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Nakagawa T, Santos J, Nasamran CA, Sen P, Sadat S, Monther A, Bendik J, Ebisumoto K, Hu J, Preissl S, Guo T, Vavinskaya V, Fisch KM, Califano JA. Defining the relationship of salivary gland malignancies to novel cell subpopulations in human salivary glands using single nucleus RNA-sequencing. Int J Cancer 2024; 154:1492-1503. [PMID: 37971144 DOI: 10.1002/ijc.34790] [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: 02/20/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Salivary glands have essential roles in maintaining oral health, mastication, taste and speech, by secreting saliva. Salivary glands are composed of several types of cells, and each cell type is predicted to be involved in the carcinogenesis of different types of cancers including adenoid cystic carcinoma (ACC), acinic cell carcinoma (AciCC), salivary duct carcinoma (SDC), myoepithelial carcinoma (MECA) and other histology. In our study, we performed single nucleus RNA-seq on three human salivary gland samples to clarify the gene expression profile of each complex cellular component of the salivary glands and related these expression patterns to expression found in salivary gland cancers (SGC) to infer cell of origin. By single nucleus RNA-seq, salivary gland cells were stratified into four clusters: acinar cells, ductal cells 1, ductal cells 2 and myoepithelial cells/stromal cells. The localization of each cell group was verified by IHC of each cluster marker gene, and one group of ductal cells was found to represent intercalated ductal cells labeled with HES1. Furthermore, in comparison with SGC RNA-seq data, acinar cell markers were upregulated in AciCC, but downregulated in ACC and ductal cell markers were upregulated in SDC but downregulated in MECA, suggesting that markers of origin are highly expressed in some SGC. Cell type expressions in specific SGC histology are similar to those found in normal salivary gland populations, indicating a potential etiologic relationship.
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Affiliation(s)
- Takuya Nakagawa
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Jessica Santos
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California, USA
| | - Prakriti Sen
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Sayed Sadat
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Abdula Monther
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Joseph Bendik
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Koji Ebisumoto
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Jingjing Hu
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Theresa Guo
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, California, USA
| | - Vera Vavinskaya
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California, USA
| | - Joseph A Califano
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, California, USA
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Aisagbonhi O, Bui T, Nasamran CA, St Louis H, Pizzo D, Meads M, Mulholland M, Magallanes C, Lamale-Smith L, Laurent LC, Morey R, Jacobs MB, Fisch KM, Horii M. High placental expression of FLT1, LEP, PHYHIP and IL3RA - In persons of African ancestry with severe preeclampsia. Placenta 2023; 144:13-22. [PMID: 37949031 PMCID: PMC10843761 DOI: 10.1016/j.placenta.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
INTRODUCTION Mortality from preeclampsia (PE) and PE-associated morbidities are 3-to 5-fold higher in persons of African ancestry than in those of Asian and European ancestries. METHODS To elucidate placental contribution to worse PE outcomes in African ancestry pregnancies, we performed bulk RNA sequencing on 50 placentas from persons with severe PE (sPE) of African (n = 9), Asian (n = 18) and European (n = 23) ancestries and 73 normotensive controls of African (n = 10), Asian (n = 15) and European (n = 48) ancestries. RESULTS Previously described canonical preeclampsia genes, involved in metabolism and hypoxia/angiogenesis including: LEP, HK2, FSTL3, FLT1, ENG, TMEM45A, ARHGEF4 and HTRA1 were upregulated sPE versus normotensive placentas across ancestries. LTF, NPR3 and PHYHIP were higher in African vs. Asian ancestry sPE placentas. Allograft rejection/adaptive immune response genes were upregulated in placentas from African but not in Asian or European ancestry sPE patients; IL3RA was of particular interest because the patient with the highest placental IL3RA expression, a person of African ancestry with sPE, developed postpartum cardiomyopathy, and was the only patient out of 123, that developed this condition. Interestingly, the sPE patients with the highest IL3RA expression among persons of Asian and European ancestries developed unexplained tachycardia peripartum, necessitating echocardiography in the European ancestry patient. The association between elevated placental IL3RA levels and unexplained tachycardia or peripartum cardiomyopathy was found to be significant in the 50 sPE patients (p = .0005). DISCUSSION High placental upregulation of both canonical preeclampsia and allograft rejection/adaptive immune response genes may contribute to worse PE outcomes in African ancestry sPE patients.
