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Sohi GK, Farooqui N, Mohan A, Rajagopalan KS, Xing L, Zhu XY, Jordan K, Krier JD, Saadiq IM, Tang H, Hickson LJ, Eirin A, Lerman LO, Herrmann SM. The impact of hypoxia preconditioning on mesenchymal stem cells performance in hypertensive kidney disease. Stem Cell Res Ther 2024; 15:162. [PMID: 38853239 PMCID: PMC11163800 DOI: 10.1186/s13287-024-03778-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Autologous mesenchymal stem cells (MSCs) have emerged as a therapeutic option for many diseases. Hypertensive kidney disease (HKD) might impair MSCs' reparative ability by altering the biomolecular properties, but the characteristics of this impairment are unclear. In our previous pre-clinical studies, we found hypoxic preconditioning (HPC) enhanced angiogenesis and suppressed senescence gene expression. Thus, we hypothesize that HPC would improve human MSCs by enhancing their functionality and angiogenesis, creating an anti-inflammatory and anti-senescence environment. METHODS MSC samples (n = 12 each) were collected from the abdominal fat of healthy kidney donors (HC), hypertensive patients (HTN), and patients with hypertensive kidney disease (HKD). MSCs were harvested and cultured in Normoxic (20% O2) or Hypoxic (1% O2) conditions. MSC functionality was measured by proliferation assays and cytokine released in conditioned media. Senescence was evaluated by senescence-associated beta-galactosidase (SA-beta-gal) activity. Additionally, transcriptome analysis using RNA-sequencing and quantitative PCR (qPCR) were performed. RESULTS At baseline, normoxic HTN-MSCs had higher proliferation capacity compared to HC. However, HPC augmented proliferation in HC. HPC did not affect the release of pro-angiogenic protein VEGF, but increased EGF in HC-MSC, and decreased HGF in HC and HKD MSCs. Under HPC, SA-β-gal activity tended to decrease, particularly in HC group. HPC upregulated mostly the pro-angiogenic and inflammatory genes in HC and HKD and a few senescence genes in HKD. CONCLUSIONS HPC has a more favorable functional effect on HC- than on HKD-MSC, reflected in increased proliferation and EGF release, and modest decrease in senescence, whereas it has little effect on HTN or HKD MSCs.
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Affiliation(s)
- Gurparneet Kaur Sohi
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | - Naba Farooqui
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | - Arjunmohan Mohan
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | | | - Li Xing
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, Jiangsu province, China
| | - Xiang Y Zhu
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | - Kyra Jordan
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | - James D Krier
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | - Ishran M Saadiq
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | - Hui Tang
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | - LaTonya J Hickson
- Division of Nephrology and Hypertension, Mayo Clinic, Jacksonville, FL, USA
| | - Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA
| | - Sandra M Herrmann
- Division of Nephrology and Hypertension, Mayo Clinic, 200, First Street SW, Rochester, 55902, MN, USA.
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Chade AR, Sitz R, Kelty TJ, McCarthy E, Tharp DL, Rector RS, Eirin A. Chronic kidney disease and left ventricular diastolic dysfunction (CKD-LVDD) alter cardiac expression of mitochondria-related genes in swine. Transl Res 2024; 267:67-78. [PMID: 38262578 PMCID: PMC11001533 DOI: 10.1016/j.trsl.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/13/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024]
Abstract
Cardiovascular disease and heart failure doubles in patients with chronic kidney disease (CKD), but the underlying mechanisms remain obscure. Mitochondria are central to maintaining cellular respiration and modulating cardiomyocyte function. We took advantage of our novel swine model of CKD and left ventricular diastolic dysfunction (CKD-LVDD) to investigate the expression of mitochondria-related genes and potential mechanisms regulating their expression. CKD-LVDD and normal control pigs (n=6/group, 3 males/3 females) were studied for 14 weeks. Renal and cardiac hemodynamics were quantified by multidetector-CT, echocardiography, and pressure-volume loop studies, respectively. Mitochondrial morphology (electron microscopy) and function (Oroboros) were assessed ex vivo. In randomly selected pigs (n=3/group), cardiac mRNA-, MeDIP-, and miRNA-sequencing (seq) were performed to identify mitochondria-related genes and study their pre- and post -transcriptional regulation. CKD-LVDD exhibited cardiac mitochondrial structural abnormalities and elevated mitochondrial H2O2 emission but preserved mitochondrial function. Cardiac mRNA-seq identified 862 mitochondria-related genes, of which 69 were upregulated and 33 downregulated (fold-change ≥2, false discovery rate≤0.05). Functional analysis showed that upregulated genes were primarily implicated in processes associated with oxidative stress, whereas those downregulated mainly participated in respiration and ATP synthesis. Integrated mRNA/miRNA/MeDIP-seq analysis showed that upregulated genes were modulated predominantly by miRNAs, whereas those downregulated were by miRNA and epigenetic mechanisms. CKD-LVDD alters cardiac expression of mitochondria-related genes, associated with mitochondrial structural damage but preserved respiratory function, possibly reflecting intrinsic compensatory mechanisms. Our findings may guide the development of early interventions at stages of cardiac dysfunction in which mitochondrial injury could be prevented, and the development of LVDD ameliorated.
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Affiliation(s)
- Alejandro R Chade
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, USA; Department of Medicine, University of Missouri, Columbia, USA; NextGen Precision Health, University of Missouri, Columbia, USA.
| | - Rhys Sitz
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, USA; NextGen Precision Health, University of Missouri, Columbia, USA
| | - Taylor J Kelty
- NextGen Precision Health, University of Missouri, Columbia, USA; Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, USA
| | - Elizabeth McCarthy
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, USA; NextGen Precision Health, University of Missouri, Columbia, USA
| | - Darla L Tharp
- NextGen Precision Health, University of Missouri, Columbia, USA; Department of Biomedical Sciences, University of Missouri, Columbia, USA
| | - R Scott Rector
- NextGen Precision Health, University of Missouri, Columbia, USA; Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, USA; Research Service, Harry S Truman Memorial Veterans Medical Center, University of Missouri, Columbia, USA; Division of Gastroenterology and Hepatology, University of Missouri, Columbia, USA
| | - Alfonso Eirin
- The Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA; Department of Cardiovascular Diseases Mayo Clinic, Rochester, MN, USA
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Reddy JS, Heath L, Vander Linden A, Allen M, de Paiva Lopes K, Seifar F, Wang E, Ma Y, Poehlman WL, Quicksall ZS, Runnels A, Wang Y, Duong DM, Yin L, Xu K, Modeste ES, Shantaraman A, Dammer EB, Ping L, Oatman SR, Scanlan J, Ho C, Carrasquillo MM, Atik M, Yepez G, Mitchell AO, Nguyen TT, Chen X, Marquez DX, Reddy H, Xiao H, Seshadri S, Mayeux R, Prokop S, Lee EB, Serrano GE, Beach TG, Teich AF, Haroutunian V, Fox EJ, Gearing M, Wingo A, Wingo T, Lah JJ, Levey AI, Dickson DW, Barnes LL, De Jager P, Zhang B, Bennett D, Seyfried NT, Greenwood AK, Ertekin-Taner N. Bridging the Gap: Multi-Omics Profiling of Brain Tissue in Alzheimer's Disease and Older Controls in Multi-Ethnic Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589592. [PMID: 38659743 PMCID: PMC11042309 DOI: 10.1101/2024.04.16.589592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
INTRODUCTION Multi-omics studies in Alzheimer's disease (AD) revealed many potential disease pathways and therapeutic targets. Despite their promise of precision medicine, these studies lacked African Americans (AA) and Latin Americans (LA), who are disproportionately affected by AD. METHODS To bridge this gap, Accelerating Medicines Partnership in AD (AMP-AD) expanded brain multi-omics profiling to multi-ethnic donors. RESULTS We generated multi-omics data and curated and harmonized phenotypic data from AA (n=306), LA (n=326), or AA and LA (n=4) brain donors plus Non-Hispanic White (n=252) and other (n=20) ethnic groups, to establish a foundational dataset enriched for AA and LA participants. This study describes the data available to the research community, including transcriptome from three brain regions, whole genome sequence, and proteome measures. DISCUSSION Inclusion of traditionally underrepresented groups in multi-omics studies is essential to discover the full spectrum of precision medicine targets that will be pertinent to all populations affected with AD.
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Affiliation(s)
- Joseph S Reddy
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Laura Heath
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121
| | | | - Mariet Allen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Katia de Paiva Lopes
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Fatemeh Seifar
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029
| | - Yiyi Ma
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | | | | | - Alexi Runnels
- New York Genome Center, 101 6th Ave, New York, NY 10013
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Duc M Duong
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Luming Yin
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Kaiming Xu
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Erica S Modeste
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | | | - Eric B Dammer
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Lingyan Ping
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | | | - Jo Scanlan
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121
| | - Charlotte Ho
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | | | - Merve Atik
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Geovanna Yepez
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | | | - Thuy T Nguyen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Xianfeng Chen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - David X Marquez
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
- University of Illinois Chicago, 1200 West Harrison St., Chicago, Illinois 60607
| | - Hasini Reddy
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Harrison Xiao
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Sudha Seshadri
- The Glen Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas, 8300 Floyd Curl Drive, San Antonio TX 78229
| | - Richard Mayeux
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | | | - Edward B Lee
- Center for Neurodegenerative Disease Brain Bank at the University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104-2676
| | - Geidy E Serrano
- Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351
| | - Thomas G Beach
- Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351
| | - Andrew F Teich
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Varham Haroutunian
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
| | - Edward J Fox
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Marla Gearing
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Aliza Wingo
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Thomas Wingo
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - James J Lah
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Allan I Levey
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Dennis W Dickson
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Philip De Jager
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
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Udine E, DeJesus-Hernandez M, Tian S, das Neves SP, Crook R, Finch NA, Baker MC, Pottier C, Graff-Radford NR, Boeve BF, Petersen RC, Knopman DS, Josephs KA, Oskarsson B, Da Mesquita S, Petrucelli L, Gendron TF, Dickson DW, Rademakers R, van Blitterswijk M. Abundant transcriptomic alterations in the human cerebellum of patients with a C9orf72 repeat expansion. Acta Neuropathol 2024; 147:73. [PMID: 38641715 PMCID: PMC11031479 DOI: 10.1007/s00401-024-02720-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
The most prominent genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) is a repeat expansion in the gene C9orf72. Importantly, the transcriptomic consequences of the C9orf72 repeat expansion remain largely unclear. Here, we used short-read RNA sequencing (RNAseq) to profile the cerebellar transcriptome, detecting alterations in patients with a C9orf72 repeat expansion. We focused on the cerebellum, since key C9orf72-related pathologies are abundant in this neuroanatomical region, yet TDP-43 pathology and neuronal loss are minimal. Consistent with previous work, we showed a reduction in the expression of the C9orf72 gene and an elevation in homeobox genes, when comparing patients with the expansion to both patients without the C9orf72 repeat expansion and control subjects. Interestingly, we identified more than 1000 alternative splicing events, including 4 in genes previously associated with ALS and/or FTLD. We also found an increase of cryptic splicing in C9orf72 patients compared to patients without the expansion and controls. Furthermore, we demonstrated that the expression level of select RNA-binding proteins is associated with cryptic splice junction inclusion. Overall, this study explores the presence of widespread transcriptomic changes in the cerebellum, a region not confounded by severe neurodegeneration, in post-mortem tissue from C9orf72 patients.
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Affiliation(s)
- Evan Udine
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Shulan Tian
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Richard Crook
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - NiCole A Finch
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - Matthew C Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - Cyril Pottier
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | | | | | | | | | | | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Sandro Da Mesquita
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA.
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA.
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5
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Fadra N, Schultz-Rogers LE, Chanana P, Cousin MA, Macke EL, Ferrer A, Pinto E Vairo F, Olson RJ, Oliver GR, Mulvihill LA, Jenkinson G, Klee EW. Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease. BMC Genomics 2024; 25:371. [PMID: 38627676 PMCID: PMC11020449 DOI: 10.1186/s12864-024-10240-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of the X chromosome in each cell. The preferential inactivation of either the maternal or paternal copy of the X chromosome in a majority of cells results in a skewed or non-random pattern of X inactivation and is observed in over 25% of adult females. Identifying skewed X inactivation is of clinical significance in patients with suspected rare genetic diseases due to the possibility of biased expression of disease-causing genes present on the active X chromosome. The current clinical test for the detection of skewed XCI relies on the methylation status of the methylation-sensitive restriction enzyme (Hpall) binding site present in proximity of short tandem polymorphic repeats on the androgen receptor (AR) gene. This approach using one locus results in uninformative or inconclusive data for 10-20% of tests. Further, recent studies have shown inconsistency between methylation of the AR locus and the state of inactivation of the X chromosome. Herein, we develop a method for estimating X inactivation status, using exome and transcriptome sequencing data derived from blood in 227 female samples. We built a reference model for evaluation of XCI in 135 females from the GTEx consortium. We tested and validated the model on 11 female individuals with different types of undiagnosed rare genetic disorders who were clinically tested for X-skew using the AR gene assay and compared results to our outlier-based analysis technique. RESULTS In comparison to the AR clinical test for identification of X inactivation, our method was concordant with the AR method in 9 samples, discordant in 1, and provided a measure of X inactivation in 1 sample with uninformative clinical results. We applied this method on an additional 81 females presenting to the clinic with phenotypes consistent with different hereditary disorders without a known genetic diagnosis. CONCLUSIONS This study presents the use of transcriptome and exome sequencing data to provide an accurate and complete estimation of X-inactivation and skew status in a cohort of female patients with different types of suspected rare genetic disease.
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Affiliation(s)
- Numrah Fadra
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Pritha Chanana
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Margot A Cousin
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Garrett Jenkinson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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Haralambieva IH, Chen J, Quach HQ, Ratishvili T, Warner ND, Ovsyannikova IG, Poland GA, Kennedy RB. Early B cell transcriptomic markers of measles-specific humoral immunity following a 3 rd dose of MMR vaccine. Front Immunol 2024; 15:1358477. [PMID: 38633249 PMCID: PMC11021587 DOI: 10.3389/fimmu.2024.1358477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
B cell transcriptomic signatures hold promise for the early prediction of vaccine-induced humoral immunity and vaccine protective efficacy. We performed a longitudinal study in 232 healthy adult participants before/after a 3rd dose of MMR (MMR3) vaccine. We assessed baseline and early transcriptional patterns in purified B cells and their association with measles-specific humoral immunity after MMR vaccination using two analytical methods ("per gene" linear models and joint analysis). Our study identified distinct early transcriptional signatures/genes following MMR3 that were associated with measles-specific neutralizing antibody titer and/or binding antibody titer. The most significant genes included: the interleukin 20 receptor subunit beta/IL20RB gene (a subunit receptor for IL-24, a cytokine involved in the germinal center B cell maturation/response); the phorbol-12-myristate-13-acetate-induced protein 1/PMAIP1, the brain expressed X-linked 2/BEX2 gene and the B cell Fas apoptotic inhibitory molecule/FAIM, involved in the selection of high-affinity B cell clones and apoptosis/regulation of apoptosis; as well as IL16 (encoding the B lymphocyte-derived IL-16 ligand of CD4), involved in the crosstalk between B cells, dendritic cells and helper T cells. Significantly enriched pathways included B cell signaling, apoptosis/regulation of apoptosis, metabolic pathways, cell cycle-related pathways, and pathways associated with viral infections, among others. In conclusion, our study identified genes/pathways linked to antigen-induced B cell proliferation, differentiation, apoptosis, and clonal selection, that are associated with, and impact measles virus-specific humoral immunity after MMR vaccination.
