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Davyson E, Shen X, Huider F, Adams M, Borges K, McCartney D, Barker L, Van Dongen J, Boomsma D, Weihs A, Grabe H, Kühn L, Teumer A, Völzke H, Zhu T, Kaprio J, Ollikainen M, David FS, Meinert S, Stein F, Forstner AJ, Dannlowski U, Kircher T, Tapuc A, Czamara D, Binder EB, Brückl T, Kwong A, Yousefi P, Wong C, Arseneault L, Fisher HL, Mill J, Cox S, Redmond P, Russ TC, van den Oord E, Aberg KA, Penninx B, Marioni RE, Wray NR, McIntosh AM. Antidepressant Exposure and DNA Methylation: Insights from a Methylome-Wide Association Study. medRxiv 2024:2024.05.01.24306640. [PMID: 38746357 PMCID: PMC11092700 DOI: 10.1101/2024.05.01.24306640] [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: 05/16/2024]
Abstract
Importance Understanding antidepressant mechanisms could help design more effective and tolerated treatments. Objective Identify DNA methylation (DNAm) changes associated with antidepressant exposure. Design Case-control methylome-wide association studies (MWAS) of antidepressant exposure were performed from blood samples collected between 2006-2011 in Generation Scotland (GS). The summary statistics were tested for enrichment in specific tissues, gene ontologies and an independent MWAS in the Netherlands Study of Depression and Anxiety (NESDA). A methylation profile score (MPS) was derived and tested for its association with antidepressant exposure in eight independent cohorts, alongside prospective data from GS. Setting Cohorts; GS, NESDA, FTC, SHIP-Trend, FOR2107, LBC1936, MARS-UniDep, ALSPAC, E-Risk, and NTR. Participants Participants with DNAm data and self-report/prescription derived antidepressant exposure. Main Outcomes and Measures Whole-blood DNAm levels were assayed by the EPIC/450K Illumina array (9 studies, N exposed = 661, N unexposed = 9,575) alongside MBD-Seq in NESDA (N exposed = 398, N unexposed = 414). Antidepressant exposure was measured by self- report and/or antidepressant prescriptions. Results The self-report MWAS (N = 16,536, N exposed = 1,508, mean age = 48, 59% female) and the prescription-derived MWAS (N = 7,951, N exposed = 861, mean age = 47, 59% female), found hypermethylation at seven and four DNAm sites (p < 9.42x10 -8 ), respectively. The top locus was cg26277237 ( KANK1, p self-report = 9.3x10 -13 , p prescription = 6.1x10 -3 ). The self-report MWAS found a differentially methylated region, mapping to DGUOK-AS1 ( p adj = 5.0x10 -3 ) alongside significant enrichment for genes expressed in the amygdala, the "synaptic vesicle membrane" gene ontology and the top 1% of CpGs from the NESDA MWAS (OR = 1.39, p < 0.042). The MPS was associated with antidepressant exposure in meta-analysed data from external cohorts (N studies = 9, N = 10,236, N exposed = 661, f3 = 0.196, p < 1x10 -4 ). Conclusions and Relevance Antidepressant exposure is associated with changes in DNAm across different cohorts. Further investigation into these changes could inform on new targets for antidepressant treatments. 3 Key Points Question: Is antidepressant exposure associated with differential whole blood DNA methylation?Findings: In this methylome-wide association study of 16,536 adults across Scotland, antidepressant exposure was significantly associated with hypermethylation at CpGs mapping to KANK1 and DGUOK-AS1. A methylation profile score trained on this sample was significantly associated with antidepressant exposure (pooled f3 [95%CI]=0.196 [0.105, 0.288], p < 1x10 -4 ) in a meta-analysis of external datasets. Meaning: Antidepressant exposure is associated with hypermethylation at KANK1 and DGUOK-AS1 , which have roles in mitochondrial metabolism and neurite outgrowth. If replicated in future studies, targeting these genes could inform the design of more effective and better tolerated treatments for depression.
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Grit JL, McGee LE, Tovar EA, Essenburg CJ, Wolfrum E, Beddows I, Williams K, Sheridan RTC, Schipper JL, Adams M, Arumugam M, Vander Woude T, Gurunathan S, Field JM, Wulfkuhle J, Petricoin EF, Graveel CR, Steensma MR. p53 modulates kinase inhibitor resistance and lineage plasticity in NF1-related MPNSTs. Oncogene 2024; 43:1411-1430. [PMID: 38480916 PMCID: PMC11068581 DOI: 10.1038/s41388-024-03000-9] [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: 06/06/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 05/05/2024]
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are chemotherapy resistant sarcomas that are a leading cause of death in neurofibromatosis type 1 (NF1). Although NF1-related MPNSTs derive from neural crest cell origin, they also exhibit intratumoral heterogeneity. TP53 mutations are associated with significantly decreased survival in MPNSTs, however the mechanisms underlying TP53-mediated therapy responses are unclear in the context of NF1-deficiency. We evaluated the role of two commonly altered genes, MET and TP53, in kinome reprograming and cellular differentiation in preclinical MPNST mouse models. We previously showed that MET amplification occurs early in human MPNST progression and that Trp53 loss abrogated MET-addiction resulting in MET inhibitor resistance. Here we demonstrate a novel mechanism of therapy resistance whereby p53 alters MET stability, localization, and downstream signaling leading to kinome reprogramming and lineage plasticity. Trp53 loss also resulted in a shift from RAS/ERK to AKT signaling and enhanced sensitivity to MEK and mTOR inhibition. In response to MET, MEK and mTOR inhibition, we observed broad and heterogeneous activation of key differentiation genes in Trp53-deficient lines suggesting Trp53 loss also impacts lineage plasticity in MPNSTs. These results demonstrate the mechanisms by which p53 loss alters MET dependency and therapy resistance in MPNSTS through kinome reprogramming and phenotypic flexibility.
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Affiliation(s)
- Jamie L Grit
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Lauren E McGee
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Elizabeth A Tovar
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Curt J Essenburg
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Emily Wolfrum
- Bioinformatics & Biostatistics Core, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Ian Beddows
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Kaitlin Williams
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | | | - Joshua L Schipper
- Flow Cytometry Core, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Menusha Arumugam
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Thomas Vander Woude
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Sharavana Gurunathan
- Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jeffrey M Field
- Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA
| | - Carrie R Graveel
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Matthew R Steensma
- Department of Cell Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.
- Helen DeVos Children's Hospital, Corewell Health System, Grand Rapids, MI, 49503, USA.
- Michigan State University College of Human Medicine, Grand Rapids, MI, 49503, USA.
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Kochmanski J, Virani M, Kuhn NC, Boyd SL, Becker K, Adams M, Bernstein AI. Developmental origins of Parkinson's disease risk: perinatal exposure to the organochlorine pesticide dieldrin leads to sex-specific DNA modifications in critical neurodevelopmental pathways in the mouse midbrain. bioRxiv 2024:2024.04.26.590998. [PMID: 38746441 PMCID: PMC11092502 DOI: 10.1101/2024.04.26.590998] [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: 05/16/2024]
Abstract
Epidemiological studies show that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson's disease (PD). Animal studies support a link between developmental dieldrin exposure and increased neuronal susceptibility in the α-synuclein preformed fibril (α-syn PFF) and MPTP models in adult male C57BL/6 mice. In a previous study, we showed that developmental dieldrin exposure was associated with sex-specific changes in DNA modifications within genes related to dopaminergic neuron development and maintenance at 12 weeks of age. Here, we used capture hybridization-sequencing with custom baits to interrogate DNA modifications across the entire genetic loci of the previously identified genes at multiple time points - birth, 6 weeks, 12 weeks, and 36 weeks old. We identified largely sex-specific dieldrin-induced changes in DNA modifications at each time point that annotated to pathways important for neurodevelopment, potentially related to critical steps in early neurodevelopment, dopaminergic neuron differentiation, synaptogenesis, synaptic plasticity, and glial-neuron interactions. Despite large numbers of age-specific DNA modifications, longitudinal analysis identified a small number of DMCs with dieldrin-induced deflection of epigenetic aging. The sex-specificity of these results adds to evidence that sex-specific responses to PD-related exposures may underly sex-specific differences in disease. Overall, these data support the idea that developmental dieldrin exposure leads to changes in epigenetic patterns that persist after the exposure period and disrupt critical neurodevelopmental pathways, thereby impacting risk of late life diseases, including PD.
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Goralski TM, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse DJ, Henderson MX. Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology. Nat Commun 2024; 15:2642. [PMID: 38531900 PMCID: PMC10966039 DOI: 10.1038/s41467-024-47027-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
A key hallmark of Parkinson's disease (PD) is Lewy pathology. Composed of α-synuclein, Lewy pathology is found both in dopaminergic neurons that modulate motor function, and cortical regions that control cognitive function. Recent work has established the molecular identity of dopaminergic neurons susceptible to death, but little is known about cortical neurons susceptible to Lewy pathology or molecular changes induced by aggregates. In the current study, we use spatial transcriptomics to capture whole transcriptome signatures from cortical neurons with α-synuclein pathology compared to neurons without pathology. We find, both in PD and related PD dementia, dementia with Lewy bodies and in the pre-formed fibril α-synucleinopathy mouse model, that specific classes of excitatory neurons are vulnerable to developing Lewy pathology. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. Neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and describe a conserved signature of molecular dysfunction in both mice and humans.
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Affiliation(s)
- Thomas M Goralski
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lindsay Meyerdirk
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Libby Breton
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Laura Brasseur
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Kevin Kurgat
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Daniella DeWeerd
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lisa Turner
- Van Andel Institute Pathology Core, Grand Rapids, MI, 49503, USA
| | - Katelyn Becker
- Van Andel Institute Genomics Core, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Van Andel Institute Genomics Core, Grand Rapids, MI, 49503, USA
| | | | - Michael X Henderson
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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Bosak J, Messersmith L, Bryer C, Drainoni M, Goodman D, Adams M, Barry T, Flanagan C, Flanagan V, Wolff K, Declercq E. "They just looked at me like I was human": The experiences of parenting women and providers with substance use disorder treatment. J Subst Use Addict Treat 2024; 157:209240. [PMID: 38061633 DOI: 10.1016/j.josat.2023.209240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/11/2023] [Accepted: 11/30/2023] [Indexed: 02/20/2024]
Abstract
BACKGROUND The current US addiction treatment system does not effectively meet the needs of pregnant and parenting women with substance use disorder (SUD). The aim of this research was to identify barriers and facilitators to engagement and retention in SUD residential treatment for pregnant and parenting women. This research was part of a co-design process to collaboratively create a more patient-centered long-term residential program. DESIGN AND METHODS The study conducted semi-structured individual interviews with both parenting women with lived experience (WWLE) in residential SUD treatment and SUD treatment providers. Interviews aimed to elicit participants' experiences either receiving or providing care. The study team analyzed data in NVivo-12 using a deductive codebook based on the six principles of trauma informed care (TIC). RESULTS We conducted a total of 32 interviews (WWLE =13, SUD providers =19). The study identified four major themes: 1) peer relationships provide inspiration and diminish shame; 2) providing individuals safe space to stumble in recovery creates opportunities for growth and builds self-efficacy; 3) reasonable, clear boundaries create a structured, protective environment for early recovery; 4) nonjudgmental connections facilitate engagement and build trust. We identified small pivotal moments along the continuum of care that showed how the elements in the four themes enhanced engagement and retention in treatment. These interactions, along the care continuum, are either structural (workflow process) or relational (interpersonal). CONCLUSION This research increases understanding of the interplay of the structural and relational barriers and facilitators to engagement and retention in treatment. These seemingly minor positive or negative interactions along the care continuum are pivotal to fully operationalizing TIC and optimizing women's engagement in treatment. Improvement strategies that integrate the voices of WWLE and collaboratively co-design a more patient-centered system are critical steps to improving engagement in SUD treatment and more equitable SUD treatment services.
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Affiliation(s)
- J Bosak
- Community Health Services, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118, United States; Dartmouth Hitchcock Medical Center, 1 Medical Drive, Lebanon, NH 03766, United States; Dartmouth Geisel School of Medicine, 1 Medical Drive, Lebanon, NH 03766, United States.
| | - L Messersmith
- Department of Global Health, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118, United States
| | - C Bryer
- Dartmouth Hitchcock Medical Center, 1 Medical Drive, Lebanon, NH 03766, United States
| | - M Drainoni
- Section of Infectious Diseases, Department of Medicine, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 801 Massachusetts Ave, Boston, MA 02118, United States; Department of Health Law Policy & Management, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA, United States
| | - D Goodman
- Dartmouth Hitchcock Medical Center, 1 Medical Drive, Lebanon, NH 03766, United States; Dartmouth Geisel School of Medicine, 1 Medical Drive, Lebanon, NH 03766, United States
| | - M Adams
- Families Flourish Northeast, P.O Box 20, Enfield Center, NH 03749, United States
| | - T Barry
- Dartmouth Hitchcock Medical Center, 1 Medical Drive, Lebanon, NH 03766, United States
| | - C Flanagan
- Families Flourish Northeast, P.O Box 20, Enfield Center, NH 03749, United States
| | - V Flanagan
- Dartmouth Hitchcock Medical Center, 1 Medical Drive, Lebanon, NH 03766, United States
| | - K Wolff
- Independent Researcher, 566 Hanover Center Rd, Hanover, NH 03755, United States
| | - E Declercq
- Community Health Services, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118, United States
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Sad K, Jones CY, Adams M, Lustenberger S, Lee RS, Elayavalli SR, Farhi J, Lemon LD, Fasken MB, Corbett AH, Spangle JM. Histone H3 E50K mutation confers oncogenic activity and supports an EMT phenotype. bioRxiv 2023:2023.10.11.561775. [PMID: 37873162 PMCID: PMC10592736 DOI: 10.1101/2023.10.11.561775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequencing of human patient tumors has identified recurrent missense mutations in genes encoding core histones. We report that mutations that convert histone H3 amino acid 50 from a glutamate to a lysine (H3E50K) support an oncogenic phenotype in human cells. Expression of H3E50K is sufficient to transform human cells as evidenced by a dramatic increase in cell migration and invasion, and a statistically significant increase in proliferation and clonogenicity. H3E50K also increases the invasive phenotype in the context of co-occurring BRAF mutations, which are present in patient tumors characterized by H3E50K. H3E50 lies on the globular domain surface in a region that contacts H4 within the nucleosome. We find that H3E50K perturbs proximal H3 post-translational modifications globally and dysregulates gene expression, activating the epithelial to mesenchymal transition. Functional studies using S. cerevisiae reveal that, while yeast cells that express H3E50K as the sole copy of histone H3 show sensitivity to cellular stressors, including caffeine, H3E50K cells display some genetic interactions that are distinct from the characterized H3K36M oncohistone yeast model. Taken together, these data suggest that additional histone H3 mutations have the potential to be oncogenic drivers and function through distinct mechanisms that dysregulate gene expression.
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Affiliation(s)
- K Sad
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - CY Jones
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
| | - M Adams
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - S Lustenberger
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - RS Lee
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - SR Elayavalli
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
| | - J Farhi
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - LD Lemon
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
| | - MB Fasken
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
| | - AH Corbett
- Department of Biology; Emory College of Arts and Sciences, Atlanta GA 30322
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322
| | - JM Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322
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Adams M, Nardella N, Bryant JMM, Palm RF, Frakes JM, Hodul P, Hoffe S. Borderline Resectable Pancreatic Cancer: Impact on Neoadjuvant Response Post Integration of MRI Guided Adaptive Radiation Therapy. Int J Radiat Oncol Biol Phys 2023; 117:e281-e282. [PMID: 37785051 DOI: 10.1016/j.ijrobp.2023.06.1264] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The optimal neoadjuvant therapy regimen for patients with borderline resectable pancreas cancer (BRPC) remains to be defined, with a recent ALLIANCE study reporting that chemotherapy alone prior to resection is an acceptable standard of care. However, pathologic differences in response between patients receiving chemotherapy alone and chemotherapy with radiation with stereotactic technique is not clear. In this study, we sought to compare differences in pathologic outcomes between patients undergoing surgery in 2018 compared with 2021 at our comprehensive cancer center, after the new data of chemotherapy alone had been reported and after our center integrated stereotactic MRI guided online adaptive radiotherapy (SMART). MATERIALS/METHODS Newly diagnosed BRPC patients were included on this IRB approved study if they were treated on our institutional clinical pathway with initial chemotherapy (FOLFIRINOX or Gemcitabine based) followed by 5 fraction stereotactic body radiation therapy (SBRT) with the intention of primary tumor resection. After surgical resection, tumor response was classified by the Tumor Regression Grading (TRG) System of the College of American Pathology on a scale from 0 (complete response) to 3 (poor response). RESULTS In 2018 when patients were treated on a conventional Linac, the median SBRT dose was 40.5 Gy compared with 46.1 Gy in 2021 after SMART integration. In 2018, 54 BRPC patients were treated and 52% were explored. Of those, 72% were resected with a 95% (19/20) rate of R0 resection. In 2021, 66 BRPC patients were treated and 45% were explored. Of those, 74% were resected with a 100% (22/22) rate of R0 resection. In 2018, pathological results showed that 55% (11/20) had lymphovascular invasion (LVI) and 90% (18/20) had perineural invasion (PNI) with a median tumor size of 2.5 cm. The average lymph node ratio in 2018 was 0.06 in 2018 and 0.05 in 2021. In 2021, pathological results showed that 36% (8/22) had LVI and 64% (14/22) had PNI with a median tumor size of 2.2 cm. In 2018, 43% of surgeries required portal vein (PV) resection compared with 27% in 2021. In 2018, of those patients who underwent surgery, 65% (13/20) received both chemotherapy and SBRT compared to 10% (2/20) with chemotherapy alone. In 2021, 73% (16/22) received chemotherapy and SBRT prior to surgery compared with 27% (6/22) who received chemotherapy only. Patients who received chemotherapy only (n = 8) had an average TRG of 2.1 compared to the patients receiving combination therapy (29) with an average TRG of 1.8. CONCLUSION This data suggests that higher ablative dose delivery with SMART following systemic therapy may be associated with improved pathologic outcomes, with less LVI, PNI, portal vein resection and improved TRG scores. Further prospective study is needed to confirm improved pathologic outcomes with SMART and to optimize patient selection regarding which patients benefit the most from the combination of chemotherapy and SBRT.
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Affiliation(s)
- M Adams
- Lake Erie College of Osteopathic Medicine, Lakewood Ranch, FL
| | | | | | - R F Palm
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - J M Frakes
- H. Lee Moffitt Cancer Center and Research Institute, Department of Radiation Oncology, Tampa, FL
| | - P Hodul
- H. Lee Moffitt Cancer Center and Research Institute, Department of Surgical Oncology, Tampa, FL
| | - S Hoffe
- H. Lee Moffitt Cancer Center and Research Institute, Department of Radiation Oncology, Tampa, FL
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Smitherman EA, Chahine RA, Beukelman T, Lewandowski LB, Rahman AKMF, Wenderfer SE, Curtis JR, Hersh AO, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar‐Smiley F, Barillas‐Arias L, Basiaga M, Baszis K, Becker M, Bell‐Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang‐Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel‐Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie‐Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui‐Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein‐Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PM, McGuire S, McHale I, McMonagle A, McMullen‐Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O'Brien B, O'Brien T, Okeke O, Oliver M, Olson J, O'Neil K, Onel K, Orandi A, Orlando M, Osei‐Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan‐Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas‐Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth‐Wojcicki E, Rouster – Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert‐Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner‐Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Childhood-Onset Lupus Nephritis in the Childhood Arthritis and Rheumatology Research Alliance Registry: Short-Term Kidney Status and Variation in Care. Arthritis Care Res (Hoboken) 2023; 75:1553-1562. [PMID: 36775844 PMCID: PMC10500561 DOI: 10.1002/acr.25002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 11/23/2021] [Revised: 07/14/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE The goal was to characterize short-term kidney status and describe variation in early care utilization in a multicenter cohort of patients with childhood-onset systemic lupus erythematosus (cSLE) and nephritis. METHODS We analyzed previously collected prospective data from North American patients with cSLE with kidney biopsy-proven nephritis enrolled in the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry from March 2017 through December 2019. We determined the proportion of patients with abnormal kidney status at the most recent registry visit and applied generalized linear mixed models to identify associated factors. We also calculated frequency of medication use, both during induction and ever recorded. RESULTS We identified 222 patients with kidney biopsy-proven nephritis, with 64% class III/IV nephritis on initial biopsy. At the most recent registry visit at median (interquartile range) of 17 (8-29) months from initial kidney biopsy, 58 of 106 patients (55%) with available data had abnormal kidney status. This finding was associated with male sex (odds ratio [OR] 3.88, 95% confidence interval [95% CI] 1.21-12.46) and age at cSLE diagnosis (OR 1.23, 95% CI 1.01-1.49). Patients with class IV nephritis were more likely than class III to receive cyclophosphamide and rituximab during induction. There was substantial variation in mycophenolate, cyclophosphamide, and rituximab ever use patterns across rheumatology centers. CONCLUSION In this cohort with predominately class III/IV nephritis, male sex and older age at cSLE diagnosis were associated with abnormal short-term kidney status. We also observed substantial variation in contemporary medication use for pediatric lupus nephritis between pediatric rheumatology centers. Additional studies are needed to better understand the impact of this variation on long-term kidney outcomes.
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Goralski T, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse D, Henderson MX. Spatial transcriptomics reveals molecular dysfunction associated with Lewy pathology. bioRxiv 2023:2023.05.17.541144. [PMID: 37292685 PMCID: PMC10245657 DOI: 10.1101/2023.05.17.541144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lewy pathology composed of α-synuclein is the key pathological hallmark of Parkinson's disease (PD), found both in dopaminergic neurons that control motor function, and throughout cortical regions that control cognitive function. Recent work has investigated which dopaminergic neurons are most susceptible to death, but little is known about which neurons are vulnerable to developing Lewy pathology and what molecular changes an aggregate induces. In the current study, we use spatial transcriptomics to selectively capture whole transcriptome signatures from cortical neurons with Lewy pathology compared to those without pathology in the same brains. We find, both in PD and in a mouse model of PD, that there are specific classes of excitatory neurons that are vulnerable to developing Lewy pathology in the cortex. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. This gene signature indicates that neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. However, beyond DNA repair gene upregulation, we find that neurons also activate apoptotic pathways, suggesting that if DNA repair fails, neurons undergo programmed cell death. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and identify a conserved signature of molecular dysfunction in both mice and humans.
