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Baljon J, Kwiatkowski AJ, Pagendarm HM, Stone PT, Kumar A, Bharti V, Schulman JA, Becker KW, Roth EW, Christov PP, Joyce S, Wilson JT. A Cancer Nanovaccine for Co-Delivery of Peptide Neoantigens and Optimized Combinations of STING and TLR4 Agonists. ACS Nano 2024; 18:6845-6862. [PMID: 38386282 PMCID: PMC10919087 DOI: 10.1021/acsnano.3c04471] [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] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Immune checkpoint blockade (ICB) has revolutionized cancer treatment and led to complete and durable responses, but only for a minority of patients. Resistance to ICB can largely be attributed to insufficient number and/or function of antitumor CD8+ T cells in the tumor microenvironment. Neoantigen targeted cancer vaccines can activate and expand the antitumor T cell repertoire, but historically, clinical responses have been poor because immunity against peptide antigens is typically weak, resulting in insufficient activation of CD8+ cytotoxic T cells. Herein, we describe a nanoparticle vaccine platform that can overcome these barriers in several ways. First, the vaccine can be reproducibly formulated using a scalable confined impingement jet mixing method to coload a variety of physicochemically diverse peptide antigens and multiple vaccine adjuvants into pH-responsive, vesicular nanoparticles that are monodisperse and less than 100 nm in diameter. Using this approach, we encapsulated synergistically acting adjuvants, cGAMP and monophosphoryl lipid A (MPLA), into the nanocarrier to induce a robust and tailored innate immune response that increased peptide antigen immunogenicity. We found that incorporating both adjuvants into the nanovaccine synergistically enhanced expression of dendritic cell costimulatory markers, pro-inflammatory cytokine secretion, and peptide antigen cross-presentation. Additionally, the nanoparticle delivery increased lymph node accumulation and uptake of peptide antigen by dendritic cells in the draining lymph node. Consequently, nanoparticle codelivery of peptide antigen, cGAMP, and MPLA enhanced the antigen-specific CD8+ T cell response and delayed tumor growth in several mouse models. Finally, the nanoparticle platform improved the efficacy of ICB immunotherapy in a murine colon carcinoma model. This work establishes a versatile nanoparticle vaccine platform for codelivery of peptide neoantigens and synergistic adjuvants to enhance responses to cancer vaccines.
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Affiliation(s)
- Jessalyn
J. Baljon
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Alexander J. Kwiatkowski
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Hayden M. Pagendarm
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Payton T. Stone
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Amrendra Kumar
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Vijaya Bharti
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jacob A. Schulman
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Kyle W. Becker
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Eric W. Roth
- Northwestern
University Atomic and Nanoscale Characterization Experimental (NUANCE)
Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Plamen P. Christov
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University Medical Center, Nashville, Tennessee 37232, United States
| | - Sebastian Joyce
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Veteran Affairs Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
- Vanderbilt
Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Center for Immunobiology, Vanderbilt University
Medical Center, Nashville, Tennessee 37232, United States
| | - John T. Wilson
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Center for Immunobiology, Vanderbilt University
Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt-Ingram
Cancer Center, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
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Blee AM, Gallagher K, Kim HS, Kim M, Kharat S, Troll C, D’Souza A, Park J, Neufer P, Schärer O, Chazin W. XPA tumor variant leads to defects in NER that sensitize cells to cisplatin. NAR Cancer 2024; 6:zcae013. [PMID: 38500596 PMCID: PMC10946055 DOI: 10.1093/narcan/zcae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/27/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Nucleotide excision repair (NER) reduces efficacy of treatment with platinum (Pt)-based chemotherapy by removing Pt lesions from DNA. Previous study has identified that missense mutation or loss of the NER genes Excision Repair Cross Complementation Group 1 and 2 (ERCC1 and ERCC2) leads to improved patient outcomes after treatment with Pt-based chemotherapies. Although most NER gene alterations found in patient tumors are missense mutations, the impact of mutations in the remaining nearly 20 NER genes is unknown. Towards this goal, we previously developed a machine learning strategy to predict genetic variants in an essential NER protein, Xeroderma Pigmentosum Complementation Group A (XPA), that disrupt repair. In this study, we report in-depth analyses of a subset of the predicted variants, including in vitro analyses of purified recombinant protein and cell-based assays to test Pt agent sensitivity in cells and determine mechanisms of NER dysfunction. The most NER deficient variant Y148D had reduced protein stability, weaker DNA binding, disrupted recruitment to damage, and degradation. Our findings demonstrate that tumor mutations in XPA impact cell survival after cisplatin treatment and provide valuable mechanistic insights to improve variant effect prediction. Broadly, these findings suggest XPA tumor variants should be considered when predicting chemotherapy response.
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Affiliation(s)
- Alexandra M Blee
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kaitlyn S Gallagher
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Suhas S Kharat
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Christina R Troll
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Areetha D’Souza
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Jiyoung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - P Drew Neufer
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Orlando D Schärer
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA
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3
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Wong J, Trinh VQ, Jyotsana N, Baig JF, Revetta F, Shi C, Means AL, DelGiorno KE, Tan M. Differential spatial distribution of HNF4α isoforms during dysplastic progression of intraductal papillary mucinous neoplasms of the pancreas. Sci Rep 2023; 13:20088. [PMID: 37974020 PMCID: PMC10654504 DOI: 10.1038/s41598-023-47238-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
Hepatocyte Nuclear Factor 4-alpha (HNF4α) comprises a nuclear receptor superfamily of ligand-dependent transcription factors that yields twelve isoforms in humans, classified into promoters P1 or P2-associated groups with specific functions. Alterations in HNF4α isoforms have been associated with tumorigenesis. However, the distribution of its isoforms during progression from dysplasia to malignancy has not been studied, nor has it yet been studied in intraductal papillary mucinous neoplasms, where both malignant and pre-malignant forms are routinely clinically identified. We examined the expression patterns of pan-promoter, P1-specific, and P2-specific isoform groups in normal pancreatic components and IPMNs. Pan-promoter, P1 and P2 nuclear expression were weakly positive in normal pancreatic components. Nuclear expression for all isoform groups was increased in low-grade IPMN, high-grade IPMN, and well-differentiated invasive adenocarcinoma. Poorly differentiated invasive components in IPMNs showed loss of all forms of HNF4α. Pan-promoter, and P1-specific HNF4α expression showed shifts in subnuclear and sub-anatomical distribution in IPMN, whereas P2 expression was consistently nuclear. Tumor cells with high-grade dysplasia at the basal interface with the stroma showed reduced expression of P1, while P2 was equally expressed in both components. Additional functional studies are warranted to further explore the mechanisms underlying the spatial and differential distribution of HNF4α isoforms in IPMNs.
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Affiliation(s)
- Jahg Wong
- Department of Pathology, University of Montreal, Montreal, QC, Canada
| | - Vincent Q Trinh
- Department of Pathology, University of Montreal, Montreal, QC, Canada
- Institute for Research in Immunology and Cancer of the University of Montreal, Montreal, QC, Canada
- Centre Hospitalier de l'Université de Montréal Research Center, Montreal, QC, Canada
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nidhi Jyotsana
- Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Jumanah F Baig
- Department of Pathology, University of Montreal, Montreal, QC, Canada
- Institute for Research in Immunology and Cancer of the University of Montreal, Montreal, QC, Canada
| | - Frank Revetta
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chanjuan Shi
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Anna L Means
- Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Division of Surgical Oncology and Endocrine Surgery, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
- Vanderbilt Ingram Cancer Center, Nashville, TN, USA
| | - Kathleen E DelGiorno
- Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Nashville, TN, USA
- Vanderbilt Digestive Disease Research Center, Nashville, TN, USA
| | - Marcus Tan
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.
- Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
- Division of Surgical Oncology and Endocrine Surgery, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA.
- Vanderbilt Ingram Cancer Center, Nashville, TN, USA.
- Vanderbilt Digestive Disease Research Center, Nashville, TN, USA.