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Affiliation(s)
- Iana H. Haralambieva
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Jun Chen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Huy Quang Quach
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Tamar Ratishvili
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Nathaniel D. Warner
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
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Arai H, Yang Y, Baca Y, Millstein J, Denda T, Ou FS, Innocenti F, Takeda H, Kubota Y, Doi A, Horie Y, Umemoto K, Izawa N, Wang J, Battaglin F, Jayachandran P, Algaze S, Soni S, Zhang W, Goldberg RM, Hall MJ, Scott AJ, Hwang JJ, Lou E, Weinberg BA, Marshall J, Goel S, Xiu J, Michael Korn W, Venook AP, Sunakawa Y, Lenz HJ. Predictive value of CDC37 gene expression for targeted therapy in metastatic colorectal cancer. Eur J Cancer 2024; 201:113914. [PMID: 38359495 DOI: 10.1016/j.ejca.2024.113914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/25/2024] [Accepted: 02/04/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND CDC37 is a key determinant of client kinase recruitment to the HSP90 chaperoning system. We hypothesized that kinase-specific dependency on CDC37 alters the efficacy of targeted therapies for metastatic colorectal cancer (mCRC). MATERIAL AND METHODS Two independent mCRC cohorts were analyzed to compare the survival outcomes between CDC37-high and CDC37-low patients (stratified by the median cutoff values): the CALGB/SWOG 80405 trial (226 and 207 patients receiving first-line bevacizumab- and cetuximab-containing chemotherapies, respectively) and Japanese retrospective (50 refractory patients receiving regorafenib) cohorts. A dataset of specimens submitted to a commercial CLIA-certified laboratory was utilized to characterize molecular profiles of CDC37-high (top quartile, N = 5055) and CDC37-low (bottom quartile, N = 5055) CRCs. RESULTS In the bevacizumab-treated group, CDC37-high patients showed significantly better progression-free survival (PFS) (median 13.3 vs 9.6 months, hazard ratio [HR] 0.59, 95% confidence interval [CI] 0.44-0.79, p < 0.01) than CDC37-low patients. In the cetuximab-treated group, CDC37-high and CDC37-low patients had similar outcomes. In the regorafenib-treated group, CDC37-high patients showed significantly better overall survival (median 11.3 vs 6.0 months, HR 0.24, 95% CI 0.11-0.54, p < 0.01) and PFS (median 3.5 vs 1.9 months, HR 0.51, 95% CI 0.28-0.94, p = 0.03). Comprehensive molecular profiling revealed that CDC37-high CRCs were associated with higher VEGFA, FLT1, and KDR expressions and activated hypoxia signature. CONCLUSIONS CDC37-high mCRC patients derived more benefit from anti-VEGF therapies, including bevacizumab and regorafenib, but not from cetuximab. Molecular profiles suggested that such tumors were dependent on angiogenesis-relating pathways.
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Affiliation(s)
- Hiroyuki Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yan Yang
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yasmine Baca
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Joshua Millstein
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tadamichi Denda
- Department of Gastroenterology, Chiba Cancer Center, Chiba, Japan
| | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Federico Innocenti
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hiroyuki Takeda
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yohei Kubota
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ayako Doi
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshiki Horie
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kumiko Umemoto
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Naoki Izawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Jingyuan Wang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Priya Jayachandran
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sandra Algaze
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Michael J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Aaron James Scott
- Department of Medicine, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Jimmy J Hwang
- Department of Solid Tumor Oncology, GI Medical Oncology, Levine Cancer Institute, Charlotte, NC, USA
| | - Emil Lou
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - John Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Sanjay Goel
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Joanne Xiu
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - W Michael Korn
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Alan P Venook
- University of California, San Francisco, San Francisco, CA, USA
| | - Yu Sunakawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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8
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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. Brief Bioinform 2024; 25:bbae164. [PMID: 38605641 PMCID: PMC11009461 DOI: 10.1093/bib/bbae164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Amruta Naik
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
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9
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Krull JE, Wenzl K, Hopper MA, Manske MK, Sarangi V, Maurer MJ, Larson MC, Mondello P, Yang Z, Novak JP, Serres M, Whitaker KR, Villasboas Bisneto JC, Habermann TM, Witzig TE, Link BK, Rimsza LM, King RL, Ansell SM, Cerhan JR, Novak AJ. Follicular lymphoma B cells exhibit heterogeneous transcriptional states with associated somatic alterations and tumor microenvironments. Cell Rep Med 2024; 5:101443. [PMID: 38428430 PMCID: PMC10983045 DOI: 10.1016/j.xcrm.2024.101443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 08/14/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Follicular lymphoma (FL) is an indolent non-Hodgkin lymphoma of germinal center origin, which presents with significant biologic and clinical heterogeneity. Using RNA-seq on B cells sorted from 87 FL biopsies, combined with machine-learning approaches, we identify 3 transcriptional states that divide the biological ontology of FL B cells into inflamed, proliferative, and chromatin-modifying states, with relationship to prior GC B cell phenotypes. When integrated with whole-exome sequencing and immune profiling, we find that each state was associated with a combination of mutations in chromatin modifiers, copy-number alterations to TNFAIP3, and T follicular helper cells (Tfh) cell interactions, or primarily by a microenvironment rich in activated T cells. Altogether, these data define FL B cell transcriptional states across a large cohort of patients, contribute to our understanding of FL heterogeneity at the tumor cell level, and provide a foundation for guiding therapeutic intervention.
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Affiliation(s)
| | - Kerstin Wenzl
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Matthew J Maurer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Melissa C Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - ZhiZhang Yang
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | - Brian K Link
- Division of Hematology, Oncology, and Blood & Marrow Transplantation, University of Iowa, Iowa City, IA, USA
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Rebecca L King
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anne J Novak
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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10
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Pollin G, Mathison AJ, de Assuncao TM, Thomas A, Zeighami L, Salmonson A, Liu H, Urrutia G, Vankayala P, Pandol SJ, Zimmermann MT, Iovanna J, Jin VX, Urrutia R, Lomberk G. EHMT2 Inactivation in Pancreatic Epithelial Cells Shapes the Transcriptional Landscape and Inflammation Response of the Whole Pancreas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.584700. [PMID: 38529489 PMCID: PMC10962735 DOI: 10.1101/2024.03.14.584700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The Euchromatic Histone Methyl Transferase Protein 2 (EHMT2), also known as G9a, deposits transcriptionally repressive chromatin marks that play pivotal roles in the maturation and homeostasis of multiple organs. Recently, we have shown that EHMT2 inactivation alters growth and immune gene expression networks, antagonizing KRAS-mediated pancreatic cancer initiation and promotion. Here, we elucidate the essential role of EHMT2 in maintaining a transcriptional landscape that protects organs from inflammation. Comparative RNA-seq studies between normal postnatal and young adult pancreatic tissue from EHMT2 conditional knockout animals ( EHMT2 fl/fl ) targeted to the exocrine pancreatic epithelial cells ( Pdx1-Cre and P48 Cre/+ ), reveal alterations in gene expression networks in the whole organ related to injury-inflammation-repair, suggesting an increased predisposition to damage. Thus, we induced an inflammation repair response in the EHMT2 fl/fl pancreas and used a data science-based approach to integrate RNA-seq-derived pathways and networks, deconvolution digital cytology, and spatial transcriptomics. We also analyzed the tissue response to damage at the morphological, biochemical, and molecular pathology levels. The EHMT2 fl/fl pancreas displays an enhanced injury-inflammation-repair response, offering insights into fundamental molecular and cellular mechanisms involved in this process. More importantly, these data show that conditional EHMT2 inactivation in exocrine cells reprograms the local environment to recruit mesenchymal and immunological cells needed to mount an increased inflammatory response. Mechanistically, this response is an enhanced injury-inflammation-repair reaction with a small contribution of specific EHMT2-regulated transcripts. Thus, this new knowledge extends the mechanisms underlying the role of the EHMT2-mediated pathway in suppressing pancreatic cancer initiation and modulating inflammatory pancreatic diseases.
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11
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Yazdani A, Yazdani A, Mendez-Giraldez R, Pillonetto G, Samiei E, Hadi R, Lenz HJ, Venook A, Samiei A, Nixon A, Lucci J, Kopetz S, Bertagnolli M, Perou C, Innocenti F. Gene expression biomarkers differentiate overall survival of colorectal cancer upon targeted therapies. RESEARCH SQUARE 2024:rs.3.rs-4047331. [PMID: 38559223 PMCID: PMC10980102 DOI: 10.21203/rs.3.rs-4047331/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
While monoclonal antibody-based targeted therapies have substantially improved progression-free survival in cancer patients, the variability in individual responses poses a significant challenge in patient care. Therefore, identifying cancer subtypes and their associated biomarkers is required for assigning effective treatment. In this study, we integrated genotype and pre-treatment tissue RNA-seq data and identified biomarkers causally associated with the overall survival (OS) of colorectal cancer (CRC) patients treated with either cetuximab or bevacizumab. We performed enrichment analysis for specific consensus molecular subtypes (CMS) of colorectal cancer and evaluated differential expression of identified genes using paired tumor and normal tissue from an external cohort. In addition, we replicated the causal effect of these genes on OS using validation cohort and assessed their association with the Cancer Genome Atlas Program data as an external cohort. One of the replicated findings was WDR62, whose overexpression shortened OS of patients treated with cetuximab. Enrichment of its over expression in CMS1 and low expression in CMS4 suggests that patients with CMS4 subtype may drive greater benefit from cetuximab. In summary, this study highlights the importance of integrating different omics data for identifying promising biomarkers specific to a treatment or a cancer subtype.
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Affiliation(s)
| | | | | | | | | | - Reza Hadi
- University of Science and Technology of Iran
| | | | | | | | | | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center
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12
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Kawatani K, Holm ML, Starling SC, Martens YA, Zhao J, Lu W, Ren Y, Li Z, Jiang P, Jiang Y, Baker SK, Wang N, Roy B, Parsons TM, Perkerson RB, Bao H, Han X, Bu G, Kanekiyo T. ABCA7 deficiency causes neuronal dysregulation by altering mitochondrial lipid metabolism. Mol Psychiatry 2024; 29:809-819. [PMID: 38135757 PMCID: PMC11153016 DOI: 10.1038/s41380-023-02372-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023]
Abstract
ABCA7 loss-of-function variants are associated with increased risk of Alzheimer's disease (AD). Using ABCA7 knockout human iPSC models generated with CRISPR/Cas9, we investigated the impacts of ABCA7 deficiency on neuronal metabolism and function. Lipidomics revealed that mitochondria-related phospholipids, such as phosphatidylglycerol and cardiolipin were reduced in the ABCA7-deficient iPSC-derived cortical organoids. Consistently, ABCA7 deficiency-induced alterations of mitochondrial morphology accompanied by reduced ATP synthase activity and exacerbated oxidative damage in the organoids. Furthermore, ABCA7-deficient iPSC-derived neurons showed compromised mitochondrial respiration and excess ROS generation, as well as enlarged mitochondrial morphology compared to the isogenic controls. ABCA7 deficiency also decreased spontaneous synaptic firing and network formation in iPSC-derived neurons, in which the effects were rescued by supplementation with phosphatidylglycerol or NAD+ precursor, nicotinamide mononucleotide. Importantly, effects of ABCA7 deficiency on mitochondria morphology and synapses were recapitulated in synaptosomes isolated from the brain of neuron-specific Abca7 knockout mice. Together, our results provide evidence that ABCA7 loss-of-function contributes to AD risk by modulating mitochondria lipid metabolism.
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Affiliation(s)
- Keiji Kawatani
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Marie-Louise Holm
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Skylar C Starling
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yuka A Martens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- SciNeuro Pharmaceuticals, Rockville, MD, 20850, USA
| | - Jing Zhao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Center for Regenerative Biotherapeutics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Wenyan Lu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Center for Regenerative Biotherapeutics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yingxue Ren
- Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Zonghua Li
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Peizhou Jiang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yangying Jiang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Samantha K Baker
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ni Wang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Bhaskar Roy
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Tammee M Parsons
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Center for Regenerative Biotherapeutics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ralph B Perkerson
- Center for Regenerative Biotherapeutics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Hanmei Bao
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA.
- Center for Regenerative Biotherapeutics, Mayo Clinic, Jacksonville, FL, 32224, USA.
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13
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Watkins R, Gamo A, Choi SH, Kumar M, Buckarma E, McCabe C, Tomlinson J, Pereya D, Lupse B, Geravandi S, Werneburg NW, Wang C, Starlinger P, Zhu S, Li S, Yu S, Surakattula M, Baguley T, Ardestani A, Maedler K, Roland J, Nguyen-Tran V, Joseph S, Petrassi M, Rogers N, Gores G, Chatterjee A, Tremblay M, Shen W, Smoot R. A small molecule MST1/2 inhibitor accelerates murine liver regeneration with improved survival in models of steatohepatitis. PNAS NEXUS 2024; 3:pgae096. [PMID: 38528952 PMCID: PMC10962727 DOI: 10.1093/pnasnexus/pgae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Dysfunctional liver regeneration following surgical resection remains a major cause of postoperative mortality and has no therapeutic options. Without targeted therapies, the current treatment paradigm relies on supportive therapy until homeostasis can be achieved. Pharmacologic acceleration of regeneration represents an alternative therapeutic avenue. Therefore, we aimed to generate a small molecule inhibitor that could accelerate liver regeneration with an emphasis on diseased models, which represent a significant portion of patients who require surgical resection and are often not studied. Utilizing a clinically approved small molecule inhibitor as a parent compound, standard medicinal chemistry approaches were utilized to generate a small molecule inhibitor targeting serine/threonine kinase 4/3 (MST1/2) with reduced off-target effects. This compound, mCLC846, was then applied to preclinical models of murine partial hepatectomy, which included models of diet-induced metabolic dysfunction-associated steatohepatitis (MASH). mCLC846 demonstrated on target inhibition of MST1/2 and reduced epidermal growth factor receptor inhibition. The inhibitory effects resulted in restored pancreatic beta-cell function and survival under diabetogenic conditions. Liver-specific cell-line exposure resulted in Yes-associated protein activation. Oral delivery of mCLC846 perioperatively resulted in accelerated murine liver regeneration and improved survival in diet-induced MASH models. Bulk transcriptional analysis of regenerating liver remnants suggested that mCLC846 enhanced the normal regenerative pathways and induced them following liver resection. Overall, pharmacological acceleration of liver regeneration with mCLC846 was feasible, had an acceptable therapeutic index, and provided a survival benefit in models of diet-induced MASH.
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Affiliation(s)
- Ryan Watkins
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Ana Gamo
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Seung Hyuk Choi
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Manoj Kumar
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - EeeLN Buckarma
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Chantal McCabe
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | | | - David Pereya
- Department of Surgery, Medical University of Vienna, General Hospital, Vienna 1090, Austria
| | - Blaz Lupse
- Centre for Biomolecular Interactions Bremen, University of Bremen, 28359 Bremen, Germany
| | - Shirin Geravandi
- Centre for Biomolecular Interactions Bremen, University of Bremen, 28359 Bremen, Germany
| | - Nathan W Werneburg
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chen Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Patrick Starlinger
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
- Center of Physiology and Pharmacology, Medical University of Vienna, Vienna 1090, Austria
| | - Siying Zhu
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sijia Li
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shan Yu
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Murali Surakattula
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tyler Baguley
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amin Ardestani
- Centre for Biomolecular Interactions Bremen, University of Bremen, 28359 Bremen, Germany
- Biomedical Institute for Multimorbidity (BIM), Centre for Biomedicine, Hull York Medical School, University of Hull, Hull YO10 5DD, UK
| | - Kathrin Maedler
- Centre for Biomolecular Interactions Bremen, University of Bremen, 28359 Bremen, Germany
| | - Jason Roland
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Van Nguyen-Tran
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Joseph
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mike Petrassi
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nikki Rogers
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gregory Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Arnab Chatterjee
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthew Tremblay
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Weijun Shen
- Calibr at Scripps Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rory Smoot
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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14
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Hwang AS, Kechter JA, Li X, Hughes A, Severson KJ, Boudreaux B, Bhullar P, Nassir S, Yousif M, Zhang N, Butterfield RJ, Nelson S, Xing X, Tsoi LC, Zunich S, Sekulic A, Pittelkow M, Gudjonsson JE, Mangold A. Topical Ruxolitinib in the Treatment of Necrobiosis Lipoidica: A Prospective, Open-Label Study. J Invest Dermatol 2024:S0022-202X(24)00159-3. [PMID: 38417541 DOI: 10.1016/j.jid.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 03/01/2024]
Abstract
Necrobiosis lipoidica (NL) is a rare granulomatous disease. There are few effective treatments for NL. We sought to investigate the efficacy and safety of the Jak1/2 inhibitor, ruxolitnib, in the treatment of NL and identify the biomarkers associated with the disease and treatment response. We conducted an open-label, phase 2 study of ruxolitinib in 12 patients with NL. We performed transcriptomic analysis of tissue samples before and after treatment. At week 12, the mean NL lesion score decreased by 58.2% (SD = 28.7%, P = .003). Transcriptomic analysis demonstrated enrichment of type I and type II IFN pathways in baseline disease. Weighted gene coexpression network analysis demonstrated post-treatment changes in IFN pathways with key hub genes IFNG and signal transducer and activator of transcription 1 gene STAT1. Limitations include small sample size and a study group limited to patients with <10% body surface area. In conclusion, ruxolitinib is an effective treatment for NL and targets the key pathogenic mediators of the disease.
