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Guzman-Gomez A, Ahmed HF, Dani A, Zafar F, Lehenbauer DG, Potter AS, Morales DLS, Ziady AG, Hayes D. Corrigendum to 'Center volume effect on acute cellular rejection and outcomes in pediatric lung transplant recipients' [J Heart Lung Transplant 2023; 42(8):1030-1039]. J Heart Lung Transplant 2024; 43:184-187. [PMID: 37978970 DOI: 10.1016/j.healun.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Affiliation(s)
- Amalia Guzman-Gomez
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hosam F Ahmed
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Alia Dani
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Farhan Zafar
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - David G Lehenbauer
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Andrew S Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - David L S Morales
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Assem G Ziady
- Cancer and Blood Disorder Institute, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Don Hayes
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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Guzman-Gomez A, Ahmed HF, Dani A, Zafar F, Lehenbauer DG, Potter AS, Morales DLS, Ziady AG, Hayes D. Center volume effect on acute cellular rejection and outcomes in pediatric lung transplant recipients. J Heart Lung Transplant 2023; 42:1030-1039. [PMID: 37088340 PMCID: PMC10524259 DOI: 10.1016/j.healun.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Acute cellular rejection (ACR) is common after lung transplant (LTx). We sought to determine if transplant center volume affected ACR-related outcomes in children after LTx. METHODS The United Network for Organ Sharing (UNOS) Registry was queried for patients <18-years-of-age who underwent LTx 1987-2020. Cohorts were children who survived the first-year post transplant and were treated for ACR within that first year (ACR group) and those not treated for ACR (non-ACR). LTx center volume was defined as: high volume center (HVC) (>5LTxs/year), medium volume center (MVC) (>1≤5 LTxs/year), and low volume center (LVC) (≤1LTxs/year). RESULTS 1320 patients were enrolled into the study; 269 (20.4%) did not experience ACR. The ACR cohort was older (median 14 [11-16] vs 13 [7-16] years, p < 0.001), female (65.3% vs 57.3%, p = 0.016), had cystic fibrosis (62.3% vs 45.5%, p < 0.001), and had a higher lung allocation score (37.3 [34.6-47.8] vs 35.8 [33-42.6], p = 0.029). The ACR cohort trended (p = 0.06) towards lower survival at 5-year (37% vs 47%) and 10-year (25% vs 34%) post-LTx. Among children at HVCs, ACR occurred in 17% of recipients (n = 98/574), compared to 18.5% (n = 73/395) at MVCs and 27% (n = 100/369) at LVCs. Children treated for ACR at HVCs had higher survival than LVCs at 5-years (52% vs 29%) and 10-years (36% vs 15%) (p < 0.001) but similar survival to MVCs at 5-years (52% vs 43%) and 10-years (36% vs 24%) (p = 0.081). No survival differences were detected in MVCs vs LVCs (p = 0.14). CONCLUSIONS ACR treated within the first post-LTx year influence survival of children. ACR incidence was lowest at higher volume centers whereas post-ACR treatment survival outcomes were also superior.
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Affiliation(s)
- Amalia Guzman-Gomez
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hosam F Ahmed
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Alia Dani
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Farhan Zafar
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - David G Lehenbauer
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Andrew S Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - David L S Morales
- Department of Cardiothoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Assem G Ziady
- Cancer and Blood Disorder Institute, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Don Hayes
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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Zheng J, Ru W, Adolacion JR, Spurgat MS, Liu X, Yuan S, Liang RX, Dong J, Potter AS, Potter SS, Chen K, Chen R, Varadarajan N, Tang SJ. Single-cell RNA-seq analysis reveals compartment-specific heterogeneity and plasticity of microglia. iScience 2021; 24:102186. [PMID: 33718838 PMCID: PMC7921843 DOI: 10.1016/j.isci.2021.102186] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/31/2020] [Accepted: 02/09/2021] [Indexed: 12/31/2022] Open
Abstract
Microglia are ubiquitous central nervous system (CNS)-resident macrophages that maintain homeostasis of neural tissues and protect them from pathogen attacks. Yet, their differentiation in different compartments remains elusive. We performed single-cell RNA-seq to compare microglial subtypes in the cortex and the spinal cord. A multi-way comparative analysis was carried out on samples from C57/BL and HIV gp120 transgenic mice at two, four, and eight months of age. The results revealed overlapping but distinct microglial populations in the cortex and the spinal cord. The differential heterogeneity of microglia in these CNS regions was further suggested by their disparity of plasticity in response to life span progression and HIV-1 pathogenic protein gp120. Our findings indicate that microglia in different CNS compartments are adapted to their local environments to fulfill region-specific biological functions.