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Affiliation(s)
- Thomas Goralski
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Lindsay Meyerdirk
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Libby Breton
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Laura Brasseur
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
| | - Kevin Kurgat
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Daniella DeWeerd
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | | | | | | | | | - Michael X. Henderson
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
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Wilson MR, Harkins S, Reske JJ, Siwicki RA, Adams M, Bae-Jump VL, Teixeira JM, Chandler RL. PIK3CA mutation in endometriotic epithelial cells promotes viperin-dependent inflammatory response to insulin. Reprod Biol Endocrinol 2023; 21:43. [PMID: 37170094 PMCID: PMC10173629 DOI: 10.1186/s12958-023-01094-6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/30/2023] [Indexed: 05/13/2023] Open
Abstract
Endometrial epithelia are known to harbor cancer driver mutations in the absence of any pathologies, including mutations in PIK3CA. Insulin plays an important role in regulating uterine metabolism during pregnancy, and hyperinsulinemia is associated with conditions impacting fertility. Hyperinsulinemia also promotes cancer, but the direct action of insulin on mutated endometrial epithelial cells is unknown. Here, we treated 12Z endometriotic epithelial cells carrying the PIK3CAH1047R oncogene with insulin and examined transcriptomes by RNA-seq. While cells naively responded to insulin, the magnitude of differential gene expression (DGE) was nine times greater in PIK3CAH1047R cells, representing a synergistic effect between insulin signaling and PIK3CAH1047R expression. Interferon signaling and the unfolded protein response (UPR) were enriched pathways among affected genes. Insulin treatment in wild-type cells activated normal endoplasmic reticulum stress (ERS) response programs, while PIK3CAH1047R cells activated programs necessary to avoid ERS-induced apoptosis. PIK3CAH1047R expression alone resulted in overexpression (OE) of Viperin (RSAD2), which is involved in viral response and upregulated in the endometrium during early pregnancy. The transcriptional changes induced by insulin in PIK3CAH1047R cells were rescued by knockdown of Viperin, while Viperin OE alone was insufficient to induce a DGE response to insulin, suggesting that Viperin is necessary but not sufficient for the synergistic effect of PIK3CAH1047R and insulin treatment. We identified interferon signaling, viral response, and protein targeting pathways that are induced by insulin but dependent on Viperin in PIK3CAH1047R mutant cells. These results suggest that response to insulin signaling is altered in mutated endometriotic epithelial cells.
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Affiliation(s)
- Mike R Wilson
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Shannon Harkins
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Jake J Reske
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Rebecca A Siwicki
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Victoria L Bae-Jump
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jose M Teixeira
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Ronald L Chandler
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA.
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
- Department for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.
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Kinn-Gurzo SS, Kitchen-Goosen SM, Chasse M, Adams M, Kaufman R, Grohar PJ. Abstract 1466: Heterogeneity of the EWS-FLI1 transcriptome drives differences in the cellular phenotype of Ewing sarcoma cell lines. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-1466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Ewing sarcoma (ES) is dependent on the oncogenic transcription factor EWS-FLI1 for oncogenesis and progression. EWS-FLI1 binds to chromatin to both induce and repress gene expression. These gene expression changes drive proliferation, disrupt the cell cycle, and block cellular differentiation. One approach to target EWS-FLI1 is to reverse the gene signature. However, we have observed an underappreciated but striking heterogeneity of the EWS-FLI1 transcriptome among cell lines. While many common downstream targets exist, at least an equal number of cell-line specific large magnitude gene expression changes are also present. In this study, we evaluate the phenotypic importance of these cell-line specific changes and evaluate potential mechanisms that EWS-FLI1 may use to drive divergent transcription.
Methods: The EWS-FLI1 transcriptome was characterized by RNA sequencing, following siRNA silencing of EWS-FLI1 at two time points in 6 cell lines. Effects on specific genes was confirmed by qPCR and western blot analysis. Cellular migration was evaluated using scratch assays on the Incucyte Zoom. EWS-FLI1binding was evaluated using Cleavage Under Targets and Tagmentation assay (CUT&Tag) and the transcriptome of Ewing subpopulations was determined by single cell RNA sequencing.
Results: Next generation RNA sequencing of highly optimized siRNA knockdowns of EWS-FLI1 in 6 ES cell lines showed striking differences in gene expression. Conditions were optimized to capture the same magnitude change in EWS-FLI1 expression at the shortest time point ever reported. Fewer common targets were identified across all cell lines than previously reported, perhaps due to the short time frame and focus on direct targets. Independently generated well-established lists of targets were enriched in the data. However, there were 184 genes that changed by a Log2FC > 3 (P < 0.0001) in only one cell line including important genes like WNT7B and CTLA4. Marked heterogeneity was observed in a previously described migratory transcriptional signature including the key effectors Zyxin and Integrin Alpha-5; an observation confirmed by unbiased pathway analysis and cellular migration assays. Importantly, increased cellular migration was only seen in one cell line with siRNA silencing and not with any EWS-FLI1 targeted small molecules. To characterize the source of heterogeneity, we evaluated EWS-FLI1 binding at Zyxin and Alpha-5 integrin and single cell RNA sequencing of the migratory sub-signature. CUT&Tag demonstrates that EWS-FLI1 is found bound at these genes even in non-migratory cell lines.
Conclusion: Careful consideration of Ewing sarcoma model-specific gene expression changes is important to future therapeutic approaches as these unique changes influence cellular phenotype.
Citation Format: Seneca S. Kinn-Gurzo, Susan M. Kitchen-Goosen, Maggie Chasse, Marie Adams, Rebecca Kaufman, Patrick J. Grohar. Heterogeneity of the EWS-FLI1 transcriptome drives differences in the cellular phenotype of Ewing sarcoma cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1466.
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Affiliation(s)
| | | | | | - Marie Adams
- 2Van Andel Research Institute, Grand Rapids, MI
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Peris D, Ubbelohde EJ, Kuang MC, Kominek J, Langdon QK, Adams M, Koshalek JA, Hulfachor AB, Opulente DA, Hall DJ, Hyma K, Fay JC, Leducq JB, Charron G, Landry CR, Libkind D, Gonçalves C, Gonçalves P, Sampaio JP, Wang QM, Bai FY, Wrobel RL, Hittinger CT. Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. Nat Commun 2023; 14:690. [PMID: 36755033 PMCID: PMC9908912 DOI: 10.1038/s41467-023-36139-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.
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Grants
- R01 GM080669 NIGMS NIH HHS
- T32 GM007133 NIGMS NIH HHS
- We thank the University of Wisconsin Biotechnology Center DNA Sequencing Facility for providing Illumina and Sanger sequencing facilities and services; Maria Sardi, Audrey Gasch, and Ursula Bond for providing strains; Sean McIlwain for providing guidance for genome ultra-scaffolding; Yury V. Bukhman for discussing applications of the Growth Curve Analysis Tool (GCAT); Mick McGee for HPLC analysis; Raúl Ortíz-Merino for assistance during YGAP annotations; Jessica Leigh for assistance with PopART; Cecile Ané for suggestions about BUCKy utilization and phylogenetic network analyses; Samina Naseeb and Daniela Delneri for sharing preliminary multi-locus Saccharomyces jurei data; and Branden Timm, Brian Kyle, and Dan Metzger for computational assistance. Some computations were performed on Tirant III of the Spanish Supercomputing Network (‘‘Servei d’Informàtica de la Universitat de València”) under the project BCV-2021-1-0001 granted to DP, while others were performed at the Wisconsin Energy Institute and the Center for High-Throughput Computing of the University of Wisconsin-Madison. During a portion of this project, DP was a researcher funded by the European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie, grant agreement No. 747775, the Research Council of Norway (RCN) grant Nos. RCN 324253 and 274337, and the Generalitat Valenciana plan GenT grant No. CIDEGENT/2021/039. DP is a recipient of an Illumina Grant for Illumina Sequencing Saccharomyces strains in this study. QKL was supported by the National Science Foundation under Grant No. DGE-1256259 (Graduate Research Fellowship) and the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (5T32GM007133). This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Nos. DEB-1253634, DEB-1442148, and DEB-2110403; and the USDA National Institute of Food and Agriculture Hatch Project Number 1020204. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from Wisconsin Alumni Research Foundation. QMW was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. 31770018 and 31961133020. CRL holds the Canada Research Chair in Cellular Systems and Synthetic Biology, and his research on wild yeast is supported by a NSERC Discovery Grant.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain.
| | - Emily J Ubbelohde
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Meihua Christina Kuang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacek Kominek
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin A Koshalek
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Katie Hyma
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C Fay
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Guillaume Charron
- Canada Natural Resources, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO, Pavillon Charles‑Eugène‑Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Carla Gonçalves
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Vanderbilt University, Department of Biological Sciences, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Paula Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Qi-Ming Wang
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Russel L Wrobel
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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Madaj ZB, Dahabieh MS, Kamalumpundi V, Muhire B, Pettinga J, Siwicki RA, Ellis AE, Isaguirre C, Escobar Galvis ML, DeCamp L, Jones RG, Givan SA, Adams M, Sheldon RD. Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-'omics analysis of the liver metabolic response to viral infection. RNA Biol 2023; 20:186-197. [PMID: 37095747 PMCID: PMC10132226 DOI: 10.1080/15476286.2023.2204586] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Here, we provide an in-depth analysis of the usefulness of single-sample metabolite/RNA extraction for multi-'omics readout. Using pulverized frozen livers of mice injected with lymphocytic choriomeningitis virus (LCMV) or vehicle (Veh), we isolated RNA prior (RNA) or following metabolite extraction (MetRNA). RNA sequencing (RNAseq) data were evaluated for differential expression analysis and dispersion, and differential metabolite abundance was determined. Both RNA and MetRNA clustered together by principal component analysis, indicating that inter-individual differences were the largest source of variance. Over 85% of LCMV versus Veh differentially expressed genes were shared between extraction methods, with the remaining 15% evenly and randomly divided between groups. Differentially expressed genes unique to the extraction method were attributed to randomness around the 0.05 FDR cut-off and stochastic changes in variance and mean expression. In addition, analysis using the mean absolute difference showed no difference in the dispersion of transcripts between extraction methods. Altogether, our data show that prior metabolite extraction preserves RNAseq data quality, which enables us to confidently perform integrated pathway enrichment analysis on metabolomics and RNAseq data from a single sample. This analysis revealed pyrimidine metabolism as the most LCMV-impacted pathway. Combined analysis of genes and metabolites in the pathway exposed a pattern in the degradation of pyrimidine nucleotides leading to uracil generation. In support of this, uracil was among the most differentially abundant metabolites in serum upon LCMV infection. Our data suggest that hepatic uracil export is a novel phenotypic feature of acute infection and highlight the usefulness of our integrated single-sample multi-'omics approach.
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Affiliation(s)
- Zachary B Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
| | - Michael S Dahabieh
- Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Vijayvardhan Kamalumpundi
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Brejnev Muhire
- Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - J Pettinga
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
| | - Rebecca A Siwicki
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Genomics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Abigail E Ellis
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Christine Isaguirre
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Lisa DeCamp
- Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Russell G Jones
- Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Scott A Givan
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
| | - Marie Adams
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Genomics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Ryan D Sheldon
- Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
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14
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Hahn T, Daymont C, Beukelman T, Groh B, Hays K, Bingham CA, Scalzi L, Abel N, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar-Smiley F, Barillas-Arias L, Basiaga M, Baszis K, Becker M, Bell-Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang-Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel-Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie-Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui-Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein-Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PMC, McGuire S, McHale I, McMonagle A, McMullen-Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O’Brien B, O’Brien T, Okeke O, Oliver M, Olson J, O’Neil K, Onel K, Orandi A, Orlando M, Osei-Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan-Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas-Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth-Wojcicki E, Rouster-Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert-Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner-Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Intraarticular steroids as DMARD-sparing agents for juvenile idiopathic arthritis flares: Analysis of the Childhood Arthritis and Rheumatology Research Alliance Registry. Pediatr Rheumatol Online J 2022; 20:107. [PMID: 36434731 PMCID: PMC9701017 DOI: 10.1186/s12969-022-00770-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/08/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Children with juvenile idiopathic arthritis (JIA) who achieve a drug free remission often experience a flare of their disease requiring either intraarticular steroids (IAS) or systemic treatment with disease modifying anti-rheumatic drugs (DMARDs). IAS offer an opportunity to recapture disease control and avoid exposure to side effects from systemic immunosuppression. We examined a cohort of patients treated with IAS after drug free remission and report the probability of restarting systemic treatment within 12 months. METHODS We analyzed a cohort of patients from the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry who received IAS for a flare after a period of drug free remission. Historical factors and clinical characteristics and of the patients including data obtained at the time of treatment were analyzed. RESULTS We identified 46 patients who met the inclusion criteria. Of those with follow up data available 49% had restarted systemic treatment 6 months after IAS injection and 70% had restarted systemic treatment at 12 months. The proportion of patients with prior use of a biologic DMARD was the only factor that differed between patients who restarted systemic treatment those who did not, both at 6 months (79% vs 35%, p < 0.01) and 12 months (81% vs 33%, p < 0.05). CONCLUSION While IAS are an option for all patients who flare after drug free remission, it may not prevent the need to restart systemic treatment. Prior use of a biologic DMARD may predict lack of success for IAS. Those who previously received methotrexate only, on the other hand, are excellent candidates for IAS.
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Affiliation(s)
- Timothy Hahn
- Department of Pediatrics, Penn State Children's Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA, 17033-0855, USA.
| | - Carrie Daymont
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | - Timothy Beukelman
- grid.265892.20000000106344187Department of Pediatrics, University of Alabama at Birmingham, CPPN G10, 1600 7th Ave South, Birmingham, AL 35233 USA
| | - Brandt Groh
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | | | - Catherine April Bingham
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | - Lisabeth Scalzi
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
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Wilson MR, Skalski H, Reske JJ, Wegener M, Adams M, Hostetter G, Hoffmann HM, Bernard JJ, Bae-Jump VL, Teixeira JM, Chandler RL. Obesity alters the mouse endometrial transcriptome in a cell context-dependent manner. Reprod Biol Endocrinol 2022; 20:163. [PMID: 36424602 PMCID: PMC9686036 DOI: 10.1186/s12958-022-01030-0] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022] Open
Abstract
Obesity impacts fertility and is positively correlated with endometrial hyperplasia and endometrial cancer occurrence. Endometrial epithelia often harbor disease driver-mutations, while endometrial stroma are highly regulative of neighboring epithelia. Here, we sought to determine distinct transcriptome changes occurring in individual cell types in the obese mouse uterus. Outbred CD-1 mice were fed high-fat or control diets for 18 weeks, estrous cycle staged, and endometrial epithelia, macrophages, and stroma isolated for transcriptomic analysis. High-fat diet mice displayed increased body mass and developed glucose intolerance, hyperinsulinemia, and fatty liver. Obese mouse epithelia displayed differential gene expression for genes related to innate immunity and leukocyte chemotaxis. The obese mouse stroma differentially expressed factors related to circadian rhythm, and expression of these genes correlated with glucose tolerance or body mass. We observed correlations between F4/80 + macrophage numbers, Cleaved Caspase 3 (CC3) apoptosis marker staining and glucose intolerance among obese mice, including a subgroup of obese mice with high CC3 + luminal epithelia. This subgroup displayed differential gene expression among all cell types, with pathways related to immune escape in epithelia and macrophages, while the stroma dysregulated pathways related to regulation of epithelia. These results suggest an important role for differential response of both the epithelia and stroma in their response to obesity, while macrophages are dysregulated in the context of apoptotic epithelia. The obesity-related gene expression programs in cells within the uterine microenvironment may influence the ability of the endometrium to function during pregnancy and influence disease pathogenesis.
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Affiliation(s)
- Mike R Wilson
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Hilary Skalski
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Jake J Reske
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Marc Wegener
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Hanne M Hoffmann
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Jamie J Bernard
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA
- Division of Dermatology, Department of Medicine, Michigan State University, East Lansing, MI, USA
| | - Victoria L Bae-Jump
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jose M Teixeira
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Ronald L Chandler
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA.
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.
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Reske JJ, Wilson MR, Armistead B, Harkins S, Perez C, Hrit J, Adams M, Rothbart SB, Missmer SA, Fazleabas AT, Chandler RL. ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers. BMC Biol 2022; 20:209. [PMID: 36153585 PMCID: PMC9509632 DOI: 10.1186/s12915-022-01407-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND SWI/SNF (BAF) chromatin remodeling complexes regulate lineage-specific enhancer activity by promoting accessibility for diverse DNA-binding factors and chromatin regulators. Additionally, they are known to modulate the function of the epigenome through regulation of histone post-translational modifications and nucleosome composition, although the way SWI/SNF complexes govern the epigenome remains poorly understood. Here, we investigate the function of ARID1A, a subunit of certain mammalian SWI/SNF chromatin remodeling complexes associated with malignancies and benign diseases originating from the uterine endometrium. RESULTS Through genome-wide analysis of human endometriotic epithelial cells, we show that more than half of ARID1A binding sites are marked by the variant histone H3.3, including active regulatory elements such as super-enhancers. ARID1A knockdown leads to H3.3 depletion and gain of canonical H3.1/3.2 at ARID1A-bound active regulatory elements, and a concomitant redistribution of H3.3 toward genic elements. ARID1A interactions with the repressive chromatin remodeler CHD4 (NuRD) are associated with H3.3, and ARID1A is required for CHD4 recruitment to H3.3. ZMYND8 interacts with CHD4 to suppress a subset of ARID1A, CHD4, and ZMYND8 co-bound, H3.3+ H4K16ac+ super-enhancers near genes governing extracellular matrix, motility, adhesion, and epithelial-to-mesenchymal transition. Moreover, these gene expression alterations are observed in human endometriomas. CONCLUSIONS These studies demonstrate that ARID1A-containing BAF complexes are required for maintenance of the histone variant H3.3 at active regulatory elements, such as super-enhancers, and this function is required for the physiologically relevant activities of alternative chromatin remodelers.