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Affiliation(s)
- Omonigho Aisagbonhi
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA.
| | - Tony Bui
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Hailee St Louis
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Donald Pizzo
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Morgan Meads
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Megan Mulholland
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Celestine Magallanes
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Leah Lamale-Smith
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Robert Morey
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marni B Jacobs
- Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mariko Horii
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
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Zapata RC, Zhang D, Yoon D, Nasamran CA, Chilin-Fuentes DR, Libster A, Chaudry BS, Lopez-Valencia M, Ponnalagu D, Singh H, Petrascheck M, Osborn O. Targeting Clic1 for the treatment of obesity: A novel therapeutic strategy to reduce food intake and body weight. Mol Metab 2023; 76:101794. [PMID: 37604246 PMCID: PMC10480059 DOI: 10.1016/j.molmet.2023.101794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
OBJECTIVE Despite great advances in obesity therapeutics in recent years, there is still a need to identify additional therapeutic targets for the treatment of this disease. We previously discovered a signature of genes, including Chloride intracellular channel 1 (Clic1), whose expression was associated with drug-induced weight gain, and in these studies, we assess the effect of Clic1 inhibition on food intake and body weight in mice. METHODS We studied the impact of Clic1 inhibition in mouse models of binge-eating, diet-induced obese mice and genetic models of obesity (Magel2 KO mice). RESULTS Clic1 knockout (KO) mice ate significantly less and had a lower body weight than WT littermates when either fed chow or high fat diet. Furthermore, pharmacological inhibition of Clic1 in diet-induced obese mice resulted in suppression of food intake and promoted highly efficacious weight loss. Clic1 inhibition also reduced food intake in binge-eating models and hyperphagic Magel2 KO mice. We observed that chronic obesity resulted in a significant change in subcellular localization of Clic1 with an increased ratio of Clic1 in the membrane in the obese state. These observations provide a novel therapeutic strategy to block Clic1 translocation as a potential mechanism to reduce food intake and lower body weight. CONCLUSIONS These studies attribute a novel role of Clic1 as a driver of food intake and overconsumption. In summary, we have identified hypothalamic expression of Clic1 plays a key role in food intake, providing a novel therapeutic target to treat overconsumption that is the root cause of modern obesity.
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Affiliation(s)
- Rizaldy C Zapata
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dinghong Zhang
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dongmin Yoon
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Chanond A Nasamran
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daisy R Chilin-Fuentes
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Avraham Libster
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Besma S Chaudry
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mariela Lopez-Valencia
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Devasena Ponnalagu
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Harpreet Singh
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Michael Petrascheck
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA; Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Olivia Osborn