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Affiliation(s)
- Junying Zheng
- Department of Neuroscience, Cell Biology, & Anatomy, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Wenjuan Ru
- Department of Neuroscience, Cell Biology, & Anatomy, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Jay R. Adolacion
- Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77004, USA
| | - Michael S. Spurgat
- Department of Neuroscience, Cell Biology, & Anatomy, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Xin Liu
- Department of Neuroscience, Cell Biology, & Anatomy, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Subo Yuan
- Department of Neuroscience, Cell Biology, & Anatomy, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Rommel X. Liang
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jianli Dong
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew S. Potter
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - S Steven Potter
- Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston 77030, TX, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston 77030, TX, USA
| | - Navin Varadarajan
- Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77004, USA
| | - Shao-Jun Tang
- Department of Neuroscience, Cell Biology, & Anatomy, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
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Hinze C, Karaiskos N, Boltengagen A, Walentin K, Redo K, Himmerkus N, Bleich M, Potter SS, Potter AS, Eckardt KU, Kocks C, Rajewsky N, Schmidt-Ott KM. Kidney Single-cell Transcriptomes Predict Spatial Corticomedullary Gene Expression and Tissue Osmolality Gradients. J Am Soc Nephrol 2021; 32:291-306. [PMID: 33239393 PMCID: PMC8054904 DOI: 10.1681/asn.2020070930] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/15/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Single-cell transcriptomes from dissociated tissues provide insights into cell types and their gene expression and may harbor additional information on spatial position and the local microenvironment. The kidney's cells are embedded into a gradient of increasing tissue osmolality from the cortex to the medulla, which may alter their transcriptomes and provide cues for spatial reconstruction. METHODS Single-cell or single-nuclei mRNA sequencing of dissociated mouse kidneys and of dissected cortex, outer, and inner medulla, to represent the corticomedullary axis, was performed. Computational approaches predicted the spatial ordering of cells along the corticomedullary axis and quantitated expression levels of osmo-responsive genes. In situ hybridization validated computational predictions of spatial gene-expression patterns. The strategy was used to compare single-cell transcriptomes from wild-type mice to those of mice with a collecting duct-specific knockout of the transcription factor grainyhead-like 2 (Grhl2CD-/-), which display reduced renal medullary osmolality. RESULTS Single-cell transcriptomics from dissociated kidneys provided sufficient information to approximately reconstruct the spatial position of kidney tubule cells and to predict corticomedullary gene expression. Spatial gene expression in the kidney changes gradually and osmo-responsive genes follow the physiologic corticomedullary gradient of tissue osmolality. Single-nuclei transcriptomes from Grhl2CD-/- mice indicated a flattened expression gradient of osmo-responsive genes compared with control mice, consistent with their physiologic phenotype. CONCLUSIONS Single-cell transcriptomics from dissociated kidneys facilitated the prediction of spatial gene expression along the corticomedullary axis and quantitation of osmotically regulated genes, allowing the prediction of a physiologic phenotype.