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Affiliation(s)
- Jake J. Reske
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Mike R. Wilson
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Brooke Armistead
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Shannon Harkins
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Cristina Perez
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Joel Hrit
- grid.251017.00000 0004 0406 2057Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Marie Adams
- grid.251017.00000 0004 0406 2057Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Scott B. Rothbart
- grid.251017.00000 0004 0406 2057Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Stacey A. Missmer
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA ,grid.416230.20000 0004 0406 3236Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341 USA
| | - Asgerally T. Fazleabas
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA ,grid.416230.20000 0004 0406 3236Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341 USA
| | - Ronald L. Chandler
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA ,grid.251017.00000 0004 0406 2057Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA ,grid.416230.20000 0004 0406 3236Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341 USA
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Proietti M, Romiti GF, Vitolo M, Harrison SL, Lane DA, Fauchier L, Marin F, Näbauer M, Potpara TS, Dan GA, Maggioni AP, Cesari M, Boriani G, Lip GYH, Ekmekçiu U, Paparisto V, Tase M, Gjergo H, Dragoti J, Goda A, Ciutea M, Ahadi N, el Husseini Z, Raepers M, Leroy J, Haushan P, Jourdan A, Lepiece C, Desteghe L, Vijgen J, Koopman P, Van Genechten G, Heidbuchel H, Boussy T, De Coninck M, Van Eeckhoutte H, Bouckaert N, Friart A, Boreux J, Arend C, Evrard P, Stefan L, Hoffer E, Herzet J, Massoz M, Celentano C, Sprynger M, Pierard L, Melon P, Van Hauwaert B, Kuppens C, Faes D, Van Lier D, Van Dorpe A, Gerardy A, Deceuninck O, Xhaet O, Dormal F, Ballant E, Blommaert D, Yakova D, Hristov M, Yncheva T, Stancheva N, Tisheva S, Tokmakova M, Nikolov F, Gencheva D, Shalganov T, Kunev B, Stoyanov M, Marchov D, Gelev V, Traykov V, Kisheva A, Tsvyatkov H, Shtereva R, Bakalska-Georgieva S, Slavcheva S, Yotov Y, Kubíčková M, Marni Joensen A, Gammelmark A, Hvilsted Rasmussen L, Dinesen P, Riahi S, Krogh Venø S, Sorensen B, Korsgaard A, Andersen K, Fragtrup Hellum C, Svenningsen A, Nyvad O, Wiggers P, May O, Aarup A, Graversen B, Jensen L, Andersen M, Svejgaard M, Vester S, Hansen S, Lynggaard V, Ciudad M, Vettus R, Muda P, Maestre A, Castaño S, Cheggour S, Poulard J, Mouquet V, Leparrée S, Bouet J, Taieb J, Doucy A, Duquenne H, Furber A, Dupuis J, Rautureau J, Font M, Damiano P, Lacrimini M, Abalea J, Boismal S, Menez T, Mansourati J, Range G, Gorka H, Laure C, Vassalière C, Elbaz N, Lellouche N, Djouadi K, Roubille F, Dietz D, Davy J, Granier M, Winum P, Leperchois-Jacquey C, Kassim H, Marijon E, Le Heuzey J, Fedida J, Maupain C, Himbert C, Gandjbakhch E, Hidden-Lucet F, Duthoit G, Badenco N, Chastre T, Waintraub X, Oudihat M, Lacoste J, Stephan C, Bader H, Delarche N, Giry L, Arnaud D, Lopez C, Boury F, Brunello I, Lefèvre M, Mingam R, Haissaguerre M, Le Bidan M, Pavin D, Le Moal V, Leclercq C, Piot O, Beitar T, Martel I, Schmid A, Sadki N, Romeyer-Bouchard C, Da Costa A, Arnault I, Boyer M, Piat C, Fauchier L, Lozance N, Nastevska S, Doneva A, Fortomaroska Milevska B, Sheshoski B, Petroska K, Taneska N, Bakrecheski N, Lazarovska K, Jovevska S, Ristovski V, Antovski A, Lazarova E, Kotlar I, Taleski J, Poposka L, Kedev S, Zlatanovik N, Jordanova S, Bajraktarova Proseva T, Doncovska S, Maisuradze D, Esakia A, Sagirashvili E, Lartsuliani K, Natelashvili N, Gumberidze N, Gvenetadze R, Etsadashvili K, Gotonelia N, Kuridze N, Papiashvili G, Menabde I, Glöggler S, Napp A, Lebherz C, Romero H, Schmitz K, Berger M, Zink M, Köster S, Sachse J, Vonderhagen E, Soiron G, Mischke K, Reith R, Schneider M, Rieker W, Boscher D, Taschareck A, Beer A, Oster D, Ritter O, Adamczewski J, Walter S, Frommhold A, Luckner E, Richter J, Schellner M, Landgraf S, Bartholome S, Naumann R, Schoeler J, Westermeier D, William F, Wilhelm K, Maerkl M, Oekinghaus R, Denart M, Kriete M, Tebbe U, Scheibner T, Gruber M, Gerlach A, Beckendorf C, Anneken L, Arnold M, Lengerer S, Bal Z, Uecker C, Förtsch H, Fechner S, Mages V, Martens E, Methe H, Schmidt T, Schaeffer B, Hoffmann B, Moser J, Heitmann K, Willems S, Willems S, Klaus C, Lange I, Durak M, Esen E, Mibach F, Mibach H, Utech A, Gabelmann M, Stumm R, Ländle V, Gartner C, Goerg C, Kaul N, Messer S, Burkhardt D, Sander C, Orthen R, Kaes S, Baumer A, Dodos F, Barth A, Schaeffer G, Gaertner J, Winkler J, Fahrig A, Aring J, Wenzel I, Steiner S, Kliesch A, Kratz E, Winter K, Schneider P, Haag A, Mutscher I, Bosch R, Taggeselle J, Meixner S, Schnabel A, Shamalla A, Hötz H, Korinth A, Rheinert C, Mehltretter G, Schön B, Schön N, Starflinger A, Englmann E, Baytok G, Laschinger T, Ritscher G, Gerth A, Dechering D, Eckardt L, Kuhlmann M, Proskynitopoulos N, Brunn J, Foth K, Axthelm C, Hohensee H, Eberhard K, Turbanisch S, Hassler N, Koestler A, Stenzel G, Kschiwan D, Schwefer M, Neiner S, Hettwer S, Haeussler-Schuchardt M, Degenhardt R, Sennhenn S, Steiner S, Brendel M, Stoehr A, Widjaja W, Loehndorf S, Logemann A, Hoskamp J, Grundt J, Block M, Ulrych R, Reithmeier A, Panagopoulos V, Martignani C, Bernucci D, Fantecchi E, Diemberger I, Ziacchi M, Biffi M, Cimaglia P, Frisoni J, Boriani G, Giannini I, Boni S, Fumagalli S, Pupo S, Di Chiara A, Mirone P, Fantecchi E, Boriani G, Pesce F, Zoccali C, Malavasi VL, Mussagaliyeva A, Ahyt B, Salihova Z, Koshum-Bayeva K, Kerimkulova A, Bairamukova A, Mirrakhimov E, Lurina B, Zuzans R, Jegere S, Mintale I, Kupics K, Jubele K, Erglis A, Kalejs O, Vanhear K, Burg M, Cachia M, Abela E, Warwicker S, Tabone T, Xuereb R, Asanovic D, Drakalovic D, Vukmirovic M, Pavlovic N, Music L, Bulatovic N, Boskovic A, Uiterwaal H, Bijsterveld N, De Groot J, Neefs J, van den Berg N, Piersma F, Wilde A, Hagens V, Van Es J, Van Opstal J, Van Rennes B, Verheij H, Breukers W, Tjeerdsma G, Nijmeijer R, Wegink D, Binnema R, Said S, Erküner Ö, Philippens S, van Doorn W, Crijns H, Szili-Torok T, Bhagwandien R, Janse P, Muskens A, van Eck M, Gevers R, van der Ven N, Duygun A, Rahel B, Meeder J, Vold A, Holst Hansen C, Engset I, Atar D, Dyduch-Fejklowicz B, Koba E, Cichocka M, Sokal A, Kubicius A, Pruchniewicz E, Kowalik-Sztylc A, Czapla W, Mróz I, Kozlowski M, Pawlowski T, Tendera M, Winiarska-Filipek A, Fidyk A, Slowikowski A, Haberka M, Lachor-Broda M, Biedron M, Gasior Z, Kołodziej M, Janion M, Gorczyca-Michta I, Wozakowska-Kaplon B, Stasiak M, Jakubowski P, Ciurus T, Drozdz J, Simiera M, Zajac P, Wcislo T, Zycinski P, Kasprzak J, Olejnik A, Harc-Dyl E, Miarka J, Pasieka M, Ziemińska-Łuć M, Bujak W, Śliwiński A, Grech A, Morka J, Petrykowska K, Prasał M, Hordyński G, Feusette P, Lipski P, Wester A, Streb W, Romanek J, Woźniak P, Chlebuś M, Szafarz P, Stanik W, Zakrzewski M, Kaźmierczak J, Przybylska A, Skorek E, Błaszczyk H, Stępień M, Szabowski S, Krysiak W, Szymańska M, Karasiński J, Blicharz J, Skura M, Hałas K, Michalczyk L, Orski Z, Krzyżanowski K, Skrobowski A, Zieliński L, Tomaszewska-Kiecana M, Dłużniewski M, Kiliszek M, Peller M, Budnik M, Balsam P, Opolski G, Tymińska A, Ozierański K, Wancerz A, Borowiec A, Majos E, Dabrowski R, Szwed H, Musialik-Lydka A, Leopold-Jadczyk A, Jedrzejczyk-Patej E, Koziel M, Lenarczyk R, Mazurek M, Kalarus Z, Krzemien-Wolska K, Starosta P, Nowalany-Kozielska E, Orzechowska A, Szpot M, Staszel M, Almeida S, Pereira H, Brandão Alves L, Miranda R, Ribeiro L, Costa F, Morgado F, Carmo P, Galvao Santos P, Bernardo R, Adragão P, Ferreira da Silva G, Peres M, Alves M, Leal M, Cordeiro A, Magalhães P, Fontes P, Leão S, Delgado A, Costa A, Marmelo B, Rodrigues B, Moreira D, Santos J, Santos L, Terchet A, Darabantiu D, Mercea S, Turcin Halka V, Pop Moldovan A, Gabor A, Doka B, Catanescu G, Rus H, Oboroceanu L, Bobescu E, Popescu R, Dan A, Buzea A, Daha I, Dan G, Neuhoff I, Baluta M, Ploesteanu R, Dumitrache N, Vintila M, Daraban A, Japie C, Badila E, Tewelde H, Hostiuc M, Frunza S, Tintea E, Bartos D, Ciobanu A, Popescu I, Toma N, Gherghinescu C, Cretu D, Patrascu N, Stoicescu C, Udroiu C, Bicescu G, Vintila V, Vinereanu D, Cinteza M, Rimbas R, Grecu M, Cozma A, Boros F, Ille M, Tica O, Tor R, Corina A, Jeewooth A, Maria B, Georgiana C, Natalia C, Alin D, Dinu-Andrei D, Livia M, Daniela R, Larisa R, Umaar S, Tamara T, Ioachim Popescu M, Nistor D, Sus I, Coborosanu O, Alina-Ramona N, Dan R, Petrescu L, Ionescu G, Popescu I, Vacarescu C, Goanta E, Mangea M, Ionac A, Mornos C, Cozma D, Pescariu S, Solodovnicova E, Soldatova I, Shutova J, Tjuleneva L, Zubova T, Uskov V, Obukhov D, Rusanova G, Soldatova I, Isakova N, Odinsova S, Arhipova T, Kazakevich E, Serdechnaya E, Zavyalova O, Novikova T, Riabaia I, Zhigalov S, Drozdova E, Luchkina I, Monogarova Y, Hegya D, Rodionova L, Rodionova L, Nevzorova V, Soldatova I, Lusanova O, Arandjelovic A, Toncev D, Milanov M, Sekularac N, Zdravkovic M, Hinic S, Dimkovic S, Acimovic T, Saric J, Polovina M, Potpara T, Vujisic-Tesic B, Nedeljkovic M, Zlatar M, Asanin M, Vasic V, Popovic Z, Djikic D, Sipic M, Peric V, Dejanovic B, Milosevic N, Stevanovic A, Andric A, Pencic B, Pavlovic-Kleut M, Celic V, Pavlovic M, Petrovic M, Vuleta M, Petrovic N, Simovic S, Savovic Z, Milanov S, Davidovic G, Iric-Cupic V, Simonovic D, Stojanovic M, Stojanovic S, Mitic V, Ilic V, Petrovic D, Deljanin Ilic M, Ilic S, Stoickov V, Markovic S, Kovacevic S, García Fernandez A, Perez Cabeza A, Anguita M, Tercedor Sanchez L, Mau E, Loayssa J, Ayarra M, Carpintero M, Roldán Rabadan I, Leal M, Gil Ortega M, Tello Montoliu A, Orenes Piñero E, Manzano Fernández S, Marín F, Romero Aniorte A, Veliz Martínez A, Quintana Giner M, Ballesteros G, Palacio M, Alcalde O, García-Bolao I, Bertomeu Gonzalez V, Otero-Raviña F, García Seara J, Gonzalez Juanatey J, Dayal N, Maziarski P, Gentil-Baron P, Shah D, Koç M, Onrat E, Dural IE, Yilmaz K, Özin B, Tan Kurklu S, Atmaca Y, Canpolat U, Tokgozoglu L, Dolu AK, Demirtas B, Sahin D, Ozcan Celebi O, Diker E, Gagirci G, Turk UO, Ari H, Polat N, Toprak N, Sucu M, Akin Serdar O, Taha Alper A, Kepez A, Yuksel Y, Uzunselvi A, Yuksel S, Sahin M, Kayapinar O, Ozcan T, Kaya H, Yilmaz MB, Kutlu M, Demir M, Gibbs C, Kaminskiene S, Bryce M, Skinner A, Belcher G, Hunt J, Stancombe L, Holbrook B, Peters C, Tettersell S, Shantsila A, Lane D, Senoo K, Proietti M, Russell K, Domingos P, Hussain S, Partridge J, Haynes R, Bahadur S, Brown R, McMahon S, Y H Lip G, McDonald J, Balachandran K, Singh R, Garg S, Desai H, Davies K, Goddard W, Galasko G, Rahman I, Chua Y, Payne O, Preston S, Brennan O, Pedley L, Whiteside C, Dickinson C, Brown J, Jones K, Benham L, Brady R, Buchanan L, Ashton A, Crowther H, Fairlamb H, Thornthwaite S, Relph C, McSkeane A, Poultney U, Kelsall N, Rice P, Wilson T, Wrigley M, Kaba R, Patel T, Young E, Law J, Runnett C, Thomas H, McKie H, Fuller J, Pick S, Sharp A, Hunt A, Thorpe K, Hardman C, Cusack E, Adams L, Hough M, Keenan S, Bowring A, Watts J, Zaman J, Goffin K, Nutt H, Beerachee Y, Featherstone J, Mills C, Pearson J, Stephenson L, Grant S, Wilson A, Hawksworth C, Alam I, Robinson M, Ryan S, Egdell R, Gibson E, Holland M, Leonard D, Mishra B, Ahmad S, Randall H, Hill J, Reid L, George M, McKinley S, Brockway L, Milligan W, Sobolewska J, Muir J, Tuckis L, Winstanley L, Jacob P, Kaye S, Morby L, Jan A, Sewell T, Boos C, Wadams B, Cope C, Jefferey P, Andrews N, Getty A, Suttling A, Turner C, Hudson K, Austin R, Howe S, Iqbal R, Gandhi N, Brophy K, Mirza P, Willard E, Collins S, Ndlovu N, Subkovas E, Karthikeyan V, Waggett L, Wood A, Bolger A, Stockport J, Evans L, Harman E, Starling J, Williams L, Saul V, Sinha M, Bell L, Tudgay S, Kemp S, Brown J, Frost L, Ingram T, Loughlin A, Adams C, Adams M, Hurford F, Owen C, Miller C, Donaldson D, Tivenan H, Button H, Nasser A, Jhagra O, Stidolph B, Brown C, Livingstone C, Duffy M, Madgwick P, Roberts P, Greenwood E, Fletcher L, Beveridge M, Earles S, McKenzie D, Beacock D, Dayer M, Seddon M, Greenwell D, Luxton F, Venn F, Mills H, Rewbury J, James K, Roberts K, Tonks L, Felmeden D, Taggu W, Summerhayes A, Hughes D, Sutton J, Felmeden L, Khan M, Walker E, Norris L, O’Donohoe L, Mozid A, Dymond H, Lloyd-Jones H, Saunders G, Simmons D, Coles D, Cotterill D, Beech S, Kidd S, Wrigley B, Petkar S, Smallwood A, Jones R, Radford E, Milgate S, Metherell S, Cottam V, Buckley C, Broadley A, Wood D, Allison J, Rennie K, Balian L, Howard L, Pippard L, Board S, Pitt-Kerby T. Epidemiology and impact of frailty in patients with atrial fibrillation in Europe. Age Ageing 2022; 51:6670566. [PMID: 35997262 DOI: 10.1093/ageing/afac192] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 03/17/2022] [Revised: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Frailty is a medical syndrome characterised by reduced physiological reserve and increased vulnerability to stressors. Data regarding the relationship between frailty and atrial fibrillation (AF) are still inconsistent. OBJECTIVES We aim to perform a comprehensive evaluation of frailty in a large European cohort of AF patients. METHODS A 40-item frailty index (FI) was built according to the accumulation of deficits model in the AF patients enrolled in the ESC-EHRA EORP-AF General Long-Term Registry. Association of baseline characteristics, clinical management, quality of life, healthcare resources use and risk of outcomes with frailty was examined. RESULTS Among 10,177 patients [mean age (standard deviation) 69.0 (11.4) years, 4,103 (40.3%) females], 6,066 (59.6%) were pre-frail and 2,172 (21.3%) were frail, whereas only 1,939 (19.1%) were considered robust. Baseline thromboembolic and bleeding risks were independently associated with increasing FI. Frail patients with AF were less likely to be treated with oral anticoagulants (OACs) (odds ratio 0.70, 95% confidence interval 0.55-0.89), especially with non-vitamin K antagonist OACs and managed with a rhythm control strategy, compared with robust patients. Increasing frailty was associated with a higher risk for all outcomes examined, with a non-linear exponential relationship. The use of OAC was associated with a lower risk of outcomes, except in patients with very/extremely high frailty. CONCLUSIONS In this large cohort of AF patients, there was a high burden of frailty, influencing clinical management and risk of adverse outcomes. The clinical benefit of OAC is maintained in patients with high frailty, but not in very high/extremely frail ones.
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Affiliation(s)
- Marco Proietti
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Geriatric Unit, IRCCS Istituti Clinici Scientifici Maugeri, Milan, Italy
| | - Giulio Francesco Romiti
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Department of Translational and Precision Medicine, Sapienza - University of Rome, Italy
| | - Marco Vitolo
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Cardiology Division, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Policlinico di Modena, Modena, Italy.,Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, Italy
| | - Stephanie L Harrison
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK
| | - Deirdre A Lane
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Laurent Fauchier
- Service de Cardiologie, Centre Hospitalier Universitaire Trousseau, Tours, France
| | - Francisco Marin
- Department of Cardiology, Hospital Universitario Virgen de la Arrixaca, IMIB-Arrixaca, University of Murcia, CIBER-CV, Murcia, Spain
| | - Michael Näbauer
- Department of Cardiology, Ludwig-Maximilians-University, Munich, Germany
| | - Tatjana S Potpara
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Clinical Center of Serbia, Belgrade, Serbia
| | - Gheorghe-Andrei Dan
- University of Medicine, 'Carol Davila', Colentina University Hospital, Bucharest, Romania
| | - Aldo P Maggioni
- ANMCO Research Center, Heart Care Foundation, Florence, Italy
| | - Matteo Cesari
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Geriatric Unit, IRCCS Istituti Clinici Scientifici Maugeri, Milan, Italy
| | - Giuseppe Boriani
- Cardiology Division, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Policlinico di Modena, Modena, Italy
| | - Gregory Y H Lip
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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Gedminas JM, Kaufman R, Boguslawski EA, Gross AC, Adams M, Beddows I, Kitchen-Goosen SM, Roberts RD, Grohar PJ. Lurbinectedin Inhibits the EWS-WT1 Transcription Factor in Desmoplastic Small Round Cell Tumor. Mol Cancer Ther 2022; 21:1296-1305. [PMID: 35657345 DOI: 10.1158/1535-7163.mct-21-1003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 12/13/2021] [Revised: 03/17/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022]
Abstract
Desmoplastic small round cell tumor (DSRCT) is a rare pediatric sarcoma with poor overall survival. This tumor is absolutely dependent on the continued expression and activity of its defining molecular lesion, the EWS-WT1 transcription factor. Unfortunately, the therapeutic targeting of transcription factors is challenging, and there is a critical need to identify compounds that inhibit EWS-WT1. Here we show that the compound lurbinectedin inhibits EWS-WT1 by redistributing the protein within the nucleus to the nucleolus. This nucleolar redistribution interferes with the activity of EWS-WT1 to reverse the expression of over 70% of the transcriptome. In addition, the compound blocks the expression of the EWS-WT1 fusion protein to inhibit cell proliferation at the lowest GI50 ever reported for this compound in any cell type. The effects occur at concentrations that are easily achievable in the clinic and translate to the in vivo setting to cause tumor regressions in multiple mice in a xenograft and PDX model of DSRCT. Importantly, this mechanism of nucleolar redistribution is also seen with wild-type EWSR1 and the related fusion protein EWS-FLI1. This provides evidence for a "class effect" for the more than 18 tumors driven by EWSR1 fusion proteins. More importantly, the data establish lurbinectedin as a promising clinical candidate for DSRCT.
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Affiliation(s)
- Jenna M Gedminas
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rebecca Kaufman
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elissa A Boguslawski
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Amy C Gross
- Center for Childhood Cancer, Nationwide Children's Hospital, The Ohio State University James Comprehensive Cancer Center, Columbus, Ohio
| | - Marie Adams
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Ian Beddows
- Van Andel Research Institute, Grand Rapids, Michigan
| | | | - Ryan D Roberts
- Center for Childhood Cancer, Nationwide Children's Hospital, The Ohio State University James Comprehensive Cancer Center, Columbus, Ohio
| | - Patrick J Grohar
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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Giovannetti O, Tomalty D, Greco S, Adams M. Self-Report Assessment of Sexual Function After LEEP in Women who Report Negative Outcomes. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.05.035] [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: 10/16/2022]
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King N, Linden B, Cunningham S, Rivera D, Rose J, Wagner N, Mulder J, Adams M, Baxter R, Duffy A. The feasibility and effectiveness of a novel online mental health literacy course in supporting university student mental health: a pilot study. BMC Psychiatry 2022; 22:515. [PMID: 35907852 PMCID: PMC9338643 DOI: 10.1186/s12888-022-04139-z] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND There is a need for effective universal approaches to promote and support university student mental health that are scalable and sustainable. In this pilot study we assess the feasibility and acceptability of a fully-digitalized, comprehensive mental health literacy course co-created with and tailored to the needs of undergraduate students. We also explore preliminary associations with mental health and positive behaviour change. METHODS An accredited online mental health literacy course was developed using state-of-the-art pedagogical principles and a reverse mentorship approach. The course was offered as an interdisciplinary undergraduate elective. Students completed an online survey before and after the 12-week course that collected demographic information and assessed mental health knowledge, emotional self-awareness, mental health, stigma, and health-related behaviors using validated measures. Dependent group t-tests were used to compare pre- and post-course levels of knowledge, mental health, sleep quality and substance use. Mental health outcomes of students who completed the course were compared to an age and sex-matched sample of students not enrolled in the course and who completed the same survey measures over the same academic year. Multivariable linear regression was used to examine the effect of course participation on outcomes at follow-up. RESULTS The course had good uptake and was positively reviewed by participants. Specifically, students found the course engaging, relevant, and applicable, and agreed they would recommend it to their peers. Among course participants there was improvement in mental health knowledge (p < 0.001) and emotional self-awareness (p = 0.02) at course completion. Compared to the matched comparison group, taking the course was associated with reduced alcohol (β = - 0.41, p = 0.01) and cannabis use (β = - 0.35, p = 0.03), and improved sleep quality (β = 1.56, p = 0.09) at the end of the term. CONCLUSIONS Findings suggest that delivering mental health literacy as an online accredited course may be an acceptable and effective way of promoting university student mental health through improved knowledge, emotional self-awareness, and healthy lifestyle choices. As the course is expanded to larger and more diverse student cohorts we will be able to further examine the short and long-term effectiveness of the course in supporting student mental health and the underlying mechanisms.
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Affiliation(s)
- N. King
- grid.410356.50000 0004 1936 8331Department of Public Health Sciences, Queen’s University, Kingston, Canada
| | - B. Linden
- grid.410356.50000 0004 1936 8331Department of Public Health Sciences, Queen’s University, Kingston, Canada ,grid.410356.50000 0004 1936 8331Health Services and Policy Research Institute, Queen’s University, Kingston, Canada
| | - S. Cunningham
- grid.410356.50000 0004 1936 8331Department of Biomedical & Molecular Sciences, Queen’s University, Kingston, Canada
| | - D. Rivera
- grid.17063.330000 0001 2157 2938Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - J. Rose
- grid.410356.50000 0004 1936 8331Department of Psychiatry, Queen’s University, Kingston, Canada
| | - N. Wagner
- grid.410356.50000 0004 1936 8331Department of Biomedical & Molecular Sciences, Queen’s University, Kingston, Canada ,grid.410356.50000 0004 1936 8331Office of Professional Development & Educational Scholarship, Queen’s University, Kingston, Canada
| | - J. Mulder
- grid.410356.50000 0004 1936 8331Department of Biomedical & Molecular Sciences, Queen’s University, Kingston, Canada ,grid.410356.50000 0004 1936 8331Office of Professional Development & Educational Scholarship, Queen’s University, Kingston, Canada
| | - M. Adams
- grid.410356.50000 0004 1936 8331Department of Biomedical & Molecular Sciences, Queen’s University, Kingston, Canada ,grid.410356.50000 0004 1936 8331Office of Professional Development & Educational Scholarship, Queen’s University, Kingston, Canada
| | - R. Baxter
- grid.4305.20000 0004 1936 7988Centre for Research Collections, University of Edinburgh Main Library, University of Edinburgh, Edinburgh, UK
| | - A. Duffy
- grid.410356.50000 0004 1936 8331Department of Public Health Sciences, Queen’s University, Kingston, Canada ,grid.410356.50000 0004 1936 8331Department of Psychiatry, Queen’s University, Kingston, Canada ,grid.4991.50000 0004 1936 8948Department of Psychiatry, University of Oxford, Oxford, UK
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21
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Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. Cell Genom 2022; 2:100144. [PMID: 35873672 PMCID: PMC9306256 DOI: 10.1016/j.xgen.2022.100144] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 05/20/2022] [Indexed: 05/21/2023]
Abstract
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc Min/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.