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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Cooke EJ, Joseph BC, Nasamran CA, Fisch KM, von Drygalski A. Maladaptive lymphangiogenesis is associated with synovial iron accumulation and delayed clearance in factor VIII-deficient mice after induced hemarthrosis. J Thromb Haemost 2023; 21:2390-2404. [PMID: 37116753 PMCID: PMC10792547 DOI: 10.1016/j.jtha.2023.04.022] [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: 02/22/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND Mechanisms of iron clearance from hemophilic joints are unknown. OBJECTIVES To better understand mechanisms of iron clearance following joint bleeding in a mouse model of hemophilia. METHODS Hemarthrosis was induced by subpatellar puncture in factor VIII (FVIII)-deficient (FVII-/-) mice, +/- periprocedural recombinant human FVIII, and hypocoagulable (HypoBALB/c) mice. HypoBALB/c mice experienced transient FVIII deficiency (anti-FVIII antibody) at the time of injury combined with warfarin-induced hypocoagulability. Synovial tissue was harvested weekly up to 6 weeks after injury for histological analysis, ferric iron and macrophage accumulation (CD68), blood and lymphatic vessel remodeling (αSMA; LYVE1). Synovial RNA sequencing was performed for FVIII-/- mice at days 0, 3, and 14 after injury to quantify expression changes of iron regulators and lymphatic markers. RESULTS Bleed volumes were similar in FVIII-/- and HypoBALB/c mice. However, pronounced and prolonged synovial iron accumulation colocalizing with macrophages and impaired lymphangiogenesis were detected only in FVIII-/- mice and were prevented by periprocedural FVIII. Gene expression changes involved in iron handling (some genes with dual roles in inflammation) and lymphatic markers supported proinflammatory milieu with iron retention and disturbed lymphangiogenesis. CONCLUSION Accumulation and delayed clearance of iron-laden macrophages were associated with defective lymphangiogenesis after hemarthrosis in FVIII-/- mice. The absence of such findings in HypoBALB/c mice suggests that intact lymphatics are required for removal of iron-laden macrophages and that these processes depend on FVIII availability. Studies to elucidate the biological mechanisms of disturbed lymphangiogenesis in hemophilia appear critical to develop new therapeutic targets.
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Affiliation(s)
- Esther J Cooke
- Division of Hematology/Oncology, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Bilgimol C Joseph
- Division of Hematology/Oncology, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California, USA
| | - Annette von Drygalski
- Division of Hematology/Oncology, Department of Medicine, University of California San Diego, La Jolla, California, USA.
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Zapata RC, Nasamran CA, Chilin-Fuentes DR, Dulawa SC, Osborn O. Identification of adipose tissue transcriptomic memory of anorexia nervosa. Mol Med 2023; 29:109. [PMID: 37582711 PMCID: PMC10428576 DOI: 10.1186/s10020-023-00705-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND Anorexia nervosa (AN) is a complex debilitating disease characterized by intense fear of weight gain and excessive exercise. It is the deadliest of any psychiatric disorder with a high rate of recidivism, yet its pathophysiology is unclear. The Activity-Based Anorexia (ABA) paradigm is a widely accepted mouse model of AN that recapitulates hypophagia and hyperactivity despite reduced body weight, however, not the chronicity. METHODS Here, we modified the prototypical ABA paradigm to increase the time to lose 25% of baseline body weight from less than 7 days to more than 2 weeks. We used this paradigm to identify persistently altered genes after weight restoration that represent a transcriptomic memory of under-nutrition and may contribute to AN relapse using RNA sequencing. We focused on adipose tissue as it was identified as a major location of transcriptomic memory of over-nutririon. RESULTS We identified 300 dysregulated genes that were refractory to weight restroration after ABA, including Calm2 and Vps13d, which could be potential global regulators of transcriptomic memory in both chronic over- and under-nutrition. CONCLUSION We demonstrated the presence of peristent changes in the adipose tissue transcriptome in the ABA mice after weight restoration. Despite being on the opposite spectrum of weight perturbations, majority of the transcriptomic memory genes of under- and over-nutrition did not overlap, suggestive of the different mechanisms involved in these extreme nutritional statuses.
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Affiliation(s)
- Rizaldy C Zapata
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, San Diego, USA.