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Pagendarm HM, Stone PT, Kimmel BR, Baljon JJ, Aziz MH, Pastora LE, Hubert L, Roth EW, Almunif S, Scott EA, Wilson JT. Engineering endosomolytic nanocarriers of diverse morphologies using confined impingement jet mixing. Nanoscale 2023; 15:16016-16029. [PMID: 37753868 PMCID: PMC10568979 DOI: 10.1039/d3nr02874g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
The clinical translation of many biomolecular therapeutics has been hindered by undesirable pharmacokinetic (PK) properties, inadequate membrane permeability, poor endosomal escape and cytosolic delivery, and/or susceptibility to degradation. Overcoming these challenges merits the development of nanoscale drug carriers (nanocarriers) to improve the delivery of therapeutic cargo. Herein, we implement a flash nanoprecipitation (FNP) approach to produce nanocarriers of diverse vesicular morphologies by using various molecular weight PEG-bl-DEAEMA-co-BMA (PEG-DB) polymers. We demonstrated that FNP can produce uniform (PDI < 0.1) particles after 5 impingements, and that by varying the copolymer hydrophilic mass fraction, FNP enables access to a diverse variety of nanoarchitectures including micelles, unilamellar vesicles (polymersomes), and multi-compartment vesicles (MCVs). We synthesized a library of 2 kDa PEG block copolymers, with DEAEMA-co-BMA second block molecular weights of 3, 6, 12, 15, 20, and 30 kDa. All formulations were both pH responsive, endosomolytic, and capable of loading and cytosolically delivering small negatively charged molecules - albeit to different degrees. Using a B16.F10 melanoma model, we showcased the therapeutic potential of a lead FNP formulated PEG-DB nanocarrier, encapsulating the cyclic dinucleotide (CDN) cGAMP to activate the stimulator of interferon genes (STING) pathway in a therapeutically relevant context. Collectively, these data demonstrate that an FNP process can be used to formulate pH-responsive nanocarriers of diverse morphologies using a PEG-DB polymer system. As FNP is an industrially scalable process, these data address the critical translational challenge of producing PEG-DB nanoparticles at scale. Furthermore, the diverse morphologies produced may specialize in the delivery of distinct biomolecular cargos for other therapeutic applications, implicating the therapeutic potential of this platform in an array of disease applications.
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Affiliation(s)
- Hayden M Pagendarm
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA.
| | - Payton T Stone
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Blaise R Kimmel
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Jessalyn J Baljon
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA.
| | - Mina H Aziz
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Neuroscience, Vanderbilt University, Nashville, TN 37235, USA
| | - Lucinda E Pastora
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Lauren Hubert
- Department of Chemical Engineering, The University of Rhode Island, Kingston, RI 02881, USA
| | - Eric W Roth
- NUANCE BioCryo, Northwestern University, Evanston, IL 60208, USA
| | - Sultan Almunif
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Evan A Scott
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - John T Wilson
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA.
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute for Infection Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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5
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Lewis JA, Bonnet K, Schlundt DG, Byerly S, Lindsell CJ, Henschke CI, Yankelevitz DF, York SJ, Hendler F, Dittus RS, Vogus TJ, Kripalani S, Moghanaki D, Audet CM, Roumie CL, Spalluto LB. Rural barriers and facilitators of lung cancer screening program implementation in the veterans health administration: a qualitative study. Front Health Serv 2023; 3:1209720. [PMID: 37674596 PMCID: PMC10477991 DOI: 10.3389/frhs.2023.1209720] [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] [Received: 04/21/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Introduction To assess healthcare professionals' perceptions of rural barriers and facilitators of lung cancer screening program implementation in a Veterans Health Administration (VHA) setting through a series of one-on-one interviews with healthcare team members. Methods Based on measures developed using Reach Effectiveness Adoption Implementation Maintenance (RE-AIM), we conducted a cross-sectional qualitative study consisting of one-on-one semi-structured telephone interviews with VHA healthcare team members at 10 Veterans Affairs medical centers (VAMCs) between December 2020 and September 2021. An iterative inductive and deductive approach was used for qualitative analysis of interview data, resulting in the development of a conceptual model to depict rural barriers and facilitators of lung cancer screening program implementation. Results A total of 30 interviews were completed among staff, providers, and lung cancer screening program directors and a conceptual model of rural barriers and facilitators of lung cancer screening program implementation was developed. Major themes were categorized within institutional and patient environments. Within the institutional environment, participants identified systems-level (patient communication, resource availability, workload), provider-level (attitudes and beliefs, knowledge, skills and capabilities), and external (regional and national networks, incentives) barriers to and facilitators of lung cancer screening program implementation. Within the patient environment, participants revealed patient-level (modifiable vulnerabilities) barriers and facilitators as well as ecological modifiers (community) that influence screening behavior. Discussion Understanding rural barriers to and facilitators of lung cancer screening program implementation as perceived by healthcare team members points to opportunities and approaches for improving lung cancer screening reach, implementation and effectiveness in VHA rural settings.
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Affiliation(s)
- Jennifer A. Lewis
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, United States
- Veterans Health Administration-Tennessee Valley Healthcare System, Medicine Service, Nashville, TN, United States
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
| | - Kemberlee Bonnet
- Department of Psychology, Vanderbilt University, Nashville, TN, United States
- Qualitative Research Core, Vanderbilt University Medical Center, Nashville, TN, United States
| | - David G. Schlundt
- Department of Psychology, Vanderbilt University, Nashville, TN, United States
- Qualitative Research Core, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Susan Byerly
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, United States
- Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Christopher J. Lindsell
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Claudia I. Henschke
- Department of Radiology, Icahn School of Medicine at Mount Sinai, NY, New York, United States
- Veterans Health Administration—Phoenix VA Health Care System, Radiology Service, Phoenix, AZ, United States
| | - David F. Yankelevitz
- Department of Radiology, Icahn School of Medicine at Mount Sinai, NY, New York, United States
| | - Sally J. York
- Veterans Health Administration-Tennessee Valley Healthcare System, Medicine Service, Nashville, TN, United States
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
| | - Fred Hendler
- Rex Robley VA Medical Center, Medicine Service, Louisville, KY, United States
| | - Robert S. Dittus
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, United States
- Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Timothy J. Vogus
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, United States
- Owen Graduate School of Management, Vanderbilt University, Nashville, TN, United States
| | - Sunil Kripalani
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, United States
- Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Drew Moghanaki
- Veterans Health Administration—Greater Los Angeles Veterans Affairs Medical Center, Radiation Oncology Service, Los Angeles, CA, United States
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Carolyn M. Audet
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Christianne L. Roumie
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, United States
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, United States
- Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Lucy B. Spalluto
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, United States
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, United States
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Ngo K, Gittens TH, Gonzalez DI, Hatmaker EA, Plotkin S, Engle M, Friedman GA, Goldin M, Hoerr RE, Eichman BF, Rokas A, Benton ML, Friedman KL. A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae. Genetics 2023; 224:iyad076. [PMID: 37119805 PMCID: PMC10474931 DOI: 10.1093/genetics/iyad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023] Open
Abstract
Telomere healing occurs when telomerase, normally restricted to chromosome ends, acts upon a double-strand break to create a new, functional telomere. De novo telomere addition (dnTA) on the centromere-proximal side of a break truncates the chromosome but, by blocking resection, may allow the cell to survive an otherwise lethal event. We previously identified several sequences in the baker's yeast, Saccharomyces cerevisiae, that act as hotspots of dnTA [termed Sites of Repair-associated Telomere Addition (SiRTAs)], but the distribution and functional relevance of SiRTAs is unclear. Here, we describe a high-throughput sequencing method to measure the frequency and location of telomere addition within sequences of interest. Combining this methodology with a computational algorithm that identifies SiRTA sequence motifs, we generate the first comprehensive map of telomere-addition hotspots in yeast. Putative SiRTAs are strongly enriched in subtelomeric regions where they may facilitate formation of a new telomere following catastrophic telomere loss. In contrast, outside of subtelomeres, the distribution and orientation of SiRTAs appears random. Since truncating the chromosome at most SiRTAs would be lethal, this observation argues against selection for these sequences as sites of telomere addition per se. We find, however, that sequences predicted to function as SiRTAs are significantly more prevalent across the genome than expected by chance. Sequences identified by the algorithm bind the telomeric protein Cdc13, raising the possibility that association of Cdc13 with single-stranded regions generated during the response to DNA damage may facilitate DNA repair more generally.
