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Smith AM, Challagundla L, McGee IG, Warfield ZJ, Santos CDSE, Garrett MR, Grayson BE. Temporal shifts to the gut microbiome associated with cognitive dysfunction following high-fat diet consumption in a juvenile model of traumatic brain injury. Physiol Genomics 2024; 56:301-316. [PMID: 38145288 DOI: 10.1152/physiolgenomics.00113.2023] [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: 10/03/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 12/26/2023] Open
Abstract
The gut-brain axis interconnects the central nervous system (CNS) and the commensal bacteria of the gastrointestinal tract. The composition of the diet consumed by the host influences the richness of the microbial populations. Traumatic brain injury (TBI) produces profound neurocognitive damage, but it is unknown how diet influences the microbiome following TBI. The present work investigates the impact of a chow diet versus a 60% fat diet (HFD) on fecal microbiome populations in juvenile rats following TBI. Twenty-day-old male rats were placed on one of two diets for 9 days before sustaining either a Sham or TBI via the Closed Head Injury Model of Engineered Rotational Acceleration (CHIMERA). Fecal samples were collected at both 1- and 9-days postinjury. Animals were cognitively assessed in the novel object recognition tests at 8 days postinjury. Fecal microbiota DNA was isolated and sequenced. Twenty days of HFD feeding did not alter body weight, but fat mass was elevated in HFD compared with Chow rats. TBI animals had a greater percentage of entries to the novel object quadrant than Sham counterparts, P < 0.05. The Firmicutes/Bacteroidetes ratio was significantly higher in TBI than in the Sham, P < 0.05. Microbiota of the Firmicutes lineage exhibited perturbations by both injury and diet that were sustained at both time points. Linear regression analyses were performed to associate bacteria with metabolic and neurocognitive endpoints. For example, counts of Lachnospiraceae were negatively associated with percent entries into the novel object quadrant. Taken together, these data suggest that both diet and injury produce robust shifts in microbiota, which may have long-term implications for chronic health.NEW & NOTEWORTHY Traumatic brain injury (TBI) produces memory and learning difficulties. Diet profoundly influences the populations of gut microbiota. Following traumatic brain injury in a pediatric model consuming either a healthy or high-fat diet (HFD), significant shifts in bacterial populations occur, of which, some are associated with diet, whereas others are associated with neurocognitive performance. More work is needed to determine whether these microbes can therapeutically improve learning following trauma to the brain.
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Affiliation(s)
- Allie M Smith
- Department of Neurology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Lavanya Challagundla
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Ian G McGee
- Department of Neurology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Zyra J Warfield
- Department of Neurology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | | | - Michael R Garrett
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Bernadette E Grayson
- Department of Neurology, University of Mississippi Medical Center, Jackson, Mississippi, United States
- Department of Anesthesiology, University of Mississippi Medical Center, Jackson, Mississippi, United States
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2
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Rexrode LE, Hartley J, Showmaker KC, Challagundla L, Vandewege MW, Martin BE, Blair E, Bollavarapu R, Antonyraj RB, Hilton K, Gardiner A, Valeri J, Gisabella B, Garrett MR, Theoharides TC, Pantazopoulos H. Molecular profiling of the hippocampus of children with autism spectrum disorder. Mol Psychiatry 2024:10.1038/s41380-024-02441-8. [PMID: 38355786 DOI: 10.1038/s41380-024-02441-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
Several lines of evidence point to a key role of the hippocampus in Autism Spectrum Disorders (ASD). Altered hippocampal volume and deficits in memory for person and emotion related stimuli have been reported, along with enhanced ability for declarative memories. Mouse models have demonstrated a critical role of the hippocampus in social memory dysfunction, associated with ASD, together with decreased synaptic plasticity. Chondroitin sulfate proteoglycans (CSPGs), a family of extracellular matrix molecules, represent a potential key link between neurodevelopment, synaptic plasticity, and immune system signaling. There is a lack of information regarding the molecular pathology of the hippocampus in ASD. We conducted RNAseq profiling on postmortem human brain samples containing the hippocampus from male children with ASD (n = 7) and normal male children (3-14 yrs old), (n = 6) from the NIH NeuroBioBank. Gene expression profiling analysis implicated molecular pathways involved in extracellular matrix organization, neurodevelopment, synaptic regulation, and immune system signaling. qRT-PCR and Western blotting were used to confirm several of the top markers identified. The CSPG protein BCAN was examined with multiplex immunofluorescence to analyze cell-type specific expression of BCAN and astrocyte morphology. We observed decreased expression of synaptic proteins PSD95 (p < 0.02) and SYN1 (p < 0.02), increased expression of the extracellular matrix (ECM) protease MMP9 (p < 0.03), and decreased expression of MEF2C (p < 0.03). We also observed increased BCAN expression with astrocytes in children with ASD, together with altered astrocyte morphology. Our results point to alterations in immune system signaling, glia cell differentiation, and synaptic signaling in the hippocampus of children with ASD, together with alterations in extracellular matrix molecules. Furthermore, our results demonstrate altered expression of genes implicated in genetic studies of ASD including SYN1 and MEF2C.