| | - Chanond A Nasamran
- Center for Computational Biology & Bioinformatics, School of Medicine, University of California San Diego, San Diego, USA
| | - Daisy R Chilin-Fuentes
- Center for Computational Biology & Bioinformatics, School of Medicine, University of California San Diego, San Diego, USA
| | - Stephanie C Dulawa
- Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, 92093, San Diego, CA, USA
| | - Olivia Osborn
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, San Diego, USA
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Vasquez-Bolanos LS, Gibbons MC, Ruoss S, Wu IT, Esparza MC, Fithian DC, Lane JG, Singh A, Nasamran CA, Fisch KM, Ward SR. Transcriptional time course after rotator cuff repair in 6 month old female rabbits. Front Physiol 2023; 14:1164055. [PMID: 37228812 PMCID: PMC10203179 DOI: 10.3389/fphys.2023.1164055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction: Rotator cuff tears are prevalent in the population above the age of 60. The disease progression leads to muscle atrophy, fibrosis, and fatty infiltration, which is not improved upon with surgical repair, highlighting the need to better understand the underlying biology impairing more favorable outcomes. Methods: In this study, we collected supraspinatus muscle tissue from 6 month old female rabbits who had undergone unilateral tenotomy for 8 weeks at 1, 2, 4, or 8 weeks post-repair (n = 4/group). RNA sequencing and enrichment analyses were performed to identify a transcriptional timeline of rotator cuff muscle adaptations and related morphological sequelae. Results: There were differentially expressed (DE) genes at 1 (819 up/210 down), 2 (776/120), and 4 (63/27) weeks post-repair, with none at 8 week post-repair. Of the time points with DE genes, there were 1092 unique DE genes and 442 shared genes, highlighting that there are changing processes in the muscle at each time point. Broadly, 1-week post-repair differentially expressed genes were significantly enriched in pathways of metabolism and energetic activity, binding, and regulation. Many were also significantly enriched at 2 weeks, with the addition of NIF/NF-kappaB signaling, transcription in response to hypoxia, and mRNA stability alongside many additional pathways. There was also a shift in transcriptional activity at 4 weeks post-repair with significantly enriched pathways for lipids, hormones, apoptosis, and cytokine activity, despite an overall decrease in the number of differentially expressed genes. At 8 weeks post-repair there were no DE genes when compared to control. These transcriptional profiles were correlated with the histological findings of increased fat, degeneration, and fibrosis. Specifically, correlated gene sets were enriched for fatty acid metabolism, TGF-B-related, and other pathways. Discussion: This study identifies the timeline of transcriptional changes in muscle after RC repair, which by itself, does not induce a growth/regenerative response as desired. Instead, it is predominately related to metabolism/energetics changes at 1 week post-repair, unclear or asynchronous transcriptional diversity at 2 weeks post-repair, increased adipogenesis at 4 weeks post-repair, and a low transcriptional steady state or a dysregulated stress response at 8 weeks post-repair.
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Affiliation(s)
- Laura S. Vasquez-Bolanos
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Michael C. Gibbons
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Severin Ruoss
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Isabella T. Wu
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Mary C. Esparza
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Donald C. Fithian
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - John G. Lane
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Anshuman Singh
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
- Department of Orthopaedic Surgery, Kaiser Permanente, San Diego, CA, United States
| | - Chanond A. Nasamran
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, San Diego, CA, United States
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Diego, San Diego, CA, United States
| | - Samuel R. Ward
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
- Department of Radiology, University of California, San Diego, San Diego, CA, United States
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Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R. Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools. Lancet Reg Health Am 2023; 19:100449. [PMID: 36844610 PMCID: PMC9939935 DOI: 10.1016/j.lana.2023.100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Background Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. Methods The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 to March 2021. Findings In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88%-98%); 67% were associated with a positive wastewater sample (95% CI: 57%-77%), and 40% were associated with a positive surface sample (95% CI: 29%-52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. Interpretation Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy. Funding County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.