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Affiliation(s)
- Katrina Ngo
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Tristen H Gittens
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - David I Gonzalez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - E Anne Hatmaker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37232 USA
| | - Simcha Plotkin
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Mason Engle
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Geofrey A Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Melissa Goldin
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Remington E Hoerr
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232 USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37232 USA
| | | | - Katherine L Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA
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7
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Strayer TE, Spalluto LB, Burns A, Lindsell CJ, Henschke CI, Yankelevitz DF, Moghanaki D, Dittus RS, Vogus TJ, Audet C, Kripalani S, Roumie CL, Lewis JA. Using the Framework for Reporting Adaptations and Modifications-Expanded (FRAME) to study adaptations in lung cancer screening delivery in the Veterans Health Administration: a cohort study. Implement Sci Commun 2023; 4:5. [PMID: 36635719 PMCID: PMC9836333 DOI: 10.1186/s43058-022-00388-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/20/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Lung cancer screening is a complex clinical process that includes identification of eligible individuals, shared decision-making, tobacco cessation, and management of screening results. Adaptations to the delivery process for lung cancer screening in situ are understudied and underreported, with the potential loss of important considerations for improved implementation. The Framework for Reporting Adaptations and Modifications-Expanded (FRAME) allows for a systematic enumeration of adaptations to implementation of evidence-based practices. We applied FRAME to study adaptations in lung cancer screening delivery processes implemented by lung cancer screening programs in a Veterans Health Administration (VHA) Enterprise-Wide Initiative. METHODS We prospectively conducted semi-structured interviews at baseline and 1-year intervals with lung cancer screening program navigators at 10 Veterans Affairs Medical Centers (VAMCs) between 2019 and 2021. Using this data, we developed baseline (1st) process maps for each program. In subsequent years (year 1 and year 2), each program navigator reviewed the process maps. Adaptations in screening processes were identified, documented, and mapped to FRAME categories. RESULTS We conducted a total of 16 interviews across 10 VHA lung cancer screening programs (n=6 in year 1, n=10 in year 2) to collect adaptations. In year 1 (2020), six programs were operational and eligible. Of these, three reported adaptations to their screening process that were planned or in response to COVID-19. In year 2 (2021), all 10 programs were operational and eligible. Programs reported 14 adaptations in year 2. These adaptations were planned and unplanned and often triggered by increased workload; 57% of year 2 adaptations were related to the identification and eligibility of Veterans and 43% were related to follow-up with Veterans for screening results. Throughout the 2 years, adaptations related to data management and patient tracking occurred in 60% of programs to improve the data collection and tracking of Veterans in the screening process. CONCLUSIONS Using FRAME, we found that adaptations occurred primarily in the areas of patient identification and communication of results due to increased workload. These findings highlight navigator time and resource considerations for sustainability and scalability of existing and future lung cancer screening programs as well as potential areas for future intervention.
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Affiliation(s)
- Thomas E Strayer
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, USA
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lucy B Spalluto
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Abby Burns
- Veterans Health Administration-Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA
| | - Christopher J Lindsell
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Claudia I Henschke
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Veterans Health Administration - Phoenix VA Health Care System, Phoenix, AZ, USA
| | - David F Yankelevitz
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Drew Moghanaki
- Veterans Health Administration - Greater Los Angeles Veterans Affairs Medical Center, Los Angeles, CA, USA
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert S Dittus
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, USA
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy J Vogus
- Owen Graduate School of Management, Vanderbilt University, Nashville, TN, USA
| | - Carolyn Audet
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sunil Kripalani
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christianne L Roumie
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, USA
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer A Lewis
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA.
- Veterans Health Administration-Tennessee Valley Healthcare System, Geriatric Research, Education and Clinical Center (GRECC) and Medicine Service, Nashville, TN, USA.
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, 2525 West End Ave, Suite 1200, Nashville, TN, 37203, USA.
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8
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Hanna A, Nixon MJ, Estrada MV, Sanchez V, Sheng Q, Opalenik SR, Toren AL, Bauer J, Owens P, Mason FM, Cook RS, Sanders ME, Arteaga CL, Balko JM. Combined Dusp4 and p53 loss with Dbf4 amplification drives tumorigenesis via cell cycle restriction and replication stress escape in breast cancer. Breast Cancer Res 2022; 24:51. [PMID: 35850776 PMCID: PMC9290202 DOI: 10.1186/s13058-022-01542-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
AIM Deregulated signaling pathways are a hallmark feature of oncogenesis and driver of tumor progression. Dual specificity protein phosphatase 4 (DUSP4) is a critical negative regulator of the mitogen-activated protein kinase (MAPK) pathway and is often deleted or epigenetically silenced in tumors. DUSP4 alterations lead to hyperactivation of MAPK signaling in many cancers, including breast cancer, which often harbor mutations in cell cycle checkpoint genes, particularly in TP53. METHODS Using a genetically engineered mouse model, we generated mammary-specific Dusp4-deleted primary epithelial cells to investigate the necessary conditions in which DUSP4 loss may drive breast cancer oncogenesis. RESULTS We found that Dusp4 loss alone is insufficient in mediating tumorigenesis, but alternatively converges with loss in Trp53 and MYC amplification to induce tumorigenesis primarily through chromosome 5 amplification, which specifically upregulates Dbf4, a cell cycle gene that promotes cellular replication by mediating cell cycle checkpoint escape. CONCLUSIONS This study identifies a novel mechanism for breast tumorigenesis implicating Dusp4 loss and p53 mutations in cellular acquisition of Dbf4 upregulation as a driver of cellular replication and cell cycle checkpoint escape.
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Affiliation(s)
- Ann Hanna
- Departments of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA
| | - Mellissa J Nixon
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Early Discovery Oncology, Merck & Co., Boston, MA, USA
| | - M Valeria Estrada
- Department of Pathology, Microbiology & Immunology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA
| | - Violeta Sanchez
- Department of Pathology, Microbiology & Immunology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Susan R Opalenik
- Departments of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA
| | - Abigail L Toren
- Departments of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA
| | - Joshua Bauer
- Vanderbilt Institute of Chemical Biology, Nashville, TN, USA
| | - Phillip Owens
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Frank M Mason
- Departments of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA
| | - Rebecca S Cook
- Biomedical Engineering, Vanderbilt University School of Engineering, Nashville, TN, USA
| | - Melinda E Sanders
- Department of Pathology, Microbiology & Immunology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA
| | - Carlos L Arteaga
- Simmons Comprehensive Cancer Center, University of Texas Southwester, Dallas, TX, USA
| | - Justin M Balko
- Departments of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA.
- Department of Pathology, Microbiology & Immunology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA.
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2200 Pierce Ave, 777 PRB, Nashville, TN, 37232, USA.
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9
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Leachman JR, Heier K, Lei F, Ahmed N, Dalmasso C, Duncan MS, Loria AS. Sex and race define the effects of adverse childhood experiences on self-reported BMI and metabolic health biomarkers. Biol Sex Differ 2022; 13:29. [PMID: 35706066 PMCID: PMC9202152 DOI: 10.1186/s13293-022-00439-x] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adverse childhood experiences (ACEs) are an independent risk factor for chronic diseases, including type 2 diabetes, stroke and ischemic heart disease. However, the effect of ACEs considering sex and race are not often reported in cohorts showing multiracial composition, with power to evaluate effects on underrepresented populations. AIM To determine how sex and race affected the association of combined and individual ACEs with metabolic health biomarkers in the Southern Community Cohort Study (2012-2015). METHODS Self-reported data were analyzed from ACE surveys performed during the second follow-up of a cohort comprised by over 60% of Black subjects and with an overall mean age of 60 years. RESULTS BMI steadily increased with cumulative ACEs among Black and White women, but remained relatively stable in White men with ≥ 4 ACEs. Contrary, Black men showed an inverse association between ACE and BMI. Secondary analysis of metabolic outcomes showed that physical abuse was correlated with a 4.85 cm increase in waist circumference in Black subjects. Total cholesterol increased among individuals with more than 4 ACEs. In addition, increases in HbA1c were associated with emotional and maternal abuse in Black women and sexual abuse in White women. CONCLUSIONS BMI is strongly associated with cumulative ACEs in women regardless the race, while waist circumference is strongly associated with ACEs in Black individuals, which combined with reduced BMI may indicate increased central adiposity in Black men. Our study suggests that sex and race influence the contribution of certain ACEs to impair metabolic health.
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Affiliation(s)
- Jacqueline R Leachman
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, 40536-0200, USA
| | - Kory Heier
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
| | - Feitong Lei
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
| | - Nermin Ahmed
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, 40536-0200, USA
| | - Carolina Dalmasso
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, 40536-0200, USA
| | - Meredith S Duncan
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA.