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Affiliation(s)
- Angelina S Hwang
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Jacob A Kechter
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Xing Li
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Alysia Hughes
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Kevin J Severson
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Blake Boudreaux
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Puneet Bhullar
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Shams Nassir
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Miranda Yousif
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Nan Zhang
- Department of Quantitative Health Sciences, Mayo Clinic, Scottsdale, Arizona, USA
| | | | - Steven Nelson
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Samantha Zunich
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | | | - Mark Pittelkow
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA
| | | | - Aaron Mangold
- Department of Dermatology, Mayo Clinic, Scottsdale, Arizona, USA.
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15
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Dudakovic A, Limberg AK, Bothun CE, Dilger OB, Bayram B, Bettencourt JW, Salmons HI, Thaler R, Karczewski DC, Owen AR, Iyer VG, Payne AN, Carstens MF, van Wijnen AJ, Berry DJ, Sanchez-Sotelo J, Morrey ME, Abdel MP. AdipoRon reduces TGFβ1-mediated collagen deposition in vitro and alleviates knee stiffness in vivo. J Cell Physiol 2024; 239:e31168. [PMID: 38149794 PMCID: PMC10922972 DOI: 10.1002/jcp.31168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/10/2023] [Accepted: 11/28/2023] [Indexed: 12/28/2023]
Abstract
Arthrofibrosis, which causes joint motion restrictions, is a common complication following total knee arthroplasty (TKA). Key features associated with arthrofibrosis include myofibroblast activation, knee stiffness, and excessive scar tissue formation. We previously demonstrated that adiponectin levels are suppressed within the knee tissues of patients affected by arthrofibrosis and showed that AdipoRon, an adiponectin receptor agonist, exhibited anti-fibrotic properties in human mesenchymal stem cells. In this study, the therapeutic potential of AdipoRon was evaluated on TGFβ1-mediated myofibroblast differentiation of primary human knee fibroblasts and in a mouse model of knee stiffness. Picrosirius red staining revealed that AdipoRon reduced TGFβ1-induced collagen deposition in primary knee fibroblasts derived from patients undergoing primary TKA and revision TKA for arthrofibrosis. AdipoRon also reduced mRNA and protein levels of ACTA2, a key myofibroblast marker. RNA-seq analysis corroborated the anti-myofibrogenic effects of AdipoRon. In our knee stiffness mouse model, 6 weeks of knee immobilization, to induce a knee contracture, in conjunction with daily vehicle (DMSO) or AdipoRon (1, 5, and 25 mg/kg) via intraperitoneal injections were well tolerated based on animal behavior and weight measurements. Biomechanical testing demonstrated that passive extension angles (PEAs) of experimental knees were similar between vehicle and AdipoRon treatment groups in mice evaluated immediately following immobilization. Interestingly, relative to vehicle-treated mice, 5 mg/kg AdipoRon therapy improved the PEA of the experimental knees in mice that underwent 4 weeks of knee remobilization following the immobilization and therapy. Together, these studies revealed that AdipoRon may be an effective therapeutic modality for arthrofibrosis.
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Affiliation(s)
- Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Afton K. Limberg
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Cole E. Bothun
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Oliver B. Dilger
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Banu Bayram
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | | | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Aaron R. Owen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Varun G. Iyer
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Ashley N. Payne
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Andre J. van Wijnen
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, VT, USA
| | - Daniel J. Berry
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Mark E. Morrey
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Matthew P. Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
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16
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Markham BN, Ramnarine C, Kim S, Grever WE, Soto-Beasley AI, Heckman M, Ren Y, Osborne AC, Bhagwate AV, Liu Y, Wang C, Kim J, Wszolek ZK, Ross OA, Springer W, Fiesel FC. miRNA family miR-29 inhibits PINK1-PRKN dependent mitophagy via ATG9A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576122. [PMID: 38293184 PMCID: PMC10827147 DOI: 10.1101/2024.01.17.576122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Loss-of-function mutations in the genes encoding PINK1 and PRKN result in early-onset Parkinson disease (EOPD). Together the encoded enzymes direct a neuroprotective pathway that ensures the elimination of damaged mitochondria via autophagy. We performed a genome-wide high content imaging miRNA screen for inhibitors of the PINK1-PRKN pathway and identified all three members of the miRNA family 29 (miR-29). Using RNAseq we identified target genes and found that siRNA against ATG9A phenocopied the effects of miR-29 and inhibited the initiation of PINK1-PRKN mitophagy. Furthermore, we discovered two rare, potentially deleterious, missense variants (p.R631W and p.S828L) in our EOPD cohort and tested them experimentally in cells. While expression of wild-type ATG9A was able to rescue the effects of miR-29a, the EOPD-associated variants behaved like loss-of-function mutations. Together, our study validates miR-29 and its target gene ATG9A as novel regulators of mitophagy initiation. It further serves as proof-of-concept of finding novel, potentially disease-causing EOPD-linked variants specifically in mitophagy regulating genes. The nomination of genetic variants and biological pathways is important for the stratification and treatment of patients that suffer from devastating diseases, such as EOPD.
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Affiliation(s)
- Briana N Markham
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Chloe Ramnarine
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Songeun Kim
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | | | - Michael Heckman
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Yingxue Ren
- Department of Quantitative Health Science, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Andrew C Osborne
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Aditya V Bhagwate
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuanhang Liu
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Chen Wang
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN 55905, USA
| | - Jungsu Kim
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224, USA
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17
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Agra Almeida Quadros AR, Li Z, Wang X, Ndayambaje IS, Aryal S, Ramesh N, Nolan M, Jayakumar R, Han Y, Stillman H, Aguilar C, Wheeler HJ, Connors T, Lopez-Erauskin J, Baughn MW, Melamed Z, Beccari MS, Olmedo Martínez L, Canori M, Lee CZ, Moran L, Draper I, Kopin AS, Oakley DH, Dickson DW, Cleveland DW, Hyman BT, Das S, Ertekin-Taner N, Lagier-Tourenne C. Cryptic splicing of stathmin-2 and UNC13A mRNAs is a pathological hallmark of TDP-43-associated Alzheimer's disease. Acta Neuropathol 2024; 147:9. [PMID: 38175301 PMCID: PMC10766724 DOI: 10.1007/s00401-023-02655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Nuclear clearance and cytoplasmic accumulations of the RNA-binding protein TDP-43 are pathological hallmarks in almost all patients with amyotrophic lateral sclerosis (ALS) and up to 50% of patients with frontotemporal dementia (FTD) and Alzheimer's disease. In Alzheimer's disease, TDP-43 pathology is predominantly observed in the limbic system and correlates with cognitive decline and reduced hippocampal volume. Disruption of nuclear TDP-43 function leads to abnormal RNA splicing and incorporation of erroneous cryptic exons in numerous transcripts including Stathmin-2 (STMN2, also known as SCG10) and UNC13A, recently reported in tissues from patients with ALS and FTD. Here, we identify both STMN2 and UNC13A cryptic exons in Alzheimer's disease patients, that correlate with TDP-43 pathology burden, but not with amyloid-β or tau deposits. We also demonstrate that processing of the STMN2 pre-mRNA is more sensitive to TDP-43 loss of function than UNC13A. In addition, full-length RNAs encoding STMN2 and UNC13A are suppressed in large RNA-seq datasets generated from Alzheimer's disease post-mortem brain tissue. Collectively, these results open exciting new avenues to use STMN2 and UNC13A as potential therapeutic targets in a broad range of neurodegenerative conditions with TDP-43 proteinopathy including Alzheimer's disease.
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Affiliation(s)
- Ana Rita Agra Almeida Quadros
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Zhaozhi Li
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - I Sandra Ndayambaje
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandeep Aryal
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Nandini Ramesh
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Matthew Nolan
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rojashree Jayakumar
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Han
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Stillman
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Corey Aguilar
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hayden J Wheeler
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theresa Connors
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jone Lopez-Erauskin
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Michael W Baughn
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ze'ev Melamed
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Laura Olmedo Martínez
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Canori
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Chao-Zong Lee
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Moran
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Derek H Oakley
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Bradley T Hyman
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA.
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18
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Swanson AA, Michal M, Xing D, Dashti NK, Židlík V, Cheek-Norgan EH, Keeney ME, Keeney GL, Sukov WR, Gupta S, Nucci MR, Schoolmeester JK. Malignant female genital tract smooth muscle tumors with adipocytic differentiation: A morphologic, immunohistochemical, MDM2 fluorescence in situ hybridization and molecular genetic study of 6 lipoleiomyosarcomas. Hum Pathol 2024; 143:24-32. [PMID: 38000678 DOI: 10.1016/j.humpath.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Leiomyosarcoma with adipocytic differentiation or lipoleiomyosarcoma is an uncommon sarcoma of the female genital tract with only a few individual reports in the literature. We therefore performed a morphologic, immunohistochemical, MDM2 gene amplification and RNA and DNA sequencing analysis of a series of gynecologic lipoleiomyosarcoma to better define the clinicopathologic spectrum. Six tumors from 6 patients were identified and classified as spindled lipoleiomyosarcoma (n = 2), mixed spindled and myxoid lipoleiomyosarcoma (n = 1), epithelioid lipoleiomyosarcoma with focal myxoid features (n = 1) and mixed spindled and epithelioid lipoleiomyosarcoma (n = 2). Patient age ranged from 41 to 64 years (mean: 49; median: 50). Primary location included uterine corpus (3), uterine corpus/cervix (2) and broad ligament (1). Tumor size ranged from 4.5 to 22 cm (mean: 11.2; median: 9.8). Four patients had metastasis at presentation or subsequently developed recurrent or distant disease. Patient status was known for 5: 2 dead of disease, 2 alive with disease and 1 alive without evidence of disease. Immunohistochemical expression of smooth muscle markers, ER, PR and WT-1 showed patterns similar to non-adipocytic gynecologic leiomyosarcomas. MDM2 amplification fluorescence in situ hybridization performed on 2 tumors was negative in 1 and equivocal in 1. Sequencing studies performed on 3 tumors found TP53 mutations in 3, with 1 tumor also having an ATRX alteration. No gene fusions were identified. Although lipoleiomyosarcomas have a diverse morphologic spectrum, our findings suggest the smooth muscle component shares morphologic and immunohistochemical features with female genital tract non-adipocytic leiomyosarcomas. Lipoleiomyosarcomas also have genetic alterations associated with non-adipocytic gynecologic leiomyosarcomas.
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Affiliation(s)
- Amy A Swanson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Michael Michal
- Department of Pathology, Charles University, Faculty of Medicine in Pilsen, Pilsen, Czech Republic; Bioptical Laboratory, Ltd., Pilsen, Czech Republic
| | - Deyin Xing
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Nooshin K Dashti
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Vladimir Židlík
- Department of Pathology, University of Ostrava, Faculty of Medicine, Ostrava, Czech Republic
| | - E Heidi Cheek-Norgan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew E Keeney
- Department of Pathology, Northwestern Medicine Central DuPage Hospital, Winfield, Il, USA
| | - Gary L Keeney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Marisa R Nucci
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Boston, MA, USA
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19
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Miley DR, Andrews-Pfannkoch CM, Pulido JS, Erickson SA, Vile RG, Fautsch MP, Marmorstein AD, Dalvin LA. Direct early growth response-1 knockdown decreases melanoma viability independent of mitogen-activated extracellular signal-related kinase inhibition. Melanoma Res 2023; 33:482-491. [PMID: 37650708 PMCID: PMC10615778 DOI: 10.1097/cmr.0000000000000921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
To investigate downstream molecular changes caused by mitogen-activated protein kinase (MEK) inhibitor treatment and further explore the impact of direct knockdown of early growth response-1 ( EGR1 ) in melanoma cell culture. RNA-sequencing (RNA-Seq) was performed to determine gene expression changes with MEK inhibitor treatment. Treatment with MEK inhibitor (trametinib) was then assessed in two cutaneous (MEL888, MEL624) and one conjunctival (YUARGE 13-3064) melanoma cell line. Direct knockdown of EGR1 was accomplished using lentiviral vectors containing shRNA. Cell viability was measured using PrestoBlueHS Cell Viability Reagent. Total RNA and protein were assessed by qPCR and SimpleWestern. RNA-Seq demonstrated a profound reduction in EGR1 with MEK inhibitor treatment, prompting further study of melanoma cell lines. Following trametinib treatment of melanoma cells, viability was reduced in both cutaneous (MEL888 26%, P < 0.01; MEL624 27%, P < 0.001) and conjunctival (YUARGE 13-3064 33%, P < 0.01) melanoma compared with DMSO control, with confirmed EGR1 knockdown to 0.04-, 0.01-, and 0.16-fold DMSO-treated levels (all P < 0.05) in MEL888, MEL624, and YUARGE 13-3064, respectively. Targeted EGR1 knockdown using shRNA reduced viability in both cutaneous (MEL624 78%, P = 0.05) and conjunctival melanoma (YUARGE-13-3064 67%, P = 0.02). RNA-Sequencing in MEK inhibitor-treated cells identified EGR1 as a candidate effector molecule of interest. In a malignant melanoma cell population, MEK inhibition reduced viability in both cutaneous and conjunctival melanoma with a profound downstream reduction in EGR1 expression. Targeted knockdown of EGR1 reduced both cutaneous and conjunctival melanoma cell viability independent of MEK inhibition, suggesting a key role for EGR1 in melanoma pathobiology.
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Affiliation(s)
- David R Miley
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | | | - Jose S Pulido
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
- Wills Eye Hospital, Philadelphia, Pennsylvania
| | | | - Richard G Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Lauren A Dalvin
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
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20
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Sun Z, Braga-Neto MB, Xiong Y, Bhagwate AV, Gibbons HR, Sagstetter MR, Hamdan FH, Baheti S, Friton J, Nair A, Ye Z, Faubion WA. Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4+ Lymphocytes in Crohn's Disease. J Crohns Colitis 2023; 17:1847-1857. [PMID: 37280154 PMCID: PMC10673812 DOI: 10.1093/ecco-jcc/jjad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/14/2023] [Accepted: 06/06/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND The development of Crohn's disease [CD] involves immune cell signalling pathways regulated by epigenetic modifications. Aberrant DNA methylation has been identified in peripheral blood and bulk intestinal tissue from CD patients. However, the DNA methylome of disease-associated intestinal CD4+ lymphocytes has not been evaluated. MATERIALS AND METHODS Genome-wide DNA methylation sequencing was performed from terminal ileum CD4+ cells from 21 CD patients and 12 age- and sex-matched controls. Data were analysed for differentially methylated CpGs [DMCs] and methylated regions [DMRs]. Integration was performed with RNA-sequencing data to evaluate the functional impact of DNA methylation changes on gene expression. DMRs were overlapped with regions of differentially open chromatin [by ATAC-seq] and CCCTC-binding factor [CTCF] binding sites [by ChIP-seq] between peripherally derived Th17 and Treg cells. RESULTS CD4+ cells in CD patients had significantly increased DNA methylation compared to those from the controls. A total of 119 051 DMCs and 8113 DMRs were detected. While hypermethylated genes were mostly related to cell metabolism and homeostasis, hypomethylated genes were significantly enriched within the Th17 signalling pathway. The differentially enriched ATAC regions in Th17 cells [compared to Tregs] were hypomethylated in CD patients, suggesting heightened Th17 activity. There was significant overlap between hypomethylated DNA regions and CTCF-associated binding sites. CONCLUSIONS The methylome of CD patients shows an overall dominant hypermethylation yet hypomethylation is more concentrated in proinflammatory pathways, including Th17 differentiation. Hypomethylation of Th17-related genes associated with areas of open chromatin and CTCF binding sites constitutes a hallmark of CD-associated intestinal CD4+ cells.