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Affiliation(s)
- Lindsay E Rexrode
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Joshua Hartley
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | | | - Lavanya Challagundla
- Department of Cell and Molecular Biology, University of Mississippi Medical School, Jackson, MS, USA
| | | | - Brigitte E Martin
- Department of Cell and Molecular Biology, University of Mississippi Medical School, Jackson, MS, USA
| | - Estelle Blair
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Ratna Bollavarapu
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Rhenius B Antonyraj
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Keauna Hilton
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Alex Gardiner
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
| | - Jake Valeri
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
- Program in Neuroscience, University of Mississippi Medical School, Jackson, MS, USA
| | - Barbara Gisabella
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA
- Program in Neuroscience, University of Mississippi Medical School, Jackson, MS, USA
| | - Michael R Garrett
- Department of Cell and Molecular Biology, University of Mississippi Medical School, Jackson, MS, USA
| | - Theoharis C Theoharides
- Institute of Neuro-Immune Medicine, Nova Southeastern University, Clearwater, FL, USA
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
| | - Harry Pantazopoulos
- Department of Psychiatry and Human Behavior, University of Mississippi Medical School, Jackson, MS, USA.
- Program in Neuroscience, University of Mississippi Medical School, Jackson, MS, USA.
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3
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Hellmann KT, Challagundla L, Gray BM, Robinson DA. Improved Genomic Prediction of Staphylococcus epidermidis Isolation Sources with a Novel Polygenic Score. J Clin Microbiol 2023; 61:e0141222. [PMID: 36840569 PMCID: PMC10035303 DOI: 10.1128/jcm.01412-22] [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: 09/23/2022] [Accepted: 01/22/2023] [Indexed: 02/25/2023] Open
Abstract
Staphylococcus epidermidis infections can be challenging to diagnose due to the species frequent contamination of clinical specimens and indolent course of infection. Nevertheless, S. epidermidis is the major cause of late-onset sepsis among premature infants and of intravascular infection in all age groups. Prior work has shown that bacterial virulence factors, antimicrobial resistances, and strains have up to 80% in-sample accuracy to distinguish hospital from community sources, but are unable to distinguish true bacteremia from blood culture contamination. Here, a phylogeny-informed genome-wide association study of 88 isolates was used to estimate effect sizes of particular genomic variants for isolation sources. A "polygenic score" was calculated for each isolate as the summed effect sizes of its repertoire of genomic variants. Predictive models of isolation sources based on polygenic scores were tested with in-samples and out-samples from prior studies of different patient populations. Polygenic scores from accessory genes (AGs) distinguished hospital from community sources with the highest accuracy to date, up to 98% for in-samples and 65% to 91% for various out-samples, whereas scores from single nucleotide polymorphisms (SNPs) had lower accuracy. Scores from AGs and SNPs achieved the highest in-sample accuracy to date, up to 76%, in distinguishing infection from contaminant sources within a hospital. Model training and testing data sets with more similar population structures resulted in more accurate predictions. This study reports the first use of a polygenic score for predicting a complex bacterial phenotype and shows the potential of this approach for enhancing S. epidermidis diagnosis.