- Center for Health Equity Transformation, University of Kentucky, Lexington, USA.
| | - Analia S Loria
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, 40536-0200, USA.
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10
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Kaur R, Leigh BA, Ritchie IT, Bordenstein SR. The Cif proteins from Wolbachia prophage WO modify sperm genome integrity to establish cytoplasmic incompatibility. PLoS Biol 2022; 20:e3001584. [PMID: 35609042 PMCID: PMC9128985 DOI: 10.1371/journal.pbio.3001584] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/25/2022] [Indexed: 01/27/2023] Open
Abstract
Inherited microorganisms can selfishly manipulate host reproduction to drive through populations. In Drosophila melanogaster, germline expression of the native Wolbachia prophage WO proteins CifA and CifB cause cytoplasmic incompatibility (CI) in which embryos from infected males and uninfected females suffer catastrophic mitotic defects and lethality; however, in infected females, CifA expression rescues the embryonic lethality and thus imparts a fitness advantage to the maternally transmitted Wolbachia. Despite widespread relevance to sex determination, evolution, and vector control, the mechanisms underlying when and how CI impairs male reproduction remain unknown and a topic of debate. Here, we use cytochemical, microscopic, and transgenic assays in D. melanogaster to demonstrate that CifA and CifB proteins of wMel localize to nuclear DNA throughout the process of spermatogenesis. Cif proteins cause abnormal histone retention in elongating spermatids and protamine deficiency in mature sperms that travel to the female reproductive tract with Cif proteins. Notably, protamine gene knockouts enhance wild-type CI. In ovaries, CifA localizes to germ cell nuclei and cytoplasm of early-stage egg chambers; however, Cifs are absent in late-stage oocytes and subsequently in fertilized embryos. Finally, CI and rescue are contingent upon a newly annotated CifA bipartite nuclear localization sequence. Together, our results strongly support the Host modification model of CI in which Cifs initially modify the paternal and maternal gametes to bestow CI-defining embryonic lethality and rescue.
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Affiliation(s)
- Rupinder Kaur
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brittany A. Leigh
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Isabella T. Ritchie
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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11
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Monga N, Davis KM, Cardona-Del Valle A, Sieck L, DeBenedectis CM, Spalluto LB. Strategies to Improve Racial and Ethnic Diversity in Breast Imaging Training and Beyond. J Breast Imaging 2022; 4:202-208. [PMID: 38417003 DOI: 10.1093/jbi/wbac001] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Indexed: 03/01/2024]
Abstract
Diversity and inclusion in breast imaging can improve creativity and innovation, enrich the workplace environment, and enhance culturally appropriate care for an increasingly diverse patient population. Current estimates predict the racial and ethnic demographics of the United States population will change markedly by the year 2060, with increases in representation of the Black demographic projected to comprise 15% of the population (currently 13.3%) and the Hispanic/Latinx demographic projected to comprise 27.5% of the population (currently 17.8%). However, matriculation rates for those who are underrepresented in medicine (URM), defined as "racial and ethnic populations that are underrepresented in the medical profession relative to their numbers in the general population," have remained largely stagnant. Black students comprise only 7.1% of medical student matriculants, and Hispanic/Latinx students comprise only 6.2% of medical school matriculants compared to the general population. The matriculation rate of URM students into diagnostic radiology is even lower, with Black trainees comprising 3.1% of radiology residents and Hispanic/Latinx trainees comprising 4.8% of radiology residents. This lack of URM radiology resident representation leads to a lack of URM potential applicants to breast imaging fellowships due to the pipeline effect. Strategies to improve diversity and inclusion in breast imaging include recruiting a diverse breast imaging workforce, establishing robust mentorship and sponsorship programs, fostering an inclusive training and workplace environment, and retaining and promoting a diverse workforce.
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Affiliation(s)
- Natasha Monga
- Memorial Sloan Kettering Cancer Center, Department of Radiology, New York, NY, USA
| | - Katie M Davis
- Vanderbilt University Medical Center, Department of Radiology and Radiological Sciences, Nashville, TN, USA
| | | | - Leah Sieck
- Indiana University School of Medicine, Department of Radiology, Indianapolis, IN, USA
| | | | - Lucy B Spalluto
- Vanderbilt University Medical Center, Department of Radiology and Radiological Sciences, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
- Veterans Health Administration-Tennessee Valley Healthcare System Geriatric Research, Education, and Clinical Center (GRECC), Nashville, TN, USA
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12
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Liu H, Li D, Sun L, Qin H, Fan A, Meng L, Graves-Deal R, Glass SE, Franklin JL, Liu Q, Wang J, Yeatman TJ, Guo H, Zong H, Jin S, Chen Z, Deng T, Fang Y, Li C, Karijolich J, Patton JG, Wang X, Nie Y, Fan D, Coffey RJ, Zhao X, Lu Y. Interaction of lncRNA MIR100HG with hnRNPA2B1 facilitates m 6A-dependent stabilization of TCF7L2 mRNA and colorectal cancer progression. Mol Cancer 2022; 21:74. [PMID: 35279145 PMCID: PMC8917698 DOI: 10.1186/s12943-022-01555-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [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: 11/23/2021] [Accepted: 03/02/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Epithelial-to-mesenchymal transition (EMT) is a process linked to metastasis and drug resistance with non-coding RNAs (ncRNAs) playing pivotal roles. We previously showed that miR-100 and miR-125b, embedded within the third intron of the ncRNA host gene MIR100HG, confer resistance to cetuximab, an anti-epidermal growth factor receptor (EGFR) monoclonal antibody, in colorectal cancer (CRC). However, whether the MIR100HG transcript itself has a role in cetuximab resistance or EMT is unknown. METHODS The correlation between MIR100HG and EMT was analyzed by curating public CRC data repositories. The biological roles of MIR100HG in EMT, metastasis and cetuximab resistance in CRC were determined both in vitro and in vivo. The expression patterns of MIR100HG, hnRNPA2B1 and TCF7L2 in CRC specimens from patients who progressed on cetuximab and patients with metastatic disease were analyzed by RNAscope and immunohistochemical staining. RESULTS The expression of MIR100HG was strongly correlated with EMT markers and acted as a positive regulator of EMT. MIR100HG sustained cetuximab resistance and facilitated invasion and metastasis in CRC cells both in vitro and in vivo. hnRNPA2B1 was identified as a binding partner of MIR100HG. Mechanistically, MIR100HG maintained mRNA stability of TCF7L2, a major transcriptional coactivator of the Wnt/β-catenin signaling, by interacting with hnRNPA2B1. hnRNPA2B1 recognized the N6-methyladenosine (m6A) site of TCF7L2 mRNA in the presence of MIR100HG. TCF7L2, in turn, activated MIR100HG transcription, forming a feed forward regulatory loop. The MIR100HG/hnRNPA2B1/TCF7L2 axis was augmented in specimens from CRC patients who either developed local or distant metastasis or had disease progression that was associated with cetuximab resistance. CONCLUSIONS MIR100HG and hnRNPA2B1 interact to control the transcriptional activity of Wnt signaling in CRC via regulation of TCF7L2 mRNA stability. Our findings identified MIR100HG as a potent EMT inducer in CRC that may contribute to cetuximab resistance and metastasis by activation of a MIR100HG/hnRNPA2B1/TCF7L2 feedback loop.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Danxiu Li
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Lina Sun
- The Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China
| | - Ahui Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Lingnan Meng
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Ramona Graves-Deal
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA
| | - Sarah E Glass
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA
| | - Jeffrey L Franklin
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA
| | - Qi Liu
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jing Wang
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Timothy J Yeatman
- Departments of Surgery and Molecular Medicine, TGH Cancer Institute and University of South Florida, Tampa, FL, 33620, USA
| | - Hao Guo
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, 210042, Jiangsu, China
| | - Hong Zong
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shuilin Jin
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhiyu Chen
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Ting Deng
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Ying Fang
- The Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China
| | - Cunxi Li
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, 100191, China
| | - John Karijolich
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Xin Wang
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China.
| | - Robert J Coffey
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA.
| | - Xiaodi Zhao
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China.
| | - Yuanyuan Lu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China.