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Affiliation(s)
- Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
| | - Toshinori Hinoue
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bret Barnes
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | - Owen Mitchell
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Waleed Iqbal
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly K. Foy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kwang-Ho Lee
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ethan J. Moyer
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra VanderArk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie M. Koeman
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Wubin Ding
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manpreet Kalkat
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Nathan J. Spix
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bryn Eagleson
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Liang Kang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Peter A. Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Rishi Porecha
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | | | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
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Kouli O, Murray V, Bhatia S, Cambridge WA, Kawka M, Shafi S, Knight SR, Kamarajah SK, McLean KA, Glasbey JC, Khaw RA, Ahmed W, Akhbari M, Baker D, Borakati A, Mills E, Thavayogan R, Yasin I, Raubenheimer K, Ridley W, Sarrami M, Zhang G, Egoroff N, Pockney P, Richards T, Bhangu A, Creagh-Brown B, Edwards M, Harrison EM, Lee M, Nepogodiev D, Pinkney T, Pearse R, Smart N, Vohra R, Sohrabi C, Jamieson A, Nguyen M, Rahman A, English C, Tincknell L, Kakodkar P, Kwek I, Punjabi N, Burns J, Varghese S, Erotocritou M, McGuckin S, Vayalapra S, Dominguez E, Moneim J, Salehi M, Tan HL, Yoong A, Zhu L, Seale B, Nowinka Z, Patel N, Chrisp B, Harris J, Maleyko I, Muneeb F, Gough M, James CE, Skan O, Chowdhury A, Rebuffa N, Khan H, Down B, Fatimah Hussain Q, Adams M, Bailey A, Cullen G, Fu YXJ, McClement B, Taylor A, Aitken S, Bachelet B, Brousse de Gersigny J, Chang C, Khehra B, Lahoud N, Lee Solano M, Louca M, Rozenbroek P, Rozitis E, Agbinya N, Anderson E, Arwi G, Barry I, Batchelor C, Chong T, Choo LY, Clark L, Daniels M, Goh J, Handa A, Hanna J, Huynh L, Jeon A, Kanbour A, Lee A, Lee J, Lee T, Leigh J, Ly D, McGregor F, Moss J, Nejatian M, O'Loughlin E, Ramos I, Sanchez B, Shrivathsa A, Sincari A, Sobhi S, Swart R, Trimboli J, Wignall P, Bourke E, Chong A, Clayton S, Dawson A, Hardy E, Iqbal R, Le L, Mao S, Marinelli I, Metcalfe H, Panicker D, R HH, Ridgway S, Tan HH, Thong S, Van M, Woon S, Woon-Shoo-Tong XS, Yu S, Ali K, Chee J, Chiu C, Chow YW, Duller A, Nagappan P, Ng S, Selvanathan M, Sheridan C, Temple M, Do JE, Dudi-Venkata NN, Humphries E, Li L, Mansour LT, Massy-Westropp C, Fang B, Farbood K, Hong H, Huang Y, Joan M, Koh C, Liu YHA, Mahajan T, Muller E, Park R, Tanudisastro M, Wu JJG, Chopra P, Giang S, Radcliffe S, Thach P, Wallace D, Wilkes A, Chinta SH, Li J, Phan J, Rahman F, Segaran A, Shannon J, Zhang M, Adams N, Bonte A, Choudhry A, Colterjohn N, Croyle JA, Donohue J, Feighery A, Keane A, McNamara D, Munir K, Roche D, Sabnani R, Seligman D, Sharma S, Stickney Z, Suchy H, Tan R, Yordi S, Ahmed I, Aranha M, El Sabawy D, Garwood P, Harnett M, Holohan R, Howard R, Kayyal Y, Krakoski N, Lupo M, McGilberry W, Nepon H, Scoleri Y, Urbina C, Ahmad Fuad MF, Ahmed O, Jaswantlal D, Kelly E, Khan MHT, Naidu D, Neo WX, O'Neill R, Sugrue M, Abbas JD, Abdul-Fattah S, Azlan A, Barry K, Idris NS, Kaka N, Mc Dermott D, Mohammad Nasir MN, Mozo M, Rehal A, Shaikh Yousef M, Wong RH, Curran E, Gardner M, Hogan A, Julka R, Lasser G, Ní Chorráin N, Ting J, Browne R, George S, Janjua Z, Leung Shing V, Megally M, Murphy S, Ravenscroft L, Vedadi A, Vyas V, Bryan A, Sheikh A, Ubhi J, Vannelli K, Vawda A, Adeusi L, Doherty C, Fitzgerald C, Gallagher H, Gill P, Hamza H, Hogan M, Kelly S, Larry J, Lynch P, Mazeni NA, O'Connell R, O'Loghlin R, Singh K, Abbas Syed R, Ali A, Alkandari B, Arnold A, Arora E, Azam R, Breathnach C, Cheema J, Compton M, Curran S, Elliott JA, Jayasamraj O, Mohammed N, Noone A, Pal A, Pandey S, Quinn P, Sheridan R, Siew L, Tan EP, Tio SW, Toh VTR, Walsh M, Yap C, Yassa J, Young T, Agarwal N, Almoosawy SA, Bowen K, Bruce D, Connachan R, Cook A, Daniell A, Elliott M, Fung HKF, Irving A, Laurie S, Lee YJ, Lim ZX, Maddineni S, McClenaghan RE, Muthuganesan V, Ravichandran P, Roberts N, Shaji S, Solt S, Toshney E, Arnold C, Baker O, Belais F, Bojanic C, Byrne M, Chau CYC, De Soysa S, Eldridge M, Fairey M, Fearnhead N, Guéroult A, Ho JSY, Joshi K, Kadiyala N, Khalid S, Khan F, Kumar K, Lewis E, Magee J, Manetta-Jones D, Mann S, McKeown L, Mitrofan C, Mohamed T, Monnickendam A, Ng AYKC, Ortu A, Patel M, Pope T, Pressling S, Purohit K, Saji S, Shah Foridi J, Shah R, Siddiqui SS, Surman K, Utukuri M, Varghese A, Williams CYK, Yang JJ, Billson E, Cheah E, Holmes P, Hussain S, Murdock D, Nicholls A, Patel P, Ramana G, Saleki M, Spence H, Thomas D, Yu C, Abousamra M, Brown C, Conti I, Donnelly A, Durand M, French N, Goan R, O'Kane E, Rubinchik P, Gardiner H, Kempf B, Lai YL, Matthews H, Minford E, Rafferty C, Reid C, Sheridan N, Al Bahri T, Bhoombla N, Rao BM, Titu L, Chatha S, Field C, Gandhi T, Gulati R, Jha R, Jones Sam MT, Karim S, Patel R, Saunders M, Sharma K, Abid S, Heath E, Kurup D, Patel A, Ali M, Cresswell B, Felstead D, Jennings K, Kaluarachchi T, Lazzereschi L, Mayson H, Miah JE, Reinders B, Rosser A, Thomas C, Williams H, Al-Hamid Z, Alsadoun L, Chlubek M, Fernando P, Gaunt E, Gercek Y, Maniar R, Ma R, Matson M, Moore S, Morris A, Nagappan PG, Ratnayake M, Rockall L, Shallcross O, Sinha A, Tan KE, Virdee S, Wenlock R, Donnelly HA, Ghazal R, Hughes I, Liu X, McFadden M, Misbert E, Mogey P, O'Hara A, Peace C, Rainey C, Raja P, Salem M, Salmon J, Tan CH, Alves D, Bahl S, Baker C, Coulthurst J, Koysombat K, Linn T, Rai P, Sharma A, Shergill A, Ahmed M, Ahmed S, Belk LH, Choudhry H, Cummings D, Dixon Y, Dobinson C, Edwards J, Flint J, Franco Da Silva C, Gallie R, Gardener M, Glover T, Greasley M, Hatab A, Howells R, Hussey T, Khan A, Mann A, Morrison H, Ng A, Osmond R, Padmakumar N, Pervaiz F, Prince R, Qureshi A, Sawhney R, Sigurdson B, Stephenson L, Vora K, Zacken A, Cope P, Di Traglia R, Ferarrio I, Hackett N, Healicon R, Horseman L, Lam LI, Meerdink M, Menham D, Murphy R, Nimmo I, Ramaesh A, Rees J, Soame R, Dilaver N, Adebambo D, Brown E, Burt J, Foster K, Kaliyappan L, Knight P, Politis A, Richardson E, Townsend J, Abdi M, Ball M, Easby S, Gill N, Ho E, Iqbal H, Matthews M, Nubi S, Nwokocha JO, Okafor I, Perry G, Sinartio B, Vanukuru N, Walkley D, Welch T, Yates J, Yeshitila N, Bryans K, Campbell B, Gray C, Keys R, Macartney M, Chamberlain G, Khatri A, Kucheria A, Lee STP, Reese G, Roy choudhury J, Tan WYR, Teh JJ, Ting A, Kazi S, Kontovounisios C, Vutipongsatorn K, Amarnath T, Balasubramanian N, Bassett E, Gurung P, Lim J, Panjikkaran A, Sanalla A, Alkoot M, Bacigalupo V, Eardley N, Horton M, Hurry A, Isti C, Maskell P, Nursiah K, Punn G, Salih H, Epanomeritakis E, Foulkes A, Henderson R, Johnston E, McCullough H, McLarnon M, Morrison E, Cheung A, Cho SH, Eriksson F, Hedges J, Low Z, May C, Musto L, Nagi S, Nur S, Salau E, Shabbir S, Thomas MC, Uthayanan L, Vig S, Zaheer M, Zeng G, Ashcroft-Quinn S, Brown R, Hayes J, McConville R, French R, Gilliam A, Sheetal S, Shehzad MU, Bani W, Christie I, Franklyn J, Khan M, Russell J, Smolarek S, Varadarassou R, Ahmed SK, Narayanaswamy S, Sealy J, Shah M, Dodhia V, Manukyan A, O'Hare R, Orbell J, Chung I, Forenc K, Gupta A, Agarwal A, Al Dabbagh A, Bennewith R, Bottomley J, Chu TSM, Chu YYA, Doherty W, Evans B, Hainsworth P, Hosfield T, Li CH, McCullagh I, Mehta A, Thaker A, Thompson B, Virdi A, Walker H, Wilkins E, Dixon C, Hassan MR, Lotca N, Tong KS, Batchelor-Parry H, Chaudhari S, Harris T, Hooper J, Johnson C, Mulvihill C, Nayler J, Olutobi O, Piramanayagam B, Stones K, Sussman M, Weaver C, Alam F, Al Rawi M, Andrew F, Arrayeh A, Azizan N, Hassan A, Iqbal Z, John I, Jones M, Kalake O, Keast M, Nicholas J, Patil A, Powell K, Roberts P, Sabri A, Segue AK, Shah A, Shaik Mohamed SA, Shehadeh A, Shenoy S, Tong A, Upcott M, Vijayasingam D, Anarfi S, Dauncey J, Devindaran A, Havalda P, Komninos G, Mwendwa E, Norman C, Richards J, Urquhart A, Allan J, Cahya E, Hunt H, McWhirter C, Norton R, Roxburgh C, Tan JY, Ali Butt S, Hansdot S, Haq I, Mootien A, Sanchez I, Vainas T, Deliyannis E, Tan M, Vipond M, Chittoor Satish NN, Dattani A, De Carvalho L, Gaston-Grubb M, Karunanithy L, Lowe B, Pace C, Raju K, Roope J, Taylor C, Youssef H, Munro T, Thorn C, Wong KHF, Yunus A, Chawla S, Datta A, Dinesh AA, Field D, Georgi T, Gwozdz A, Hamstead E, Howard N, Isleyen N, Jackson N, Kingdon J, Sagoo KS, Schizas A, Yin L, Aung E, Aung YY, Franklin S, Han SM, Kim WC, Martin Segura A, Rossi M, Ross T, Tirimanna R, Wang B, Zakieh O, Ben-Arzi H, Flach A, Jackson E, Magers S, Olu abara C, Rogers E, Sugden K, Tan H, Veliah S, Walton U, Asif A, Bharwada Y, Bowley D, Broekhuizen A, Cooper L, Evans N, Girdlestone H, Ling C, Mann H, Mehmood N, Mulvenna CL, Rainer N, Trout I, Gujjuri R, Jeyaraman D, Leong E, Singh D, Smith E, Anderton J, Barabas M, Goyal S, Howard D, Joshi A, Mitchell D, Weatherby T, Badminton R, Bird R, Burtle D, Choi NY, Devalia K, Farr E, Fischer F, Fish J, Gunn F, Jacobs D, Johnston P, Kalakoutas A, Lau E, Loo YNAF, Louden H, Makariou N, Mohammadi K, Nayab Y, Ruhomaun S, Ryliskyte R, Saeed M, Shinde P, Sudul M, Theodoropoulou K, Valadao-Spoorenberg J, Vlachou F, Arshad SR, Janmohamed AM, Noor M, Oyerinde O, Saha A, Syed Y, Watkinson W, Ahmadi H, Akintunde A, Alsaady A, Bradley J, Brothwood D, Burton M, Higgs M, Hoyle C, Katsura C, Lathan R, Louani A, Mandalia R, Prihartadi AS, Qaddoura B, Sandland-Taylor L, Thadani S, Thompson A, Walshaw J, Teo S, Ali S, Bawa JH, Fox S, Gargan K, Haider SA, Hanna N, Hatoum A, Khan Z, Krzak AM, Li T, Pitt J, Tan GJS, Ullah Z, Wilson E, Cleaver J, Colman J, Copeland L, Coulson A, Davis P, Faisal H, Hassan F, Hughes JT, Jabr Y, Mahmoud Ali F, Nahaboo Solim ZN, Sangheli A, Shaya S, Thompson R, Cornwall H, De Andres Crespo M, Fay E, Findlay J, Groves E, Jones O, Killen A, Millo J, Thomas S, Ward J, Wilkins M, Zaki F, Zilber E, Bhavra K, Bilolikar A, Charalambous M, Elawad A, Eleni A, Fawdon R, Gibbins A, Livingstone D, Mala D, Oke SE, Padmakumar D, Patsalides MA, Payne D, Ralphs C, Roney A, Sardar N, Stefanova K, Surti F, Timms R, Tosney G, Bannister J, Clement NS, Cullimore V, Kamal F, Lendor J, McKay J, Mcswiggan J, Minhas N, Seneviratne K, Simeen S, Valverde J, Watson N, Bloom I, Dinh TH, Hirniak J, Joseph R, Kansagra M, Lai CKN, Melamed N, Patel J, Randev J, Sedighi T, Shurovi B, Sodhi J, Vadgama N, Abdulla S, Adabavazeh B, Champion A, Chennupati R, Chu K, Devi S, Haji A, Schulz J, Testa F, Davies P, Gurung B, Howell S, Modi P, Pervaiz A, Zahid M, Abdolrazaghi S, Abi Aoun R, Anjum Z, Bawa G, Bhardwaj R, Brown S, Enver M, Gill D, Gopikrishna D, Gurung D, Kanwal A, Kaushal P, Khanna A, Lovell E, McEvoy C, Mirza M, Nabeel S, Naseem S, Pandya K, Perkins R, Pulakal R, Ray M, Reay C, Reilly S, Round A, Seehra J, Shakeel NM, Singh B, Vijay Sukhnani M, Brown L, Desai B, Elzanati H, Godhaniya J, Kavanagh E, Kent J, Kishor A, Liu A, Norwood M, Shaari N, Wood C, Wood M, Brown A, Chellapuri A, Ferriman A, Ghosh I, Kulkarni N, Noton T, Pinto A, Rajesh S, Varghese B, Wenban C, Aly R, Barciela C, Brookes T, Corrin E, Goldsworthy M, Mohamed Azhar MS, Moore J, Nakhuda S, Ng D, Pillay S, Port S, Abdullah M, Akinyemi J, Islam S, Kale A, Lewis A, Manjunath T, McCabe H, Misra S, Stubley T, Tam JP, Waraich N, Chaora T, Ford C, Osinkolu I, Pong G, Rai J, Risquet R, Ainsworth J, Ayandokun P, Barham E, Barrett G, Barry J, Bisson E, Bridges I, Burke D, Cann J, Cloney M, Coates S, Cripps P, Davies C, Francis N, Green S, Handley G, Hathaway D, Hurt L, Jenkins S, Johnston C, Khadka A, McGee U, Morris D, Murray R, Norbury C, Pierrepont Z, Richards C, Ross O, Ruddy A, Salmon C, Shield M, Soanes K, Spencer N, Taverner S, Williams C, Wills-Wood W, Woodward S, Chow J, Fan J, Guest O, Hunter I, Moon WY, Arthur-Quarm S, Edwards P, Hamlyn V, 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K, Cinnamond A, Coleman S, George HA, Goulder L, Hare N, Hawksley J, Kret A, Luesley A, Mecia L, Porter H, Puddy E, Richardson G, Sohail B, Srikaran V, Tadross D, Tobin J, Tokidis E, Young L, Ashdown T, Bratsos S, Koomson A, Kufuor A, Lim MQ, Shah S, Thorne EPC, Warusavitarne J, Xu S, Abigail S, Ahmed A, Ahmed J, Akmal A, Al-Khafaji M, Amini B, Arshad M, Bogie E, Brazkiewicz M, Carroll M, Chandegra A, Cirelli C, Deng A, Fairclough S, Fung YJ, Gornell C, Green RL, Green SV, Gulamhussein AHM, Isaac AG, Jan R, Jegatheeswaran L, Knee M, Kotecha J, Kotecha S, Maxwell-Armstrong C, McIntyre C, Mendis N, Naing TKP, Oberman J, Ong ZX, Ramalingam A, Saeed Adam A, Tan LL, Towell S, Yadav J, Anandampillai R, Chung S, Hounat A, Ibrahim B, Jeyakumar G, Khalil A, Khan UA, Nair G, Owusu-Ayim M, Wilson M, Kanani A, Kilkelly B, Ogunmwonyi I, Ong L, Samra B, Schomerus L, Shea J, Turner O, Yang Y, Amin M, Blott N, Clark A, Feather A, Forrest M, Hague S, Hamilton K, Higginbotham G, Hope E, Karimian S, Loveday K, Malik H, McKenna O, Noor A, Onsiong C, Patel B, Radcliffe N, Shah P, Tye L, Verma K, Walford R, Yusufi U, Zachariah M, Casey A, Doré C, Fludder V, Fortescue L, Kalapu SS, Karel E, Khera G, Smith C, Appleton B, Ashaye A, Boggon E, Evans A, Faris Mahmood H, Hinchcliffe Z, Marei O, Silva I, Spooner C, Thomas G, Timlin M, Wellington J, Yao SL, Abdelrazek M, Abdelrazik Y, Bee F, Joseph A, Mounce A, Parry G, Vignarajah N, Biddles D, Creissen A, Kolhe S, K T, Lea A, Ledda V, O'Loughlin P, Scanlon J, Shetty N, Weller C, Abdalla M, Adeoye A, Bhatti M, Chadda KR, Chu J, Elhakim H, Foster-Davies H, Rabie M, Tailor B, Webb S, Abdelrahim ASA, Choo SY, Jiwa A, Mangam S, Murray S, Shandramohan A, Aghanenu O, Budd W, Hayre J, Khanom S, Liew ZY, McKinney R, Moody N, Muhammad-Kamal H, Odogwu J, Patel D, Roy C, Sattar Z, Shahrokhi N, Sinha I, Thomson E, Wonga L, Bain J, Khan J, Ricardo D, Bevis R, Cherry C, Darkwa S, Drew W, Griffiths E, Konda N, Madani D, Mak JKC, Meda B, Odunukwe U, Preest G, Raheel F, Rajaseharan A, Ramgopal A, Risbrooke C, Selvaratnam K, Sethunath G, Tabassum R, Taylor J, Thakker A, Wijesingha N, Wybrew R, Yasin T, Ahmed Osman A, Alfadhel S, Carberry E, Chen JY, Drake I, Glen P, Jayasuriya N, Kawar L, Myatt R, Sinan LOH, Siu SSY, Tjen V, Adeboyejo O, Bacon H, Barnes R, Birnie C, D'Cunha Kamath A, Hughes E, Middleton S, Owen R, Schofield E, Short C, Smith R, Wang H, Willett M, Zimmerman M, Balfour J, Chadwick T, Coombe-Jones M, Do Le HP, Faulkner G, Hobson K, Shehata Z, Beattie M, Chmielewski G, Chong C, Donnelly B, Drusch B, Ellis J, Farrelly C, Feyi-Waboso J, Hibell I, Hoade L, Ho C, Jones H, Kodiatt B, Lidder P, Ni Cheallaigh L, Norman R, Patabendi I, Penfold H, Playfair M, Pomeroy S, Ralph C, Rottenburg H, Sebastian J, Sheehan M, Stanley V, Welchman J, Ajdarpasic D, Antypas A, Azouaghe O, Basi S, Bettoli G, Bhattarai S, Bommireddy L, Bourne K, Budding J, Cookey-Bresi R, Cummins T, Davies G, Fabelurin C, Gwilliam R, Hanley J, Hird A, Kruczynska A, Langhorne B, Lund J, Lutchman I, McGuinness R, Neary M, Pampapathi S, Pang E, Podbicanin S, Rai N, Redhouse White G, Sujith J, Thomas P, Walker I, Winterton R, Anderson P, Barrington M, Bhadra K, Clark G, Fowler G, Gibson C, Hudson S, Kaminskaite V, Lawday S, Longshaw A, MacKrill E, McLachlan F, Murdeshwar A, Nieuwoudt R, Parker P, Randall R, Rawlins E, Reeves SA, Rye D, Sirkis T, Sykes B, Ventress N, Wosinska N, Akram B, Burton L, Coombs A, Long R, Magowan D, Ong C, Sethi M, Williams G, Chan C, Chan LH, Fernando D, Gaba F, Khor Z, Les JW, Mak R, Moin S, Ng Kee Kwong KC, Paterson-Brown S, Tew YY, Bardon A, Burrell K, Coldwell C, Costa I, Dexter E, Hardy A, Khojani M, Mazurek J, Raymond T, Reddy V, Reynolds J, Soma A, Agiotakis S, Alsusa H, Desai N, Peristerakis I, Adcock A, Ayub H, Bennett T, Bibi F, Brenac S, Chapman T, Clarke G, Clark F, Galvin C, Gwyn-Jones A, Henry-Blake C, Kerner S, Kiandee M, Lovett A, Pilecka A, Ravindran R, Siddique H, Sikand T, Treadwell K, Akmal K, Apata A, Barton O, Broad G, Darling H, Dhuga Y, Emms L, Habib S, Jain R, Jeater J, Kan CYP, Kathiravelupillai A, Khatkar H, Kirmani S, Kulasabanathan K, Lacey H, Lal K, Manafa C, Mansoor M, McDonald S, Mittal A, Mustoe S, Nottrodt L, Oliver P, Papapetrou I, Pattinson F, Raja M, Reyhani H, Shahmiri A, Small O, Soni U, Aguirrezabala Armbruster B, Bunni J, Hakim MA, Hawkins-Hooker L, Howell KA, Hullait R, Jaskowska A, Ottewell L, Thomas-Jones I, Vasudev A, Clements B, Fenton J, Gill M, Haider S, Lim AJM, Maguire H, McMullan J, Nicoletti J, Samuel S, Unais MA, White N, Yao PC, Yow L, Boyle C, Brady R, Cheekoty P, Cheong J, Chew SJHL, Chow R, Ganewatta Kankanamge D, Mamer L, Mohammed B, Ng Chieng Hin J, Renji Chungath R, Royston A, Sharrad E, Sinclair R, Tingle S, Treherne K, Wyatt F, Maniarasu VS, Moug S, Appanna T, Bucknall T, Hussain F, Owen A, Parry M, Parry R, Sagua N, Spofforth K, Yuen ECT, Bosley N, Hardie W, Moore T, Regas C, Abdel-Khaleq S, Ali N, Bashiti H, Buxton-Hopley R, Constantinides M, D'Afflitto M, Deshpande A, Duque Golding J, Frisira E, Germani Batacchi M, Gomaa A, Hay D, Hutchison R, Iakovou A, Iakovou D, Ismail E, Jefferson S, Jones L, Khouli Y, Knowles C, Mason J, McCaughan R, Moffatt J, Morawala A, Nadir H, Neyroud F, Nikookam Y, Parmar A, Pinto L, Ramamoorthy R, Richards E, Thomson S, Trainer C, Valetopoulou A, Vassiliou A, Wantman A, Wilde S, Dickinson M, Rockall T, Senn D, Wcislo K, Zalmay P, Adelekan K, Allen K, Bajaj M, Gatumbu P, Hang S, Hashmi Y, Kaur T, Kawesha A, Kisiel A, Woodmass M, Adelowo T, Ahari D, Alhwaishel K, Atherton R, Clayton B, Cockroft A, Curtis Lopez C, Hilton M, Ismail N, Kouadria M, Lee L, MacConnachie A, Monks F, Mungroo S, Nikoletopoulou C, Pearce L, Sara X, Shahid A, Suresh G, Wilcha R, Atiyah A, Davies E, Dermanis