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Affiliation(s)
- Zhifu Sun
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Manuel B Braga-Neto
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuning Xiong
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Adytia V Bhagwate
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Saurabh Baheti
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jessica Friton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Asha Nair
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenqing Ye
- Greehey Children’s Cancer Research Institute, UT Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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21
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Atasoy-Zeybek A, Hawse GP, Nagelli CV, Lopez De Padilla C, Abdel MP, Evans CH. Transcriptomic changes during the replicative senescence of human articular chondrocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.565835. [PMID: 37986862 PMCID: PMC10659330 DOI: 10.1101/2023.11.07.565835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Osteoarthritis (OA) is a degenerative joint disease and a leading cause of disability worldwide. Aging is a major risk factor for OA, but the specific mechanisms underlying this connection remain unclear. Although chondrocytes rarely divide in adult articular cartilage, they undergo replicative senescence in vitro which provides an opportunity to study changes related to aging under controlled laboratory conditions. In this pilot study, we performed bulk RNA sequencing on early- and late-passage human articular chondrocytes to identify transcriptomic changes associated with cellular aging. Chondrocytes were isolated from the articular cartilage of three donors, two with OA (age 70-80 years) and one with healthy cartilage (age 26 years). Chondrocytes were serially passaged until replicative senescence and RNA extracted from early- and late-passage cells. Principal component analysis of all genes showed clear separation between early- and late-passage chondrocytes, indicating substantial age-related differences in gene expression. Differentially expressed genes (DEGs) analysis confirmed distinct transcriptomic profiles between early- and late-passage chondrocytes. Hierarchical clustering revealed contrasting expression patterns between the two isolates from osteoarthritic samples and the healthy sample. Focused analysis of DEGs on transcripts associated with turnover of the extra-cellular matrix and the senescence-associated secretory phenotype (SASP) showed consistent downregulation of Col2A1 and ACAN, and upregulation of MMP19, ADAMTS4, and ADAMTS8 in late passage chondrocytes across all samples. SASP components including IL-1α, IL-1β, IL-6, IL-7, p16INK4A (CDKN2A) and CCL2 demonstrated significant upregulation in late passage chondrocytes originally isolated from OA samples. Pathway analysis between sexes with OA revealed shared pathways such as extracellular matrix (ECM) organization, collagen formation, skeletal and muscle development, and nervous system development. Sex-specific differences were observed, with males showing distinctions in ECM organization, regulation of the cell cycle process as well as neuron differentiation. In contrast, females exhibited unique variations in the regulation of the cell cycle process, DNA metabolic process, and the PID-PLK1 pathway.
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Affiliation(s)
- Aysegul Atasoy-Zeybek
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Gresin P. Hawse
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Christopher V. Nagelli
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Consuelo Lopez De Padilla
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Matthew P. Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Christopher H. Evans
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
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22
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Pataky MW, Dasari S, Michie KL, Sevits KJ, Kumar AA, Klaus KA, Heppelmann CJ, Robinson MM, Carter RE, Lanza IR, Nair KS. Impact of biological sex and sex hormones on molecular signatures of skeletal muscle at rest and in response to distinct exercise training modes. Cell Metab 2023; 35:1996-2010.e6. [PMID: 37939659 PMCID: PMC10659143 DOI: 10.1016/j.cmet.2023.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 05/09/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Substantial divergence in cardio-metabolic risk, muscle size, and performance exists between men and women. Considering the pivotal role of skeletal muscle in human physiology, we investigated and found, based on RNA sequencing (RNA-seq), that differences in the muscle transcriptome between men and women are largely related to testosterone and estradiol and much less related to genes located on the Y chromosome. We demonstrate inherent unique, sex-dependent differences in muscle transcriptional responses to aerobic, resistance, and combined exercise training in young and older cohorts. The hormonal changes with age likely explain age-related differential expression of transcripts. Furthermore, in primary human myotubes we demonstrate the profound but distinct effects of testosterone and estradiol on amino acid incorporation to multiple individual proteins with specific functions. These results clearly highlight the potential of designing exercise programs tailored specifically to men and women and have implications for people who change gender by altering their hormone profile.
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Affiliation(s)
- Mark W Pataky
- Division of Endocrinology and Metabolism, Mayo Clinic, Rochester, MN, USA
| | - Surendra Dasari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Kelly L Michie
- Division of Endocrinology and Metabolism, Mayo Clinic, Rochester, MN, USA
| | - Kyle J Sevits
- Division of Endocrinology and Metabolism, Mayo Clinic, Rochester, MN, USA
| | - A Aneesh Kumar
- Division of Endocrinology and Metabolism, Mayo Clinic, Rochester, MN, USA
| | - Katherine A Klaus
- Division of Endocrinology and Metabolism, Mayo Clinic, Rochester, MN, USA
| | | | - Matthew M Robinson
- School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Rickey E Carter
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Ian R Lanza
- Division of Endocrinology and Metabolism, Mayo Clinic, Rochester, MN, USA
| | - K Sreekumaran Nair
- Division of Endocrinology and Metabolism, Mayo Clinic, Rochester, MN, USA.
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23
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Min Y, Wang X, İş Ö, Patel TA, Gao J, Reddy JS, Quicksall ZS, Nguyen T, Lin S, Tutor-New FQ, Chalk JL, Mitchell AO, Crook JE, Nelson PT, Van Eldik LJ, Golde TE, Carrasquillo MM, Dickson DW, Zhang K, Allen M, Ertekin-Taner N. Cross species systems biology discovers glial DDR2, STOM, and KANK2 as therapeutic targets in progressive supranuclear palsy. Nat Commun 2023; 14:6801. [PMID: 37919278 PMCID: PMC10622416 DOI: 10.1038/s41467-023-42626-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Progressive supranuclear palsy (PSP) is a neurodegenerative parkinsonian disorder characterized by cell-type-specific tau lesions in neurons and glia. Prior work uncovered transcriptome changes in human PSP brains, although their cell-specificity is unknown. Further, systematic data integration and experimental validation platforms to prioritize brain transcriptional perturbations as therapeutic targets in PSP are currently lacking. In this study, we combine bulk tissue (n = 408) and single nucleus RNAseq (n = 34) data from PSP and control brains with transcriptome data from a mouse tauopathy and experimental validations in Drosophila tau models for systematic discovery of high-confidence expression changes in PSP with therapeutic potential. We discover, replicate, and annotate thousands of differentially expressed genes in PSP, many of which reside in glia-enriched co-expression modules and cells. We prioritize DDR2, STOM, and KANK2 as promising therapeutic targets in PSP with striking cross-species validations. We share our findings and data via our interactive application tool PSP RNAseq Atlas ( https://rtools.mayo.edu/PSP_RNAseq_Atlas/ ). Our findings reveal robust glial transcriptome changes in PSP, provide a cross-species systems biology approach, and a tool for therapeutic target discoveries in PSP with potential application in other neurodegenerative diseases.
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Affiliation(s)
- Yuhao Min
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Özkan İş
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Tulsi A Patel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Junli Gao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Joseph S Reddy
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Zachary S Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Shu Lin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Jessica L Chalk
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Julia E Crook
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - Linda J Van Eldik
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Todd E Golde
- Department of Pharmacology and Chemical Biology, Department of Neurology, Emory Center for Neurodegenerative Disease, Emory University, Atlanta, GA, USA
| | | | | | - Ke Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
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24
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Grams KJ, Neumueller SE, Mouradian GC, Burgraff NJ, Hodges MR, Pan L, Forster HV. Mild and moderate chronic hypercapnia elicit distinct transcriptomic responses of immune function in cardiorespiratory nuclei. Physiol Genomics 2023; 55:487-503. [PMID: 37602394 DOI: 10.1152/physiolgenomics.00038.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023] Open
Abstract
Chronic hypercapnia (CH) is a hallmark of respiratory-related diseases, and the level of hypercapnia can acutely or progressively become more severe. Previously, we have shown time-dependent adaptations in steady-state physiology during mild (arterial Pco2 ∼55 mmHg) and moderate (∼60 mmHg) CH in adult goats, including transient (mild CH) or sustained (moderate CH) suppression of acute chemosensitivity suggesting limitations in adaptive respiratory control mechanisms as the level of CH increases. Changes in specific markers of glutamate receptor plasticity, interleukin-1ß, and serotonergic modulation within key nodes of cardiorespiratory control do not fully account for the physiological adaptations to CH. Here, we used an unbiased approach (bulk tissue RNA sequencing) to test the hypothesis that mild or moderate CH elicits distinct gene expression profiles in important brain stem regions of cardiorespiratory control, which may explain the contrasting responses to CH. Gene expression profiles from the brain regions validated the accuracy of tissue biopsy methodology. Differential gene expression analyses revealed greater effects of CH on brain stem sites compared with the medial prefrontal cortex. Mild CH elicited an upregulation of predominantly immune-related genes and predicted activation of immune-related pathways and functions. In contrast, moderate CH broadly led to downregulation of genes and predicted inactivation of cellular pathways related to the immune response and vascular function. These data suggest that mild CH leads to a steady-state activation of neuroinflammatory pathways within the brain stem, whereas moderate CH drives the opposite response. Transcriptional shifts in immune-related functions may underlie the cardiorespiratory network's capability to respond to acute, more severe hypercapnia when in a state of progressively increased CH.NEW & NOTEWORTHY Mild chronic hypercapnia (CH) broadly upregulated immune-related genes and a predicted activation of biological pathways related to immune cell activity and the overall immune response. In contrast, moderate CH primarily downregulated genes related to major histocompatibility complex signaling and vasculature function that led to a predicted inactivation of pathways involving the immune response and vascular endothelial function. The severity-dependent effect on immune responses suggests that neuroinflammation has an important role in CH and may be important in the maintenance of proper ventilatory responses to acute and chronic hypercapnia.
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Affiliation(s)
- Kirstyn J Grams
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Suzanne E Neumueller
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Gary C Mouradian
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Nicholas J Burgraff
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
| | - Matthew R Hodges
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Lawrence Pan
- Department of Physical Therapy, Marquette University, Milwaukee, Wisconsin, United States
| | - Hubert V Forster
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Zablocki Veterans Affairs Medical Center, Milwaukee, Wisconsin, United States
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25
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Jachim SK, Zhong J, Ordog T, Lee JH, Bhagwate AV, Nagaraj NK, Westendorf JJ, Passos JF, Matveyenko AV, LeBrasseur NK. BMAL1 modulates senescence programming via AP-1. Aging (Albany NY) 2023; 15:9984-10009. [PMID: 37819791 PMCID: PMC10599731 DOI: 10.18632/aging.205112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Cellular senescence and circadian dysregulation are biological hallmarks of aging. Whether they are coordinately regulated has not been thoroughly studied. We hypothesize that BMAL1, a pioneer transcription factor and master regulator of the molecular circadian clock, plays a role in the senescence program. Here, we demonstrate BMAL1 is significantly upregulated in senescent cells and has altered rhythmicity compared to non-senescent cells. Through BMAL1-ChIP-seq, we show that BMAL1 is uniquely localized to genomic motifs associated with AP-1 in senescent cells. Integration of BMAL1-ChIP-seq data with RNA-seq data revealed that BMAL1 presence at AP-1 motifs is associated with active transcription. Finally, we showed that BMAL1 contributes to AP-1 transcriptional control of key features of the senescence program, including altered regulation of cell survival pathways, and confers resistance to drug-induced apoptosis. Overall, these results highlight a previously unappreciated role of the core circadian clock component BMAL1 on the molecular phenotype of senescent cells.
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Affiliation(s)
- Sarah K. Jachim
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Zhong
- Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
- Center for Cell Signaling in Gastroenterology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Center for Cell Signaling in Gastroenterology, Mayo Clinic, Rochester, MN 55905, USA
| | - Aditya V. Bhagwate
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - João F. Passos
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Aleksey V. Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
- Department of Medicine, Division of Endocrinology, Metabolism, Diabetes, and Nutrition, Mayo Clinic, Rochester, MN 55905, USA
| | - Nathan K. LeBrasseur
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN 55905, USA
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26
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Grande J, Jones TL, Sun Z, Chanana P, Jaiswal I, Leontovich A, Carapanceanu N, Carapanceanu V, Saadalla A, Osman A, Famuyide AO, Daftary GS, Khan Z, Khazaie K. Host immunity and KLF 11 deficiency together promote fibrosis in a mouse model of endometriosis. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166784. [PMID: 37321514 DOI: 10.1016/j.bbadis.2023.166784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Endometriosis is a debilitating disease typically characterized by prolific fibrotic scarring. Earlier we reported downregulation of two transcription factors belonging TGF-βR signaling pathway Sp/Krüppel-like factor 11 (KLF11) and 10 (KLF10) in human endometriosis lesions. Here we investigated the role of these nuclear factors and immunity in the scaring fibrosis associated with endometriosis. METHODS We used a well characterized experimental mouse model of endometriosis. WT, KLF10 or KLF11 deficient mice were compared. The lesions were evaluated histologically, fibrosis was quantified with Masons' Trichome staining, immune-infiltrates were quantified by immunohistochemistry, peritoneal adhesions were score, gene expression was evaluated by bulk RNA sequencing. RESULTS Intense fibrotic reactions and large changes in gene expression were detected in KLF11 deficient implants associated with squamous metaplasia of the ectopic endometrium, as compared to KLF10 deficient or WT implants. Fibrosis was mitigated with pharmacologic agents that blocked histone acetylation or TGF-βR signaling or with genetic deficiency for SMAD3. The lesions were richly infiltrated with T-cells, regulatory T-cells, and innate immune cells. Fibrosis was exacerbated when implants expressed ectopic genes implicating autoimmunity as a major factor contributing to the scaring fibrosis. CONCLUSIONS Our findings identify KLF11 and TGF-βR signaling as cell intrinsic mechanisms and autoimmune responses as cell extrinsic mechanisms of scaring fibrosis in ectopic endometrium lesions. GENERAL SIGNIFICANCE Immunological factors associated with inflammation and tissue repair drive scaring fibrosis in experimental endometriosis, providing the rationale for immune therapy of endometriosis.
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Affiliation(s)
- Joseph Grande
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States of America
| | - Tiffanny L Jones
- Department of Obstetrics and Gynecology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States of America
| | - Zhifu Sun
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States of America
| | - Pritha Chanana
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States of America
| | - Indu Jaiswal
- Department of Immunology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States of America
| | - Alexey Leontovich
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States of America
| | - Nicoletta Carapanceanu
- Department of Immunology, Mayo Clinic, CRB, 2-221, 13400 E. Shea Blvd., Scottsdale, AZ 85259, United States of America
| | - Valentin Carapanceanu
- Department of Immunology, Mayo Clinic, CRB, 2-221, 13400 E. Shea Blvd., Scottsdale, AZ 85259, United States of America
| | - Abdulrahman Saadalla
- Department of Immunology, Mayo Clinic, CRB, 2-221, 13400 E. Shea Blvd., Scottsdale, AZ 85259, United States of America
| | - Abu Osman
- Department of Immunology, Mayo Clinic, CRB, 2-221, 13400 E. Shea Blvd., Scottsdale, AZ 85259, United States of America
| | - Abimbola O Famuyide
- Department of Obstetrics and Gynecology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States of America
| | - Gaurang S Daftary
- Department of Obstetrics and Gynecology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States of America.
| | - Zaraq Khan
- Department of Obstetrics and Gynecology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States of America.
| | - Khashayarsha Khazaie
- Department of Immunology, Mayo Clinic, CRB, 2-221, 13400 E. Shea Blvd., Scottsdale, AZ 85259, United States of America.
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27
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Brar T, McCabe C, Miglani A, Marino M, Lal D. Tissue Eosinophilia is Superior to an Analysis by Polyp Status for the Chronic Rhinosinusitis Transcriptome: An RNA Study. Laryngoscope 2023; 133:2480-2489. [PMID: 36594502 DOI: 10.1002/lary.30544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/29/2022] [Accepted: 12/11/2022] [Indexed: 01/04/2023]
Abstract
OBJECTIVE RNA sequencing (transcriptomics) is used to study biological pathways. However, the yield of data depends on comparing well-characterized cohorts. We compared tissue eosinophilia versus nasal polyp (NP) status as the metric to characterize transcriptomic mechanisms at play in eosinophilic and non-eosinophilic chronic rhinosinusitis (CRS) versus controls. METHODS RNA sequencing was conducted on sinonasal tissue samples of CRS and controls. Analyses were conducted based on polyp status [with nasal polyps (CRSwNP) and without nasal polyps (CRSsNP)] as well as tissue eosinophil levels per high power field (eos/hpf)[non-eosinophilic (<10 eos/hpf, neCRS) or eosinophilic (≥10 eos/hpf, eCRS)]. The yield of differentially expressed genes (DEGs) and biological pathways through Ingenuity Pathway Analysis (IPA) were compared. RESULTS CRS tissue differed from controls by 736 statistically significant DEGs. Both NP status and tissue eosinophilia were effective in differentiating CRS from controls and into two distinct subgroups. Statistically significant DEGs identified when comparing CRS by NP status were 60, whereas 110 DEGs were identified using eosinophil cutoff ≥10 and <10 eos/hpf. Additionally, heatmaps showed greater homogeneity within each CRS subgroup when analyzed by tissue eosinophilia versus NP status. On IPA, the IL-17 signaling pathway was significantly different only by tissue eosinophilia status, not NP status, being higher in CRS <10 eos/hpf. CONCLUSION Tissue eosinophilia is superior to an analysis by NP status for the study of CRS transcriptome by RNA sequencing in identifying DEGs. Classification of CRS samples by eosinophil counts agnostic of NP status may offer advantageous insights into CRS pathogenetic mechanisms. LEVEL OF EVIDENCE 3 Laryngoscope, 133:2480-2489, 2023.