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13
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Huang S, Shu X, Ping J, Wu J, Wang J, Shidal C, Guo X, Bauer JA, Long J, Shu XO, Zheng W, Cai Q. TBX1 functions as a putative oncogene of breast cancer through promoting cell cycle progression. Carcinogenesis 2022; 43:12-20. [PMID: 34919666 PMCID: PMC8832409 DOI: 10.1093/carcin/bgab111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/04/2021] [Accepted: 11/25/2021] [Indexed: 12/24/2022] Open
Abstract
We have previously identified a genetic variant, rs34331122 in the 22q11.21 locus, as being associated with breast cancer risk in a genome-wide association study. This novel variant is located in the intronic region of the T-box transcription factor 1 (TBX1) gene. Cis-expression quantitative trait loci analysis showed that expression of TBX1 was regulated by the rs34331122 variant. In the current study, we investigated biological functions and potential molecular mechanisms of TBX1 in breast cancer. We found that TBX1 expression was significantly higher in breast cancer tumor tissues than adjacent normal breast tissues and increased with tumor stage (P < 0.05). We further knocked-down TBX1 gene expression in three breast cancer cell lines, MDA-MB-231, MCF-7 and T47D, using small interfering RNAs and examined consequential changes on cell oncogenicity and gene expression. TBX1 knock-down significantly inhibited breast cancer cell proliferation, colony formation, migration and invasion. RNA sequencing and flow cytometry analysis revealed that TBX1 knock-down in breast cancer cells induced cell cycle arrest in the G1 phase through disrupting expression of genes involved in the cell cycle pathway. Furthermore, survival analysis using the online Kaplan-Meier Plotter suggested that higher TBX1 expression was associated with worse outcomes in breast cancer patients, especially for estrogen receptor-positive breast cancer, with HRs (95% CIs) for overall survival (OS) and distant metastasis free survival (DMFS) of 1.5 (1.05-2.15) and 1.55 (1.10-2.18), respectively. In conclusion, our results suggest that the TBX1 gene may act as a putative oncogene of breast cancer through regulating expressions of cell cycle-related genes.
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Affiliation(s)
- Shuya Huang
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P. R. China
| | - Xiang Shu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jie Ping
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jie Wu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jifeng Wang
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Chris Shidal
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Xingyi Guo
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Joshua A Bauer
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jirong Long
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Xiao-Ou Shu
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wei Zheng
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qiuyin Cai
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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14
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Pan XF, Yang JJ, Shu XO, Moore SC, Palmer ND, Guasch-Ferré M, Herrington DM, Harada S, Eliassen H, Wang TJ, Gerszten RE, Albanes D, Tzoulaki I, Karaman I, Elliott P, Zhu H, Wagenknecht LE, Zheng W, Cai H, Cai Q, Matthews CE, Menni C, Meyer KA, Lipworth LP, Ose J, Fornage M, Ulrich CM, Yu D. Associations of circulating choline and its related metabolites with cardiometabolic biomarkers: an international pooled analysis. Am J Clin Nutr 2021; 114:893-906. [PMID: 34020444 PMCID: PMC8408854 DOI: 10.1093/ajcn/nqab152] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/09/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Choline is an essential nutrient; however, the associations of choline and its related metabolites with cardiometabolic risk remain unclear. OBJECTIVE We examined the associations of circulating choline, betaine, carnitine, and dimethylglycine (DMG) with cardiometabolic biomarkers and their potential dietary and nondietary determinants. METHODS The cross-sectional analyses included 32,853 participants from 17 studies, who were free of cancer, cardiovascular diseases, chronic kidney diseases, and inflammatory bowel disease. In each study, metabolites and biomarkers were log-transformed and standardized by means and SDs, and linear regression coefficients (β) and 95% CIs were estimated with adjustments for potential confounders. Study-specific results were combined by random-effects meta-analyses. A false discovery rate <0.05 was considered significant. RESULTS We observed moderate positive associations of circulating choline, carnitine, and DMG with creatinine [β (95% CI): 0.136 (0.084, 0.188), 0.106 (0.045, 0.168), and 0.128 (0.087, 0.169), respectively, for each SD increase in biomarkers on the log scale], carnitine with triglycerides (β = 0.076; 95% CI: 0.042, 0.109), homocysteine (β = 0.064; 95% CI: 0.033, 0.095), and LDL cholesterol (β = 0.055; 95% CI: 0.013, 0.096), DMG with homocysteine (β = 0.068; 95% CI: 0.023, 0.114), insulin (β = 0.068; 95% CI: 0.043, 0.093), and IL-6 (β = 0.060; 95% CI: 0.027, 0.094), but moderate inverse associations of betaine with triglycerides (β = -0.146; 95% CI: -0.188, -0.104), insulin (β = -0.106; 95% CI: -0.130, -0.082), homocysteine (β = -0.097; 95% CI: -0.149, -0.045), and total cholesterol (β = -0.074; 95% CI: -0.102, -0.047). In the whole pooled population, no dietary factor was associated with circulating choline; red meat intake was associated with circulating carnitine [β = 0.092 (0.042, 0.142) for a 1 serving/d increase], whereas plant protein was associated with circulating betaine [β = 0.249 (0.110, 0.388) for a 5% energy increase]. Demographics, lifestyle, and metabolic disease history showed differential associations with these metabolites. CONCLUSIONS Circulating choline, carnitine, and DMG were associated with unfavorable cardiometabolic risk profiles, whereas circulating betaine was associated with a favorable cardiometabolic risk profile. Future prospective studies are needed to examine the associations of these metabolites with incident cardiovascular events.
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Affiliation(s)
- Xiong-Fei Pan
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jae Jeong Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Steven C Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Marta Guasch-Ferré
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - David M Herrington
- Section on Cardiology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Heather Eliassen
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Thomas J Wang
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Robert E Gerszten
- Broad Institute of Harvard and Massachusetts Institute of Technology and Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Dementia Research Institute, Imperial College London, London, United Kingdom
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Ibrahim Karaman
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Dementia Research Institute, Imperial College London, London, United Kingdom
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Dementia Research Institute, Imperial College London, London, United Kingdom
| | - Huilian Zhu
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Lynne E Wagenknecht
- Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Charles E Matthews
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Katie A Meyer
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Loren P Lipworth
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer Ose
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Cornelia M Ulrich
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Danxia Yu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
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15
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Barone SM, Paul AGA, Muehling LM, Lannigan JA, Kwok WW, Turner RB, Woodfolk JA, Irish JM. Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy. eLife 2021; 10:e64653. [PMID: 34350827 PMCID: PMC8370768 DOI: 10.7554/elife.64653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 08/02/2021] [Indexed: 12/31/2022] Open
Abstract
For an emerging disease like COVID-19, systems immunology tools may quickly identify and quantitatively characterize cells associated with disease progression or clinical response. With repeated sampling, immune monitoring creates a real-time portrait of the cells reacting to a novel virus before disease-specific knowledge and tools are established. However, single cell analysis tools can struggle to reveal rare cells that are under 0.1% of the population. Here, the machine learning workflow Tracking Responders EXpanding (T-REX) was created to identify changes in both rare and common cells across human immune monitoring settings. T-REX identified cells with highly similar phenotypes that localized to hotspots of significant change during rhinovirus and SARS-CoV-2 infections. Specialized MHCII tetramer reagents that mark rhinovirus-specific CD4+ cells were left out during analysis and then used to test whether T-REX identified biologically significant cells. T-REX identified rhinovirus-specific CD4+ T cells based on phenotypically homogeneous cells expanding by ≥95% following infection. T-REX successfully identified hotspots of virus-specific T cells by comparing infection (day 7) to either pre-infection (day 0) or post-infection (day 28) samples. Plotting the direction and degree of change for each individual donor provided a useful summary view and revealed patterns of immune system behavior across immune monitoring settings. For example, the magnitude and direction of change in some COVID-19 patients was comparable to blast crisis acute myeloid leukemia patients undergoing a complete response to chemotherapy. Other COVID-19 patients instead displayed an immune trajectory like that seen in rhinovirus infection or checkpoint inhibitor therapy for melanoma. The T-REX algorithm thus rapidly identifies and characterizes mechanistically significant cells and places emerging diseases into a systems immunology context for comparison to well-studied immune changes.