A, Gibbons H, Hyde A, Lawson A, Lee C, Leung-Tack M, Li Saw Hee J, Mostafa O, Nair D, Pattani N, Plumbley-Jones J, Pufal K, Ramesh P, Sanghera J, Saram S, Scadding S, See S, Stringer H, Torrance A, Vardon H, Wyn-Griffiths F, Brew A, Kaur G, Soni D, Tickle A, Akbar Z, Appleyard T, Figg K, Jayawardena P, Johnson A, Kamran Siddiqui Z, Lacy-Colson J, Oatham R, Rowlands B, Sludden E, Turnbull C, Allin D, Ansar Z, Azeez Z, Dale VH, Garg J, Horner A, Jones S, Knight S, McGregor C, McKenna J, McLelland T, Packham-Smith A, Rowsell K, Spector-Hill I, Adeniken E, Baker J, Bartlett M, Chikomba L, Connell B, Deekonda P, Dhar M, Elmansouri A, Gamage K, Goodhew R, Hanna P, Knight J, Luca A, Maasoumi N, Mahamoud F, Manji S, Marwaha PK, Mason F, Oluboyede A, Pigott L, Razaq AM, Richardson M, Saddaoui I, Wijeyendram P, Yau S, Atkins W, Liang K, Miles N, Praveen B, Ashai S, Braganza J, Common J, Cundy A, Davies R, Guthrie J, Handa I, Iqbal M, Ismail R, Jones C, Jones I, Lee KS, Levene A, Okocha M, Olivier J, Smith A, Subramaniam E, Tandle S, Wang A, Watson A, Wilson C, Chan XHF, Khoo E, Montgomery C, Norris M, Pugalenthi PP, Common T, Cook E, Mistry H, Shinmar HS, Agarwal G, Bandyopadhyay S, Brazier B, Carroll L, Goede A, Harbourne A, Lakhani A, Lami M, Larwood J, Martin J, Merchant J, Pattenden S, Pradhan A, Raafat N, Rothwell E, Shammoon Y, Sudarshan R, Vickers E, Wingfield L, Ashworth I, Azizi S, Bhate R, Chowdhury T, Christou A, Davies L, Dwaraknath M, Farah Y, Garner J, Gureviciute E, Hart E, Jain A, Javid S, Kankam HK, Kaur Toor P, Kaz R, Kermali M, Khan I, Mattson A, McManus A, Murphy M, Nair K, Ngemoh D, Norton E, Olabiran A, Parry L, Payne T, Pillai K, Price S, Punjabi K, Raghunathan A, Ramwell A, Raza M, Ritehnia J, Simpson G, Smith W, Sodeinde S, Studd L, Subramaniam M, Thomas J, Towey S, Tsang E, Tuteja D, Vasani J, Vio M, Badran A, Adams J, Anthony Wilkinson J, Asvandi S, Austin T, Bald A, Bix E, Carrick M, Chander B, Chowdhury S, Cooper Drake B, Crosbie S, D Portela S, Francis D, Gallagher C, Gillespie R, Gravett H, Gupta P, Ilyas C, James G, Johny J, Jones A, Kinder F, MacLeod C, Macrow C, Maqsood-Shah A, Mather J, McCann L, McMahon R, Mitham E, Mohamed M, Munton E, Nightingale K, O'Neill K, Onyemuchara I, Senior R, Shanahan A, Sherlock J, Spyridoulias A, Stavrou C, Stokes D, Tamang R, Taylor E, Trafford C, Uden C, Waddington C, Yassin D, Zaman M, Bangi S, Cheng T, Chew D, Hussain N, Imani-Masouleh S, Mahasivam G, McKnight G, Ng HL, Ota HC, Pasha T, Ravindran W, Shah K, Vishnu K S, Zaman S, Carr W, Cope S, Eagles EJ, Howarth-Maddison M, Li CY, Reed J, Ridge A, Stubbs T, Teasdaled D, Umar R, Worthington J, Dhebri A, Kalenderov R, Alattas A, Arain Z, Bhudia R, Chia D, Daniel S, Dar T, Garland H, Girish M, Hampson A, Kyriacou H, Lehovsky K, Mullins W, Omorphos N, Vasdev N, Venkatesh A, Waldock W, Bhandari A, Brown G, Choa G, Eichenauer CE, Ezennia K, Kidwai Z, Lloyd-Thomas A, Macaskill Stewart A, Massardi C, Sinclair E, Skajaa N, Smith M, Tan I, Afsheen N, Anuar A, Azam Z, Bhatia P, Davies-kelly N, Dickinson S, Elkawafi M, Ganapathy M, Gupta S, Khoury EG, Licudi D, Mehta V, Neequaye S, Nita G, Tay VL, Zhao S, Botsa E, Cuthbert H, Elliott J, Furlepa M, Lehmann J, Mangtani A, Narayan A, Nazarian S, Parmar C, Shah D, Shaw C, Zhao Z, Beck C, Caldwell S, Clements JM, French B, Kenny R, Kirk S, Lindsay J, McClung A, McLaughlin N, Watson S, Whiteside E, Alyacoubi S, Arumugam V, Beg R, Dawas K, Garg S, Lloyd ER, Mahfouz Y, Manobharath N, Moonesinghe R, Morka N, Patel K, Prashar J, Yip S, Adeeko ES, Ajekigbe F, Bhat A, Evans C, Farrugia A, Gurung C, Long T, Malik B, Manirajan S, Newport D, Rayer J, Ridha A, Ross E, Saran T, Sinker A, Waruingi D, Allen R, Al Sadek Y, Alves do Canto Brum H, Asharaf H, Ashman M, Balakumar V, Barrington J, Baskaran R, Berry A, Bhachoo H, Bilal A, Boaden L, Chia WL, Covell G, Crook D, Dadnam F, Davis L, De Berker H, Doyle C, Fox C, Gruffydd-Davies M, Hafouda Y, Hill A, Hubbard E, Hunter A, Inpadhas V, Jamshaid M, Jandu G, Jeyanthi M, Jones T, Kantor C, Kwak SY, Malik N, Matt R, McNulty P, Miles C, Mohomed A, Myat P, Niharika J, Nixon A, O'Reilly D, Parmar K, Pengelly S, Price L, Ramsden M, Turnor R, Wales E, Waring H, Wu M, Yang T, Ye TTS, Zander A, Zeicu C, Bellam S, Francombe J, Kawamoto N, Rahman MR, Sathyanarayana A, Tang HT, Cheung J, Hollingshead J, Page V, Sugarman J, Wong E, Chiong J, Fung E, Kan SY, Kiang J, Kok J, Krahelski O, Liew MY, Lyell B, Sharif Z, Speake D, Alim L, Amakye NY, Chandrasekaran J, Chandratreya N, Drake J, Owoso T, Thu YM, Abou El Ela Bourquin B, Alberts J, Chapman D, Rehnnuma N, Ainsworth K, Carpenter H, Emmanuel T, Fisher T, Gabrel M, Guan Z, Hollows S, Hotouras A, Ip Fung Chun N, Jaffer S, Kallikas G, Kennedy N, Lewinsohn B, Liu FY, Mohammed S, Rutherfurd A, Situ T, Stammer A, Taylor F, Thin N, Urgesi E, Zhang N, Ahmad MA, Bishop A, Bowes A, Dixit A, Glasson R, Hatta S, Hatt K, Larcombe S, Preece J, Riordan E, Fegredo D, Haq MZ, Li C, McCann G, Stewart D, Baraza W, Bhullar D, Burt G, Coyle J, Deans J, Devine A, Hird R, Ikotun O, Manchip G, Ross C, Storey L, Tan WWL, Tse C, Warner C, Whitehead M, Wu F, Court EL, Crisp E, Huttman M, Mayes F, Robertson H, Rosen H, Sandberg C, Smith H, Al Bakry M, Ashwell W, Bajaj S, Bandyopadhyay D, Browlee O, Burway S, Chand CP, Elsayeh K, Elsharkawi A, Evans E, Ferrin S, Fort-Schaale A, Iacob M, I K, Impelliziere Licastro G, Mankoo AS, Olaniyan T, Otun J, Pereira R, Reddy R, Saeed D, Simmonds O, Singhal G, Tron K, Wickstone C, Williams R, Bradshaw E, De Kock Jewell V, Houlden C, Knight C, Metezai H, Mirza-Davies A, Seymour Z, Spink D, Wischhusen S. Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study. Lancet Digit Health 2022; 4:e520-e531. [PMID: 35750401 DOI: 10.1016/s2589-7500(22)00069-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/07/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications. METHODS We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC). FINDINGS In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]). INTERPRETATION In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required. FUNDING British Journal of Surgery Society.
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Wilson MR, Reske JJ, Koeman J, Adams M, Joshi NR, Fazleabas AT, Chandler RL. SWI/SNF Antagonism of PRC2 Mediates Estrogen-Induced Progesterone Receptor Expression. Cells 2022; 11:1000. [PMID: 35326450 PMCID: PMC8946988 DOI: 10.3390/cells11061000] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/08/2022] [Accepted: 03/12/2022] [Indexed: 12/11/2022] Open
Abstract
Endometrial cancer (EC) is characterized by high estrogen levels unopposed by progesterone. Treatment with progestins is standard for early EC, but the response to progestins is dependent on progesterone receptor (PGR) expression. Here, we show that the expression of PGR in endometrial epithelial cells is dependent on ARID1A, a DNA-binding subunit of the SWI/SNF chromatin-remodeling complex that is commonly mutated in EC. In endometrial epithelial cells with estrogen receptor overexpression, we find that ARID1A promotes estrogen signaling and regulates common gene expression programs. Normally, endometrial epithelial cells expressing estrogen receptors respond to estrogen by upregulating the PGR. However, when ARID1A expression is lost, upregulation of PGR expression is significantly reduced. This phenomenon can also occur following the loss of the SWI/SNF subunit BRG1, suggesting a role for ARID1A- and BRG1-containing complexes in PGR regulation. We find that PGR is regulated by a bivalent promoter, which harbors both H3K4me3 and H3K27me3 histone tail modifications. H3K27me3 is deposited by EZH2, and inhibition of EZH2 in the context of ARID1A loss results in restoration of estrogen-induced PGR expression. Our results suggest a role for ARID1A deficiency in the loss of PGR in late-stage EC and a therapeutic utility for EZH2 inhibitors in this disease.
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Affiliation(s)
- Mike R. Wilson
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (M.R.W.); (J.J.R.); (N.R.J.); (A.T.F.)
| | - Jake J. Reske
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (M.R.W.); (J.J.R.); (N.R.J.); (A.T.F.)
| | - Julie Koeman
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA; (J.K.); (M.A.)
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA; (J.K.); (M.A.)
| | - Niraj R. Joshi
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (M.R.W.); (J.J.R.); (N.R.J.); (A.T.F.)
| | - Asgerally T. Fazleabas
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (M.R.W.); (J.J.R.); (N.R.J.); (A.T.F.)
- Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Ronald L. Chandler
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (M.R.W.); (J.J.R.); (N.R.J.); (A.T.F.)
- Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341, USA
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
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Soulsby WD, Balmuri N, Cooley V, Gerber LM, Lawson E, Goodman S, Onel K, Mehta B, Abel N, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar-Smiley F, Barillas-Arias L, Basiaga M, Baszis K, Becker M, Bell-Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang-Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel-Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie-Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui-Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein-Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PMC, McGuire S, McHale I, McMonagle A, McMullen-Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O’Brien B, O’Brien T, Okeke O, Oliver M, Olson J, O’Neil K, Onel K, Orandi A, Orlando M, Osei-Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan-Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas-Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth-Wojcicki E, Rouster-Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert-Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner-Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Social determinants of health influence disease activity and functional disability in Polyarticular Juvenile Idiopathic Arthritis. Pediatr Rheumatol Online J 2022; 20:18. [PMID: 35255941 PMCID: PMC8903717 DOI: 10.1186/s12969-022-00676-9] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/07/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Social determinants of health (SDH) greatly influence outcomes during the first year of treatment in rheumatoid arthritis, a disease similar to polyarticular juvenile idiopathic arthritis (pJIA). We investigated the correlation of community poverty level and other SDH with the persistence of moderate to severe disease activity and functional disability over the first year of treatment in pJIA patients enrolled in the Childhood Arthritis and Rheumatology Research Alliance Registry. METHODS In this cohort study, unadjusted and adjusted generalized linear mixed effects models analyzed the effect of community poverty and other SDH on disease activity, using the clinical Juvenile Arthritis Disease Activity Score-10, and disability, using the Child Health Assessment Questionnaire, measured at baseline, 6, and 12 months. RESULTS One thousand six hundred eighty-four patients were identified. High community poverty (≥20% living below the federal poverty level) was associated with increased odds of functional disability (OR 1.82, 95% CI 1.28-2.60) but was not statistically significant after adjustment (aOR 1.23, 95% CI 0.81-1.86) and was not associated with increased disease activity. Non-white race/ethnicity was associated with higher disease activity (aOR 2.48, 95% CI: 1.41-4.36). Lower self-reported household income was associated with higher disease activity and persistent functional disability. Public insurance (aOR 1.56, 95% CI 1.06-2.29) and low family education (aOR 1.89, 95% CI 1.14-3.12) was associated with persistent functional disability. CONCLUSION High community poverty level was associated with persistent functional disability in unadjusted analysis but not with persistent moderate to high disease activity. Race/ethnicity and other SDH were associated with persistent disease activity and functional disability.
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Affiliation(s)
- William Daniel Soulsby
- University of California, San Francisco, 550 16th Street, 4th Floor, Box #0632, San Francisco, CA, 94158, USA.
| | - Nayimisha Balmuri
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Victoria Cooley
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Linda M. Gerber
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Erica Lawson
- grid.266102.10000 0001 2297 6811University of California, San Francisco, 550 16th Street, 4th Floor, Box #0632, San Francisco, CA 94158 USA
| | - Susan Goodman
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Karen Onel
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Bella Mehta
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
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Thuillard S, Adams M, Jelmini G, Schmutz S, Sonderegger A, Sauer J. When humans and computers induce social stress through negative feedback: Effects on performance and subjective state. Computers in Human Behavior 2022. [DOI: 10.1016/j.chb.2022.107270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Rubinstein CD, McLean DT, Lehman BP, Meudt JJ, Schomberg DT, Krentz KJ, Reichert JL, Meyer MB, Adams M, Konsitzke CM, Shanmuganayagam D. Assessment of Mosaicism and Detection of Cryptic Alleles in CRISPR/Cas9-Engineered Neurofibromatosis Type 1 and TP53 Mutant Porcine Models Reveals Overlooked Challenges in Precision Modeling of Human Diseases. Front Genet 2021; 12:721045. [PMID: 34630515 PMCID: PMC8495252 DOI: 10.3389/fgene.2021.721045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/18/2021] [Indexed: 12/20/2022] Open
Abstract
Genome editing in pigs has been made efficient, practical, and economically viable by the CRISPR/Cas9 platform, representing a promising new era in translational modeling of human disease for research and preclinical development of therapies and devices. Porcine embryo microinjection provides a universally available, efficient option over somatic-cell nuclear transfer, but requires that critical considerations be made in genotypic validation of the models that routinely go unaddressed. Accurate validation of genotypes is especially important when modeling genetic disorders, such as neurofibromatosis type 1 (NF1) that exhibits complex genotype–phenotypic relationships. NF1, an autosomal dominant disorder, is particularly hard to model as it manifests very differently across patients, and even within families, with over 3,000 disease-associated mutations of the neurofibromin 1 (NF1) gene identified. The precise nature of the mutations plays a role in the complex phenotypic presentation of the disorder that includes benign and malignant peripheral and central nervous system tumors, a variety of motor deficits and debilitating cognitive impairments and musculoskeletal, cardiovascular, and gastrointestinal disorders. NF1 can also often involve mutations in passenger genes such as TP53. In this manuscript, we describe the creation of three novel porcine models of NF1 and a model additionally harboring a mutation in TP53 by embryo microinjection of CRISPR/Cas9. We present the challenges encountered in validation of genotypes and the methodological strategies developed to counter the hurdles. We present simple options for quantifying level of mosaicism: a quantitative method (targeted amplicon sequencing) for small edits such as SNPs and indels and a semiquantitative method (competitive PCR) for large edits. Characterization of mosaicism allowed for strategic selection of founder pigs for rapid, economical expansion of genetically defined lines. We also present commonly observed unexpected DNA repair products (i.e., structural variants or cryptic alleles) that are refractory to PCR amplification and thus evade detection. We present the use of copy number variance assays to overcome hurdles in detecting cryptic alleles. The report provides a framework for genotypic validation of porcine models created by embryo microinjection and the expansion of lines in an efficient manner.
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Affiliation(s)
| | - Dalton T McLean
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Brent P Lehman
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jennifer J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Dominic T Schomberg
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Kathy J Krentz
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jamie L Reichert
- Swine Research and Teaching Center, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Charles M Konsitzke
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States.,Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
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Smith K, Moore A, Popov S, Adams M, Folaranmi E, Sekaran P. 671 Fetus-In-Fetu Found at Excision of An Antenatally Diagnosed Abdominal Mass: Multi-Disciplinary Approach. Br J Surg 2021. [DOI: 10.1093/bjs/znab259.681] [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: 11/13/2022]
Abstract
Abstract
We present a case of antenatally detected abdominal mass and an alternative diagnostic course for suspected neonatal neuroblastoma as a result of investigative findings. A female infant presented antenatally with a left upper quadrant mass initially managed as a suspected neonatal neuroblastoma; further cross-sectional imaging suggested a wider differential including teratoma and aided surgical planning. The multi-disciplinary team (MDT) decision was for an early excision at 31 days and post-operative histology identified a diagnosis of fetus-in-fetu (FIF). We describe this case as a compliment to the current literature and an example of a necessary variation to recognised diagnostic and treatment pathways as a result of investigative findings.