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Affiliation(s)
- Tripti Brar
- Division of Rhinology, Department of Otolaryngology, Mayo Clinic in Arizona, Phoenix, Arizona, USA
| | - Chantal McCabe
- Department of Quantitative Health Sciences, Mayo Clinic, Phoenix, Arizona, USA
| | - Amar Miglani
- Division of Rhinology, Department of Otolaryngology, Mayo Clinic in Arizona, Phoenix, Arizona, USA
| | - Michael Marino
- Division of Rhinology, Department of Otolaryngology, Mayo Clinic in Arizona, Phoenix, Arizona, USA
| | - Devyani Lal
- Division of Rhinology, Department of Otolaryngology, Mayo Clinic in Arizona, Phoenix, Arizona, USA
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28
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Gross JM, Perret R, Coindre JM, Le Loarer F, Michal M, Michal M, Miettinen M, McCabe CE, Nair AA, Swanson AA, Thangaiah JJ, Torres-Mora J, Bonadio A, Voltaggio L, Epstein JI, Gupta S, Folpe AL, Schoolmeester JK. Lipoblastoma-Like Tumor and Fibrosarcoma-Like Lipomatous Neoplasm Represent the Same Entity: A Clinicopathologic and Molecular Genetic Study of 23 Cases Occurring in Both Men and Women at Diverse Locations. Mod Pathol 2023; 36:100246. [PMID: 37307874 PMCID: PMC10530403 DOI: 10.1016/j.modpat.2023.100246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023]
Abstract
Lipoblastoma-like tumor (LLT) is a benign soft tissue tumor demonstrating mixed morphologic features of lipoblastoma, myxoid liposarcoma, and spindle cell lipoma but lacking genetic alterations associated with those tumors. LLT was originally thought to be specific to the vulva but has since been reported in the paratesticular region. The morphologic features of LLT overlap with those of "fibrosarcoma-like lipomatous neoplasm" (FLLN), a rare, indolent adipocytic neoplasm considered by some to form part of the spectrum of atypical spindle cell and pleomorphic lipomatous tumor. We compared the morphologic, immunohistochemical, and genetic features of 23 tumors previously classified as LLT (n = 17) and FLLN (n = 6). The 23 tumors occurred in 13 women and 10 men (mean age, 42 years; range, 17 to 80 years). Eighteen (78%) cases arose in the inguinogenital region, whereas 5 tumors (22%) involved noninguinogenital soft tissue, including the flank (n = 1), shoulder (n = 1), foot (n = 1), forearm (n = 1), and chest wall (n = 1). Microscopically, the tumors were lobulated and septated, with variably collagenized fibromyxoid stroma, prominent thin-walled vessels, scattered univacuolated or bivacuolated lipoblasts, and a minor component of mature adipose tissue. Using immunohistochemistry, 5 tumors (42%) showed complete RB1 loss, with partial loss in 7 cases (58%). RNA sequencing, chromosomal microarray, and DNA next-generation sequencing study results were negative for significant alterations. There were no clinical, morphologic, immunohistochemical, or molecular genetic differences between cases previously classified as LLT or FLLN. Clinical follow-up (11 patients [48%]; range, 2-276 months; mean, 48.2 months) showed all patients were alive without disease, and only one patient had experienced a single local recurrence. We conclude that LLT and FLLN represent the same entity, for which "LLT" seems most appropriate. LLT may occur in either sex and any superficial soft tissue location. Careful morphologic study and appropriate ancillary testing should allow for the distinction of LLT from its potential mimics.
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Affiliation(s)
- John M Gross
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Raul Perret
- Department of Biopathology, Institut Bergonié, Comprehensive Cancer Center, Bordeaux, France; Bordeaux Institute of Oncology, Université de Bordeaux, Institut Bergonié, Bordeaux, France
| | - Jean Michel Coindre
- Department of Biopathology, Institut Bergonié, Comprehensive Cancer Center, Bordeaux, France; Bordeaux Institute of Oncology, Université de Bordeaux, Institut Bergonié, Bordeaux, France; University of Bordeaux, Talence, France
| | - Francois Le Loarer
- Department of Biopathology, Institut Bergonié, Comprehensive Cancer Center, Bordeaux, France; Bordeaux Institute of Oncology, Université de Bordeaux, Institut Bergonié, Bordeaux, France; University of Bordeaux, Talence, France
| | - Michael Michal
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Michal Michal
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Chantal E McCabe
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, Minnesota
| | - Asha A Nair
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, Minnesota
| | - Amy A Swanson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Judith J Thangaiah
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jorge Torres-Mora
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Angelo Bonadio
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Lysandra Voltaggio
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jonathan I Epstein
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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29
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Belliveau J, Papoutsakis ET. The microRNomes of Chinese hamster ovary (CHO) cells and their extracellular vesicles, and how they respond to osmotic and ammonia stress. Biotechnol Bioeng 2023; 120:2700-2716. [PMID: 36788116 DOI: 10.1002/bit.28356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/23/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
A new area of focus in Chinese hamster ovary (CHO) biotechnology is the role of small (exosomes) and large (microvesicles or microparticles) extracellular vesicles (EVs). CHO cells in culture exchange large quantities of proteins and RNA through these EVs, yet the content and role of these EVs remain elusive. MicroRNAs (miRs or miRNA) are central to adaptive responses to stress and more broadly to changes in culture conditions. Given that EVs are highly enriched in miRs, and that EVs release large quantities of miRs both in vivo and in vitro, EVs and their miR content likely play an important role in adaptive responses. Here we report the miRNA landscape of CHO cells and their EVs under normal culture conditions and under ammonia and osmotic stress. We show that both cells and EVs are highly enriched in five miRs (among over 600 miRs) that make up about half of their total miR content, and that these highly enriched miRs differ significantly between normal and stress culture conditions. Notable is the high enrichment in miR-92a and miR-23a under normal culture conditions, in contrast to the high enrichment in let-7 family miRs (let-7c, let-7b, and let-7a) under both stress conditions. The latter suggests a preserved stress-responsive function of the let-7 miR family, one of the most highly preserved miR families across species, where among other functions, let-7 miRs regulate core oncogenes, which, depending on the biological context, may tip the balance between cell cycle arrest and apoptosis. While the expected-based on their profound enrichment-important role of these highly enriched miRs remains to be dissected, our data and analysis constitute an important resource for exploring the role of miRs in cell adaptation as well as for synthetic applications.
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Affiliation(s)
- Jessica Belliveau
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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Kosari F, Sosa C, Kilic I, Acosta AM, Raghunathan A, Herrera Hernandez L, Sharma V, Cheville JC, Gupta S. Comparative gene expression profiling reveals differential expression of GATA3 and Wnt signaling in juxtaglomerular cell tumors compared to renal glomus tumors. Hum Pathol 2023; 139:138-140. [PMID: 37478920 DOI: 10.1016/j.humpath.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Affiliation(s)
- Farhad Kosari
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Carlos Sosa
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Irem Kilic
- Department of Pathology, Indiana University, Indianapolis, IN, 46202, USA
| | - Andres M Acosta
- Department of Pathology, Indiana University, Indianapolis, IN, 46202, USA
| | - Aditya Raghunathan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Vidit Sharma
- Department of Urology, Mayo Clinic, Rochester, MN, 55905, USA
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
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Chatzopoulos K, Davila JI, Fadra N, Jackson RA, Minn KT, Sotiriou S, Oliveira AM, Erickson LA, Halling KC, Rumilla KM, Rivera M. Transcriptomic and immunophenotypic characterization of two cases of adamantinoma-like Ewing sarcoma of the thyroid gland. Histopathology 2023; 83:426-434. [PMID: 37195579 DOI: 10.1111/his.14961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/22/2023] [Accepted: 05/08/2023] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Adamantinoma-like Ewing sarcoma (ALES) is a rare aggressive malignancy occasionally diagnosed in the thyroid gland. ALES shows basaloid cytomorphology, expresses keratins, p63, p40, frequently CD99, and harbours the t(11;22) EWSR1::FLI1 translocation. There is debate on whether ALES resembles more sarcoma or carcinoma. METHODS We performed RNA sequencing from two ALES cases and compared findings with skeletal Ewing's sarcomas and nonneoplastic thyroid tissue. ALES was investigated by in situ hybridization (ISH) for high-risk human papillomavirus (HPV) DNA and immunohistochemistry for the following antigens: keratin 7, keratin 20, keratin 5, keratins (AE1/AE3 and CAM5.2), CD45, CD20, CD5, CD99, chromogranin, synaptophysin, calcitonin, thyroglobulin, PAX8, TTF1, S100, p40, p63, p16, NUT, desmin, ER, FLI1, INI1, and myogenin. RESULTS An uncommon EWSR1::FLI transcript with retained EWSR1 exon 8 was detected in both ALES cases. Regulators of EWSR1::FLI1 splicing (HNRNPH1, SUPT6H, SF3B1) necessary for production of a functional fusion oncoprotein, as well as 53 genes (including TNNT1, NKX2.2) activated downstream to the EWSR1::FLI1 cascade, were overexpressed. Eighty-six genes were uniquely overexpressed in ALES, most of which were related to squamous differentiation. Immunohistochemically, ALES strongly expressed keratins 5, AE1/AE3 and CAM5.2, p63, p40, p16, and focally CD99. INI1 was retained. The remaining immunostains and HPV DNA ISH were negative. CONCLUSION Comparative transcriptomic profiling reveals overlapping features of ALES with skeletal Ewing's sarcoma and an epithelial carcinoma, as evidenced by immunohistochemical expression of keratin 5, p63, p40, CD99, the transcriptome profile, and detection of EWSR1::FLI1 fusion transcript by RNA sequencing.
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Affiliation(s)
- Kyriakos Chatzopoulos
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Department of General and Anatomic Pathology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Jaime I Davila
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Numrah Fadra
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rory A Jackson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- NeoGenomics Laboratories, Aliso Viejo, CA, USA
| | - Kay T Minn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sotiris Sotiriou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Department of General and Anatomic Pathology, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andre M Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Lori A Erickson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kandelaria M Rumilla
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Michael Rivera
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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Kazeminia S, Zhu XY, Tang H, Jordan KL, Saadiq IM, Herrmann SM, Chade AR, Irazabal MV, Lerman LO, Eirin A. Renal ischemia alters the transcriptomic and epigenetic profile of inflammatory genes in swine scattered tubular-like cells. Clin Sci (Lond) 2023; 137:1265-1283. [PMID: 37606084 PMCID: PMC10644845 DOI: 10.1042/cs20230555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/31/2023] [Accepted: 08/11/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Scattered tubular-like cells (STCs) are differentiated renal tubular cells that during recovery from ischemic injury dedifferentiate to repair other injured renal cells. Renal artery stenosis (RAS), often associated with chronic inflammatory injury, compromises the integrity and function of STCs, but the underlying mechanisms remain unknown. We hypothesized that RAS alters the transcriptomic and epigenetic profile of inflammatory genes in swine STCs. METHODS STCs were harvested from pig kidneys after 10 weeks of RAS or sham (n=6 each). STC mRNA profiles of inflammatory genes were analyzed using high-throughput mRNA-sequencing (seq) and their DNA methylation (5mC) and hydroxymethylation (5hmC) profiles by DNA immunoprecipitation and next-generation sequencing (MeDIP-seq) (n=3 each), followed by an integrated (mRNA-seq/MeDIP-seq) analysis. STC protein expression of candidate differentially expressed (DE) genes and common proinflammatory proteins were subsequently assessed in vitro before and after epigenetic (Bobcat339) modulation. RESULTS mRNA-seq identified 57 inflammatory genes up-regulated in RAS-STCs versus Normal-STCs (>1.4 or <0.7-fold, P<0.05), of which 14% exhibited lower 5mC and 5% higher 5hmC levels in RAS-STCs versus Normal-STCs, respectively. Inflammatory gene and protein expression was higher in RAS-STCs compared with Normal-STCs but normalized after epigenetic modulation. CONCLUSIONS These observations highlight a novel modulatory mechanism of this renal endogenous repair system and support development of epigenetic or anti-inflammatory therapies to preserve the reparative capacity of STCs in individuals with RAS.
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Affiliation(s)
- Sara Kazeminia
- Department of Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Xiang-Yang Zhu
- Department of Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Hui Tang
- Department of Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Kyra L. Jordan
- Department of Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Ishran M. Saadiq
- Department of Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Sandra M. Herrmann
- Department of Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Alejandro R. Chade
- Department of Medical Pharmacology and Physiology and Department of Medicine, University of Missouri-Columbia
| | - Maria V. Irazabal
- Department of Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Lilach O. Lerman
- Department of Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, United States
| | - Alfonso Eirin
- Department of Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, United States
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Norton ES, Whaley LA, Jones VK, Brooks MM, Russo MN, Morderer D, Jessen E, Schiapparelli P, Ramos-Fresnedo A, Zarco N, Carrano A, Rossoll W, Asmann YW, Lam TT, Chaichana KL, Anastasiadis PZ, Quiñones-Hinojosa A, Guerrero-Cázares H. Cell-specific crosstalk proteomics reveals cathepsin B signaling as a driver of glioblastoma malignancy near the subventricular zone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553966. [PMID: 37662251 PMCID: PMC10473635 DOI: 10.1101/2023.08.19.553966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Glioblastoma (GBM) is the most prevalent and aggressive malignant primary brain tumor. GBM proximal to the lateral ventricles (LVs) is more aggressive, potentially due to subventricular zone (SVZ) contact. Despite this, crosstalk between GBM and neural stem/progenitor cells (NSC/NPCs) is not well understood. Using cell-specific proteomics, we show that LV-proximal GBM prevents neuronal maturation of NSCs through induction of senescence. Additionally, GBM brain tumor initiating cells (BTICs) increase expression of CTSB upon interaction with NPCs. Lentiviral knockdown and recombinant protein experiments reveal both cell-intrinsic and soluble CTSB promote malignancy-associated phenotypes in BTICs. Soluble CTSB stalls neuronal maturation in NPCs while promoting senescence, providing a link between LV-tumor proximity and neurogenesis disruption. Finally, we show LV-proximal CTSB upregulation in patients, showing the relevance of this crosstalk in human GBM biology. These results demonstrate the value of proteomic analysis in tumor microenvironment research and provide direction for new therapeutic strategies in GBM. Highlights Periventricular GBM is more malignant and disrupts neurogenesis in a rodent model.Cell-specific proteomics elucidates tumor-promoting crosstalk between GBM and NPCs.NPCs induce upregulated CTSB expression in GBM, promoting tumor progression.GBM stalls neurogenesis and promotes NPC senescence via CTSB.
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Quach HQ, Goergen KM, Grill DE, Haralambieva IH, Ovsyannikova IG, Poland GA, Kennedy RB. Virus-specific and shared gene expression signatures in immune cells after vaccination in response to influenza and vaccinia stimulation. Front Immunol 2023; 14:1168784. [PMID: 37600811 PMCID: PMC10436507 DOI: 10.3389/fimmu.2023.1168784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Background In the vaccine era, individuals receive multiple vaccines in their lifetime. Host gene expression in response to antigenic stimulation is usually virus-specific; however, identifying shared pathways of host response across a wide spectrum of vaccine pathogens can shed light on the molecular mechanisms/components which can be targeted for the development of broad/universal therapeutics and vaccines. Method We isolated PBMCs, monocytes, B cells, and CD8+ T cells from the peripheral blood of healthy donors, who received both seasonal influenza vaccine (within <1 year) and smallpox vaccine (within 1 - 4 years). Each of the purified cell populations was stimulated with either influenza virus or vaccinia virus. Differentially expressed genes (DEGs) relative to unstimulated controls were identified for each in vitro viral infection, as well as for both viral infections (shared DEGs). Pathway enrichment analysis was performed to associate identified DEGs with KEGG/biological pathways. Results We identified 2,906, 3,888, 681, and 446 DEGs in PBMCs, monocytes, B cells, and CD8+ T cells, respectively, in response to influenza stimulation. Meanwhile, 97, 120, 20, and 10 DEGs were identified as gene signatures in PBMCs, monocytes, B cells, and CD8+ T cells, respectively, upon vaccinia stimulation. The majority of DEGs identified in PBMCs were also found in monocytes after either viral stimulation. Of the virus-specific DEGs, 55, 63, and 9 DEGs occurred in common in PBMCs, monocytes, and B cells, respectively, while no DEGs were shared in infected CD8+ T cells after influenza and vaccinia. Gene set enrichment analysis demonstrated that these shared DEGs were over-represented in innate signaling pathways, including cytokine-cytokine receptor interaction, viral protein interaction with cytokine and cytokine receptor, Toll-like receptor signaling, RIG-I-like receptor signaling pathways, cytosolic DNA-sensing pathways, and natural killer cell mediated cytotoxicity. Conclusion Our results provide insights into virus-host interactions in different immune cells, as well as host defense mechanisms against viral stimulation. Our data also highlights the role of monocytes as a major cell population driving gene expression in ex vivo PBMCs in response to viral stimulation. The immune response signaling pathways identified in this study may provide specific targets for the development of novel virus-specific therapeutics and improved vaccines for vaccinia and influenza. Although influenza and vaccinia viruses have been selected in this study as pathogen models, this approach could be applicable to other pathogens.