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Affiliation(s)
- Rebecca Fielding-Miller
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Richard S. Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Rodolfo A. Salido
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Victor J. Cantu
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Laura Kohn
- Kohn Education Consulting, San Diego, CA, USA
| | - Natasha K. Martin
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Adriane Wynn
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Carrissa Wijaya
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Marlene Flores
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Vinton Omaleki
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Araz Majnoonian
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Patricia Gonzalez-Zuniga
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Megan Nguyen
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Anh V. Vo
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Tina Le
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Dawn Duong
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ashkan Hassani
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Samantha Tweeten
- County of San Diego, Health and Human Services Agency, 1600 Pacific Highway, San Diego, CA, 92101, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Abbas Hakim
- Department of Obstetrics Gynecology and Reproductive Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Peter De Hoff
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Adam M. Mark
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chanond A. Nasamran
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Kathleen M. Fisch
- Department of Obstetrics Gynecology and Reproductive Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Helena M. Tubb
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Justin Morris
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Electrical and Computer Engineering, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Jaeyoung Kang
- Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Behnam Khaleghi
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Colin Young
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ameen D. Akel
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Sean Eilert
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Justin Eno
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Ken Curewitz
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Louise C. Laurent
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tajana Rosing
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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8
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Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R. Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project. medRxiv 2023:2021.10.19.21265226. [PMID: 34704096 PMCID: PMC8547528 DOI: 10.1101/2021.10.19.21265226] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. Methods The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 - March 2021. Findings In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88% - 98%); 67% were associated with a positive wastewater sample (95% CI: 57% - 77%), and 40% were associated with a positive surface sample (95% CI: 29% - 52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. Interpretation Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy. Funding County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.
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Affiliation(s)
- Rebecca Fielding-Miller
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | | | - Tommi Gaines
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | - Richard S. Garfein
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | | | - Victor J. Cantu
- University of California San Diego, Department of Bioengineering
| | | | - Natasha K Martin
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | - Adriane Wynn
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | - Carrissa Wijaya
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Marlene Flores
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Vinton Omaleki
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Araz Majnoonian
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health
| | - Patricia Gonzalez-Zuniga
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Megan Nguyen
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions
| | - Anh V Vo
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions
| | - Tina Le
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Dawn Duong
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Ashkan Hassani
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | | | - Kristen Jepsen
- University of California San Diego, Institute for Genomic Medicine
| | - Benjamin Henson
- University of California San Diego, Institute for Genomic Medicine
| | - Abbas Hakim
- University of California San Diego, Department of Obstetrics Gynecology and Reproductive Sciences
| | - Amanda Birmingham
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Peter De Hoff
- University of California San Diego, Department of Pediatrics
| | - Adam M. Mark
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Chanond A Nasamran
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Sara Brin Rosenthal
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Niema Moshiri
- University of California San Diego, Department of Computer Science & Engineering
| | - Kathleen M. Fisch
- University of California San Diego, Department of Obstetrics Gynecology and Reproductive Sciences
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Greg Humphrey
- University of California San Diego, Department of Pediatrics
| | - Sawyer Farmer
- University of California San Diego, Department of Pediatrics
| | - Helena M. Tubb
- University of California San Diego, Department of Pediatrics
| | - Tommy Valles
- University of California San Diego, Department of Pediatrics
| | - Justin Morris
- University of California San Diego, Department of Computer Science & Engineering
- San Diego State University, Department of Electrical and Computer Engineering
| | - Jaeyoung Kang
- University of California San Diego, Department of Electrical and Computer Engineering
| | - Behnam Khaleghi
- University of California San Diego, Department of Computer Science & Engineering
| | - Colin Young
- University of California San Diego, Department of Computer Science & Engineering
| | | | | | | | | | - Louise C Laurent
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health
| | - Tajana Rosing
- University of California San Diego, Department of Computer Science & Engineering
| | - Rob Knight