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Affiliation(s)
- K Smith
- University Hospital Wales, Cardiff, United Kingdom
| | - A Moore
- University Hospital Wales, Cardiff, United Kingdom
| | - S Popov
- University Hospital Wales, Cardiff, United Kingdom
| | - M Adams
- University Hospital Wales, Cardiff, United Kingdom
| | - E Folaranmi
- University Hospital Wales, Cardiff, United Kingdom
| | - P Sekaran
- University Hospital Wales, Cardiff, United Kingdom
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O'Leary C, Monkman J, Kirkby B, Matigian N, Kulasinghe A, McCaffrey E, Richard D, Adams M, O'Byrne K. 1797P Polo-like kinase-1 as a biomarker in resected non-small cell lung cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1739] [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: 11/26/2022] Open
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Abazov VM, Abbott B, Acharya BS, Adams M, Adams T, Agnew JP, Alexeev GD, Alkhazov G, Alton A, Alves GA, Antchev G, Askew A, Aspell P, Assis Jesus ACS, Atanassov I, Atkins S, Augsten K, Aushev V, Aushev Y, Avati V, Avila C, Badaud F, Baechler J, Bagby L, Baldenegro Barrera C, Baldin B, Bandurin DV, Banerjee S, Barberis E, Baringer P, Barreto J, Bartlett JF, Bassler U, Bazterra V, Bean A, Begalli M, Bellantoni L, Berardi V, Beri SB, Bernardi G, Bernhard R, Berretti M, Bertram I, Besançon M, Beuselinck R, Bhat PC, Bhatia S, Bhatnagar V, Blazey G, Blessing S, Bloom K, Boehnlein A, Boline D, Boos EE, Borchsh V, Borissov G, Borysova M, Bossini E, Bottigli U, Bozzo M, Brandt A, Brandt O, Brochmann M, Brock R, Bross A, Brown D, Bu XB, Buehler M, Buescher V, Bunichev V, Burdin S, Burkhardt H, Buszello CP, Cafagna FS, Camacho-Pérez E, Carvalho W, Casey BCK, Castilla-Valdez H, Catanesi MG, Caughron S, Chakrabarti S, Chan KM, Chandra A, Chapon E, Chen G, Cho SW, Choi S, Choudhary B, Cihangir S, Claes D, Clutter J, Cooke M, Cooper WE, Corcoran M, Couderc F, Cousinou MC, Csanád M, Csörgő T, Cuth J, Cutts D, da Motta H, Das A, Davies G, Deile M, de Jong SJ, De La Cruz-Burelo E, De Leonardis F, Déliot F, Demina R, Denisov D, Denisov SP, De Oliveira Martins C, Desai S, Deterre C, DeVaughan K, Diehl HT, Diesburg M, Ding PF, Dominguez A, Doubek M, Drutskoy A, Druzhkin D, Dubey A, Dudko LV, Duperrin A, Dutt S, Eads M, Edmunds D, Eggert K, Ellison J, Elvira VD, Enari Y, Eremin V, Evans H, Evdokimov A, Evdokimov VN, Fauré A, Feng L, Ferbel T, Ferro F, Fiedler F, Fiergolski A, Filthaut F, Fisher W, Fisk HE, Forthomme L, Fortner M, Fox H, Franc J, Fuess S, Garbincius PH, Garcia F, Garcia-Bellido A, García-González JA, Gavrilov V, Geng W, Georgiev V, Gerber CE, Gershtein Y, Giani S, Ginther G, Gogota O, Golovanov G, Grannis PD, Greder S, Greenlee H, Grenier G, Gris P, Grivaz JF, Grohsjean A, Grünendahl S, Grünewald MW, Grzanka L, Guillemin T, Gutierrez G, Gutierrez P, Haley J, Hammerbauer J, Han L, Harder K, Harel A, Hauptman JM, Hays J, Head T, Hebbeker T, Hedin D, Hegab H, Heinson AP, Heintz U, Hensel C, Heredia-De La Cruz I, Herner K, Hesketh G, Hildreth MD, Hirosky R, Hoang T, Hobbs JD, Hoeneisen B, Hogan J, Hohlfeld M, Holzbauer JL, Howley I, Hubacek Z, Hynek V, Iashvili I, Ilchenko Y, Illingworth R, Isidori T, Ito AS, Ivanchenko V, Jabeen S, Jaffré M, Janda M, Jayasinghe A, Jeong MS, Jesik R, Jiang P, Johns K, Johnson E, Johnson M, Jonckheere A, Jonsson P, Joshi J, Jung AW, Juste A, Kajfasz E, Karev A, Karmanov D, Kašpar J, Katsanos I, Kaur M, Kaynak B, Kehoe R, Kermiche S, Khalatyan N, Khanov A, Kharchilava A, Kharzheev YN, Kiselevich I, Kohli JM, Kopal J, Kozelov AV, Kraus J, Kumar A, Kundrát V, Kupco A, Kurča T, Kuzmin VA, Lami S, Lammers S, Latino G, Lebrun P, Lee HS, Lee SW, Lee WM, Le X, Lellouch J, Li D, Li H, Li L, Li QZ, Lim JK, Lincoln D, Lindsey C, Linhart R, Linnemann J, Lipaev VV, Lipton R, Liu H, Liu Y, Lobodenko A, Lokajicek M, Lokajíček MV, Lopes de Sa R, Losurdo L, Lucas Rodríguez F, Luna-Garcia R, Lyon AL, Maciel AKA, Macrí M, Madar R, Magaña-Villalba R, Malawski M, Malbouisson HB, Malik S, Malyshev VL, Mansour J, Martínez-Ortega J, McCarthy R, McGivern CL, Meijer MM, Melnitchouk A, Menezes D, Mercadante PG, Merkin M, Meyer A, Meyer J, Miconi F, Minafra N, Minutoli S, Molina J, Mondal NK, Mulhearn M, Mundim L, Naaranoja T, Nagy E, Narain M, Nayyar R, Neal HA, Negret JP, Nemes F, Neustroev P, Nguyen HT, Niewiadomski H, Novák T, Nunnemann T, Oguri V, Oliveri E, Oljemark F, Orduna J, Oriunno M, Osman N, Österberg K, Pal A, Palazzi P, Parashar N, Parihar V, Park SK, Partridge R, Parua N, Pasechnik R, Passaro V, Patwa A, Penning B, Perfilov M, Peroutka Z, Peters Y, Petridis K, Petrillo G, Pétroff P, Pleier MA, Podstavkov VM, Popov AV, Prado da Silva WL, Prewitt M, Price D, Procházka J, Prokopenko N, Qian J, Quadt A, Quinn B, Quinto M, Raben TG, Radermacher E, Radicioni E, Rangel M, Ratoff PN, Ravotti F, Razumov I, Ripp-Baudot I, 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Watts G, Wayne M, Weichert J, Welti J, Welty-Rieger L, Williams J, Williams MRJ, Wilson GW, Wobisch M, Wood DR, Wyatt TR, Xie Y, Yamada R, Yang S, Yasuda T, Yatsunenko YA, Ye W, Ye Z, Yin H, Yip K, Youn SW, Yu JM, Zennamo J, Zhao TG, Zhou B, Zhu J, Zich J, Zielinski K, Zielinski M, Zieminska D, Zivkovic L. Odderon Exchange from Elastic Scattering Differences between pp and pp[over ¯] Data at 1.96 TeV and from pp Forward Scattering Measurements. Phys Rev Lett 2021; 127:062003. [PMID: 34420329 DOI: 10.1103/physrevlett.127.062003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/19/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
We describe an analysis comparing the pp[over ¯] elastic cross section as measured by the D0 Collaboration at a center-of-mass energy of 1.96 TeV to that in pp collisions as measured by the TOTEM Collaboration at 2.76, 7, 8, and 13 TeV using a model-independent approach. The TOTEM cross sections, extrapolated to a center-of-mass energy of sqrt[s]=1.96 TeV, are compared with the D0 measurement in the region of the diffractive minimum and the second maximum of the pp cross section. The two data sets disagree at the 3.4σ level and thus provide evidence for the t-channel exchange of a colorless, C-odd gluonic compound, also known as the odderon. We combine these results with a TOTEM analysis of the same C-odd exchange based on the total cross section and the ratio of the real to imaginary parts of the forward elastic strong interaction scattering amplitude in pp scattering for which the significance is between 3.4σ and 4.6σ. The combined significance is larger than 5σ and is interpreted as the first observation of the exchange of a colorless, C-odd gluonic compound.
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Affiliation(s)
- V M Abazov
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - B Abbott
- University of Oklahoma, Norman, Oklahoma 73019, USA
| | - B S Acharya
- Tata Institute of Fundamental Research, Mumbai-400 005, India
| | - M Adams
- University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - T Adams
- Florida State University, Tallahassee, Florida 32306, USA
| | - J P Agnew
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - G D Alexeev
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - G Alkhazov
- Petersburg Nuclear Physics Institute, St. Petersburg 188300, Russia
| | - A Alton
- University of Michigan, Ann Arbor, Michigan 48109, USA
| | - G A Alves
- LAFEX, Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro, RJ 22290, Brazil
| | - G Antchev
- INRNE-BAS, Institute for Nuclear Research and Nuclear Energy, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
| | - A Askew
- Florida State University, Tallahassee, Florida 32306, USA
| | - P Aspell
- CERN, 1211 Geneva 23, Switzerland
| | - A C S Assis Jesus
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | - I Atanassov
- INRNE-BAS, Institute for Nuclear Research and Nuclear Energy, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
| | - S Atkins
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - K Augsten
- Czech Technical University in Prague, 116 36 Prague 6, Czech Republic
| | - V Aushev
- Taras Shevchenko National University of Kyiv, Kiev 01601, Ukraine
| | - Y Aushev
- Taras Shevchenko National University of Kyiv, Kiev 01601, Ukraine
| | - V Avati
- AGH University of Science and Technology, 30-059 Krakow, Poland
- CERN, 1211 Geneva 23, Switzerland
| | - C Avila
- Universidad de los Andes, Bogotá 111711, Colombia
| | - F Badaud
- LPC, Université Blaise Pascal, CNRS/IN2P3, Clermont, F-63178 Aubière Cedex, France
| | | | - L Bagby
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | | | - B Baldin
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - D V Bandurin
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - S Banerjee
- Tata Institute of Fundamental Research, Mumbai-400 005, India
| | - E Barberis
- Northeastern University, Boston, Massachusetts 02115, USA
| | - P Baringer
- University of Kansas, Lawrence, Kansas 66045, USA
| | - J Barreto
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | - J F Bartlett
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - U Bassler
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - V Bazterra
- University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - A Bean
- University of Kansas, Lawrence, Kansas 66045, USA
| | - M Begalli
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | - L Bellantoni
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - V Berardi
- INFN Sezione di Bari, 70126 Bari, Italy
- Dipartimento Interateneo di Fisica di Bari, 70126 Bari, Italy
| | - S B Beri
- Panjab University, Chandigarh 160014, India
| | - G Bernardi
- LPNHE, Universités Paris VI and VII, CNRS/IN2P3, F-75005 Paris, France
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- Physikalisches Institut, Universität Freiburg, 79085 Freiburg, Germany
| | - M Berretti
- Helsinki Institute of Physics, 00014 University of Helsinki, Helsinki, Finland
| | - I Bertram
- Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - M Besançon
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - R Beuselinck
- Imperial College London, London SW7 2AZ, United Kingdom
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - S Bhatia
- University of Mississippi, University, Mississippi 38677, USA
| | | | - G Blazey
- Northern Illinois University, DeKalb, Illinois 60115, USA
| | - S Blessing
- Florida State University, Tallahassee, Florida 32306, USA
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- University of Nebraska, Lincoln, Nebraska 68588, USA
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- State University of New York, Stony Brook, New York 11794, USA
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- Moscow State University, Moscow 119991, Russia
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- Tomsk State University, Tomsk 634050, Russia
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- Lancaster University, Lancaster LA1 4YB, United Kingdom
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- Taras Shevchenko National University of Kyiv, Kiev 01601, Ukraine
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- Università degli Studi di Siena and Gruppo Collegato INFN di Siena, 53100 Siena, Italy
- CERN, 1211 Geneva 23, Switzerland
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- Università degli Studi di Siena and Gruppo Collegato INFN di Siena, 53100 Siena, Italy
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- INFN Sezione di Genova, 16146 Genova, Italy
- Università degli Studi di Genova, 16146 Genova, Italy
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- University of Texas, Arlington, Texas 76019, USA
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- II. Physikalisches Institut, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - M Brochmann
- University of Washington, Seattle, Washington 98195, USA
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- Michigan State University, East Lansing, Michigan 48824, USA
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- LPNHE, Universités Paris VI and VII, CNRS/IN2P3, F-75005 Paris, France
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- Institut für Physik, Universität Mainz, 55099 Mainz, Germany
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- Moscow State University, Moscow 119991, Russia
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- Lancaster University, Lancaster LA1 4YB, United Kingdom
| | | | | | | | | | - W Carvalho
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | | | | | - S Caughron
- Michigan State University, East Lansing, Michigan 48824, USA
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- State University of New York, Stony Brook, New York 11794, USA
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- University of Notre Dame, Notre Dame, Indiana 46556, USA
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- Rice University, Houston, Texas 77005, USA
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- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
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- University of Kansas, Lawrence, Kansas 66045, USA
| | - S W Cho
- Korea Detector Laboratory, Korea University, Seoul 02841, Korea
| | - S Choi
- Korea Detector Laboratory, Korea University, Seoul 02841, Korea
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- University of Nebraska, Lincoln, Nebraska 68588, USA
| | - J Clutter
- University of Kansas, Lawrence, Kansas 66045, USA
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - M Corcoran
- Rice University, Houston, Texas 77005, USA
| | - F Couderc
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
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- CPPM, Aix-Marseille Université, CNRS/IN2P3, F-13288 Marseille Cedex 09, France
| | - M Csanád
- Eötvös University, 1117 Budapest, Pázmány P. sétány 1/A, Hungary
- Wigner Research Centre for Physics, RMI, 1121 Budapest, Hungary
| | - T Csörgő
- Wigner Research Centre for Physics, RMI, 1121 Budapest, Hungary
- MATE Institute of Technology KRC, 3200 Gyöngyös, Hungary
| | - J Cuth
- Institut für Physik, Universität Mainz, 55099 Mainz, Germany
| | - D Cutts
- Brown University, Providence, Rhode Island 02912, USA
| | - H da Motta
- Southern Methodist University, Dallas, Texas 75275, USA
| | - A Das
- Southern Methodist University, Dallas, Texas 75275, USA
| | - G Davies
- Imperial College London, London SW7 2AZ, United Kingdom
| | - M Deile
- CERN, 1211 Geneva 23, Switzerland
| | - S J de Jong
- Nikhef, Science Park, 1098 XG Amsterdam, Netherlands
- Radboud University Nijmegen, 6525 AJ Nijmegen, Netherlands
| | | | - F De Leonardis
- INFN Sezione di Bari, 70126 Bari, Italy
- Dipartimento di Ingegneria Elettrica e dell'Informazione-Politecnico di Bari, 70125 Bari, Italy
| | - F Déliot
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - R Demina
- University of Rochester, Rochester, New York 14627, USA
| | - D Denisov
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - S P Denisov
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | | | - S Desai
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - C Deterre
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - K DeVaughan
- University of Nebraska, Lincoln, Nebraska 68588, USA
| | - H T Diehl
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - M Diesburg
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - P F Ding
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - A Dominguez
- University of Nebraska, Lincoln, Nebraska 68588, USA
| | - M Doubek
- Czech Technical University in Prague, 116 36 Prague 6, Czech Republic
| | - A Drutskoy
- Institute for Theoretical and Experimental Physics, Moscow 117259, Russia
| | - D Druzhkin
- Tomsk State University, Tomsk 634050, Russia
- CERN, 1211 Geneva 23, Switzerland
| | - A Dubey
- Delhi University, Delhi-110 007, India
| | - L V Dudko
- Moscow State University, Moscow 119991, Russia
| | - A Duperrin
- CPPM, Aix-Marseille Université, CNRS/IN2P3, F-13288 Marseille Cedex 09, France
| | - S Dutt
- Panjab University, Chandigarh 160014, India
| | - M Eads
- Northern Illinois University, DeKalb, Illinois 60115, USA
| | - D Edmunds
- Michigan State University, East Lansing, Michigan 48824, USA
| | - K Eggert
- Case Western Reserve University, Department of Physics, Cleveland, Ohio 44106, USA
| | - J Ellison
- University of California Riverside, Riverside, California 92521, USA
| | - V D Elvira
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - Y Enari
- LPNHE, Universités Paris VI and VII, CNRS/IN2P3, F-75005 Paris, France
| | - V Eremin
- Ioffe Physical-Technical Institute of Russian Academy of Sciences, St. Petersburg 194021, Russian Federation
| | - H Evans
- Indiana University, Bloomington, Indiana 47405, USA
| | - A Evdokimov
- University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - V N Evdokimov
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | - A Fauré
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - L Feng
- Northern Illinois University, DeKalb, Illinois 60115, USA
| | - T Ferbel
- University of Rochester, Rochester, New York 14627, USA
| | - F Ferro
- INFN Sezione di Genova, 16146 Genova, Italy
| | - F Fiedler
- Institut für Physik, Universität Mainz, 55099 Mainz, Germany
| | | | - F Filthaut
- Nikhef, Science Park, 1098 XG Amsterdam, Netherlands
- Radboud University Nijmegen, 6525 AJ Nijmegen, Netherlands
| | - W Fisher
- Michigan State University, East Lansing, Michigan 48824, USA
| | - H E Fisk
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - L Forthomme
- Helsinki Institute of Physics, 00014 University of Helsinki, Helsinki, Finland
- Department of Physics, 00014 University of Helsinki, Helsinki, Finland
| | - M Fortner
- Northern Illinois University, DeKalb, Illinois 60115, USA
| | - H Fox
- Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - J Franc
- Czech Technical University in Prague, 116 36 Prague 6, Czech Republic
| | - S Fuess
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - P H Garbincius
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - F Garcia
- Helsinki Institute of Physics, 00014 University of Helsinki, Helsinki, Finland
| | | | | | - V Gavrilov
- Institute for Theoretical and Experimental Physics, Moscow 117259, Russia
| | - W Geng
- CPPM, Aix-Marseille Université, CNRS/IN2P3, F-13288 Marseille Cedex 09, France
- Michigan State University, East Lansing, Michigan 48824, USA
| | - V Georgiev
- University of West Bohemia, 301 00 Pilsen, Czech Republic
| | - C E Gerber
- University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Y Gershtein
- Rutgers University, Piscataway, New Jersey 08855, USA
| | - S Giani
- CERN, 1211 Geneva 23, Switzerland
| | - G Ginther
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - O Gogota
- Taras Shevchenko National University of Kyiv, Kiev 01601, Ukraine
| | - G Golovanov
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - P D Grannis
- State University of New York, Stony Brook, New York 11794, USA
| | - S Greder
- IPHC, Université de Strasbourg, CNRS/IN2P3, F-67037 Strasbourg, France
| | - H Greenlee
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - G Grenier
- IPNL, Université Lyon 1, CNRS/IN2P3, F-69622 Villeurbanne Cedex, France and Université de Lyon, F-69361 Lyon CEDEX 07, France
| | - Ph Gris
- LPC, Université Blaise Pascal, CNRS/IN2P3, Clermont, F-63178 Aubière Cedex, France
| | - J-F Grivaz
- LAL, Univ. Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91898 Orsay Cedex, France
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- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - S Grünendahl
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | | | - L Grzanka
- AGH University of Science and Technology, 30-059 Krakow, Poland
| | - T Guillemin
- LAL, Univ. Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91898 Orsay Cedex, France
| | - G Gutierrez
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - P Gutierrez
- University of Oklahoma, Norman, Oklahoma 73019, USA
| | - J Haley
- Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - J Hammerbauer
- University of West Bohemia, 301 00 Pilsen, Czech Republic
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- University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - K Harder
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - A Harel
- University of Rochester, Rochester, New York 14627, USA
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- Imperial College London, London SW7 2AZ, United Kingdom
| | - T Head
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - T Hebbeker
- III. Physikalisches Institut A, RWTH Aachen University, 52056 Aachen, Germany
| | - D Hedin
- Northern Illinois University, DeKalb, Illinois 60115, USA
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- Oklahoma State University, Stillwater, Oklahoma 74078, USA
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- University of California Riverside, Riverside, California 92521, USA
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- Brown University, Providence, Rhode Island 02912, USA
| | - C Hensel
- LAFEX, Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro, RJ 22290, Brazil
| | | | - K Herner
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - G Hesketh
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - M D Hildreth
- University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - R Hirosky
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - T Hoang
- Florida State University, Tallahassee, Florida 32306, USA
| | - J D Hobbs
- State University of New York, Stony Brook, New York 11794, USA
| | - B Hoeneisen
- Universidad San Francisco de Quito, Quito 170157, Ecuador
| | - J Hogan
- Rice University, Houston, Texas 77005, USA
| | - M Hohlfeld
- Institut für Physik, Universität Mainz, 55099 Mainz, Germany
| | - J L Holzbauer
- University of Mississippi, University, Mississippi 38677, USA
| | - I Howley
- University of Texas, Arlington, Texas 76019, USA
| | - Z Hubacek
- Czech Technical University in Prague, 116 36 Prague 6, Czech Republic
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - V Hynek
- Czech Technical University in Prague, 116 36 Prague 6, Czech Republic
| | - I Iashvili
- State University of New York, Buffalo, New York 14260, USA
| | - Y Ilchenko
- Southern Methodist University, Dallas, Texas 75275, USA
| | - R Illingworth
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - T Isidori
- University of Kansas, Lawrence, Kansas 66045, USA
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- LAL, Univ. Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91898 Orsay Cedex, France
| | - M Janda
- Czech Technical University in Prague, 116 36 Prague 6, Czech Republic
| | - A Jayasinghe
- University of Oklahoma, Norman, Oklahoma 73019, USA
| | - M S Jeong
- Korea Detector Laboratory, Korea University, Seoul 02841, Korea
| | - R Jesik
- Imperial College London, London SW7 2AZ, United Kingdom
| | - P Jiang
- University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - K Johns
- University of Arizona, Tucson, Arizona 85721, USA
| | - E Johnson
- Michigan State University, East Lansing, Michigan 48824, USA
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - P Jonsson
- Imperial College London, London SW7 2AZ, United Kingdom
| | - J Joshi
- University of California Riverside, Riverside, California 92521, USA
| | - A W Jung
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
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- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Institut de Física d'Altes Energies (IFAE), 08193 Bellaterra (Barcelona), Spain
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- CPPM, Aix-Marseille Université, CNRS/IN2P3, F-13288 Marseille Cedex 09, France
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- CERN, 1211 Geneva 23, Switzerland
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- Moscow State University, Moscow 119991, Russia
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- Institute of Physics, Academy of Sciences of the Czech Republic, 182 21 Prague, Czech Republic
- CERN, 1211 Geneva 23, Switzerland
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- University of Nebraska, Lincoln, Nebraska 68588, USA
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- Panjab University, Chandigarh 160014, India
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- Istanbul University, 34134 Vezneciler, Istanbul, Turkey
| | - R Kehoe
- Southern Methodist University, Dallas, Texas 75275, USA
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- CPPM, Aix-Marseille Université, CNRS/IN2P3, F-13288 Marseille Cedex 09, France
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- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - A Khanov
- Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - A Kharchilava
- State University of New York, Buffalo, New York 14260, USA
| | - Y N Kharzheev
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - I Kiselevich
- Institute for Theoretical and Experimental Physics, Moscow 117259, Russia
| | - J M Kohli
- Panjab University, Chandigarh 160014, India
| | - J Kopal
- CERN, 1211 Geneva 23, Switzerland
| | - A V Kozelov
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | - J Kraus
- University of Mississippi, University, Mississippi 38677, USA
| | - A Kumar
- State University of New York, Buffalo, New York 14260, USA
| | - V Kundrát
- Institute of Physics, Academy of Sciences of the Czech Republic, 182 21 Prague, Czech Republic
| | - A Kupco
- Institute of Physics, Academy of Sciences of the Czech Republic, 182 21 Prague, Czech Republic
| | - T Kurča
- IPNL, Université Lyon 1, CNRS/IN2P3, F-69622 Villeurbanne Cedex, France and Université de Lyon, F-69361 Lyon CEDEX 07, France
| | - V A Kuzmin
- Moscow State University, Moscow 119991, Russia
| | - S Lami
- INFN Sezione di Pisa, 56127 Pisa, Italy
| | - S Lammers
- Indiana University, Bloomington, Indiana 47405, USA
| | - G Latino
- Università degli Studi di Siena and Gruppo Collegato INFN di Siena, 53100 Siena, Italy
| | - P Lebrun
- IPNL, Université Lyon 1, CNRS/IN2P3, F-69622 Villeurbanne Cedex, France and Université de Lyon, F-69361 Lyon CEDEX 07, France
| | - H S Lee
- Korea Detector Laboratory, Korea University, Seoul 02841, Korea
| | - S W Lee
- Iowa State University, Ames, Iowa 50011, USA
| | - W M Lee
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - X Le
- University of Arizona, Tucson, Arizona 85721, USA
| | - J Lellouch
- LPNHE, Universités Paris VI and VII, CNRS/IN2P3, F-75005 Paris, France
| | - D Li
- LPNHE, Universités Paris VI and VII, CNRS/IN2P3, F-75005 Paris, France
| | - H Li
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - L Li
- University of California Riverside, Riverside, California 92521, USA
| | - Q Z Li
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - J K Lim
- Korea Detector Laboratory, Korea University, Seoul 02841, Korea
| | - D Lincoln
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - C Lindsey
- University of Kansas, Lawrence, Kansas 66045, USA
| | - R Linhart
- University of West Bohemia, 301 00 Pilsen, Czech Republic
| | - J Linnemann
- Michigan State University, East Lansing, Michigan 48824, USA
| | - V V Lipaev
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | - R Lipton
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - H Liu
- Southern Methodist University, Dallas, Texas 75275, USA
| | - Y Liu
- University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - A Lobodenko
- Petersburg Nuclear Physics Institute, St. Petersburg 188300, Russia
| | - M Lokajicek
- Institute of Physics, Academy of Sciences of the Czech Republic, 182 21 Prague, Czech Republic
| | - M V Lokajíček