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Affiliation(s)
- K. Taylor Hellmann
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Lavanya Challagundla
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Barry M. Gray
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi, USA
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4
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Chung WC, Challagundla L, Zhou Y, Li M, Atfi A, Xu K. Loss of Jag1 cooperates with oncogenic Kras to induce pancreatic cystic neoplasms. Life Sci Alliance 2020; 4:4/2/e201900503. [PMID: 33268505 PMCID: PMC7756968 DOI: 10.26508/lsa.201900503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 01/09/2023] Open
Abstract
Notch signaling exerts both oncogenic and tumor-suppressive functions in the pancreas. In this study, deletion of Jag1 in conjunction with oncogenic Kras G12D expression in the mouse pancreas induced rapid development of acinar-to-ductal metaplasia and early stage pancreatic intraepithelial neoplasm; however, culminating in cystic neoplasms rather than ductal adenocarcinoma. Most cystic lesions in these mice were reminiscent of serous cystic neoplasm, and the rest resembled intraductal papillary mucinous neoplasm. Jag1 expression was lost or decreased in cystic lesions but retained in adenocarcinoma in these mice, so was the expression of Sox9. In pancreatic cancer patients, JAG1 expression is higher in cancerous tissue, and high JAG1 is associated with poor overall survival. Expression of SOX9 is correlated with JAG1, and high SOX9 is also associated with poor survival. Mechanistically, Jag1 regulates expression of Lkb1, a tumor suppressor involved in the development of pancreatic cystic neoplasm. Collectively, Jag1 can act as a tumor suppressor in the pancreas by delaying precursor lesions, whereas loss of Jag1 promoted a phenotypic switch from malignant carcinoma to benign cystic lesions.
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Affiliation(s)
- Wen-Cheng Chung
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Lavanya Challagundla
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yunyun Zhou
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Min Li
- Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Azeddine Atfi
- Cellular and Molecular Pathogenesis Division, Department of Pathology, Virginia Commonwealth University, Richmond, VA, USA
| | - Keli Xu
- Cancer Center and Research Institute, University of Mississippi Medical Center, Jackson, MS, USA .,Department of Neurobiology and Anatomical Sciences, University of Mississippi Medical Center, Jackson, MS, USA
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5
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Challagundla L, Reyes J, Rafiqullah I, Sordelli DO, Echaniz-Aviles G, Velazquez-Meza ME, Castillo-Ramírez S, Fittipaldi N, Feldgarden M, Chapman SB, Calderwood MS, Carvajal LP, Rincon S, Hanson B, Planet PJ, Arias CA, Diaz L, Robinson DA. Phylogenomic Classification and the Evolution of Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere. Front Microbiol 2018; 9:1901. [PMID: 30186248 PMCID: PMC6113392 DOI: 10.3389/fmicb.2018.01901] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/27/2018] [Indexed: 12/30/2022] Open
Abstract
Clonal complex 5 methicillin-resistant Staphylococcus aureus (CC5-MRSA) includes multiple prevalent clones that cause hospital-associated infections in the Western Hemisphere. Here, we present a phylogenomic study of these MRSA to reveal their phylogeny, spatial and temporal population structure, and the evolution of selected traits. We studied 598 genome sequences, including 409 newly generated sequences, from 11 countries in Central, North, and South America, and references from Asia and Europe. An early-branching CC5-Basal clade is well-dispersed geographically, is methicillin-susceptible and MRSA predominantly of ST5-IV such as the USA800 clone, and includes separate subclades for avian and porcine strains. In the early 1970s and early 1960s, respectively, two clades appeared that subsequently underwent major expansions in the Western Hemisphere: a CC5-I clade in South America and a CC5-II clade largely in Central and North America. The CC5-I clade includes the ST5-I Chilean/Cordobes clone, and the ST228-I South German clone as an early offshoot, but is distinct from other ST5-I clones from Europe that nest within CC5-Basal. The CC5-II clade includes divergent strains of the ST5-II USA100 clone, various other clones, and most known vancomycin-resistant strains of S. aureus, but is distinct from ST5-II strain N315 from Japan that nests within CC5-Basal. The recombination rate of CC5 was much lower than has been reported for other S. aureus genetic