- University of California San Diego, Department of Pediatrics
- University of California San Diego, Department of Bioengineering
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9
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Ruoss S, Nasamran CA, Singh A, Lane JG, Ward SR. Are there sex-dependent transcriptional differences in human subacromial bursa from traumatic versus degenerative rotator cuff tears? J Orthop Res 2022; 40:2705-2707. [PMID: 36250743 DOI: 10.1002/jor.25450] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/03/2022] [Indexed: 02/04/2023]
Affiliation(s)
- Severin Ruoss
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, California, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, California, USA
| | - Anshuman Singh
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, California, USA.,Southern California Kaiser Permanente, San Diego, California, USA
| | - John G Lane
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, California, USA
| | - Samuel R Ward
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, California, USA.,Department of Bioengineering, UC San Diego, La Jolla, California, USA.,Department of Radiology, UC San Diego, La Jolla, California, USA
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10
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Ruoss S, Esparza MC, Vasquez-Bolanos LS, Nasamran CA, Fisch KM, Engler AJ, Ward SR. Spatial transcriptomics tools allow for regional exploration of heterogeneous muscle pathology in the pre-clinical rabbit model of rotator cuff tear. J Orthop Surg Res 2022; 17:440. [PMID: 36195913 PMCID: PMC9531386 DOI: 10.1186/s13018-022-03326-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/18/2022] [Indexed: 11/21/2022] Open
Abstract
Background Conditions affecting skeletal muscle, such as chronic rotator cuff tears, low back pain, dystrophies, and many others, often share changes in muscle phenotype: intramuscular adipose and fibrotic tissue increase while contractile tissue is lost. The underlying changes in cell populations and cell ratios observed with these phenotypic changes complicate the interpretation of tissue-level transcriptional data. Novel single-cell transcriptomics has limited capacity to address this problem because muscle fibers are too long to be engulfed in single-cell droplets and single nuclei transcriptomics are complicated by muscle fibers’ multinucleation. Therefore, the goal of this project was to evaluate the potential and challenges of a spatial transcriptomics technology to add dimensionality to transcriptional data in an attempt to better understand regional cellular activity in heterogeneous skeletal muscle tissue. Methods The 3′ Visium spatial transcriptomics technology was applied to muscle tissue of a rabbit model of rotator cuff tear. Healthy control and tissue collected at 2 and 16 weeks after tenotomy was utilized and freshly snap frozen tissue was compared with tissue stored for over 6 years to evaluate whether this technology is retrospectively useful in previously acquired tissues. Transcriptional information was overlayed with standard hematoxylin and eosin (H&E) stains of the exact same histological sections. Results Sequencing saturation and number of genes detected was not affected by sample storage duration. Unbiased clustering matched the underlying tissue type-based on H&E assessment. Connective-tissue-rich areas presented with lower unique molecular identifier counts are compared with muscle fibers even though tissue permeabilization was standardized across the section. A qualitative analysis of resulting datasets revealed heterogeneous fiber degeneration–regeneration after tenotomy based on (neonatal) myosin heavy chain 8 detection and associated differentially expressed gene analysis. Conclusions This protocol can be used in skeletal muscle to explore spatial transcriptional patterns and confidently relate them to the underlying histology, even for tissues that have been stored for up to 6 years. Using this protocol, there is potential for novel transcriptional pathway discovery in longitudinal studies since the transcriptional information is unbiased by muscle composition and cell type changes.
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Affiliation(s)
- Severin Ruoss
- Department of Orthopaedic Surgery, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0863, USA
| | - Mary C Esparza
- Department of Orthopaedic Surgery, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0863, USA
| | - Laura S Vasquez-Bolanos
- Department of Orthopaedic Surgery, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0863, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, UC San Diego, La Jolla, CA, USA
| | - Adam J Engler
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Samuel R Ward
- Department of Orthopaedic Surgery, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0863, USA. .,Department of Bioengineering, UC San Diego, La Jolla, CA, USA. .,Department of Radiology, UC San Diego, La Jolla, CA, USA.
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11
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Honda A, Hoeksema MA, Sakai M, Lund SJ, Lakhdari O, Butcher LD, Rambaldo TC, Sekiya NM, Nasamran CA, Fisch KM, Sajti E, Glass CK, Prince LS. The Lung Microenvironment Instructs Gene Transcription in Neonatal and Adult Alveolar Macrophages. J Immunol 2022; 208:1947-1959. [PMID: 35354612 PMCID: PMC9012679 DOI: 10.4049/jimmunol.2101192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
Immaturity of alveolar macrophages (AMs) around birth contributes to the susceptibility of newborns to lung disease. However, the molecular features differentiating neonatal and mature, adult AMs are poorly understood. In this study, we identify the unique transcriptomes and enhancer landscapes of neonatal and adult AMs in mice. Although the core AM signature was similar, murine adult AMs expressed higher levels of genes involved in lipid metabolism, whereas neonatal AMs expressed a largely proinflammatory gene profile. Open enhancer regions identified by an assay for transposase-accessible chromatin followed by high-throughput sequencing (ATAC-seq) contained motifs for nuclear receptors, MITF, and STAT in adult AMs and AP-1 and NF-κB in neonatal AMs. Intranasal LPS activated a similar innate immune response in both neonatal and adult mice, with higher basal expression of inflammatory genes in neonates. The lung microenvironment drove many of the distinguishing gene expression and open chromatin characteristics of neonatal and adult AMs. Neonatal mouse AMs retained high expression of some proinflammatory genes, suggesting that the differences in neonatal AMs result from both inherent cell properties and environmental influences.