- Institute of Physics, Academy of Sciences of the Czech Republic, 182 21 Prague, Czech Republic
| | - R Lopes de Sa
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - L Losurdo
- Università degli Studi di Siena and Gruppo Collegato INFN di Siena, 53100 Siena, Italy
| | | | | | - A L Lyon
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - A K A Maciel
- LAFEX, Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro, RJ 22290, Brazil
| | - M Macrí
- INFN Sezione di Genova, 16146 Genova, Italy
| | - R Madar
- Physikalisches Institut, Universität Freiburg, 79085 Freiburg, Germany
| | | | - M Malawski
- AGH University of Science and Technology, 30-059 Krakow, Poland
| | - H B Malbouisson
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | - S Malik
- University of Nebraska, Lincoln, Nebraska 68588, USA
| | - V L Malyshev
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - J Mansour
- II. Physikalisches Institut, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | | | - R McCarthy
- State University of New York, Stony Brook, New York 11794, USA
| | - C L McGivern
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - M M Meijer
- Nikhef, Science Park, 1098 XG Amsterdam, Netherlands
- Radboud University Nijmegen, 6525 AJ Nijmegen, Netherlands
| | - A Melnitchouk
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - D Menezes
- Northern Illinois University, DeKalb, Illinois 60115, USA
| | - P G Mercadante
- Universidade Federal do ABC, Santo André, SP 09210, Brazil
| | - M Merkin
- Moscow State University, Moscow 119991, Russia
| | - A Meyer
- III. Physikalisches Institut A, RWTH Aachen University, 52056 Aachen, Germany
| | - J Meyer
- II. Physikalisches Institut, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - F Miconi
- IPHC, Université de Strasbourg, CNRS/IN2P3, F-67037 Strasbourg, France
| | - N Minafra
- University of Kansas, Lawrence, Kansas 66045, USA
| | - S Minutoli
- INFN Sezione di Genova, 16146 Genova, Italy
| | - J Molina
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | - N K Mondal
- Tata Institute of Fundamental Research, Mumbai-400 005, India
| | - M Mulhearn
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - L Mundim
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | - T Naaranoja
- Helsinki Institute of Physics, 00014 University of Helsinki, Helsinki, Finland
- Department of Physics, 00014 University of Helsinki, Helsinki, Finland
| | - E Nagy
- CPPM, Aix-Marseille Université, CNRS/IN2P3, F-13288 Marseille Cedex 09, France
| | - M Narain
- Brown University, Providence, Rhode Island 02912, USA
| | - R Nayyar
- University of Arizona, Tucson, Arizona 85721, USA
| | - H A Neal
- University of Michigan, Ann Arbor, Michigan 48109, USA
| | - J P Negret
- Universidad de los Andes, Bogotá 111711, Colombia
| | - F Nemes
- Wigner Research Centre for Physics, RMI, 1121 Budapest, Hungary
- CERN, 1211 Geneva 23, Switzerland
| | - P Neustroev
- Petersburg Nuclear Physics Institute, St. Petersburg 188300, Russia
| | - H T Nguyen
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - H Niewiadomski
- Case Western Reserve University, Department of Physics, Cleveland, Ohio 44106, USA
| | - T Novák
- MATE Institute of Technology KRC, 3200 Gyöngyös, Hungary
| | - T Nunnemann
- Ludwig-Maximilians-Universität München, 80539 München, Germany
| | - V Oguri
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | | | - F Oljemark
- Helsinki Institute of Physics, 00014 University of Helsinki, Helsinki, Finland
- Department of Physics, 00014 University of Helsinki, Helsinki, Finland
| | - J Orduna
- Brown University, Providence, Rhode Island 02912, USA
| | - M Oriunno
- SLAC National Accelerator Laboratory, Stanford, California 94025, USA
| | - N Osman
- CPPM, Aix-Marseille Université, CNRS/IN2P3, F-13288 Marseille Cedex 09, France
| | - K Österberg
- Helsinki Institute of Physics, 00014 University of Helsinki, Helsinki, Finland
- Department of Physics, 00014 University of Helsinki, Helsinki, Finland
| | - A Pal
- University of Texas, Arlington, Texas 76019, USA
| | | | - N Parashar
- Purdue University Calumet, Hammond, Indiana 46323, USA
| | - V Parihar
- Brown University, Providence, Rhode Island 02912, USA
| | - S K Park
- Korea Detector Laboratory, Korea University, Seoul 02841, Korea
| | - R Partridge
- Brown University, Providence, Rhode Island 02912, USA
| | - N Parua
- Indiana University, Bloomington, Indiana 47405, USA
| | - R Pasechnik
- Department of Astronomy and Theoretical Physics, Lund University, SE-223 62 Lund, Sweden
| | - V Passaro
- INFN Sezione di Bari, 70126 Bari, Italy
- Dipartimento di Ingegneria Elettrica e dell'Informazione-Politecnico di Bari, 70125 Bari, Italy
| | - A Patwa
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - B Penning
- Imperial College London, London SW7 2AZ, United Kingdom
| | - M Perfilov
- Moscow State University, Moscow 119991, Russia
| | - Z Peroutka
- University of West Bohemia, 301 00 Pilsen, Czech Republic
| | - Y Peters
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - K Petridis
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - G Petrillo
- University of Rochester, Rochester, New York 14627, USA
| | - P Pétroff
- LAL, Univ. Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91898 Orsay Cedex, France
| | - M-A Pleier
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - V M Podstavkov
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - A V Popov
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | - W L Prado da Silva
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | - M Prewitt
- Rice University, Houston, Texas 77005, USA
| | - D Price
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - J Procházka
- Institute of Physics, Academy of Sciences of the Czech Republic, 182 21 Prague, Czech Republic
| | - N Prokopenko
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | - J Qian
- University of Michigan, Ann Arbor, Michigan 48109, USA
| | - A Quadt
- II. Physikalisches Institut, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - B Quinn
- University of Mississippi, University, Mississippi 38677, USA
| | - M Quinto
- INFN Sezione di Bari, 70126 Bari, Italy
- Dipartimento Interateneo di Fisica di Bari, 70126 Bari, Italy
| | - T G Raben
- University of Kansas, Lawrence, Kansas 66045, USA
| | | | | | - M Rangel
- LAFEX, Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro, RJ 22290, Brazil
| | - P N Ratoff
- Lancaster University, Lancaster LA1 4YB, United Kingdom
| | | | - I Razumov
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | - I Ripp-Baudot
- IPHC, Université de Strasbourg, CNRS/IN2P3, F-67037 Strasbourg, France
| | - F Rizatdinova
- Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - E Robutti
- INFN Sezione di Genova, 16146 Genova, Italy
| | - R F Rodrigues
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | - M Rominsky
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - A Ross
- Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - C Royon
- University of Kansas, Lawrence, Kansas 66045, USA
| | - P Rubinov
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - R Ruchti
- University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | | - H Saarikko
- Helsinki Institute of Physics, 00014 University of Helsinki, Helsinki, Finland
- Department of Physics, 00014 University of Helsinki, Helsinki, Finland
| | - G Sajot
- LPSC, Université Joseph Fourier Grenoble 1, CNRS/IN2P3, Institut National Polytechnique de Grenoble, F-38026 Grenoble Cedex, France
| | - V D Samoylenko
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | | | - M P Sanders
- Ludwig-Maximilians-Universität München, 80539 München, Germany
| | - A Santoro
- Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ 20550, Brazil
| | - A S Santos
- LAFEX, Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro, RJ 22290, Brazil
| | - G Savage
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - M Savitskyi
- Taras Shevchenko National University of Kyiv, Kiev 01601, Ukraine
| | - L Sawyer
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - T Scanlon
- Imperial College London, London SW7 2AZ, United Kingdom
| | - R D Schamberger
- State University of New York, Stony Brook, New York 11794, USA
| | - Y Scheglov
- Petersburg Nuclear Physics Institute, St. Petersburg 188300, Russia
| | - H Schellman
- Northwestern University, Evanston, Illinois 60208, USA
- Oregon State University, Corvallis, Oregon 97331, USA
| | - M Schott
- Institut für Physik, Universität Mainz, 55099 Mainz, Germany
| | - C Schwanenberger
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - R Schwienhorst
- Michigan State University, East Lansing, Michigan 48824, USA
| | | | - J Sekaric
- University of Kansas, Lawrence, Kansas 66045, USA
| | - H Severini
- University of Oklahoma, Norman, Oklahoma 73019, USA
| | - E Shabalina
- II. Physikalisches Institut, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - V Shary
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - S Shaw
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - A A Shchukin
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | - O Shkola
- Taras Shevchenko National University of Kyiv, Kiev 01601, Ukraine
| | - V Simak
- Czech Technical University in Prague, 116 36 Prague 6, Czech Republic
| | - J Siroky
- University of West Bohemia, 301 00 Pilsen, Czech Republic
| | - P Skubic
- University of Oklahoma, Norman, Oklahoma 73019, USA
| | - P Slattery
- University of Rochester, Rochester, New York 14627, USA
| | - J Smajek
- CERN, 1211 Geneva 23, Switzerland
| | - W Snoeys
- CERN, 1211 Geneva 23, Switzerland
| | - G R Snow
- University of Nebraska, Lincoln, Nebraska 68588, USA
| | - J Snow
- Langston University, Langston, Oklahoma 73050, USA
| | - S Snyder
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | | | - L Sonnenschein
- III. Physikalisches Institut A, RWTH Aachen University, 52056 Aachen, Germany
| | - K Soustruznik
- Charles University, Faculty of Mathematics and Physics, Center for Particle Physics, 116 36 Prague 1, Czech Republic
| | - J Stark
- LPSC, Université Joseph Fourier Grenoble 1, CNRS/IN2P3, Institut National Polytechnique de Grenoble, F-38026 Grenoble Cedex, France
| | - N Stefaniuk
- Taras Shevchenko National University of Kyiv, Kiev 01601, Ukraine
| | | | - A Ster
- Wigner Research Centre for Physics, RMI, 1121 Budapest, Hungary
| | - D A Stoyanova
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | - M Strauss
- University of Oklahoma, Norman, Oklahoma 73019, USA
| | - L Suter
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - P Svoisky
- University of Virginia, Charlottesville, Virginia 22904, USA
| | - I Szanyi
- Eötvös University, 1117 Budapest, Pázmány P. sétány 1/A, Hungary
- Wigner Research Centre for Physics, RMI, 1121 Budapest, Hungary
| | - J Sziklai
- Wigner Research Centre for Physics, RMI, 1121 Budapest, Hungary
| | - C Taylor
- Case Western Reserve University, Department of Physics, Cleveland, Ohio 44106, USA
| | | | - M Titov
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - V V Tokmenin
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Y-T Tsai
- University of Rochester, Rochester, New York 14627, USA
| | - D Tsybychev
- State University of New York, Stony Brook, New York 11794, USA
| | - B Tuchming
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - C Tully
- Princeton University, Princeton, New Jersey 08544, USA
| | - N Turini
- Università degli Studi di Siena and Gruppo Collegato INFN di Siena, 53100 Siena, Italy
| | - O Urban
- University of West Bohemia, 301 00 Pilsen, Czech Republic
| | - L Uvarov
- Petersburg Nuclear Physics Institute, St. Petersburg 188300, Russia
| | - S Uvarov
- Petersburg Nuclear Physics Institute, St. Petersburg 188300, Russia
| | - S Uzunyan
- Northern Illinois University, DeKalb, Illinois 60115, USA
| | - V Vacek
- Czech Technical University in Prague, 116 36 Prague 6, Czech Republic
| | - R Van Kooten
- Indiana University, Bloomington, Indiana 47405, USA
| | | | - N Varelas
- University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - E W Varnes
- University of Arizona, Tucson, Arizona 85721, USA
| | - I A Vasilyev
- Institute for High Energy Physics, Protvino, Moscow region 142281, Russia
| | - O Vavroch
- University of West Bohemia, 301 00 Pilsen, Czech Republic
| | - A Y Verkheev
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | | | - M Verzocchi
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - M Vesterinen
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - D Vilanova
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - P Vokac
- Czech Technical University in Prague, 116 36 Prague 6, Czech Republic
| | - H D Wahl
- Florida State University, Tallahassee, Florida 32306, USA
| | - C Wang
- University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - M H L S Wang
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - J Warchol
- University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - G Watts
- University of Washington, Seattle, Washington 98195, USA
| | - M Wayne
- University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - J Weichert
- Institut für Physik, Universität Mainz, 55099 Mainz, Germany
| | - J Welti
- Helsinki Institute of Physics, 00014 University of Helsinki, Helsinki, Finland
- Department of Physics, 00014 University of Helsinki, Helsinki, Finland
| | | | - J Williams
- University of Kansas, Lawrence, Kansas 66045, USA
| | | | - G W Wilson
- University of Kansas, Lawrence, Kansas 66045, USA
| | - M Wobisch
- Louisiana Tech University, Ruston, Louisiana 71272, USA
| | - D R Wood
- Northeastern University, Boston, Massachusetts 02115, USA
| | - T R Wyatt
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Y Xie
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - R Yamada
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - S Yang
- University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - T Yasuda
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - Y A Yatsunenko
- Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - W Ye
- State University of New York, Stony Brook, New York 11794, USA
| | - Z Ye
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - H Yin
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - K Yip
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - S W Youn
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - J M Yu
- University of Michigan, Ann Arbor, Michigan 48109, USA
| | - J Zennamo
- State University of New York, Buffalo, New York 14260, USA
| | - T G Zhao
- The University of Manchester, Manchester M13 9PL, United Kingdom
| | - B Zhou
- University of Michigan, Ann Arbor, Michigan 48109, USA
| | - J Zhu
- University of Michigan, Ann Arbor, Michigan 48109, USA
| | - J Zich
- University of West Bohemia, 301 00 Pilsen, Czech Republic
| | - K Zielinski
- AGH University of Science and Technology, 30-059 Krakow, Poland
| | - M Zielinski
- University of Rochester, Rochester, New York 14627, USA
| | - D Zieminska
- Indiana University, Bloomington, Indiana 47405, USA
| | - L Zivkovic
- LPNHE, Universités Paris VI and VII, CNRS/IN2P3, F-75005 Paris, France
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30
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Podnar JW, Pantano L, Zeller MJ, Kolling FW, Zhang Y, Alekseyev YO, Niece J, Deiderick H, Fan J, Xuei X, Kieleczawa J, Levine SS, Herbert ZT, Adams M. Cross-Site Evaluation of Commercial Sanger Sequencing Chemistries. J Biomol Tech 2021; 31:88-93. [PMID: 32831655 DOI: 10.7171/jbt.20-3103-002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sanger sequencing remains an essential tool utilized by researchers. Despite competition from commercial sequencing providers, many academic sequencing core facilities continue to offer these services based on a model of competitive pricing, knowledgeable technical support, and rapid turnaround time. In-house Sanger sequencing remains a viable core service and, until recently, Applied Biosystems BigDye Terminator chemistry was the only commercially available solution for Sanger DNA sequencing on Applied Biosystems (ABI) instruments; however, several new products employing novel dye chemistries and reaction configurations have entered the market. As a result, there is a need to benchmark the performance of these new chemistries on various DNA templates, including difficult-to-sequence templates, and their amenability to commonly employed cost-saving measures, such as dye dilution and reaction miniaturization. To evaluate these new reagents, a study was designed to compare the quality of Sanger sequencing data produced by ABI BigDye and commercially available kits from 2 other vendors using both control and difficult-to-sequence DNA templates under various reaction conditions. This study will serve as a valuable resource to core facilities conducting Sanger sequencing that wish to evaluate the use of an alternative chemistry in their sequencing core.
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Affiliation(s)
- Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Lorena Pantano
- eGenesis Engineering Life, Cambridge, Massachusetts, USA
| | - Molly J Zeller
- DNA Sequencing Facility, University of Wisconsin Biotechnology Center, Madison, Wisconsin, USA
| | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Yanping Zhang
- Gene Expression and Genotyping, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University, Boston, Massachusetts, USA
| | - Jeremy Niece
- DNA Sequencing Facility, University of Wisconsin Biotechnology Center, Madison, Wisconsin, USA
| | - Heather Deiderick
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Jun Fan
- Department of Biomedical Sciences, Genomic Core Facility, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, USA
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA; and
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
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31
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Morrison J, Koeman JM, Johnson BK, Foy KK, Beddows I, Zhou W, Chesla DW, Rossell LL, Siegwald EJ, Adams M, Shen H. Evaluation of whole-genome DNA methylation sequencing library preparation protocols. Epigenetics Chromatin 2021; 14:28. [PMID: 34147133 PMCID: PMC8214260 DOI: 10.1186/s13072-021-00401-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022] Open
Abstract
Background With rapidly dropping sequencing cost, the popularity of whole-genome DNA methylation sequencing has been on the rise. Multiple library preparation protocols currently exist. We have performed 22 whole-genome DNA methylation sequencing experiments on snap frozen human samples, and extensively benchmarked common library preparation protocols for whole-genome DNA methylation sequencing, including three traditional bisulfite-based protocols and a new enzyme-based protocol. In addition, different input DNA quantities were compared for two kits compatible with a reduced starting quantity. In addition, we also present bioinformatic analysis pipelines for sequencing data from each of these library types. Results An assortment of metrics were collected for each kit, including raw read statistics, library quality and uniformity metrics, cytosine retention, and CpG beta value consistency between technical replicates. Overall, the NEBNext Enzymatic Methyl-seq and Swift Accel-NGS Methyl-Seq kits performed quantitatively better than the other two protocols. In addition, the NEB and Swift kits performed well at low-input amounts, validating their utility in applications where DNA is the limiting factor. Results The NEBNext Enzymatic Methyl-seq kit appeared to be the best option for whole-genome DNA methylation sequencing of high-quality DNA, closely followed by the Swift kit, which potentially works better for degraded samples. Further, a general bioinformatic pipeline is applicable across the four protocols, with the exception of extra trimming needed for the Swift Biosciences’s Accel-NGS Methyl-Seq protocol to remove the Adaptase sequence. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00401-y.
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Affiliation(s)
- Jacob Morrison
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Julie M Koeman
- Genomics Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Benjamin K Johnson
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Kelly K Foy
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Ian Beddows
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, 3501 Civic Center Boulevard, Philadelphia, PA, 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David W Chesla
- Spectrum Health Office of Research and Education, Spectrum Health System, 15 Michigan Street NE, Grand Rapids, MI, 49503, USA
| | - Larissa L Rossell
- Spectrum Health Office of Research and Education, Spectrum Health System, 15 Michigan Street NE, Grand Rapids, MI, 49503, USA
| | - Emily J Siegwald
- Spectrum Health Office of Research and Education, Spectrum Health System, 15 Michigan Street NE, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA.
| | - Hui Shen
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA.
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Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech 2021; 31:47-56. [PMID: 31966025 DOI: 10.7171/jbt.20-3102-001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs in vivo. Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over- and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Carol S Ringelberg
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA
| | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, Massachusetts, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Holly S Stevenson
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shipra Gupta
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Julie Koeman
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Allison R Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Jeffrey Malik
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - Kara L Pivarski
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Xinkun Wang
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Gina Kuffel
- Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, USA
| | - Tania E Mesa
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrew T Smith
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Thomas L Volkert
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jennifer A Love
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research Gene Expression and Genotyping, University of Florida, Gainsville, Florida, USA
| | - Jun Wang
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Gupta R, Leimanis ML, Adams M, Bachmann AS, Uhl KL, Bupp CP, Hartog NL, Kort EJ, Olivero R, Comstock SS, Sanfilippo DJ, Lunt SY, Prokop JW, Rajasekaran S. Balancing precision versus cohort transcriptomic analysis of acute and recovery phase of viral bronchiolitis. Am J Physiol Lung Cell Mol Physiol 2021; 320:L1147-L1157. [PMID: 33851876 DOI: 10.1152/ajplung.00440.2020] [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] [Indexed: 01/18/2023] Open
Abstract
Viral infections affecting the lower respiratory tract place enormous burdens on hospitals. As neither vaccines nor antiviral agents exist for many viruses, understanding risk factors and outcomes in each patient using minimally invasive analysis, such as blood, can lead to improved health care delivery. A cohort of PAXgene RNA sequencing of infants admitted with moderate or severe acute bronchiolitis and respiratory syncytial virus were compared with case-control statistical analysis and cohort-based outlier mapping for precision transcriptomics. Patients with severe bronchiolitis had signatures connected to the immune system, interferon signaling, and cytokine signaling, with marked sex differences in XIST, RPS4Y1, KDM5D, and LINC00278 for severity. Several patients had unique secondary infections, cytokine activation, immune responses, biological pathways, and immune cell activation, highlighting the need for defining patient-level transcriptomic signatures. Balancing relative contributions of cohort-based biomarker discoveries with patient's biological responses is needed to understand the totality of mechanisms of adverse outcomes in viral bronchiolitis.
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Affiliation(s)
- Ruchir Gupta
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Mara L Leimanis
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - André S Bachmann
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | - Katie L Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Caleb P Bupp
- Spectrum Health Medical Genetics, Grand Rapids, Michigan
| | | | - Eric J Kort
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,DeVos Cardiovascular Research Program, Spectrum Health and Van Andel Institute, Grand Rapids, Michigan
| | - Rosemary Olivero
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Infectious Disease, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan
| | - Dominic J Sanfilippo
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Sophia Y Lunt
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan.,Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan.,Office of Research, Spectrum Health, Grand Rapids, Michigan
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Suraweera A, Duijf P, Tang M, Jekimovs C, Schrobback K, Liu C, Adams M, Richard D, O'Byrne K. 216P COMMD1 in non-small cell lung cancer: A novel DNA repair protein as a therapeutic target and diagnostic biomarker. J Thorac Oncol 2021. [DOI: 10.1016/s1556-0864(21)02058-x] [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: 11/29/2022]
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Dorkenoo A, Kouassi K, Afanyibo YG, Gbada K, Yakpa K, Têko M, Koura A, Katawa G, Adams M, Merkel M. [External Quality Assessment of Thick and Thin Blood Smear Slides for the Diagnosis of Malaria in the Lomé and Gulf Health Districts of Togo]. Med Trop Sante Int 2021; 1:S1SQ-3476. [PMID: 35586643 PMCID: PMC9022756 DOI: 10.48327/s1sq-3476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/12/2021] [Indexed: 11/24/2022]
Abstract
Objective In sub-Saharan Africa where 90% of malaria cases are concentrated, the control of this disease constitutes a major challenge whose diagnosis by thick and thin smear deserves to be exact and reproducible. The purpose of this study is to assess the performance of thick/thin blood smear in order to improve its implementation process. Material and methods This was a descriptive and analytical study that took place from May to June 2017 and involved participating laboratories (PL) coming from public, liberal and confessional sectors in Lomé. A set of 13 blood smear slides of variable parasite densities (PD) with assigned values (AV) of parasite densities and the Plasmodium species assigned was used. The criterion for establishing the parasite densities compliance interval was assigned values ± 25% and the performance rates were compared to the 80% recommended by the WHO for Africa region. Results 41.9% (13/31) of the PLs had a compliance rate greater than 80% including four with a performance of 100% for the ability to identify the Plasmodium species. For the parasitaemia < 100/μl, 51.6% of participating laboratories had a performance rate less than 80% and for parasitaemia > 2000/μl, 100% of these laboratories had a performance rate greater than 80%. Conclusion The evaluated laboratories had insufficient ability for the identification of Plasmodium falciparum and the correct estimation of low parasitaemia. A need to strength the technical skills, adapted to the context of low parasitaemia are essential to improve the biological diagnosis of malaria in Togo.