backgrounds, which indicates that recurrence of vancomycin resistance in CC5 is not likely due to an enhanced promiscuity. An increased number of antibiotic resistances and decreased number of toxins with distance from the CC5 tree root were observed. Of note, the expansions of the CC5-I and CC5-II clades in the Western Hemisphere were preceded by convergent gains of resistance to fluoroquinolone, macrolide, and lincosamide antibiotics, and convergent losses of the staphylococcal enterotoxin p (sep) gene from the immune evasion gene cluster of phage ϕSa3. Unique losses of surface proteins were also noted for these two clades. In summary, our study has determined the relationships of different clades and clones of CC5 and has revealed genomic changes for increased antibiotic resistance and decreased virulence associated with the expansions of these MRSA in the Western Hemisphere.
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Affiliation(s)
- Lavanya Challagundla
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, United States
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Iftekhar Rafiqullah
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Daniel O. Sordelli
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires and Consejo Nacional de Investigaciones Ciencias y Tecnicas, Buenos Aires, Argentina
| | | | | | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Nahuel Fittipaldi
- Public Health Ontario Laboratory, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Michael Feldgarden
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, United States
| | | | - Michael S. Calderwood
- Section of Infectious Disease and International Health, Dartmouth–Hitchcock Medical Center, Lebanon, NH, United States
| | - Lina P. Carvajal
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Sandra Rincon
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Blake Hanson
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern Medical School, Houston, TX, United States
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX, United States
| | - Paul J. Planet
- Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Cesar A. Arias
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern Medical School, Houston, TX, United States
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX, United States
| | - Lorena Diaz
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - D. Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
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6
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Mahajan GJ, Vallender EJ, Garrett MR, Challagundla L, Overholser JC, Jurjus G, Dieter L, Syed M, Romero DG, Benghuzzi H, Stockmeier CA. Altered neuro-inflammatory gene expression in hippocampus in major depressive disorder. Prog Neuropsychopharmacol Biol Psychiatry 2018; 82:177-186. [PMID: 29175309 PMCID: PMC5801125 DOI: 10.1016/j.pnpbp.2017.11.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/07/2017] [Accepted: 11/18/2017] [Indexed: 12/28/2022]
Abstract
Major Depressive Disorder (MDD) is a common psychiatric disorder for which available medications are often not effective. The high prevalence of MDD and modest response to existing therapies compels efforts to better understand and treat the disorder. Decreased hippocampal volume with increasing duration of depression suggests altered gene expression or even a decrease in neurogenesis. Tissue punches from the dentate gyrus were collected postmortem from 23 subjects with MDD and 23 psychiatrically-normal control subjects. Total RNA was isolated and whole transcriptome paired-end RNA-sequencing was performed using an Illumina NextSeq 500. For each sample, raw RNA-seq reads were aligned to the Ensembl GRCh38 human reference genome. Analysis revealed 30 genes differentially expressed in MDD compared to controls (FDR<0.05). Down-regulated genes included several with inflammatory function (ISG15, IFI44L, IFI6, NR4A1/Nur-77) and GABBR1 while up-regulated genes included several with cytokine function (CCL2/MCP-1), inhibitors of angiogenesis (ADM, ADAMTS9), and the KANSL1 gene, a histone acetyltransferase. Similar analyses of specific subsets of MDD subjects (suicide vs. non-suicide, single vs. multiple episodes) yielded similar, though not identical, results. Enrichment analysis identified an over-representation of inflammatory and neurogenesis-related (ERK/MAPK) signaling pathways significantly altered in the hippocampal dentate gyrus in MDD. Together, these data implicate neuro-inflammation as playing a crucial role in MDD. These findings support continued efforts to identify adjunctive approaches towards the treatment of MDD with drugs including anti-inflammatory and neuroprotective properties.
