCV/HIV coinfected persons may be at greater risk of viral resistance if suboptimal dosing occurs.
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Affiliation(s)
- Enass A Abdel-Hameed
- University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH, 45267-0595, USA
| | - Susan D Rouster
- University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH, 45267-0595, USA
| | - Ceejay L Boyce
- University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH, 45267-0595, USA
| | - Xiang Zhang
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Jacek Biesiada
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Kenneth E Sherman
- University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH, 45267-0595, USA.
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Jodele S, Luebbering N, Medvedovic M, Chen J, Davies SM. Complement and Interferon Pathway Activation Triggers Thrombotic Microangiopathy after Stem Cell Transplantation. Biol Blood Marrow Transplant 2018. [DOI: 10.1016/j.bbmt.2017.12.520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Huang W, Feng Y, Liang J, Yu H, Wang C, Wang B, Wang M, Jiang L, Meng W, Cai W, Medvedovic M, Chen J, Paul C, Davidson WS, Sadayappan S, Stambrook PJ, Yu XY, Wang Y. Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration. Nat Commun 2018; 9:700. [PMID: 29453456 PMCID: PMC5816015 DOI: 10.1038/s41467-018-03019-z] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [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] [Received: 03/06/2017] [Accepted: 01/12/2018] [Indexed: 12/20/2022] Open
Abstract
The goal of replenishing the cardiomyocyte (CM) population using regenerative therapies following myocardial infarction (MI) is hampered by the limited regeneration capacity of adult CMs, partially due to their withdrawal from the cell cycle. Here, we show that microRNA-128 (miR-128) is upregulated in CMs during the postnatal switch from proliferation to terminal differentiation. In neonatal mice, cardiac-specific overexpression of miR-128 impairs CM proliferation and cardiac function, while miR-128 deletion extends proliferation of postnatal CMs by enhancing expression of the chromatin modifier SUZ12, which suppresses p27 (cyclin-dependent kinase inhibitor) expression and activates the positive cell cycle regulators Cyclin E and CDK2. Furthermore, deletion of miR-128 promotes cell cycle re-entry of adult CMs, thereby reducing the levels of fibrosis, and attenuating cardiac dysfunction in response to MI. These results suggest that miR-128 serves as a critical regulator of endogenous CM proliferation, and might be a novel therapeutic target for heart repair. During early postnatal development in mammals, cardiomyocytes exit the cell cycle, losing their regenerative capacity. Here the authors show that, following myocardial infarction, loss of microRNA-128 promotes cardiomyocyte proliferation and cardiac regeneration in adult mice partly via enhancing the expression of the chromatin modifier SUZ12.
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Affiliation(s)
- Wei Huang
- Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China.,Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Yuliang Feng
- Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Jialiang Liang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Hao Yu
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Cheng Wang
- Department of Molecular Biology, Radboud Institute of Molecular Life Sciences and Faculty of Science, Radboud University, Nijmegen, 6525, Gelderland, The Netherlands
| | - Boyu Wang
- Samaritan Medical Center, 830 Washington Street, Watertown, NY, 13601, USA
| | - Mingyang Wang
- College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Lin Jiang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Wei Meng
- Division of Liver Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510630, China
| | - Wenfeng Cai
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Jenny Chen
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Christian Paul
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - W Sean Davidson
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Sakthivel Sadayappan
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Peter J Stambrook
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Xi-Yong Yu
- Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmaceutical Sciences & Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 511436, China.
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Syst 2018; 6:13-24. [PMID: 29199020 PMCID: PMC5799026 DOI: 10.1016/j.cels.2017.11.001] [Citation(s) in RCA: 241] [Impact Index Per Article: 40.2] [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: 07/27/2017] [Revised: 09/13/2017] [Accepted: 11/01/2017] [Indexed: 12/19/2022]
Abstract
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.
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Affiliation(s)
- Alexandra B Keenan
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sherry L Jenkins
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen M Jagodnik
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simon Koplev
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Edward He
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Denis Torre
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zichen Wang
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anders B Dohlman
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Moshe C Silverstein
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxim V Kuleshov
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Vasileios Stathias
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Raymond Terryn
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Daniel Cooper
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Michele Forlin
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Amar Koleti
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Dusica Vidovic
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Caty Chung
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Stephan C Schürer
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Jouzas Vasiliauskas
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Marcin Pilarczyk
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Behrouz Shamsaei
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Mehdi Fazel
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Yan Ren
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Wen Niu
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Nicholas A Clark
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Shana White
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Naim Mahi
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Lixia Zhang
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Michal Kouril
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - John F Reichard
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Siva Sivaganesan
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Mario Medvedovic
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Jaroslaw Meller
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Rick J Koch
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marc R Birtwistle
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ravi Iyengar
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric A Sobie
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Evren U Azeloglu
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julia Kaye
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jeannette Osterloh
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kelly Haston
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jaslin Kalra
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Steve Finkbiener
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jonathan Li
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Pamela Milani
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Miriam Adam
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | | | - Karen Sachs
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Alex Lenail
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Divya Ramamoorthy
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Ernest Fraenkel
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Gavin Daigle
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Uzma Hussain
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Alyssa Coye
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeffrey Rothstein
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Dhruv Sareen
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Loren Ornelas
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Maria Banuelos
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Berhan Mandefro
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ritchie Ho
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Clive N Svendsen
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ryan G Lim
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Jennifer Stocksdale
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Malcolm S Casale
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Terri G Thompson
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Jie Wu
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Leslie M Thompson
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Victoria Dardov
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Andrea Matlock
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Jacob D Jaffe
- LINCS PCCSE, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Aravind Subramanian
- LINCS Center for Transcriptomics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Todd R Golub
- LINCS Center for Transcriptomics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sean D Erickson
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Marc Hafner
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jia-Ren Lin
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin E Mills
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Niepel
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - David Wrobel
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K Sorger
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Laura M Heiser
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joe W Gray
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - James E Korkola
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gordon B Mills
- MEP-LINCS Center, Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark LaBarge
- MEP-LINCS Center, Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91011, USA; MEP-LINCS Center, Center for Cancer Biomarkers Research, University of Bergen, Bergen 5009, Norway
| | - Heidi S Feiler
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mark A Dane
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elmar Bucher
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michel Nederlof
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA; MEP-LINCS Center, Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Damir Sudar
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA; MEP-LINCS Center, Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Sean Gross
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - David F Kilburn
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rebecca Smith
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kaylyn Devlin
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
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