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Affiliation(s)
- Christian Hinze
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin, Berlin, Germany,Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany,Berlin Institute of Health, Berlin, Germany
| | - Nikos Karaiskos
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anastasiya Boltengagen
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Katharina Walentin
- Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Klea Redo
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin, Berlin, Germany,Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Nina Himmerkus
- Department of Physiology, Physiology of Membrane Transport, Christian-Albrechts-Universität, Kiel, Germany
| | - Markus Bleich
- Department of Physiology, Physiology of Membrane Transport, Christian-Albrechts-Universität, Kiel, Germany
| | - S. Steven Potter
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Andrew S. Potter
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin, Berlin, Germany
| | - Christine Kocks
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Kai M. Schmidt-Ott
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin, Berlin, Germany,Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany,Berlin Institute of Health, Berlin, Germany
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Zhang L, He X, Liu X, Zhang F, Huang LF, Potter AS, Xu L, Zhou W, Zheng T, Luo Z, Berry KP, Pribnow A, Smith SM, Fuller C, Jones BV, Fouladi M, Drissi R, Yang ZJ, Gustafson WC, Remke M, Pomeroy SL, Girard EJ, Olson JM, Morrissy AS, Vladoiu MC, Zhang J, Tian W, Xin M, Taylor MD, Potter SS, Roussel MF, Weiss WA, Lu QR. Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse. Cancer Cell 2019; 36:302-318.e7. [PMID: 31474569 PMCID: PMC6760242 DOI: 10.1016/j.ccell.2019.07.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/16/2019] [Accepted: 07/29/2019] [Indexed: 02/05/2023]
Abstract
Progenitor heterogeneity and identities underlying tumor initiation and relapse in medulloblastomas remain elusive. Utilizing single-cell transcriptomic analysis, we demonstrated a developmental hierarchy of progenitor pools in Sonic Hedgehog (SHH) medulloblastomas, and identified OLIG2-expressing glial progenitors as transit-amplifying cells at the tumorigenic onset. Although OLIG2+ progenitors become quiescent stem-like cells in full-blown tumors, they are highly enriched in therapy-resistant and recurrent medulloblastomas. Depletion of mitotic Olig2+ progenitors or Olig2 ablation impeded tumor initiation. Genomic profiling revealed that OLIG2 modulates chromatin landscapes and activates oncogenic networks including HIPPO-YAP/TAZ and AURORA-A/MYCN pathways. Co-targeting these oncogenic pathways induced tumor growth arrest. Together, our results indicate that glial lineage-associated OLIG2+ progenitors are tumor-initiating cells during medulloblastoma tumorigenesis and relapse, suggesting OLIG2-driven oncogenic networks as potential therapeutic targets.
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Affiliation(s)
- Liguo Zhang
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xuelian He
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Boston Children's Hospital, Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
| | - Xuezhao Liu
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Feng Zhang
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - L Frank Huang
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrew S Potter
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lingli Xu
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Wenhao Zhou
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Tao Zheng
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zaili Luo
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kalen P Berry
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Allison Pribnow
- Tumor Cell Biology Division, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephanie M Smith
- Tumor Cell Biology Division, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christine Fuller
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Blaise V Jones
- Radiology Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Maryam Fouladi
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Rachid Drissi
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Zeng-Jie Yang
- Cancer Biology Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - W Clay Gustafson
- Department of Neurology, Pediatrics, and Surgery and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Scott L Pomeroy
- Boston Children's Hospital, Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Emily J Girard
- Division of Pediatric Hematology/Oncology, Fred Hutchinson Cancer Research Center, University of Washington School of Medicine, Seattle Children's Hospital, Seattle, WA 98145-5005, USA
| | - James M Olson
- Division of Pediatric Hematology/Oncology, Fred Hutchinson Cancer Research Center, University of Washington School of Medicine, Seattle Children's Hospital, Seattle, WA 98145-5005, USA
| | - A Sorana Morrissy
- Department of Biochemistry and Molecular Biology, The University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maria C Vladoiu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Jiao Zhang
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Weidong Tian
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Mei Xin
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael D Taylor
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - S Steven Potter
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Martine F Roussel
- Tumor Cell Biology Division, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - William A Weiss
- Department of Neurology, Pediatrics, and Surgery and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Q Richard Lu
- Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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Mucenski ML, Mahoney R, Adam M, Potter AS, Potter SS. Single cell RNA-seq study of wild type and Hox9,10,11 mutant developing uterus. Sci Rep 2019; 9:4557. [PMID: 30872674 PMCID: PMC6418183 DOI: 10.1038/s41598-019-40923-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/25/2019] [Indexed: 12/17/2022] Open
Abstract
The uterus is a remarkable organ that must guard against infections while maintaining the ability to support growth of a fetus without rejection. The Hoxa10 and Hoxa11 genes have previously been shown to play essential roles in uterus development and function. In this report we show that the Hoxa9,10,11, Hoxc9,10,11, Hoxd9,10,11 genes play a redundant role in the formation of uterine glands. In addition, we use single cell RNA-seq to create a high resolution gene expression atlas of the developing wild type mouse uterus. Cell types and subtypes are defined, for example dividing endothelial cells into arterial, venous, capillary, and lymphatic, while epithelial cells separate into luminal and glandular subtypes. Further, a surprising heterogeneity of stromal and myocyte cell types are identified. Transcription factor codes and ligand/receptor interactions are characterized. We also used single cell RNA-seq to globally define the altered gene expression patterns in all developing uterus cell types for two Hox mutants, with 8 or 9 mutant Hox genes. The mutants show a striking disruption of Wnt signaling as well as the Cxcl12/Cxcr4 ligand/receptor axis.