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Affiliation(s)
- Huy Quang Quach
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Krista M. Goergen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Diane E. Grill
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Iana H. Haralambieva
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
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Desai AP, Kosari F, Disselhorst M, Yin J, Agahi A, Peikert T, Udell J, Johnson SH, Smadbeck J, Murphy S, Karagouga G, McCune A, Schaefer-Klein J, Borad MJ, Cheville J, Vasmatzis G, Baas P, Mansfield A. Dynamics and survival associations of T cell receptor clusters in patients with pleural mesothelioma treated with immunotherapy. J Immunother Cancer 2023; 11:e006035. [PMID: 37279993 PMCID: PMC10255162 DOI: 10.1136/jitc-2022-006035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) are now a first-line treatment option for patients with pleural mesothelioma with the recent approval of ipilimumab and nivolumab. Mesothelioma has a low tumor mutation burden and no robust predictors of survival with ICI. Since ICIs enable adaptive antitumor immune responses, we investigated T-cell receptor (TCR) associations with survival in participants from two clinical trials treated with ICI. METHODS We included patients with pleural mesothelioma who were treated with nivolumab (NivoMes, NCT02497508) or nivolumab and ipilimumab (INITIATE, NCT03048474) after first-line therapy. TCR sequencing was performed with the ImmunoSEQ assay in 49 and 39 pretreatment and post-treatment patient peripheral blood mononuclear cell (PBMC) samples. These data were integrated with TCR sequences found in bulk RNAseq data by TRUST4 program in 45 and 35 pretreatment and post-treatment tumor biopsy samples and TCR sequences from over 600 healthy controls. The TCR sequences were clustered into groups of shared antigen specificity using GIANA. Associations of TCR clusters with overall survival were determined by cox proportional hazard analysis. RESULTS We identified 4.2 million and 12 thousand complementarity-determining region 3 (CDR3) sequences from PBMCs and tumors, respectively, in patients treated with ICI. These CDR3 sequences were integrated with 2.1 million publically available CDR3 sequences from healthy controls and clustered. ICI-enhanced T-cell infiltration and expanded T cell diversity in tumors. Cases with TCR clones in the top tertile in the pretreatment tissue or in circulation had significantly better survival than the bottom two tertiles (p<0.04). Furthermore, a high number of shared TCR clones between pretreatment tissue and in circulation was associated with improved survival (p=0.01). To potentially select antitumor clusters, we filtered for clusters that were (1) not found in healthy controls, (2) recurrent in multiple patients with mesothelioma, and (3) more prevalent in post-treatment than pretreatment samples. The detection of two-specific TCR clusters provided significant survival benefit compared with detection of 1 cluster (HR<0.001, p=0.026) or the detection of no TCR clusters (HR=0.10, p=0.002). These two clusters were not found in bulk tissue RNA-seq data and have not been reported in public CDR3 databases. CONCLUSIONS We identified two unique TCR clusters that were associated with survival on treatment with ICI in patients with pleural mesothelioma. These clusters may enable approaches for antigen discovery and inform future targets for design of adoptive T cell therapies.
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Affiliation(s)
- Aakash P Desai
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Farhad Kosari
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Disselhorst
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jun Yin
- Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Alireza Agahi
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Tobias Peikert
- Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Julia Udell
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - James Smadbeck
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Stephen Murphy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Giannoula Karagouga
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Alexa McCune
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Janet Schaefer-Klein
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Mitesh J Borad
- Hematology/Medical Oncology, Mayo Clinic, Phoenix, Arizona, USA
| | - John Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul Baas
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aaron Mansfield
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
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Glasstetter LM, Oderinde TS, Mirchandani M, Rajagopalan KS, Barsom SH, Thaler R, Siddiqi S, Zhu XY, Tang H, Jordan KL, Saadiq IM, van Wijnen AJ, Eirin A, Lerman LO. Obesity and dyslipidemia are associated with partially reversible modifications to DNA hydroxymethylation of apoptosis- and senescence-related genes in swine adipose-derived mesenchymal stem/stromal cells. Stem Cell Res Ther 2023; 14:143. [PMID: 37231414 PMCID: PMC10214739 DOI: 10.1186/s13287-023-03372-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 05/09/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Obesity dysregulates key biological processes underlying the functional homeostasis, fate decisions, and reparative potential of mesenchymal stem/stromal cells (MSCs). Mechanisms directing obesity-induced phenotypic alterations in MSCs remain unclear, but emerging drivers include dynamic modification of epigenetic marks, like 5-hydroxymethylcytosine (5hmC). We hypothesized that obesity and cardiovascular risk factors induce functionally relevant, locus-specific changes in 5hmC of swine adipose-derived MSCs and evaluated their reversibility using an epigenetic modulator, vitamin-C. METHODS Female domestic pigs were fed a 16-week Lean or Obese diet (n = 6 each). MSCs were harvested from subcutaneous adipose tissue, and 5hmC profiles were examined through hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq) followed by an integrative (hMeDIP and mRNA sequencing) gene set enrichment analysis. For clinical context, we compared 5hmC profiles of adipose tissue-derived human MSCs harvested from patients with obesity and healthy controls. RESULTS hMeDIP-seq revealed 467 hyper- (fold change ≥ 1.4; p-value ≤ 0.05) and 591 hypo- (fold change ≤ 0.7; p-value ≤ 0.05) hydroxymethylated loci in swine Obese- versus Lean-MSCs. Integrative hMeDIP-seq/mRNA-seq analysis identified overlapping dysregulated gene sets and discrete differentially hydroxymethylated loci with functions related to apoptosis, cell proliferation, and senescence. These 5hmC changes were associated with increased senescence in cultured MSCs (p16/CDKN2A immunoreactivity, senescence-associated β-galactosidase [SA-β-Gal] staining), were partly reversed in swine Obese-MSCs treated with vitamin-C, and shared common pathways with 5hmC changes in human Obese-MSCs. CONCLUSIONS Obesity and dyslipidemia are associated with dysregulated DNA hydroxymethylation of apoptosis- and senescence-related genes in swine and human MSCs, potentially affecting cell vitality and regenerative functions. Vitamin-C may mediate reprogramming of this altered epigenomic landscape, providing a potential strategy to improve the success of autologous MSC transplantation in obese patients.
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Affiliation(s)
- Logan M Glasstetter
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Tomiwa S Oderinde
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Mohit Mirchandani
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Samer H Barsom
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Sarosh Siddiqi
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Xiang-Yang Zhu
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Hui Tang
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kyra L Jordan
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ishran M Saadiq
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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Ogi DA, Jin S. Transcriptome-Powered Pluripotent Stem Cell Differentiation for Regenerative Medicine. Cells 2023; 12:1442. [PMID: 37408278 DOI: 10.3390/cells12101442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 07/07/2023] Open
Abstract
Pluripotent stem cells are endless sources for in vitro engineering human tissues for regenerative medicine. Extensive studies have demonstrated that transcription factors are the key to stem cell lineage commitment and differentiation efficacy. As the transcription factor profile varies depending on the cell type, global transcriptome analysis through RNA sequencing (RNAseq) has been a powerful tool for measuring and characterizing the success of stem cell differentiation. RNAseq has been utilized to comprehend how gene expression changes as cells differentiate and provide a guide to inducing cellular differentiation based on promoting the expression of specific genes. It has also been utilized to determine the specific cell type. This review highlights RNAseq techniques, tools for RNAseq data interpretation, RNAseq data analytic methods and their utilities, and transcriptomics-enabled human stem cell differentiation. In addition, the review outlines the potential benefits of the transcriptomics-aided discovery of intrinsic factors influencing stem cell lineage commitment, transcriptomics applied to disease physiology studies using patients' induced pluripotent stem cell (iPSC)-derived cells for regenerative medicine, and the future outlook on the technology and its implementation.
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Affiliation(s)
- Derek A Ogi
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Sha Jin
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
- Center of Biomanufacturing for Regenerative Medicine, State University of New York at Binghamton, Binghamton, NY 13902, USA
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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537847. [PMID: 37162982 PMCID: PMC10168222 DOI: 10.1101/2023.04.21.537847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully-length mRNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM, or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in PCR amplification, barcode read errors, and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
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Affiliation(s)
- Thomas G Brooks
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Antonijo Mrčela
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
| | - Dimitra Sarantopoulou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Soumyashant Nayak
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Current address: Statistics and Mathematics Unit, Indian Statistical Institute, Bengaluru, Karnataka, India
| | - Amruta Naik
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shaon Sengupta
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology & Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
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Starlinger P, Brunnthaler L, McCabe C, Pereyra D, Santol J, Steadman J, Hackl M, Skalicky S, Hackl H, Gronauer R, O’Brien D, Kain R, Hirsova P, Gores GJ, Wang C, Gruenberger T, Smoot RL, Assinger A. Transcriptomic landscapes of effective and failed liver regeneration in humans. JHEP Rep 2023; 5:100683. [PMID: 36950091 PMCID: PMC10025111 DOI: 10.1016/j.jhepr.2023.100683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/19/2022] [Accepted: 01/08/2023] [Indexed: 03/24/2023] Open
Abstract
Background & Aims Although extensive experimental evidence on the process of liver regeneration exists, in humans, validation is largely missing. However, liver regeneration is critically affected by underlying liver disease. Within this project, we aimed to systematically assess early transcriptional changes during liver regeneration in humans and further assess how these processes differ in people with dysfunctional liver regeneration. Methods Blood samples of 154 patients and intraoperative tissue samples of 46 patients undergoing liver resection were collected and classified with regard to dysfunctional postoperative liver regeneration. Of those, a matched cohort of 21 patients were used for RNA sequencing. Samples were assessed for circulating cytokines, gene expression dynamics, intrahepatic neutrophil accumulation, and spatial transcriptomics. Results Individuals with dysfunctional liver regeneration demonstrated an aggravated transcriptional inflammatory response with higher intracellular adhesion molecule-1 induction. Increased induction of this critical leukocyte adhesion molecule was associated with increased intrahepatic neutrophil accumulation and activation upon induction of liver regeneration in individuals with dysfunctional liver regeneration. Comparing baseline gene expression profiles in individuals with and without dysfunctional liver regeneration, we found that dual-specificity phosphatase 4 (DUSP4) expression, a known critical regulator of intracellular adhesion molecule-1 expression in endothelial cells, was markedly reduced in patients with dysfunctional liver regeneration. Mimicking clinical risk factors for dysfunctional liver regeneration, we found liver sinusoidal endothelial cells of two liver disease models to have significantly reduced baseline levels of DUSP4. Conclusions Exploring the landscape of early transcriptional changes of human liver regeneration, we observed that people with dysfunctional regeneration experience overwhelming intrahepatic inflammation. Subclinical liver disease might account for DUSP4 reduction in liver sinusoidal endothelial cells, which ultimately primes the liver for an aggravated inflammatory response. Impact and implications Using a unique human biorepository, focused on liver regeneration (LR), we explored the landscape of circulating and tissue-level alterations associated with both functional and dysfunctional LR. In contrast to experimental animal models, people with dysfunctional LR demonstrated an aggravated transcriptional inflammatory response, higher intracellular adhesion molecule-1 (ICAM-1) induction, intrahepatic neutrophil accumulation and activation upon induction of LR. Although inflammatory responses appear rapidly after liver resection, people with dysfunctional LR have exaggerated inflammatory responses that appear to be related to decreased levels of LSEC DUSP4, challenging existing concepts of post-resectional LR.
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Key Words
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- CASH, chemotherapy associated steatohepatitis
- DLR, dysfunctional LR
- DUSP-4
- DUSP4, dual-specificity phosphatase 4
- FDR, false discovery rate
- FLR, functional LR
- FPKM, fragments per kilobase of transcript per million mapped reads
- Human
- ICAM-1, intracellular adhesion molecule-1
- IPA, Ingenuity Pathway Analysis
- IVCL, inferior vena cava ligation
- Inflammation
- LPS, lipopolysaccharide
- LR, liver regeneration
- LSEC, liver sinusoidal endothelial cell
- Liver regeneration
- MFI, mean fluorescence intensity
- MPO, myeloperoxidase
- NASH, non-alcoholic steatohepatitis
- Neutrophils
- PCA, principal component analysis
- POD1, 1 day after liver resection
- POD5, 5 days after liver resection
- STRING, Search Tool for the Retrieval of Interacting Genes/Proteins
- TMM, trimmed mean of M values
- TNF, tumour necrosis factor
- logCPM, log counts per million
- pTPM, protein-coding transcripts per million
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Affiliation(s)
- Patrick Starlinger
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Mayo Clinic, Rochester, MN, USA
- Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
- Corresponding authors. Addresses: Department of HPB Surgery, Mayo Clinic, 200 First Street SW, Rochester 55905, MN, USA; Department of Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria. Tel.: +43-1-40400-5621.
| | - Laura Brunnthaler
- Center of Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Chantal McCabe
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - David Pereyra
- Department of Surgery, Medical University of Vienna, General Hospital, Vienna, Austria
| | - Jonas Santol
- Department of Surgery, HPB Center, Viennese Health Network, Clinic Favoriten and Sigmund Freud Private University, Vienna, Austria
| | - Jessica Steadman
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | | | - Hubert Hackl
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Raphael Gronauer
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniel O’Brien
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Renate Kain
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Petra Hirsova
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Gregory J. Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Chen Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Thomas Gruenberger
- Department of Surgery, HPB Center, Viennese Health Network, Clinic Favoriten and Sigmund Freud Private University, Vienna, Austria
| | - Rory L. Smoot
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
- Department of Surgery, Mayo Clinic, 200 First Street SW, 55905 Rochester, MN, USA. Tel.: +1-507-284-1529; fax: +1-507-284-5196.
| | - Alice Assinger
- Center of Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
- Institute of Physiology, Medical University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria. Tel.: +43-1-40160-31405.
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Miller B, Kim SJ, Mehta HH, Cao K, Kumagai H, Thumaty N, Leelaprachakul N, Braniff RG, Jiao H, Vaughan J, Diedrich J, Saghatelian A, Arpawong TE, Crimmins EM, Ertekin-Taner N, Tubi MA, Hare ET, Braskie MN, Décarie-Spain L, Kanoski SE, Grodstein F, Bennett DA, Zhao L, Toga AW, Wan J, Yen K, Cohen P. Mitochondrial DNA variation in Alzheimer's disease reveals a unique microprotein called SHMOOSE. Mol Psychiatry 2023; 28:1813-1826. [PMID: 36127429 PMCID: PMC10027624 DOI: 10.1038/s41380-022-01769-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 08/15/2022] [Accepted: 08/26/2022] [Indexed: 01/22/2023]
Abstract
Mitochondrial DNA variants have previously associated with disease, but the underlying mechanisms have been largely elusive. Here, we report that mitochondrial SNP rs2853499 associated with Alzheimer's disease (AD), neuroimaging, and transcriptomics. We mapped rs2853499 to a novel mitochondrial small open reading frame called SHMOOSE with microprotein encoding potential. Indeed, we detected two unique SHMOOSE-derived peptide fragments in mitochondria by using mass spectrometry-the first unique mass spectrometry-based detection of a mitochondrial-encoded microprotein to date. Furthermore, cerebrospinal fluid (CSF) SHMOOSE levels in humans correlated with age, CSF tau, and brain white matter volume. We followed up on these genetic and biochemical findings by carrying out a series of functional experiments. SHMOOSE acted on the brain following intracerebroventricular administration, differentiated mitochondrial gene expression in multiple models, localized to mitochondria, bound the inner mitochondrial membrane protein mitofilin, and boosted mitochondrial oxygen consumption. Altogether, SHMOOSE has vast implications for the fields of neurobiology, Alzheimer's disease, and microproteins.