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Affiliation(s)
- Sierra M Barone
- Department of Cell and Developmental Biology, Vanderbilt UniversityNashvilleUnited States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical CenterNashvilleUnited States
| | - Alberta GA Paul
- Allergy Division, Department of Medicine, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Lyndsey M Muehling
- Allergy Division, Department of Medicine, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Joanne A Lannigan
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of MedicineCharlottesvilleUnited States
| | - William W Kwok
- Benaroya Research Institute at Virginia MasonSeattleUnited States
| | - Ronald B Turner
- Department of Pediatrics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Judith A Woodfolk
- Allergy Division, Department of Medicine, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt UniversityNashvilleUnited States
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical CenterNashvilleUnited States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashvilleUnited States
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16
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Abstract
Landmark discoveries in the gut microbiome field have paved the way for new research aimed at illuminating the influence of microbiota in colorectal cancer. A major challenge is to account for the effect of inherently variable environmental factors on the host and the gut microbiome, while concurrently determining their contribution to carcinogenesis. Here, we briefly discuss the role of the gut microbial community in colorectal cancer and elaborate on the recent insight that environmental factors related to a Western diet and lifestyle may drive the bloom of tumorigenic members of the gut microbiota. We also discuss how future research focused on untangling host-microbe interactions in the colon may influence medical insights that relate to the prevention and treatment of colorectal cancer.
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Affiliation(s)
- Nora J. Foegeding
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Zachary S. Jones
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Mariana X. Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
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17
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Davis KM, Monga N, Sonubi C, Asumu H, DeBenedectis CM, Spalluto LB. Educational Strategies to Achieve Equitable Breast Imaging Care. J Breast Imaging 2021; 3:231-239. [PMID: 38424828 DOI: 10.1093/jbi/wbaa082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 03/02/2024]
Abstract
As the population of the United States becomes increasingly diverse, radiologists must learn to both understand and mitigate the impact of health disparities. Significant health disparities persist in radiologic care, including breast imaging. Racial and ethnic minorities, women from lower socioeconomic status, those living in rural areas, and the uninsured bear a disproportionate burden of breast cancer morbidity and mortality. Currently, there is no centralized radiology curriculum focusing on breast health disparities available to residents, breast imaging fellows, or practicing breast radiologists. While patient-, provider-, and system-level initiatives are necessary to overcome disparities, our purpose is to describe educational strategies targeted to breast imaging radiologists at all levels to provide equitable care to a diverse population. These strategies may include, but are not limited to, diversifying the breast imaging workforce, understanding the needs of a diverse population, cultural sensitivity and bias training, and fostering awareness of the existing issues in screening mammography access, follow-up imaging, and clinical care.
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Affiliation(s)
- Katie M Davis
- Vanderbilt University Medical Center, Department of Radiology and Radiological Sciences, Nashville, TN
| | - Natasha Monga
- Case Western Reserve University - The MetroHealth System, Department of Radiology, Cleveland, OH
| | | | - Hazel Asumu
- Vanderbilt University Medical Center, Department of Radiology and Radiological Sciences, Nashville, TN
| | | | - Lucy B Spalluto
- Vanderbilt University Medical Center, Department of Radiology and Radiological Sciences, Nashville, TN
- Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center, Nashville, TN
- Veterans Health Administration, Tennessee Valley Healthcare System Geriatric Research, Education, and Clinical Center, Nashville, TN
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18
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Liu W, Krishnamoorthy A, Zhao R, Cortez D. Two replication fork remodeling pathways generate nuclease substrates for distinct fork protection factors. Sci Adv 2020; 6:6/46/eabc3598. [PMID: 33188024 PMCID: PMC7673757 DOI: 10.1126/sciadv.abc3598] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/23/2020] [Indexed: 05/11/2023]
Abstract
Fork reversal is a common response to replication stress, but it generates a DNA end that is susceptible to degradation. Many fork protection factors block degradation, but how they work remains unclear. Here, we find that 53BP1 protects forks from DNA2-mediated degradation in a cell type-specific manner. Fork protection by 53BP1 reduces S-phase DNA damage and hypersensitivity to replication stress. Unlike BRCA2, FANCD2, and ABRO1 that protect reversed forks generated by SMARCAL1, ZRANB3, and HLTF, 53BP1 protects forks remodeled by FBH1. This property is shared by the fork protection factors FANCA, FANCC, FANCG, BOD1L, and VHL. RAD51 is required to generate the resection substrate in all cases. Unexpectedly, BRCA2 is also required for fork degradation in the FBH1 pathway or when RAD51 activity is partially compromised. We conclude that there are multiple fork protection mechanisms that operate downstream of at least two RAD51-dependent fork remodeling pathways.
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Affiliation(s)
- W Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - A Krishnamoorthy
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - R Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - D Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA.
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19
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Wen X, Ou YC, Bogatcheva G, Thomas G, Mahadevan-Jansen A, Singh B, Lin EC, Bardhan R. Probing metabolic alterations in breast cancer in response to molecular inhibitors with Raman spectroscopy and validated with mass spectrometry. Chem Sci 2020; 11:9863-9874. [PMID: 34094246 PMCID: PMC8162119 DOI: 10.1039/d0sc02221g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/19/2020] [Indexed: 01/07/2023] Open
Abstract
Rapid and accurate response to targeted therapies is critical to differentiate tumors that are resistant to treatment early in the regimen. In this work, we demonstrate a rapid, noninvasive, and label-free approach to evaluate treatment response to molecular inhibitors in breast cancer (BC) cells with Raman spectroscopy (RS). Metabolic reprogramming in BC was probed with RS and multivariate analysis was applied to classify the cells into responsive or nonresponsive groups as a function of drug dosage, drug type, and cell type. Metabolites identified with RS were then validated with mass spectrometry (MS). We treated triple-negative BC cells with Trametinib, an inhibitor of the extracellular-signal-regulated kinase (ERK) pathway. Changes measured with both RS and MS corresponding to membrane phospholipids, amino acids, lipids and fatty acids indicated that these BC cells were responsive to treatment. Comparatively, minimal metabolic changes were observed post-treatment with Alpelisib, an inhibitor of the mammalian target of rapamycin (mTOR) pathway, indicating treatment resistance. These findings were corroborated with cell viability assay and immunoblotting. We also showed estrogen receptor-positive MCF-7 cells were nonresponsive to Trametinib with minimal metabolic and viability changes. Our findings support that oncometabolites identified with RS will ultimately enable rapid drug screening in patients ensuring patients receive the most effective treatment at the earliest time point.
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Affiliation(s)
- Xiaona Wen
- Department of Chemical and Biomolecular Engineering, Vanderbilt University Nashville TN 37235 USA
| | - Yu-Chuan Ou
- Department of Chemical and Biomolecular Engineering, Vanderbilt University Nashville TN 37235 USA
| | - Galina Bogatcheva
- Department of Medicine, Vanderbilt University Medical Center Nashville TN 37232 USA
| | - Giju Thomas
- Vanderbilt Biophotonics Center, Vanderbilt University Nashville TN 37232 USA
| | | | - Bhuminder Singh
- Department of Medicine, Vanderbilt University Medical Center Nashville TN 37232 USA
| | - Eugene C Lin
- Department of Chemistry and Biochemistry, National Chung Cheng University Chiayi 62106 Taiwan
| | - Rizia Bardhan
- Department of Chemical and Biological Engineering, Iowa State University Ames IA 50012 USA
- Nanovaccine Institute, Iowa State University Ames IA 50012 USA
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20
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Ping J, Guo X, Ye F, Long J, Lipworth L, Cai Q, Blot W, Shu XO, Zheng W. Differences in gene-expression profiles in breast cancer between African and European-ancestry women. Carcinogenesis 2020; 41:887-893. [PMID: 32267939 PMCID: PMC7359770 DOI: 10.1093/carcin/bgaa035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/25/2020] [Accepted: 04/07/2020] [Indexed: 12/24/2022] Open
Abstract
African American (AA) women have an excess breast cancer mortality than European American (EA) women. To investigate the contribution of tumor biology to this survival health disparity, we compared gene expression profiles in breast tumors using RNA sequencing data derived from 260 AA and 155 EA women who were prospectively enrolled in the Southern Community Cohort Study (SCCS) and developed breast cancer during follow-up. We identified 59 genes (54 protein-coding genes and 5 long intergenic non-coding RNAs) that were expressed differently between EA and AA at a stringent false discovery rate (FDR) < 0.01. A gene signature was derived with these 59 genes and externally validated using the publicly available Cancer Genome Atlas (TCGA) data from180 AA and 838 EA breast cancer patients. Applying C-statistics, we found that this 59-gene signature has a high discriminative ability in distinguishing AA and EA breast cancer patients in the TCGA dataset (C-index = 0.81). These findings may provide new insight into tumor biological differences and the causes of the survival disparity between AA and EA breast cancer patients.