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Affiliation(s)
- Asami Honda
- Department of Pediatrics, University of California, San Diego, La Jolla, CA.,Rady Children's Hospital, San Diego, CA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Sean J Lund
- Department of Pediatrics, University of California, San Diego, La Jolla, CA.,Rady Children's Hospital, San Diego, CA
| | - Omar Lakhdari
- Department of Pediatrics, University of California, San Diego, La Jolla, CA.,Rady Children's Hospital, San Diego, CA
| | - Lindsay D Butcher
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA
| | | | | | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA; and
| | - Eniko Sajti
- Department of Pediatrics, University of California, San Diego, La Jolla, CA.,Rady Children's Hospital, San Diego, CA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA.,Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Lawrence S Prince
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA;
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12
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Vasquez-Bolanos LS, Gibbons MC, Ruoss S, Wu IT, Vargas-Vila M, Hyman SA, Esparza MC, Fithian DC, Lane JG, Singh A, Nasamran CA, Fisch KM, Ward SR. Corrigendum: Transcriptional Time Course After Rotator Cuff Tear. Front Physiol 2021; 12:775297. [PMID: 34777027 PMCID: PMC8589024 DOI: 10.3389/fphys.2021.775297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Laura S Vasquez-Bolanos
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Michael C Gibbons
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Severin Ruoss
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Isabella T Wu
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Mario Vargas-Vila
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Sydnee A Hyman
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Mary C Esparza
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Donald C Fithian
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - John G Lane
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Anshuman Singh
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States.,Department of Orthopedic Surgery, Kaiser Permanente, San Diego, CA, United States
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Samuel R Ward
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States.,Department of Radiology, University of California, San Diego, San Diego, CA, United States
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13
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Moon JS, da Cunha FF, Huh JY, Andreyev AY, Lee J, Mahata SK, Reis FC, Nasamran CA, Lee YS. ANT2 drives proinflammatory macrophage activation in obesity. JCI Insight 2021; 6:147033. [PMID: 34676827 PMCID: PMC8564915 DOI: 10.1172/jci.insight.147033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
Macrophage proinflammatory activation is an important etiologic component of the development of insulin resistance and metabolic dysfunction in obesity. However, the underlying mechanisms are not clearly understood. Here, we demonstrate that a mitochondrial inner membrane protein, adenine nucleotide translocase 2 (ANT2), mediates proinflammatory activation of adipose tissue macrophages (ATMs) in obesity. Ant2 expression was increased in ATMs of obese mice compared with lean mice. Myeloid-specific ANT2-knockout (ANT2-MKO) mice showed decreased adipose tissue inflammation and improved insulin sensitivity and glucose tolerance in HFD/obesity. At the molecular level, we found that ANT2 mediates free fatty acid–induced mitochondrial permeability transition, leading to increased mitochondrial reactive oxygen species production and damage. In turn, this increased HIF-1α expression and NF-κB activation, leading to proinflammatory macrophage activation. Our results provide a previously unknown mechanism for how obesity induces proinflammatory activation of macrophages with propagation of low-grade chronic inflammation (metaflammation).