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Affiliation(s)
- Gouri J Mahajan
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Eric J Vallender
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Michael R Garrett
- Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS, USA
| | | | | | - George Jurjus
- Psychiatry, Case Western Reserve University, Cleveland, OH, USA; Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA
| | - Lesa Dieter
- Psychology, Case Western Reserve University, Cleveland, OH, USA
| | - Maryam Syed
- Biochemistry, University of Mississippi Medical Center, Jackson, MS, USA
| | - Damian G Romero
- Biochemistry, University of Mississippi Medical Center, Jackson, MS, USA
| | - Hamed Benghuzzi
- Diagnostic and Clinical Health Sciences, University of Mississippi Medical Center, Jackson, MS, USA
| | - Craig A Stockmeier
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA; Psychiatry, Case Western Reserve University, Cleveland, OH, USA.
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7
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Chung WC, Zhang S, Challagundla L, Zhou Y, Xu K. Lunatic Fringe and p53 Cooperatively Suppress Mesenchymal Stem-Like Breast Cancer. Neoplasia 2017; 19:885-895. [PMID: 28938159 PMCID: PMC5608590 DOI: 10.1016/j.neo.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 12/05/2022]
Abstract
Claudin-low breast cancer (CLBC) is a poor prognosis molecular subtype showing stemness and mesenchymal features. We previously discovered that deletion of a Notch signaling modulator, Lunatic Fringe (Lfng), in the mouse mammary gland induced a subset of tumors resembling CLBC. Here we report that deletion of one copy of p53 on this background not only accelerated mammary tumor development but also led to a complete penetrance of the mesenchymal stem-like phenotype. All mammary tumors examined in the Lfng/p53 compound mutant mice displayed a mesenchymal/spindloid pathology. These tumors showed high level expressions of epithelial-to-mesenchymal transition (EMT) markers including Vimentin, Twist, and PDGFRα, a gene known to be enriched in CLBC. Prior to tumor onset, Lfng/p53 mutant mammary glands exhibited increased levels of Vimentin and E-cadherin, but decreased expressions of cytokeratin 14 and cytokeratin 8, accompanied by elevated basal cell proliferation and an expanded mammary stem cell-enriched population. Lfng/p53 mutant glands displayed increased accumulation of Notch3 intracellular fragment, up-regulation of Hes5 and down-regulation of Hes1. Analysis in human breast cancer datasets found the lowest HES1 and second lowest LFNG expressions in CLBC among molecular subtypes, and low level of LFNG is associated with poor survival. Immunostaining of human breast cancer tissue array found correlation between survival and LFNG immunoreactivity. Finally, patients carrying TP53 mutations express lower LFNG than patients with wild type TP53. Taken together, these data revealed genetic interaction between Lfng and p53 in mammary tumorigenesis, established a new mouse model resembling CLBC, and may suggest targeting strategy for this disease.
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Affiliation(s)
- Wen-Cheng Chung
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Shubing Zhang
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Lavanya Challagundla
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yunyun Zhou
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Keli Xu
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA; Department of Neurobiology and Anatomical Sciences, University of Mississippi Medical Center, Jackson, MS, USA.