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Affiliation(s)
- A.M. Dorkenoo
- Faculté des sciences de la santé, Université de Lomé-Lomé, Togo,Ministère de la santé et de l'hygiène publique-Lomé, Togo,*
| | - K.C. Kouassi
- Ecole supérieure des techniques biologiques et alimentaires, Université de Lomé-Lomé, Togo
| | | | - K. Gbada
- Ministère de la santé et de l'hygiène publique-Lomé, Togo
| | - K. Yakpa
- Programme national de lutte contre le paludisme-Lomé, Togo
| | - M. Têko
- Ministère de la santé et de l'hygiène publique-Lomé, Togo
| | | | - G. Katawa
- Ecole supérieure des techniques biologiques et alimentaires, Université de Lomé-Lomé, Togo
| | - M. Adams
- Global Scientific Solution for Health, Maryland, USA
| | - M. Merkel
- Global Scientific Solution for Health, Maryland, USA
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36
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Wilson MR, Reske JJ, Holladay J, Neupane S, Ngo J, Cuthrell N, Wegener M, Rhodes M, Adams M, Sheridan R, Hostetter G, Alotaibi FT, Yong PJ, Anglesio MS, Lessey BA, Leach RE, Teixeira JM, Missmer SA, Fazleabas AT, Chandler RL. ARID1A Mutations Promote P300-Dependent Endometrial Invasion through Super-Enhancer Hyperacetylation. Cell Rep 2020; 33:108366. [PMID: 33176148 PMCID: PMC7682620 DOI: 10.1016/j.celrep.2020.108366] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/16/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Endometriosis affects 1 in 10 women and is characterized by the presence of abnormal endometrium at ectopic sites. ARID1A mutations are observed in deeply invasive forms of the disease, often correlating with malignancy. To identify epigenetic dependencies driving invasion, we use an unbiased approach to map chromatin state transitions accompanying ARID1A loss in the endometrium. We show that super-enhancers marked by high H3K27 acetylation are strongly associated with ARID1A binding. ARID1A loss leads to H3K27 hyperacetylation and increased chromatin accessibility and enhancer RNA transcription at super-enhancers, but not typical enhancers, indicating that ARID1A normally prevents super-enhancer hyperactivation. ARID1A co-localizes with P300 at super-enhancers, and genetic or pharmacological inhibition of P300 in ARID1A mutant endometrial epithelia suppresses invasion and induces anoikis through the rescue of super-enhancer hyperacetylation. Among hyperactivated super-enhancers, SERPINE1 (PAI-1) is identified as an essential target gene driving ARID1A mutant endometrial invasion. Broadly, our findings provide rationale for therapeutic strategies targeting super-enhancers in ARID1A mutant endometrium.
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Affiliation(s)
- Mike R Wilson
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jake J Reske
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jeanne Holladay
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Subechhya Neupane
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Julie Ngo
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Nina Cuthrell
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Marc Wegener
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Mary Rhodes
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Rachael Sheridan
- Flow Cytometry Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Fahad T Alotaibi
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; Department of Physiology, College of Medicine, Al-Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Paul J Yong
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Anglesio
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; British Columbia's Gynecological Cancer Research Team (OVCARE), University of British Columbia, Vancouver General Hospital, and BC Cancer, Vancouver, BC, Canada
| | - Bruce A Lessey
- Department of Obstetrics and Gynecology, Wake Forest Baptist Health, Winston-Salem, NC 27157, USA
| | - Richard E Leach
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Jose M Teixeira
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Stacey A Missmer
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Asgerally T Fazleabas
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA
| | - Ronald L Chandler
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; Department of Women's Health, Spectrum Health System, Grand Rapids, MI 49341, USA; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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Reske JJ, Wilson MR, Holladay J, Wegener M, Adams M, Chandler RL. SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity. Hum Mol Genet 2020; 29:3412-3430. [PMID: 33075803 PMCID: PMC7749707 DOI: 10.1093/hmg/ddaa227] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
Although ARID1A mutations are a hallmark feature, mutations in other SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling subunits are also observed in endometrial neoplasms. Here, we interrogated the roles of Brahma/SWI2-related gene 1 (BRG1, SMARCA4), the SWI/SNF catalytic subunit, in the endometrial epithelium. BRG1 loss affects more than one-third of all active genes and highly overlaps with the ARID1A gene regulatory network. Chromatin immunoprecipitation studies revealed widespread subunit-specific differences in transcriptional regulation, as BRG1 promoter interactions are associated with gene activation, while ARID1A binding is associated with gene repression. However, we identified a physiologically relevant subset of BRG1 and ARID1A co-regulated epithelial identity genes. Mice were genetically engineered to inactivate BRG1 specifically in the endometrial epithelium. Endometrial glands were observed embedded in uterine myometrium, indicating adenomyosis-like phenotypes. Molecular similarities were observed between BRG1 and ARID1A mutant endometrial cells in vivo, including loss of epithelial cell adhesion and junction genes. Collectively, these studies illustrate overlapping contributions of multiple SWI/SNF subunit mutations in the translocation of endometrium to distal sites, with loss of cell integrity being a common feature in SWI/SNF mutant endometrial epithelia.
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Affiliation(s)
- Jake J Reske
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Mike R Wilson
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jeanne Holladay
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Marc Wegener
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Ronald L Chandler
- To whom correspondence should be addressed at: Grand Rapids Research Center, 400 Monroe NW, Grand Rapids, MI 49503, USA. Tel: +1 6162340980;
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38
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Poole J, Bentley J, Barraud L, Samish I, Dalkas G, Matheson A, Clegg P, Euston S, Kauffman Johnson J, Haacke C, Westphal L, Molina Beato L, Adams M, Spiro A. Rising to the challenges: Solution‐based case studies highlighting innovation and evolution in reformulation. NUTR BULL 2020. [DOI: 10.1111/nbu.12456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- J. Poole
- Institute of Food Science and Technology London UK
| | | | - L. Barraud
- Nestlé Product Technology Centre York UK
| | | | | | | | - P. Clegg
- The University of Edinburgh Edinburgh UK
| | | | | | | | | | | | | | - A. Spiro
- British Nutrition Foundation London UK
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Giovannetti O, Forster A, Tomalty D, Hannan J, Szell N, Komisaruk B, Goldstein S, Goldstein I, Adams M. 023 Investigation of Sensory Innervation in the Surgical Field of Mid-Urethral Sling and Loop Electrosurgical Excision Procedures in Periurethral and Cervical Tissues Using Immunohistochemistry. J Sex Med 2020. [DOI: 10.1016/j.jsxm.2020.04.259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Tomalty D, Giovannetti O, Hannan J, Komisaruk B, Goldstein S, Goldstein I, Szell N, Adams M. 073 Characterization of Female Periurethral Glandular Tissue in the Periurethral Space Negatively Impacted by Mid-Urethral Sling Surgery. J Sex Med 2020. [DOI: 10.1016/j.jsxm.2020.04.309] [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: 11/25/2022]
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41
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Abbas Y, Abdelkader M, Adams M, Addison A, Advani R, Ahmed T, Alexander V, Alexander V, Alli B, Alvi S, Amiraraghi N, Ashman A, Balakumar R, Bewick J, Bhasker D, Bola S, Bowles P, Campbell N, Can Guru Naidu N, Caton N, Chapman J, Chawdhary G, Cherko M, Coates M, Conroy K, Coyle P, Cozar O, Cresswell M, Dalton L, Danino J, Daultrey C, Davies K, Carrie S, Dick D, Dimitriadis PA, Doddi N, Dowling M, Easto R, Edmiston R, Ellul D, Erskine S, Evans A, Farboud A, Forde C, Fussey J, Gaunt A, Gilchrist J, Gohil R, Gosnell E, Grech Marguerat D, Green R, Grounds R, Hall A, Hardman J, Harris A, Harrison L, Hone R, Hoskison E, Howard J, Ioannidis D, Iqbal I, Janjua N, Jolly K, Kamal S, Kanzara T, Keates N, Kelly A, Khan H, Korampalli T, Kuet M, Kul‐loo P, Lakhani R, Lambert A, Lancer H, Leonard C, Lloyd G, Lowe E, Mair J, Maughan E, Gao C, Mayberry T, McCadden L, McClenaghan F, McKenzie G, Mcleod R, Meghji S, Mian M, Millington A, Mirza O, Mistry S, Molena E, Morris J, Myuran T, Navaratnam A, Noon E, Okonkwo O, Oremule B, Pabla L, Papesch E, Puranik V, Roplekar R, Ross E, Rudd J, Schechter E, Senior A, Sethi N, Sharma S, Sharma R, Shelton F, Sherazi Z, Tahir A, Tikka T, Tkachuk Hlinicanova O, To K, Tse A, Toll E, Ubayasiri K, Unadkat S, Upile N, Vijendren A, Walijee H, Wilkie M, Williams R, Williams M, Wilson G, Wong W, Wong G, Xie C, Yao A, Zhang H, Ellis M, Mehta N, Milinis K, Tikka T, Slovick A, Swords C, Hutson K, Smith ME, Hopkins C, Ng Kee Kwong F. Nasal Packs for Epistaxis: Predictors of Success. Clin Otolaryngol 2020; 45:659-666. [DOI: 10.1111/coa.13555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 03/08/2020] [Accepted: 04/13/2020] [Indexed: 11/30/2022]
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Prokop JW, Shankar R, Gupta R, Leimanis ML, Nedveck D, Uhl K, Chen B, Hartog NL, Van Veen J, Sisco JS, Sirpilla O, Lydic T, Boville B, Hernandez A, Braunreiter C, Kuk CC, Singh V, Mills J, Wegener M, Adams M, Rhodes M, Bachmann AS, Pan W, Byrne-Steele ML, Smith DC, Depinet M, Brown BE, Eisenhower M, Han J, Haw M, Madura C, Sanfilippo DJ, Seaver LH, Bupp C, Rajasekaran S. Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19. Physiol Genomics 2020; 52:255-268. [PMID: 32437232 PMCID: PMC7303726 DOI: 10.1152/physiolgenomics.00045.2020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Precision medicine requires the translation of basic biological understanding to medical insights, mainly applied to characterization of each unique patient. In many clinical settings, this requires tools that can be broadly used to identify pathology and risks. Patients often present to the intensive care unit with broad phenotypes, including multiple organ dysfunction syndrome (MODS) resulting from infection, trauma, or other disease processes. Etiology and outcomes are unique to individuals, making it difficult to cohort patients with MODS, but presenting a prime target for testing/developing tools for precision medicine. Using multitime point whole blood (cellular/acellular) total transcriptomics in 27 patients, we highlight the promise of simultaneously mapping viral/bacterial load, cell composition, tissue damage biomarkers, balance between syndromic biology versus environmental response, and unique biological insights in each patient using a single platform measurement. Integration of a transcriptome workflow yielded unexpected insights into the complex interplay between host genetics and viral/bacterial specific mechanisms, highlighted by a unique case of virally induced genetics (VIG) within one of these 27 patients. The power of RNA-Seq to study unique patient biology while investigating environmental contributions can be a critical tool moving forward for translational sciences applied to precision medicine.
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Affiliation(s)
- Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Rama Shankar
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Ruchir Gupta
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Mara L Leimanis
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Derek Nedveck
- Office of Research, Spectrum Health, Grand Rapids, Michigan
| | - Katie Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Bin Chen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - Nicholas L Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Allergy and Immunology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
- Adult Allergy and Immunology, Spectrum Health, Grand Rapids, Michigan
| | - Jason Van Veen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Grand Rapids Community College, Grand Rapids, Michigan
| | - Joshua S Sisco
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Grand Rapids Community College, Grand Rapids, Michigan
| | - Olivia Sirpilla
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Walsh University, North Canton, Ohio
| | - Todd Lydic
- Department of Physiology, Michigan State University, East Lansing, Michigan
| | - Brian Boville
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Angel Hernandez
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Chi Braunreiter
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Hematology-Oncology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - ChiuYing Cynthia Kuk
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | - Varinder Singh
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan
| | - Joshua Mills
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Grand Rapids Community College, Grand Rapids, Michigan
| | - Marc Wegener
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - Mary Rhodes
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan
| | - Andre S Bachmann
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | | | | | | | | | | | | | - Jian Han
- iRepertoire Inc., Huntsville, Alabama
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Marcus Haw
- Congenital Heart Center, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Casey Madura
- Pediatric Neurology, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Dominic J Sanfilippo
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Laurie H Seaver
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Spectrum Health Medical Genetics, Grand Rapids, Michigan
| | - Caleb Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Spectrum Health Medical Genetics, Grand Rapids, Michigan
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
- Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan
- Office of Research, Spectrum Health, Grand Rapids, Michigan
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Mische SM, Fisher NC, Meyn SM, Sol-Church K, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Kubow KE, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL. A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups. J Biomol Tech 2020; 31:11-26. [PMID: 31969795 PMCID: PMC6959150 DOI: 10.7171/jbt.20-3101-003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Indexed: 01/12/2023]
Abstract
Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and they have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific society whose members are scientists and administrators that manage or support Cores. The ABRF Research Groups (RGs), representing expertise for an array of cutting-edge and established technology platforms, perform multicenter research studies to determine and communicate best practices and community-based standards. This review provides a summary of the contributions of the ABRF RGs to promote scientific rigor and reproducibility in Cores from the published literature, ABRF meetings, and ABRF RGs communications.
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Affiliation(s)
- Sheenah M. Mische
- New York University (NYU) Langone Medical Center, New
York, New York 10016, USA
| | - Nancy C. Fisher
- University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599, USA
| | - Susan M. Meyn
- Vanderbilt University Medical Center, Nashville,
Tennessee 37212, USA
| | - Katia Sol-Church
- University of Virginia School of Medicine,
Charlottesville, Virginia 22908, USA
| | | | | | - Marie Adams
- Van Andel Institute, Grand Rapids, Michigan 49503,
USA
| | - John M. Ashton
- University of Rochester Medical Center, West
Henrietta, New York 14642, USA
| | - Kym M. Delventhal
- Stowers Institute for Medical Research, Kansas City,
Missouri 64110, USA
| | | | - Laura Holmes
- Stowers Institute for Medical Research, Kansas City,
Missouri 64110, USA
| | - Pratik Jagtap
- University of Minnesota, Minneapolis, Minnesota
55455, USA
| | | | | | - Magnus Palmblad
- Leiden University Medical Center, Leiden 2333, The
Netherlands
| | - Brian C. Searle
- Institute for Systems Biology, Seattle, Washington
98109, USA
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Flores G, Everett JH, Boguslawski EA, Oswald BM, Madaj ZB, Beddows I, Dikalov S, Adams M, Klumpp-Thomas CA, Kitchen-Goosen SM, Martin SE, Caplen NJ, Helman LJ, Grohar PJ. CDK9 Blockade Exploits Context-dependent Transcriptional Changes to Improve Activity and Limit Toxicity of Mithramycin for Ewing Sarcoma. Mol Cancer Ther 2020; 19:1183-1196. [PMID: 32127464 DOI: 10.1158/1535-7163.mct-19-0775] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/17/2019] [Accepted: 02/19/2020] [Indexed: 11/16/2022]
Abstract
There is a need to develop novel approaches to improve the balance between efficacy and toxicity for transcription factor-targeted therapies. In this study, we exploit context-dependent differences in RNA polymerase II processivity as an approach to improve the activity and limit the toxicity of the EWS-FLI1-targeted small molecule, mithramycin, for Ewing sarcoma. The clinical activity of mithramycin for Ewing sarcoma is limited by off-target liver toxicity that restricts the serum concentration to levels insufficient to inhibit EWS-FLI1. In this study, we perform an siRNA screen of the druggable genome followed by a matrix drug screen to identify mithramycin potentiators and a synergistic "class" effect with cyclin-dependent kinase 9 (CDK9) inhibitors. These CDK9 inhibitors enhanced the mithramycin-mediated suppression of the EWS-FLI1 transcriptional program leading to a shift in the IC50 and striking regressions of Ewing sarcoma xenografts. To determine whether these compounds may also be liver protective, we performed a qPCR screen of all known liver toxicity genes in HepG2 cells to identify mithramycin-driven transcriptional changes that contribute to the liver toxicity. Mithramycin induces expression of the BTG2 gene in HepG2 but not Ewing sarcoma cells, which leads to a liver-specific accumulation of reactive oxygen species (ROS). siRNA silencing of BTG2 rescues the induction of ROS and the cytotoxicity of mithramycin in these cells. Furthermore, CDK9 inhibition blocked the induction of BTG2 to limit cytotoxicity in HepG2, but not Ewing sarcoma cells. These studies provide the basis for a synergistic and less toxic EWS-FLI1-targeted combination therapy for Ewing sarcoma.
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Affiliation(s)
- Guillermo Flores
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan.,College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | - Joel H Everett
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee
| | - Elissa A Boguslawski
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan
| | - Brandon M Oswald
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan
| | - Zachary B Madaj
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan
| | - Ian Beddows
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan
| | - Sergey Dikalov
- The Free Radicals in Medicine Core, Division of Clinical Pharmacology Vanderbilt University Medical Center, Nashville, Tennessee
| | - Marie Adams
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan
| | - Carleen A Klumpp-Thomas
- Trans-NIH RNAi Screening Facility, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Susan M Kitchen-Goosen
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan
| | - Scott E Martin
- Trans-NIH RNAi Screening Facility, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Natasha J Caplen
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Lee J Helman
- Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Patrick J Grohar
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan. .,Pediatric Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland.,Department of Pediatrics, Vanderbilt University, Nashville, Tennessee.,Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan.,Division of Pediatric Hematology-Oncology, Helen DeVos Children's Hospital, Grand Rapids, Michigan.,Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
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Ni M, Adams M, Huddy J, Carr R, Fotheringham I, Wilson C, Tsang M, Hanna G. A multi-centred, prospective, observational study of a first-generation novel human lipase pH test for siting nasogastric feeding tubes in adult patients. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2019.12.006] [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: 10/25/2022]
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Scasta JD, Adams M, Gibbs R, Fleury B. Free-ranging horse management in Australia, New Zealand and the United States: socio-ecological dimensions of a protracted environmental conflict. Rangel J 2020. [DOI: 10.1071/rj19019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Management of free-ranging horses (Equus ferus caballus) is a complex socio-ecological issue in Australia (AU), New Zealand (NZ), and the United States (US). In these countries, horses are the results of colonial introductions and occupy very harsh rangeland environments exerting a grazing disturbance that has generated ecological concerns. Although many social and ecological concerns are similar, each country also has nuances. In 2018, we conducted a field-based comparison of AU, NZ, and US using an inductive approach to identify similarities, differences, and emerging themes through conversations with >100 individuals from New South Wales Australia, the North Island of New Zealand, and the western US. Additional data sources included field observations and archival documents. Consistent emergent themes identified included: strong public emotion, politicization of management, population growth concerns, negative ecological impact concerns, agreement that horses should be treated humanely, disagreement as to what practices were the most humane, interest and scepticism about fertility control, the need for transparency, compromise to accommodating horses and acknowledgement of social values, and recognition that collaboration is the only means to achieve both healthy rangelands and healthy horses. Unique themes identified included: NZ empowering advocate groups to become part of the solution, conflict between horses and livestock is a mostly US conflict, equids originated in the US, concern about the sustainability of adoption programs, different expectations/options for management on private lands, cultural history such as brumby running in AU, permanent branding of horses in the US, litigation as a uniquely US strategy (although a judgement on recent AU litigation is pending), government data accepted to guide removals in NZ but not always in AU or US, and complex heterogeneous land surface ownership patterns makes management difficult in the US. The difficulty of horse management in these countries is attributed to social intricacies rather than biological/ecological gaps of knowledge.
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Arnold R, Amos D, Lowe H, Elder A, Martin S, Moss S, McMaster K, Juergens C, Ryan E, Larnach G, Adams M. 472 Development of a Rural NSW Cardiac Catheter and Coronary Intervention Service Over 14 Years: Impacts on Service and 30 Day AMI Mortality. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Moss S, Arnold R, Lowe H, Elder A, Juergens C, McMaster K, Roach A, Larnach G, Adams M, Amos D. 436 A Rural 24/7 Cardiac Catheter Lab Service in Western NSW Local Health District (WNSWLHD): Locally Based Acute Coronary Syndrome (ACS) Care With Low Mortality Over 5 Years. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.443] [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: 11/30/2022]
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George JW, Fan H, Johnson B, Carpenter TJ, Foy KK, Chatterjee A, Patterson AL, Koeman J, Adams M, Madaj ZB, Chesla D, Marsh EE, Triche TJ, Shen H, Teixeira JM. Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids. Cell Rep 2019; 29:4069-4085.e6. [PMID: 31851934 PMCID: PMC6956710 DOI: 10.1016/j.celrep.2019.11.077] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 09/20/2019] [Accepted: 11/19/2019] [Indexed: 11/29/2022] Open
Abstract
Uterine fibroids are benign myometrial smooth muscle tumors of unknown etiology that, when symptomatic, are the most common indication for hysterectomy in the United States. Unsupervised clustering of results from DNA methylation analyses segregates normal myometrium from fibroids and further segregates the fibroids into subtypes characterized by MED12 mutation or activation of either HMGA2 or HMGA1 expression. Upregulation of HMGA2 expression does not always appear to be dependent on translocation but is associated with hypomethylation in the HMGA2 gene body. HOXA13 expression is upregulated in fibroids and correlates with expression of typical uterine fibroid genes. Significant overlap of differentially expressed genes is observed between cervical stroma and uterine fibroids compared with normal myometrium. These analyses show a possible role of DNA methylation in fibroid biology and suggest that homeotic transformation of myometrial cells to a more cervical stroma phenotype could be an important mechanism for etiology of the disease.
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Affiliation(s)
- Jitu Wilson George
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Huihui Fan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Benjamin Johnson
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Tyler James Carpenter
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | | | - Anindita Chatterjee
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Amanda Lynn Patterson
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA; Division of Animal Sciences, Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO, USA
| | - Julie Koeman
- Genomics Core, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Marie Adams
- Genomics Core, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Zachary Brian Madaj
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, MI, USA
| | - David Chesla
- Spectrum Health Universal Biorepository, Spectrum Health System, Grand Rapids, MI, USA
| | - Erica Elizabeth Marsh
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA.
| | - Jose Manuel Teixeira
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA.
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Adams M, Burgess J, Richard D, O'Byrne K. P1.01-01 Clinical Relevance of Targeting Proteins Required for Mitotic Progression to Improve Chemotherapy Response in Non-Small Cell Lung Cancer. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.716] [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: 10/25/2022]
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