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Affiliation(s)
- Michael L Mucenski
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Robert Mahoney
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Andrew S Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
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Magella B, Adam M, Potter AS, Venkatasubramanian M, Chetal K, Hay SB, Salomonis N, Potter SS. Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf. Dev Biol 2017; 434:36-47. [PMID: 29183737 DOI: 10.1016/j.ydbio.2017.11.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022]
Abstract
The developing kidney provides a useful model for study of the principles of organogenesis. In this report we use three independent platforms, Drop-Seq, Chromium 10x Genomics and Fluidigm C1, to carry out single cell RNA-Seq (scRNA-Seq) analysis of the E14.5 mouse kidney. Using the software AltAnalyze, in conjunction with the unsupervised approach ICGS, we were unable to identify and confirm the presence of 16 distinct cell populations during this stage of active nephrogenesis. Using a novel integrative supervised computational strategy, we were able to successfully harmonize and compare the cell profiles across all three technological platforms. Analysis of possible cross compartment receptor/ligand interactions identified the nephrogenic zone stroma as a source of GDNF. This was unexpected because the cap mesenchyme nephron progenitors had been thought to be the sole source of GDNF, which is a key driver of branching morphogenesis of the collecting duct system. The expression of Gdnf by stromal cells was validated in several ways, including Gdnf in situ hybridization combined with immunohistochemistry for SIX2, and marker of nephron progenitors, and MEIS1, a marker of stromal cells. Finally, the single cell gene expression profiles generated in this study confirmed and extended previous work showing the presence of multilineage priming during kidney development. Nephron progenitors showed stochastic expression of genes associated with multiple potential differentiation lineages.
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Affiliation(s)
- Bliss Magella
- Cincinnati Children's Medical Center, Division of Developmental Biology, 3333 Burnet Ave., Cincinnati, OH 45229, USA
| | - Mike Adam
- Cincinnati Children's Medical Center, Division of Developmental Biology, 3333 Burnet Ave., Cincinnati, OH 45229, USA
| | - Andrew S Potter
- Cincinnati Children's Medical Center, Division of Developmental Biology, 3333 Burnet Ave., Cincinnati, OH 45229, USA
| | - Meenakshi Venkatasubramanian
- Cincinnati Children's Medical Center, Division of Biomedical Informatics, 3333 Burnet Ave., Cincinnati OH 45229, USA
| | - Kashish Chetal
- Cincinnati Children's Medical Center, Division of Biomedical Informatics, 3333 Burnet Ave., Cincinnati OH 45229, USA
| | - Stuart B Hay
- Cincinnati Children's Medical Center, Division of Biomedical Informatics, 3333 Burnet Ave., Cincinnati OH 45229, USA
| | - Nathan Salomonis
- Cincinnati Children's Medical Center, Division of Biomedical Informatics, 3333 Burnet Ave., Cincinnati OH 45229, USA.
| | - S Steven Potter
- Cincinnati Children's Medical Center, Division of Developmental Biology, 3333 Burnet Ave., Cincinnati, OH 45229, USA.