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8
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Rajkowska G, Mahajan G, Legutko B, Challagundla L, Griswold M, Albert PR, Daigle M, Miguel-Hidalgo JJ, Austin MC, Blakely RD, Steffens DC, Stockmeier CA. Length of axons expressing the serotonin transporter in orbitofrontal cortex is lower with age in depression. Neuroscience 2017; 359:30-39. [PMID: 28711621 DOI: 10.1016/j.neuroscience.2017.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/08/2017] [Accepted: 07/04/2017] [Indexed: 12/27/2022]
Abstract
Studies of major depressive disorder (MDD) in postmortem brain tissue report enhanced binding to inhibitory serotonin-1A autoreceptors in midbrain dorsal raphe and reductions in length of axons expressing the serotonin transporter (SERT) in dorsolateral prefrontal cortex. The length density of axons expressing SERT in the orbitofrontal cortex (OFC) was determined in 18 subjects with MDD and 17 age-matched control subjects. A monoclonal antibody was used to immunohistochemically label the SERT in fixed sections of OFC. The 3-dimensional length density of SERT-immunoreactive (ir) axons in layer VI of OFC was estimated. The age of subjects with MDD was negatively correlated with SERT axon length (r=-0.77, p<0.0005). The significant effect of age persisted when removing four depressed subjects with an antidepressant medication present at the time of death, or when removing nine depressed subjects that had a recent prescription for an antidepressant medication. Neither gender, tissue pH, postmortem interval, 5-HTTLPR genotype, time in fixative, nor death by suicide had a significant effect on axon length. The age-related decrease in SERT-ir axon length in MDD may reflect pathology of ascending axons passing through deep white matter hyperintensities. Greater length of axons expressing SERT in younger subjects with MDD may result in a significant deficit in serotonin availability in OFC.
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Affiliation(s)
- Grazyna Rajkowska
- Department of Psychiatry and Human Behavior, School of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
| | - Gouri Mahajan
- Department of Psychiatry and Human Behavior, School of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
| | - Beata Legutko
- Department of Psychiatry and Human Behavior, School of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
| | - Lavanya Challagundla
- Department of Data Science, JD Bower School of Population Health, University of Mississippi Medical Center, Jackson, MS 39216, USA.
| | - Michael Griswold
- Department of Data Science, JD Bower School of Population Health, University of Mississippi Medical Center, Jackson, MS 39216, USA.
| | - Paul R Albert
- Ottawa Hospital Research Institute (Neuroscience) and UOttawa Brain and Mind Research Institute, Ottawa, ON K1H 8M5, Canada.
| | - Mireille Daigle
- Ottawa Hospital Research Institute (Neuroscience) and UOttawa Brain and Mind Research Institute, Ottawa, ON K1H 8M5, Canada.
| | - Jose J Miguel-Hidalgo
- Department of Psychiatry and Human Behavior, School of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
| | - Mark C Austin
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA.
| | - Randy D Blakely
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| | - David C Steffens
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT 06030, USA.
| | - Craig A Stockmeier
- Department of Psychiatry and Human Behavior, School of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Psychiatry, Case Western Reserve University, Cleveland, OH 44106, USA.
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9
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Wheeler GL, Dorman HE, Buchanan A, Challagundla L, Wallace LE. A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology. Appl Plant Sci 2014; 2:apps.1400059. [PMID: 25506520 PMCID: PMC4259455 DOI: 10.3732/apps.1400059] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/06/2014] [Indexed: 05/02/2023]
Abstract
Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995-2013. These markers are an important and economical tool for plant biologists and continue to be used alongside modern genomics approaches to study genetic diversity and structure, evolutionary history, and hybridization in native and agricultural species. Studies using species-specific primers reported a greater number of polymorphic loci than those employing universal primers. A major disadvantage to cpSSRs is fragment size homoplasy; therefore, we documented its occurrence at several cpSSR loci within and between species of Acmispon (Fabaceae). Based on our empirical data set, we recommend targeted sequencing of a subset of samples combined with fragment genotyping as a cost-efficient, data-rich approach to the use of cpSSRs and as a test of homoplasy. The availability of genomic resources for plants aids in the development of primers for new study systems, thereby enhancing the utility of cpSSRs across plant biology.
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Affiliation(s)
- Gregory L. Wheeler
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Hanna E. Dorman
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Alenda Buchanan
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Lavanya Challagundla
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
| | - Lisa E. Wallace
- Department of Biological Sciences, Mississippi State University, P.O. Box GY, Mississippi State, Mississippi 39762 USA
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