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Affiliation(s)
- Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center and Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center and Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fei Ye
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center and Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center and Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Loren Lipworth
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center and Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center and Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center and Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center and Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center and Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
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21
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Bryan AF, Wang J, Howard GC, Guarnaccia AD, Woodley CM, Aho ER, Rellinger EJ, Matlock BK, Flaherty DK, Lorey SL, Chung DH, Fesik SW, Liu Q, Weissmiller AM, Tansey WP. WDR5 is a conserved regulator of protein synthesis gene expression. Nucleic Acids Res 2020; 48:2924-2941. [PMID: 31996893 PMCID: PMC7102967 DOI: 10.1093/nar/gkaa051] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/30/2019] [Accepted: 01/17/2020] [Indexed: 12/12/2022] Open
Abstract
WDR5 is a highly-conserved nuclear protein that performs multiple scaffolding functions in the context of chromatin. WDR5 is also a promising target for pharmacological inhibition in cancer, with small molecule inhibitors of an arginine-binding pocket of WDR5 (the 'WIN' site) showing efficacy against a range of cancer cell lines in vitro. Efforts to understand WDR5, or establish the mechanism of action of WIN site inhibitors, however, are stymied by its many functions in the nucleus, and a lack of knowledge of the conserved gene networks-if any-that are under its control. Here, we have performed comparative genomic analyses to identify the conserved sites of WDR5 binding to chromatin, and the conserved genes regulated by WDR5, across a diverse panel of cancer cell lines. We show that a specific cohort of protein synthesis genes (PSGs) are invariantly bound by WDR5, demonstrate that the WIN site anchors WDR5 to chromatin at these sites, and establish that PSGs are bona fide, acute, and persistent targets of WIN site blockade. Together, these data reveal that WDR5 plays a predominant transcriptional role in biomass accumulation and provide further evidence that WIN site inhibitors act to repress gene networks linked to protein synthesis homeostasis.
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Affiliation(s)
- Audra F Bryan
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Gregory C Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Alissa D Guarnaccia
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Chase M Woodley
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Erin R Aho
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Eric J Rellinger
- Department of Pediatric General and Thoracic Surgery, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Brittany K Matlock
- Vanderbilt University Medical Center Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - David K Flaherty
- Vanderbilt University Medical Center Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Dai H Chung
- Department of Pediatric General and Thoracic Surgery, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Stephen W Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37240, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
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22
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Pike M, Taylor J, Kabagambe E, Stewart TG, Robinson-Cohen C, Morse J, Akwo E, Abdel-Kader K, Siew ED, Blot WJ, Ikizler TA, Lipworth L. The association of exercise and sedentary behaviours with incident end-stage renal disease: the Southern Community Cohort Study. BMJ Open 2019; 9:e030661. [PMID: 31471443 PMCID: PMC6720137 DOI: 10.1136/bmjopen-2019-030661] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVE To examine whether lifestyle factors, including sedentary time and physical activity, could independently contribute to risk of end-stage renal disease (ESRD). STUDY DESIGN Case-cohort study. SETTING South-eastern USA. PARTICIPANTS The Southern Community Cohort Study recruited ~86 000 black and white participants from 2002 to 2009. We assembled a case cohort of 692 incident ESRD cases and a probability sample of 4113 participants. PREDICTORS Sedentary time was calculated as hours/day from daily sitting activities. Physical activity was calculated as metabolic equivalent (MET)-hours/day from engagement in light, moderate and vigorous activities. OUTCOMES Incident ESRD. RESULTS At baseline, among the subcohort, mean (SD) age was 52 (8.6) years, and median (25th, 75th centile) estimated glomerular filtration rate (eGFR) was 102.8 (85.9-117.9) mL/min/1.73 m2. Medians (25th-75th centile) for sedentary time and physical activity were 8.0 (5.5-12.0) hours/day and 17.2 (8.7-31.9) MET-hours/day, respectively. Median follow-up was 9.4 years. We observed significant interactions between eGFR and both physical activity and sedentary behaviour (p<0.001). The partial effect plot of the association between physical activity and log relative hazard of ESRD suggests that ESRD risk decreases as physical activity increases when eGFR is 90 mL/min/1.73 m2. The inverse association is most pronounced at physical activity levels >27 MET-hours/day. High levels of sitting time were associated with increased ESRD risk only among those with reduced kidney function (eGFR ≤30 mL/min/1.73 m2); this association was attenuated after excluding the first 2 years of follow-up. CONCLUSIONS In a population with a high prevalence of chronic kidney disease risk factors such as hypertension and diabetes, physical activity appears to be associated with reduced risk of ESRD among those with preserved kidney function. A positive association between sitting time and ESRD observed among those with advanced kidney disease is likely due to reverse causation.
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Affiliation(s)
- Mindy Pike
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jacob Taylor
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Edmond Kabagambe
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Thomas G Stewart
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cassianne Robinson-Cohen
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jennifer Morse
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Elvis Akwo
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Khaled Abdel-Kader
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Edward D Siew
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - T Alp Ikizler
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt O'Brien Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Loren Lipworth
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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23
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Beeghly-Fadiel A, Wilson AJ, Keene S, El Ramahi M, Xu S, Marnett LJ, Fadare O, Crispens MA, Khabele D. Differential cyclooxygenase expression levels and survival associations in type I and type II ovarian tumors. J Ovarian Res 2018; 11:17. [PMID: 29482584 PMCID: PMC5828488 DOI: 10.1186/s13048-018-0389-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/14/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND High cyclooxygenase (COX)-2 expression in ovarian tumors has been associated with poor prognosis, but the role of COX-1 expression and its relation to survival is less clear. Here, we evaluated COX expression and associations with survival outcomes between type I (clear cell, mucinous, low grade endometrioid and low grade serous) and type II (high grade serous and high grade endometrioid) ovarian tumors. METHODS We developed and validated a new COX-1 antibody, and conducted immunohistochemical (IHC) staining for COX-1 and COX-2 on a tissue microarray (TMA) of 190 primary ovarian tumors. In addition to standard IHC scoring and H-scores to combine the percentage of positive cells and staining intensity, we also measured COX-1 and COX-2 mRNA expression by QPCR. High expression was defined as greater than or equal to median values. Clinical characteristics and disease outcomes were ascertained from medical records. Associations with disease-free survival (DFS) and overall survival (OS) were quantified by hazard ratios (HRs) and confidence intervals (CIs) from proportional hazards regression. RESULTS Type I tumors had high COX-2 expression, while type II tumors had high COX-1 expression. In multivariable adjusted regression models, higher COX-1 mRNA expression was associated with shorter DFS (HR: 6.37, 95% CI: 1.84-22.01) and OS (HR: 2.26, 95% CI: 1.04-4.91), while higher H-scores for COX-2 expression were associated with shorter DFS (HR: 1.92, 95% CI: 1.06-3.49). Stratified analysis indicated that COX-2 was significantly associated with DFS among cases with Type II tumors (HR: 1.93, 95% CI: 1.06-3.53). CONCLUSIONS These findings suggest that ovarian tumor type contributes to differences in COX expression levels and associations with survival.