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Affiliation(s)
- Brendan Miller
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
| | - Su-Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Hemal H Mehta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kevin Cao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Hiroshi Kumagai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Neehar Thumaty
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Naphada Leelaprachakul
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Regina Gonzalez Braniff
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Henry Jiao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Joan Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jolene Diedrich
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Thalida E Arpawong
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eileen M Crimmins
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | | | - Meral A Tubi
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Evan T Hare
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Meredith N Braskie
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Léa Décarie-Spain
- Human and Evolutionary Biology Section, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Scott E Kanoski
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
- Human and Evolutionary Biology Section, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Francine Grodstein
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Lu Zhao
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Junxiang Wan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kelvin Yen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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Bian X, Conley SM, Eirin A, Zimmerman Zuckerman EA, Smith AL, Gowan CC, Snow ZK, Jarmi T, Farres H, Erben YM, Hakaim AG, Dietz MA, Zubair AC, Wyles SP, Wolfram JV, Lerman LO, Hickson LJ. Diabetic kidney disease induces transcriptome alterations associated with angiogenesis activity in human mesenchymal stromal cells. Stem Cell Res Ther 2023; 14:49. [PMID: 36949528 PMCID: PMC10035152 DOI: 10.1186/s13287-023-03269-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Therapeutic interventions that optimize angiogenic activities may reduce rates of end-stage kidney disease, critical limb ischemia, and lower extremity amputations in individuals with diabetic kidney disease (DKD). Infusion of autologous mesenchymal stromal cells (MSC) is a promising novel therapy to rejuvenate vascular integrity. However, DKD-related factors, including hyperglycemia and uremia, might alter MSC angiogenic repair capacity in an autologous treatment approach. METHODS To explore the angiogenic activity of MSC in DKD, the transcriptome of adipose tissue-derived MSC obtained from DKD subjects was compared to age-matched controls without diabetes or kidney impairment. Next-generation RNA sequencing (RNA-seq) was performed on MSC (DKD n = 29; Controls n = 9) to identify differentially expressed (DE; adjusted p < 0.05, |log2fold change|> 1) messenger RNA (mRNA) and microRNA (miRNA) involved in angiogenesis (GeneCards). Paracrine-mediated angiogenic repair capacity of MSC conditioned medium (MSCcm) was assessed in vitro using human umbilical vein endothelial cells incubated in high glucose and indoxyl sulfate for a hyperglycemic, uremic state. RESULTS RNA-seq analyses revealed 133 DE mRNAs (77 upregulated and 56 down-regulated) and 208 DE miRNAs (119 up- and 89 down-regulated) in DKD-MSC versus Control-MSC. Interestingly, miRNA let-7a-5p, which regulates angiogenesis and participates in DKD pathogenesis, interacted with 5 angiogenesis-associated mRNAs (transgelin/TAGLN, thrombospondin 1/THBS1, lysyl oxidase-like 4/LOXL4, collagen 4A1/COL4A1 and collagen 8A1/COL8A1). DKD-MSCcm incubation with injured endothelial cells improved tube formation capacity, enhanced migration, reduced adhesion molecules E-selectin, vascular cell adhesion molecule 1 and intercellular adhesion molecule 1 mRNA expression in endothelial cells. Moreover, angiogenic repair effects did not differ between treatment groups (DKD-MSCcm vs. Control-MSCcm). CONCLUSIONS MSC from individuals with DKD show angiogenic transcriptome alterations compared to age-matched controls. However, angiogenic repair potential may be preserved, supporting autologous MSC interventions to treat conditions requiring enhanced angiogenic activities such as DKD, diabetic foot ulcers, and critical limb ischemia.
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Affiliation(s)
- Xiaohui Bian
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
- Department of Nephrology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Sabena M Conley
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Alfonso Eirin
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Anastasia L Smith
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Cody C Gowan
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Zachary K Snow
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Tambi Jarmi
- Division of Transplant Nephrology, Department of Transplant Surgery, Mayo Clinic, Jacksonville, FL, USA
| | - Houssam Farres
- Division of Vascular Surgery, Department of Surgery, Mayo Clinic, Jacksonville, FL, USA
| | - Young M Erben
- Division of Vascular Surgery, Department of Surgery, Mayo Clinic, Jacksonville, FL, USA
| | - Albert G Hakaim
- Division of Vascular Surgery, Department of Surgery, Mayo Clinic, Jacksonville, FL, USA
| | - Matthew A Dietz
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Abba C Zubair
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL, USA
- Center for Regenerative Biotherapeutics, Mayo Clinic, Jacksonville, FL, USA
| | | | - Joy V Wolfram
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Jacksonville, FL, USA
- School of Chemical Engineering/Australian Institute for Bioengineering, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - LaTonya J Hickson
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
- Center for Regenerative Biotherapeutics, Mayo Clinic, Jacksonville, FL, USA.
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42
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Grgic O, Prijatelj V, Dudakovic A, Vucic S, Dhamo B, Trajanoska K, Monnereau C, Zrimsek M, Gautvik K, Reppe S, Shimizu E, Haworth S, Timpson N, Jaddoe V, Jarvelin MR, Evans D, Uitterlinden A, Ongkosuwito E, van Wijnen A, Medina-Gomez C, Rivadeneira F, Wolvius E. Novel Genetic Determinants of Dental Maturation in Children. J Dent Res 2023; 102:349-356. [PMID: 36437532 PMCID: PMC10083589 DOI: 10.1177/00220345221132268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Dental occlusion requires harmonious development of teeth, jaws, and other elements of the craniofacial complex, which are regulated by environmental and genetic factors. We performed the first genome-wide association study (GWAS) on dental development (DD) using the Demirjian radiographic method. Radiographic assessments from participants of the Generation R Study (primary study population, N1 = 2,793; mean age of 9.8 y) were correlated with ~30 million genetic variants while adjusting for age, sex, and genomic principal components (proxy for population stratification). Variants associated with DD at genome-wide significant level (P < 5 × 10-8) mapped to 16q12.2 (IRX5) (lead variant rs3922616, B = 0.16; P = 2.2 × 10-8). We used Fisher's combined probability tests weighted by sample size to perform a meta-analysis (N = 14,805) combining radiographic DD at a mean age of 9.8 y from Generation R with data from a previous GWAS (N2 = 12,012) on number of teeth (NT) in infants used as proxy of DD at a mean age of 9.8 y (including the ALSPAC and NFBC1966). This GWAS meta-analysis revealed 3 novel loci mapping to 7p15.3 (IGF2BP3: P = 3.2 × 10-8), 14q13.3 (PAX9: P = 1.9 × 10-8), and 16q12.2 (IRX5: P = 1.2 × 10-9) and validated 8 previously reported NT loci. A polygenic allele score constructed from these 11 loci was associated with radiographic DD in an independent Generation R set of children (N = 703; B = 0.05, P = 0.004). Furthermore, profiling of the identified genes across an atlas of murine and human stem cells observed expression in the cells involved in the formation of bone and/or dental tissues (>0.3 frequency per kilobase of transcript per million mapped reads), likely reflecting functional specialization. Our findings provide biological insight into the polygenic architecture of the pediatric dental maturation process.
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Affiliation(s)
- O. Grgic
- Department of Oral and Maxillofacial
Surgery, ErasmusMC, Rotterdam, The Netherlands
- The Generation R Study, ErasmusMC,
Rotterdam, The Netherlands
| | - V. Prijatelj
- Department of Oral and Maxillofacial
Surgery, ErasmusMC, Rotterdam, The Netherlands
- The Generation R Study, ErasmusMC,
Rotterdam, The Netherlands
| | - A. Dudakovic
- Department of Orthopedic Surgery, Mayo
Clinic, Rochester, MN, USA
| | - S. Vucic
- Department of Oral and Maxillofacial
Surgery, ErasmusMC, Rotterdam, The Netherlands
- The Generation R Study, ErasmusMC,
Rotterdam, The Netherlands
| | - B. Dhamo
- Department of Oral and Maxillofacial
Surgery, ErasmusMC, Rotterdam, The Netherlands
- The Generation R Study, ErasmusMC,
Rotterdam, The Netherlands
| | - K. Trajanoska
- Department of Human Genetics McGill
University, Montréal, Québec, Canada
- Canada Excellence Research Chair in
Genomic Medicine, McGill University, Montréal, Québec, Canada
| | - C. Monnereau
- The Generation R Study, ErasmusMC,
Rotterdam, The Netherlands
| | - M. Zrimsek
- Department of Pathology, Medical
University of Vienna, Vienna, Austria
| | - K.M. Gautvik
- Department of Medical Biochemistry,
Oslo University Hospital, Oslo, Norway
| | - S. Reppe
- Department of Medical Biochemistry,
Oslo University Hospital, Oslo, Norway
| | - E. Shimizu
- Department of Oral Biology, Rutgers
School of Dental Medicine, Newark, NJ, USA
| | - S. Haworth
- Department of Population Health
Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Dental School, University of
Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit,
University of Bristol, Bristol, UK
| | - N.J. Timpson
- Department of Population Health
Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit,
University of Bristol, Bristol, UK
| | - V.W.V. Jaddoe
- The Generation R Study, ErasmusMC,
Rotterdam, The Netherlands
| | - M.-R. Jarvelin
- Faculty of Medicine, Center for Life
Course Health Research, University of Oulu, Oulu, Finland
- Faculty of Medicine, School of Public
Health, Imperial College, London, UK
| | - D. Evans
- MRC Integrative Epidemiology Unit,
University of Bristol, Bristol, UK
- Diamantina Institute, The University
of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience,
The University of Queensland, Brisbane, Australia
| | | | - E.M. Ongkosuwito
- Dentistry, Section Orthodontics and
Craniofacial Biology, Radboud University Medical Center, Nijmegen, The
Netherlands
| | - A.J. van Wijnen
- Department of Biochemistry,
University of Vermont, Burlington, VT, USA
| | - C. Medina-Gomez
- The Generation R Study, ErasmusMC,
Rotterdam, The Netherlands
| | - F. Rivadeneira
- Department of Oral and Maxillofacial
Surgery, ErasmusMC, Rotterdam, The Netherlands
- The Generation R Study, ErasmusMC,
Rotterdam, The Netherlands
| | - E.B. Wolvius
- Department of Oral and Maxillofacial
Surgery, ErasmusMC, Rotterdam, The Netherlands
- The Generation R Study, ErasmusMC,
Rotterdam, The Netherlands
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Mumtaz N, Dudakovic A, Nair A, Koedam M, van Leeuwen JPTM, Koopmans MPG, Rockx B, van Wijnen AJ, van der Eerden BCJ. Zika virus alters osteogenic lineage progression of human mesenchymal stromal cells. J Cell Physiol 2023; 238:379-392. [PMID: 36538650 DOI: 10.1002/jcp.30933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 11/09/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
Arboviruses target bone forming osteoblasts and perturb bone remodeling via paracrine factors. We previously reported that Zika virus (ZIKV) infection of early-stage human mesenchymal stromal cells (MSCs) inhibited the osteogenic lineage commitment of MSCs. To understand the physiological interplay between bone development and ZIKV pathogenesis, we employed a primary in vitro model to examine the biological responses of MSCs to ZIKV infection at different stages of osteogenesis. Precommitted MSCs were infected at the late stage of osteogenic stimulation (Day 7) with ZIKV (multiplicity of infection of 5). We observe that MSCs infected at the late stage of differentiation are highly susceptible to ZIKV infection similar to previous observations with early stage infected MSCs (Day 0). However, in contrast to ZIKV infection at the early stage of differentiation, infection at a later stage significantly elevates the key osteogenic markers and calcium content. Comparative RNA sequencing (RNA-seq) of early and late stage infected MSCs reveals that ZIKV infection alters the mRNA transcriptome during osteogenic induction of MSCs (1251 genes). ZIKV infection provokes a robust antiviral response at both stages of osteogenic differentiation as reflected by the upregulation of interferon responsive genes (n > 140). ZIKV infection enhances the expression of immune-related genes in early stage MSCs while increasing cell cycle genes in late stage MSCs. Remarkably, ZIKA infection in early stage MSCs also activates lipid metabolism-related pathways. In conclusion, ZIKV infection has differentiation stage-dependent effects on MSCs and this mechanistic understanding may permit the development of new therapeutic or preventative measures for bone-related effects of ZIKV infection.
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Affiliation(s)
- Noreen Mumtaz
- Department of Viroscience, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Amel Dudakovic
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Asha Nair
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Marijke Koedam
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Johannes P T M van Leeuwen
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Andre J van Wijnen
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont, USA
| | - Bram C J van der Eerden
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Centre, Rotterdam, The Netherlands
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Ramos GP, Bamidele AO, Klatt EE, Sagstetter MR, Kurdi AT, Hamdan FH, Kosinsky RL, Gaballa JM, Nair A, Sun Z, Dasari S, Lanza IR, Rozeveld CN, Schott MB, Urrutia G, Westphal MS, Clarkson BD, Howe CL, Marietta EV, Luckey DH, Murray JA, Gonzalez M, Braga Neto MB, Gibbons HR, Smyrk TC, Johnsen S, Lomberk G, Faubion WA. G9a Modulates Lipid Metabolism in CD4 T Cells to Regulate Intestinal Inflammation. Gastroenterology 2023; 164:256-271.e10. [PMID: 36272457 PMCID: PMC9892272 DOI: 10.1053/j.gastro.2022.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/27/2022] [Accepted: 10/06/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND & AIMS Although T-cell intrinsic expression of G9a has been associated with murine intestinal inflammation, mechanistic insight into the role of this methyltransferase in human T-cell differentiation is ill defined, and manipulation of G9a function for therapeutic use against inflammatory disorders is unexplored. METHODS Human naive T cells were isolated from peripheral blood and differentiated in vitro in the presence of a G9a inhibitor (UNC0642) before being characterized via the transcriptome (RNA sequencing), chromatin accessibility (assay for transposase-accessible chromatin by sequencing), protein expression (cytometry by time of flight, flow cytometry), metabolism (mitochondrial stress test, ultrahigh performance liquid chromatography-tandem mas spectroscopy) and function (T-cell suppression assay). The in vivo role of G9a was assessed using 3 murine models. RESULTS We discovered that pharmacologic inhibition of G9a enzymatic function in human CD4 T cells led to spontaneous generation of FOXP3+ T cells (G9a-inibitors-T regulatory cells [Tregs]) in vitro that faithfully reproduce human Tregs, functionally and phenotypically. Mechanistically, G9a inhibition altered the transcriptional regulation of genes involved in lipid biosynthesis in T cells, resulting in increased intracellular cholesterol. Metabolomic profiling of G9a-inibitors-Tregs confirmed elevated lipid pathways that support Treg development through oxidative phosphorylation and enhanced lipid membrane composition. Pharmacologic G9a inhibition promoted Treg expansion in vivo upon antigen (gliadin) stimulation and ameliorated acute trinitrobenzene sulfonic acid-induced colitis secondary to tissue-specific Treg development. Finally, Tregs lacking G9a expression (G9a-knockout Tregs) remain functional chronically and can rescue T-cell transfer-induced colitis. CONCLUSION G9a inhibition promotes cholesterol metabolism in T cells, favoring a metabolic profile that facilitates Treg development in vitro and in vivo. Our data support the potential use of G9a inhibitors in the treatment of immune-mediated conditions including inflammatory bowel disease.
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Affiliation(s)
- Guilherme Piovezani Ramos
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Adebowale O Bamidele
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Emily E Klatt
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - Mary R Sagstetter
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Ahmed T Kurdi
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Feda H Hamdan
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Robyn Laura Kosinsky
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Joseph M Gaballa
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Asha Nair
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Zhifu Sun
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | | | - Ian R Lanza
- Metabolomics Core, Mayo Clinic, Rochester, Minnesota
| | - Cody N Rozeveld
- Department of Biology, Northwestern College, Orange City, Iowa
| | - Micah B Schott
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Guillermo Urrutia
- Genomic Sciences and Precision Medicine Center, Milwaukee, Wisconsin; Division of Research Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Maria S Westphal
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Charles L Howe
- Department of Immunology, Mayo Clinic, Rochester, Minnesota; Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | - Eric V Marietta
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - David H Luckey
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - Joseph A Murray
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Michelle Gonzalez
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Manuel B Braga Neto
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Hunter R Gibbons
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Steven Johnsen
- Robert Bosch Center for Tumor Diseases, Stuttgart, Germany
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center, Milwaukee, Wisconsin; Division of Research Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - William A Faubion
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Immunology, Mayo Clinic, Rochester, Minnesota.