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Adam M, Potter AS, Potter SS. Psychrophilic proteases dramatically reduce single-cell RNA-seq artifacts: a molecular atlas of kidney development. Development 2017; 144:3625-3632. [PMID: 28851704 DOI: 10.1242/dev.151142] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/18/2017] [Indexed: 12/18/2022]
Abstract
Single-cell RNA-seq is a powerful technique. Nevertheless, there are important limitations, including the technical challenges of breaking down an organ or tissue into a single-cell suspension. Invariably, this has required enzymatic incubation at 37°C, which can be expected to result in artifactual changes in gene expression patterns. Here, we describe a dissociation method that uses a protease with high activity in the cold, purified from a psychrophilic microorganism. The entire procedure is carried out at 6°C or colder, at which temperature mammalian transcriptional machinery is largely inactive, thereby effectively 'freezing in' the in vivo gene expression patterns. To test this method, we carried out RNA-seq on 20,424 single cells from postnatal day 1 mouse kidneys, comparing the results of the psychrophilic protease method with procedures using 37°C incubation. We show that the cold protease method provides a great reduction in gene expression artifacts. In addition, the results produce a single-cell resolution gene expression atlas of the newborn mouse kidney, an interesting time in development when mature nephrons are present yet nephrogenesis remains extremely active.
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Affiliation(s)
- Mike Adam
- Cincinnati Children's Hospital Medical Center, Division of Developmental Biology, Cincinnati, OH 45229, USA
| | - Andrew S Potter
- Cincinnati Children's Hospital Medical Center, Division of Developmental Biology, Cincinnati, OH 45229, USA
| | - S Steven Potter
- Cincinnati Children's Hospital Medical Center, Division of Developmental Biology, Cincinnati, OH 45229, USA
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Foroudi S, Potter AS, Stamatikos A, Patil BS, Deyhim F. Drinking Orange Juice Increases Total Antioxidant Status and Decreases Lipid Peroxidation in Adults. J Med Food 2014; 17:612-7. [DOI: 10.1089/jmf.2013.0034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shahrzad Foroudi
- Department of Human Sciences, Texas A&M University–Kingsville, Kingsville, Texas, USA
| | - Andrew S. Potter
- Department of Human Sciences, Texas A&M University–Kingsville, Kingsville, Texas, USA
| | - Alexis Stamatikos
- Department of Human Sciences, Texas A&M University–Kingsville, Kingsville, Texas, USA
| | - Bhimanagouda S. Patil
- Department of Horticultural Sciences, Vegetable and Fruit Improvement Center, Texas A&M University, College Station, Texas, USA
| | - Farzad Deyhim
- Department of Human Sciences, Texas A&M University–Kingsville, Kingsville, Texas, USA
- Department of Horticultural Sciences, Vegetable and Fruit Improvement Center, Texas A&M University, College Station, Texas, USA
- Citrus Center, Texas A&M University–Kingsville, Weslaco, Texas, USA
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Potter AS, Foroudi S, Stamatikos A, Patil BS, Deyhim F. Drinking carrot juice increases total antioxidant status and decreases lipid peroxidation in adults. Nutr J 2011; 10:96. [PMID: 21943297 PMCID: PMC3192732 DOI: 10.1186/1475-2891-10-96] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 09/24/2011] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND High prevalence of obesity and cardiovascular disease is attributable to sedentary lifestyle and eating diets high in fat and refined carbohydrate while eating diets low in fruit and vegetables. Epidemiological studies have confirmed a strong association between eating diets rich in fruits and vegetables and cardiovascular health. The aim of this pilot study was to determine whether drinking fresh carrot juice influences antioxidant status and cardiovascular risk markers in subjects not modifying their eating habits. METHODS An experiment was conducted to evaluate the effects of consuming 16 fl oz of daily freshly squeezed carrot juice for three months on cardiovascular risk markers, C-reactive protein, insulin, leptin, interleukin-1α, body fat percentage, body mass index (BMI), blood pressure, antioxidant status, and malondialdehyde production. Fasting blood samples were collected pre-test and 90 days afterward to conclude the study. RESULTS Drinking carrot juice did not affect (P > 0.1) the plasma cholesterol, triglycerides, Apo A, Apo B, LDL, HDL, body fat percentage, insulin, leptin, interleukin-1α, or C-reactive protein. Drinking carrot juice decreased (P = 0.06) systolic pressure, but did not influence diastolic pressure. Drinking carrot juice significantly (P < 0.05) increased the plasma total antioxidant capacity and decreased (P < 0.05) the plasma malondialdehyde production. CONCLUSION Drinking carrot juice may protect the cardiovascular system by increasing total antioxidant status and by decreasing lipid peroxidation independent of any of the cardiovascular risk markers measured in the study.
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Affiliation(s)
- Andrew S Potter
- Department of Human Sciences, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
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