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Affiliation(s)
- Alicia Beeghly-Fadiel
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN USA
| | - Andrew J. Wilson
- Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Spencer Keene
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Meral El Ramahi
- Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Shu Xu
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN USA
| | - Lawrence J. Marnett
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Oluwole Fadare
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA USA
| | - Marta A. Crispens
- Vanderbilt-Ingram Cancer Center, Nashville, TN USA
- Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Dineo Khabele
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, The University of Kansas Medical Center, MS 2028, 3901 Rainbow Boulevard, Kansas City, KS 66160 USA
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24
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Sivley RM, Sheehan JH, Kropski JA, Cogan J, Blackwell TS, Phillips JA, Bush WS, Meiler J, Capra JA. Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. BMC Bioinformatics 2018; 19:18. [PMID: 29361909 PMCID: PMC5781290 DOI: 10.1186/s12859-018-2010-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/03/2018] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Next-generation sequencing of individuals with genetic diseases often detects candidate rare variants in numerous genes, but determining which are causal remains challenging. We hypothesized that the spatial distribution of missense variants in protein structures contains information about function and pathogenicity that can help prioritize variants of unknown significance (VUS) and elucidate the structural mechanisms leading to disease. RESULTS To illustrate this approach in a clinical application, we analyzed 13 candidate missense variants in regulator of telomere elongation helicase 1 (RTEL1) identified in patients with Familial Interstitial Pneumonia (FIP). We curated pathogenic and neutral RTEL1 variants from the literature and public databases. We then used homology modeling to construct a 3D structural model of RTEL1 and mapped known variants into this structure. We next developed a pathogenicity prediction algorithm based on proximity to known disease causing and neutral variants and evaluated its performance with leave-one-out cross-validation. We further validated our predictions with segregation analyses, telomere lengths, and mutagenesis data from the homologous XPD protein. Our algorithm for classifying RTEL1 VUS based on spatial proximity to pathogenic and neutral variation accurately distinguished 7 known pathogenic from 29 neutral variants (ROC AUC = 0.85) in the N-terminal domains of RTEL1. Pathogenic proximity scores were also significantly correlated with effects on ATPase activity (Pearson r = -0.65, p = 0.0004) in XPD, a related helicase. Applying the algorithm to 13 VUS identified from sequencing of RTEL1 from patients predicted five out of six disease-segregating VUS to be pathogenic. We provide structural hypotheses regarding how these mutations may disrupt RTEL1 ATPase and helicase function. CONCLUSIONS Spatial analysis of missense variation accurately classified candidate VUS in RTEL1 and suggests how such variants cause disease. Incorporating spatial proximity analyses into other pathogenicity prediction tools may improve accuracy for other genes and genetic diseases.
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Affiliation(s)
- R Michael Sivley
- Department of Biomedical Informatics, Vanderbilt University, Nashville, USA
| | - Jonathan H Sheehan
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, USA
| | | | - Joy Cogan
- Department of Pediatrics, Vanderbilt University, Nashville, USA
| | | | - John A Phillips
- Department of Pediatrics, Vanderbilt University, Nashville, USA
| | - William S Bush
- Department of Quantitative and Population Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt Genetics Institute, and Center for Structural Biology, Vanderbilt University, Nashville, USA.
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25
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Luo W, Janoštiak R, Tolde O, Ryzhova LM, Koudelková L, Dibus M, Brábek J, Hanks SK, Rosel D. ARHGAP42 is activated by Src-mediated tyrosine phosphorylation to promote cell motility. J Cell Sci 2017; 130:2382-2393. [PMID: 28584191 PMCID: PMC5536916 DOI: 10.1242/jcs.197434] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 05/26/2017] [Indexed: 01/08/2023] Open
Abstract
The tyrosine kinase Src acts as a key regulator of cell motility by phosphorylating multiple protein substrates that control cytoskeletal and adhesion dynamics. In an earlier phosphotyrosine proteomics study, we identified a novel Rho-GTPase activating protein, now known as ARHGAP42, as a likely biologically relevant Src substrate. ARHGAP42 is a member of a family of RhoGAPs distinguished by tandem BAR-PH domains lying N-terminal to the GAP domain. Like other family members, ARHGAP42 acts preferentially as a GAP for RhoA. We show that Src principally phosphorylates ARHGAP42 on tyrosine 376 (Tyr-376) in the short linker between the BAR-PH and GAP domains. The expression of ARHGAP42 variants in mammalian cells was used to elucidate its regulation. We found that the BAR domain is inhibitory toward the GAP activity of ARHGAP42, such that BAR domain deletion resulted in decreased active GTP-bound RhoA and increased cell motility. With the BAR domain intact, ARHGAP42 GAP activity could be activated by phosphorylation of Tyr-376 to promote motile cell behavior. Thus, phosphorylation of ARHGAP42 Tyr-376 is revealed as a novel regulatory event by which Src can affect actin dynamics through RhoA inhibition.
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Affiliation(s)
- Weifeng Luo
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, 12843, Czech Republic
| | - Radoslav Janoštiak
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, 12843, Czech Republic
| | - Ondřej Tolde
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, 12843, Czech Republic
- Department of Cell Biology, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, Vestec u Prahy 25242, Czech Republic
| | - Larisa M Ryzhova
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lenka Koudelková
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, 12843, Czech Republic
- Department of Cell Biology, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, Vestec u Prahy 25242, Czech Republic
| | - Michal Dibus
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, 12843, Czech Republic
- Department of Cell Biology, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, Vestec u Prahy 25242, Czech Republic
| | - Jan Brábek
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, 12843, Czech Republic
- Department of Cell Biology, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, Vestec u Prahy 25242, Czech Republic
| | - Steven K Hanks
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Daniel Rosel
- Department of Cell Biology, Charles University in Prague, Viničná 7, Prague, 12843, Czech Republic
- Department of Cell Biology, Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, Vestec u Prahy 25242, Czech Republic
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26
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Shi J, Zhang B, Choi JY, Gao YT, Li H, Lu W, Long J, Kang D, Xiang YB, Wen W, Park SK, Ye X, Noh DY, Zheng Y, Wang Y, Chung S, Lin X, Cai Q, Shu XO. Age at menarche and age at natural menopause in East Asian women: a genome-wide association study. Age (Dordr) 2016; 38:513-523. [PMID: 27629107 PMCID: PMC5266214 DOI: 10.1007/s11357-016-9939-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 07/14/2016] [Indexed: 06/06/2023]
Abstract
Age at menarche (AM) and age at natural menopause (ANM) are complex traits with a high heritability. Abnormal timing of menarche or menopause is associated with a reduced span of fertility and risk for several age-related diseases including breast, endometrial and ovarian cancer, cardiovascular disease, and osteoporosis. To identify novel genetic loci for AM or ANM in East Asian women and to replicate previously identified loci primarily in women of European ancestry by genome-wide association studies (GWASs), we conducted a two-stage GWAS. Stage I aimed to discover promising novel AM and ANM loci using GWAS data of 8073 women from Shanghai, China. The Stage II replication study used the data from another Chinese GWAS (n = 1230 for AM and n = 1458 for ANM), a Korean GWAS (n = 4215 for AM and n = 1739 for ANM), and de novo genotyping of 2877 additional Chinese women. Previous GWAS-identified loci for AM and ANM were also evaluated. We identified two suggestive menarcheal age loci tagged by rs79195475 at 10q21.3 (beta = -0.118 years, P = 3.4 × 10-6) and rs1023935 at 4p15.1 (beta = -0.145 years, P = 4.9 × 10-6) and one menopausal age locus tagged by rs3818134 at 22q12.2 (beta = -0.276 years, P = 8.8 × 10-6). These suggestive loci warrant a further validation in independent populations. Although limited by low statistical power, we replicated 19 of the 98 menarche loci and 5 of the 20 menopause loci previously identified in women of European ancestry in East Asian women, suggesting a shared genetic architecture for these two traits across populations.
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Affiliation(s)
- Jiajun Shi
- Department of Medicine, Vanderbilt Epidemiology Center and Division of Epidemiology, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 600, IMPH, Nashville, Tennessee, 37203, USA
| | - Ben Zhang
- Department of Medicine, Vanderbilt Epidemiology Center and Division of Epidemiology, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 600, IMPH, Nashville, Tennessee, 37203, USA
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huaixing Li
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of the Chinese Academy of Sciences, Shanghai, China
| | - Wei Lu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jirong Long
- Department of Medicine, Vanderbilt Epidemiology Center and Division of Epidemiology, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 600, IMPH, Nashville, Tennessee, 37203, USA
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wanqing Wen
- Department of Medicine, Vanderbilt Epidemiology Center and Division of Epidemiology, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 600, IMPH, Nashville, Tennessee, 37203, USA
| | - Sue K Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Xingwang Ye
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of the Chinese Academy of Sciences, Shanghai, China
| | - Dong-Young Noh
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yiqin Wang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of the Chinese Academy of Sciences, Shanghai, China
| | - Seokang Chung
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Xu Lin
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of the Chinese Academy of Sciences, Shanghai, China
| | - Qiuyin Cai
- Department of Medicine, Vanderbilt Epidemiology Center and Division of Epidemiology, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 600, IMPH, Nashville, Tennessee, 37203, USA
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt Epidemiology Center and Division of Epidemiology, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 600, IMPH, Nashville, Tennessee, 37203, USA.
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