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Qiao W, Chen Y, Zhong J, Madden BJ, Charlesworth CM, Martens YA, Liu CC, Knight J, Ikezu TC, Kurti A, Zhu Y, Meneses A, Rosenberg CL, Kuchenbecker LA, Vanmaele LK, Li F, Chen K, Shue F, Dacquel MV, Fryer J, Pandey A, Zhao N, Bu G. Trem2 H157Y increases soluble TREM2 production and reduces amyloid pathology. Mol Neurodegener 2023; 18:8. [PMID: 36721205 PMCID: PMC9890893 DOI: 10.1186/s13024-023-00599-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/19/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The rare p.H157Y variant of TREM2 (Triggering Receptor Expressed on Myeloid Cells 2) was found to increase Alzheimer's disease (AD) risk. This mutation is located at the cleavage site of TREM2 extracellular domain. Ectopic expression of TREM2-H157Y in HEK293 cells resulted in increased TREM2 shedding. However, the physiological outcomes of the TREM2 H157Y mutation remain unknown in the absence and presence of AD related pathologies. METHODS We generated a novel Trem2 H157Y knock-in mouse model through CRISPR/Cas9 technology and investigated the effects of Trem2 H157Y on TREM2 proteolytic processing, synaptic function, and AD-related amyloid pathologies by conducting biochemical assays, targeted mass spectrometry analysis of TREM2, hippocampal electrophysiology, immunofluorescent staining, in vivo micro-dialysis, and cortical bulk RNA sequencing. RESULTS Consistent with previous in vitro findings, Trem2 H157Y increases TREM2 shedding with elevated soluble TREM2 levels in the brain and serum. Moreover, Trem2 H157Y enhances synaptic plasticity without affecting microglial density and morphology, or TREM2 signaling. In the presence of amyloid pathology, Trem2 H157Y accelerates amyloid-β (Aβ) clearance and reduces amyloid burden, dystrophic neurites, and gliosis in two independent founder lines. Targeted mass spectrometry analysis of TREM2 revealed higher ratios of soluble to full-length TREM2-H157Y compared to wild-type TREM2, indicating that the H157Y mutation promotes TREM2 shedding in the presence of Aβ. TREM2 signaling was further found reduced in Trem2 H157Y homozygous mice. Transcriptomic profiling revealed that Trem2 H157Y downregulates neuroinflammation-related genes and an immune module correlated with the amyloid pathology. CONCLUSION Taken together, our findings suggest beneficial effects of the Trem2 H157Y mutation in synaptic function and in mitigating amyloid pathology. Considering the genetic association of TREM2 p.H157Y with AD risk, we speculate TREM2 H157Y in humans might increase AD risk through an amyloid-independent pathway, such as its effects on tauopathy and neurodegeneration which merit further investigation.
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Affiliation(s)
- Wenhui Qiao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Yixing Chen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Jun Zhong
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - Benjamin J. Madden
- Medical Genome Facility, Proteomics Core, Mayo Clinic, Rochester, MN USA
| | | | - Yuka A. Martens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Joshua Knight
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Aishe Kurti
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Yiyang Zhu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Axel Meneses
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | | | - Lucy K. Vanmaele
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Fuyao Li
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Kai Chen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Francis Shue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - John Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ 85259 USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN USA
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104 India
| | - Na Zhao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- SciNeuro Pharmaceuticals, Rockville, MD 20805 USA
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46
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Ailawadhi S, Parrondo RD, Dutta N, Han B, Ciccio G, Cherukuri Y, Alegria VR, LaPlant BR, Roy V, Sher T, Edwards B, Lanier S, Manna A, Heslop K, Caulfield T, Maldosevic E, Storz P, Manochakian R, Asmann Y, Chanan-Khan AA, Paulus A. AT-101 Enhances the Antitumor Activity of Lenalidomide in Patients with Multiple Myeloma. Cancers (Basel) 2023; 15:477. [PMID: 36672426 PMCID: PMC9857228 DOI: 10.3390/cancers15020477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/03/2022] [Accepted: 12/09/2022] [Indexed: 01/15/2023] Open
Abstract
Bcl-2 and Mcl-1 proteins play a role in multiple myeloma (MM) cell survival, for which targeted inhibitors are being developed. AT-101 is an oral drug, which disrupts Bcl-2 and Mcl-1 function, impedes mitochondrial bioenergetic processes and induces apoptosis in MM cells. When combined with lenalidomide and dexamethasone (Rd), AT-101 significantly reduced tumor burden in an in vivo xenograft model of MM. These data provided rationale for a phase I/II study to establish the effective dose of AT-101 in combination with Rd (ARd regimen) in relapsed/refractory MM. A total of 10 patients were enrolled, most with high-risk cytogenetics (80%) and prior stem cell transplant (70%). Three patients were lenalidomide-refractory, 2 were bortezomib-refractory and 3 were daratumumab-refractory. The ARd combination was well tolerated with most common grade 3/4 adverse events being cytopenia's. The overall response rate was 40% and clinical benefit rate was 90%. The median progression free survival was 14.9 months (95% CI 7.1-NE). Patients responsive to ARd showed a decrease in Bcl-2:Bim or Mcl-1:Noxa protein complexes, increased CD8+ T and NK cells and depletion of T and B-regulatory cells. The ARd regimen demonstrated an acceptable safety profile and promising efficacy in patients with relapsed/refractory MM prompting further investigation in additional patients.
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Affiliation(s)
- Sikander Ailawadhi
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Ricardo D. Parrondo
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Navnita Dutta
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Bing Han
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Gina Ciccio
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Yesesri Cherukuri
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Victoria R. Alegria
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Betsy R. LaPlant
- Department of Biostatistics, Mayo Clinic Rochester, Rochester, MN 55902, USA
| | - Vivek Roy
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Taimur Sher
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Brett Edwards
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Stephanie Lanier
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Alak Manna
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Keisha Heslop
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Thomas Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Emir Maldosevic
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Peter Storz
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Rami Manochakian
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Yan Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Asher A. Chanan-Khan
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
| | - Aneel Paulus
- Deparment of Hematology-Oncology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
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47
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Fisher CR, Krull JE, Bhagwate A, Masters T, Greenwood-Quaintance KE, Abdel MP, Patel R. Sonicate Fluid Cellularity Predicted by Transcriptomic Deconvolution Differentiates Infectious from Non-Infectious Arthroplasty Failure. J Bone Joint Surg Am 2023; 105:63-73. [PMID: 36574631 PMCID: PMC10137834 DOI: 10.2106/jbjs.22.00605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Although cellularity is traditionally assessed morphologically, deep sequencing approaches being used for microorganism detection may be able to provide information about cellularity. We hypothesized that cellularity predicted using CIBERSORTx (Stanford University), a transcriptomic-based cellular deconvolution tool, would differentiate between infectious and non-infectious arthroplasty failure. METHODS CIBERSORTx-derived cellularity profiles of 93 sonicate fluid samples, including 53 from subjects who underwent failed arthroplasties due to periprosthetic joint infection (PJI) (abbreviated for the purpose of this study as PJIF) and 40 from subjects who had undergone non-infectious arthroplasty failure (abbreviated NIAF) that had been subjected to bulk RNA sequencing were evaluated. RESULTS Samples from PJIF and NIAF subjects were differentially clustered by principal component analysis based on the cellularity profile. Twelve of the 22 individual predicted cellular fractions were differentially expressed in the PJIF cases compared with the NIAF cases, including increased predicted neutrophils (mean and standard error, 9.73% ± 1.06% and 0.81% ± 0.60%), activated mast cells (17.12% ± 1.51% and 4.11% ± 0.44%), and eosinophils (1.96% ± 0.37% and 0.42% ± 0.21%), and decreased predicted M0 macrophages (21.33% ± 1.51% and 39.75% ± 2.45%), M2 macrophages (3.56% ± 0.52% and 8.70% ± 1.08%), and regulatory T cells (1.57% ± 0.23% and 3.20% ± 0.34%). The predicted total granulocyte fraction was elevated in the PJIF cases (32.97% ± 2.13% and 11.76% ± 1.61%), and the samples from the NIAF cases had elevated predicted total macrophage and monocyte (34.71% ± 1.71% and 55.34% ± 2.37%) and total B cell fractions (5.89% ± 0.30% and 8.62% ± 0.86%). Receiver operating characteristic curve analysis identified predicted total granulocytes, neutrophils, and activated mast cells as highly able to differentiate between the PJIF cases and the NIAF cases. Within the PJIF cases, the total granulocyte, total macrophage and monocyte, M0 macrophage, and M2 macrophage fractions were differentially expressed in Staphylococcus aureus compared with Staphylococcus epidermidis -associated samples. Within the NIAF cases, the predicted total B cell, naïve B cell, plasma cell, and M2 macrophage fractions were differentially expressed among different causes of failure. CONCLUSIONS CIBERSORTx can predict the cellularity of sonicate fluid using transcriptomic data, allowing for the evaluation of the underlying immune response during the PJIF and NIAF cases, without a need to phenotypically assess cell composition.
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Affiliation(s)
- Cody R Fisher
- Department of Immunology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jordan E Krull
- Department of Immunology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota
| | - Aditya Bhagwate
- Department of Quantitative Sciences, Mayo Clinic, Rochester, Minnesota
| | - Thao Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota
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Salvarani C, Paludo J, Hunder GG, Ansell SM, Giannini C, Parisi JE, Huston J, Koster MJ, Warrington KJ, Croci S, Brown RD. Exploring Gene Expression Profiles in Primary Central Nervous System Vasculitis. Ann Neurol 2023; 93:120-130. [PMID: 36264136 DOI: 10.1002/ana.26537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 02/05/2023]
Abstract
OBJECTIVE This study was undertaken to explore the gene expression profile of primary central nervous system vasculitis (PCNSV). METHODS Brain specimens of 4 patients with granulomatous vasculitis (GV), 5 with lymphocytic vasculitis (LV), 4 with amyloid β-related angiitis (ABRA), and 4 normal controls were studied. RNA-sequencing was performed using the Illumina Hiseq-4,000 platform and the Illumina TruSeq Total-RNA library. Student t test and false discovery rate tests were performed for each of the differentially expressed transcripts. Ingenuity Pathway Analysis was used for the pathway expression analysis. CIBERSORT was used to estimate the abundances of different immune cell subsets in the tissues based on gene expression data. RESULTS Transcripts differentially expressed between PCNSV and normal brain indicated that endosomal, mitochondrial, and ribosome dysfunction, alterations in protein synthesis, and noncoding RNAs might be involved in PCNSV. Pathway analysis revealed the activation of dendritic cell maturation and antigen processing as well as neuroinflammation in PCNSV versus normal brain, whereas oxidative phosphorylation was inhibited. CIBERSORT estimation of immune cell subsets suggested that activated NK cells, M1 macrophages, memory B cells, and follicular helper T cells were likely to be more prevalent in PCNSV samples. Naïve CD4 T cells and monocytes were mainly estimated to be present in GV and ABRA. Plasma cell and γδ T-cell signatures were mainly found in LV and normal brain. GV showed higher levels of genes associated with macrophage activities and T cells. ABRA showed higher levels of long noncoding RNAs and miR-616. LV showed higher levels of genes encoding immunoglobulins. INTERPRETATION RNA sequencing confirmed PCNSV heterogeneity. ANN NEUROL 2023;93:120-130.
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Affiliation(s)
- Carlo Salvarani
- Department of Neurology, Mayo Clinic, Rochester, MN, USA.,Division of Rheumatology, Local Health Unit Company-Institute of Hospitalization and Scientific Care, Reggio Emilia, Italy
| | - Jonas Paludo
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Gene G Hunder
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Joseph E Parisi
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - John Huston
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Stefania Croci
- Clinical Immunology, Allergy and Advanced Biotechnologies Unit, USL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - Robert D Brown
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
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49
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Stabenau KA, Samuels TL, Lam TK, Mathison AJ, Wells C, Altman KW, Battle MA, Johnston N. Pepsinogen/Proton Pump Co-Expression in Barrett's Esophageal Cells Induces Cancer-Associated Changes. Laryngoscope 2023; 133:59-69. [PMID: 35315085 DOI: 10.1002/lary.30109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/27/2022] [Accepted: 03/04/2022] [Indexed: 02/02/2023]
Abstract
EDUCATIONAL OBJECTIVE At the conclusion of this presentation, participants should better understand the carcinogenic potential of pepsin and proton pump expression in Barrett's esophagus. OBJECTIVE Barrett's esophagus (BE) is a well-known risk factor for esophageal adenocarcinoma (EAC). Gastric H+ /K+ ATPase proton pump and pepsin expression has been demonstrated in some cases of BE; however, the contribution of local pepsin and proton pump expression to carcinogenesis is unknown. In this study, RNA sequencing was used to examine global transcriptomic changes in a BE cell line ectopically expressing pepsinogen and/or gastric H+ /K+ ATPase proton pumps. STUDY DESIGN In vitro translational. METHODS BAR-T, a human BE cell line devoid of expression of pepsinogen or proton pumps, was transduced by lentivirus-encoding pepsinogen (PGA5) and/or gastric proton pump subunits (ATP4A, ATP4B). Changes relative to the parental line were assessed by RNA sequencing. RESULTS Top canonical pathways associated with protein-coding genes differentially expressed in pepsinogen and/or proton pump expressing BAR-T cells included those involved in the tumor microenvironment and epithelial-mesenchymal transition. Top upstream regulators of coding transcripts included TGFB1 and ERBB2, which are associated with the pathogenesis and prognosis of BE and EAC. Top upstream regulators of noncoding transcripts included p300-CBP, I-BET-151, and CD93, which have previously described associations with EAC or carcinogenesis. The top associated disease of both coding and noncoding transcripts was cancer. CONCLUSIONS These data support the carcinogenic potential of pepsin and proton pump expression in BE and reveal molecular pathways affected by their expression. Further study is warranted to investigate the role of these pathways in carcinogenesis associated with BE. LEVEL OF EVIDENCE NA Laryngoscope, 133:59-69, 2023.
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Affiliation(s)
- Kaleigh A Stabenau
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Tina L Samuels
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Tina K Lam
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Clive Wells
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kenneth W Altman
- Department of Otolaryngology, Geisinger Health System, Danville, California, USA
| | - Michele A Battle
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nikki Johnston
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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50
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Eirin A, Chade AR. Cardiac epigenetic changes in VEGF signaling genes associate with myocardial microvascular rarefaction in experimental chronic kidney disease. Am J Physiol Heart Circ Physiol 2023; 324:H14-H25. [PMID: 36367693 PMCID: PMC9762979 DOI: 10.1152/ajpheart.00522.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Chronic kidney disease (CKD) is common in patients with heart failure and often results in left ventricular diastolic dysfunction (LVDD). However, the mechanisms responsible for cardiac damage in CKD-LVDD remain to be elucidated. Epigenetic alterations may impose long-lasting effects on cellular transcription and function, but their exact role in CKD-LVDD is unknown. We investigate whether changes in cardiac site-specific DNA methylation profiles might be implicated in cardiac abnormalities in CKD-LVDD. CKD-LVDD and normal control pigs (n = 6 each) were studied for 14 wk. Renal and cardiac hemodynamics were quantified by multidetector CT and echocardiography. In randomly selected pigs (n = 3/group), cardiac site-specific 5-methylcytosine (5mC) immunoprecipitation (MeDIP)- and mRNA-sequencing (seq) were performed, followed by integrated (MeDiP-seq/mRNA-seq analysis), and confirmatory ex vivo studies. MeDIP-seq analysis revealed 261 genes with higher (fold change > 1.4; P < 0.05) and 162 genes with lower (fold change < 0.7; P < 0.05) 5mC levels in CKD-LVDD versus normal pigs, which were primarily implicated in vascular endothelial growth factor (VEGF)-related signaling and angiogenesis. Integrated MeDiP-seq/mRNA-seq analysis identified a select group of VEGF-related genes in which 5mC levels were higher, but mRNA expression was lower in CKD-LVDD versus normal pigs. Cardiac VEGF signaling gene and VEGF protein expression were blunted in CKD-LVDD compared with controls and were associated with decreased subendocardial microvascular density. Cardiac epigenetic changes in VEGF-related genes are associated with impaired angiogenesis and cardiac microvascular rarefaction in swine CKD-LVDD. These observations may assist in developing novel therapies to ameliorate cardiac damage in CKD-LVDD.NEW & NOTEWORTHY Chronic kidney disease (CKD) often leads to left ventricular diastolic dysfunction (LVDD) and heart failure. Using a novel translational swine model of CKD-LVDD, we characterize the cardiac epigenetic landscape, identifying site-specific 5-methylcytosine changes in vascular endothelial growth factor (VEGF)-related genes associated with impaired angiogenesis and cardiac microvascular rarefaction. These observations shed light on the mechanisms of cardiac microvascular damage in CKD-LVDD and may assist in developing novel therapies for these patients.
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Affiliation(s)
- Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Alejandro R Chade
- Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, Missouri
- Department of Medicine, University of Missouri-Columbia, Columbia, Missouri
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