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Affiliation(s)
- Jae-Su Moon
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, California, USA
| | - Flavia Franco da Cunha
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, California, USA
| | - Jin Young Huh
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, California, USA
| | - Alexander Yu Andreyev
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, California, USA
| | - Jihyung Lee
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, California, USA
| | - Sushil K Mahata
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, California, USA.,VA San Diego Healthcare System, San Diego, California, USA
| | - Felipe Cg Reis
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, California, USA
| | - Chanond A Nasamran
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Yun Sok Lee
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, California, USA
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14
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Vasquez-Bolanos LS, Gibbons MC, Ruoss S, Wu IT, Vargas-Vila M, Hyman SA, Esparza MC, Fithian DC, Lane JG, Singh A, Nasamran CA, Fisch KM, Ward SR. Transcriptional Time Course After Rotator Cuff Tear. Front Physiol 2021; 12:707116. [PMID: 34421646 PMCID: PMC8378535 DOI: 10.3389/fphys.2021.707116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
Rotator cuff (RC) tears are prevalent in the population above the age of 60. The disease progression leads to muscle atrophy, fibrosis, and fatty infiltration in the chronic state, which is not improved with intervention or surgical repair. This highlights the need to better understand the underlying dysfunction in muscle after RC tendon tear. Contemporary studies aimed at understanding muscle pathobiology after RC tear have considered transcriptional data in mice, rats and sheep models at 2–3 time points (1 to 16 weeks post injury). However, none of these studies observed a transition or resurgence of gene expression after the initial acute time points. In this study, we collected rabbit supraspinatus muscle tissue with high temporal resolution (1, 2, 4, 8, and 16 weeks) post-tenotomy (n = 6/group), to determine if unique, time-dependent transcriptional changes occur. RNA sequencing and analyses were performed to identify a transcriptional timeline of RC muscle changes and related morphological sequelae. At 1-week post-tenotomy, the greatest number of differentially expressed genes was observed (1,069 up/873 down) which decreases through 2 (170/133), 4 (86/41), and 8 weeks (16/18), followed by a resurgence and transition of expression at 16 weeks (1,421/293), a behavior which previously has not been captured or reported. Broadly, 1-week post-tenotomy is an acute time point with expected immune system responses, catabolism, and changes in energy metabolism, which continues into 2 weeks with less intensity and greater contribution from mitochondrial effects. Expression shifts at 4 weeks post-tenotomy to fatty acid oxidation, lipolysis, and general upregulation of adipogenesis related genes. The effects of previous weeks’ transcriptional dysfunction present themselves at 8 weeks post-tenotomy with enriched DNA damage binding, aggresome activity, extracellular matrix-receptor changes, and significant expression of genes known to induce apoptosis. At 16 weeks post-tenotomy, there is a range of enriched pathways including extracellular matrix constituent binding, mitophagy, neuronal activity, immune response, and more, highlighting the chaotic nature of this time point and possibility of a chronic classification. Transcriptional activity correlated significantly with histological changes and were enriched for biologically relevant pathways such as lipid metabolism. These data provide platform for understanding the biological mechanisms of chronic muscle degeneration after RC tears.
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Affiliation(s)
- Laura S Vasquez-Bolanos
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Michael C Gibbons
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Severin Ruoss
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Isabella T Wu
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Mario Vargas-Vila
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Sydnee A Hyman
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Mary C Esparza
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Donald C Fithian
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - John G Lane
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States
| | - Anshuman Singh
- Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States.,Department of Orthopedic Surgery, Kaiser Permanente, San Diego, CA, United States
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Samuel R Ward
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Department of Orthopaedic Surgery, University of California, San Diego, San Diego, CA, United States.,Department of Radiology, University of California, San Diego, San Diego, CA, United States
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15
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Ruoss S, Walker JT, Nasamran CA, Fisch KM, Paez C, Parekh JN, Ball ST, Chen JL, Ahmed SS, Ward SR. Strategies to Identify Mesenchymal Stromal Cells in Minimally Manipulated Human Bone Marrow Aspirate Concentrate Lack Consensus. Am J Sports Med 2021; 49:1313-1322. [PMID: 33646886 PMCID: PMC8409176 DOI: 10.1177/0363546521993788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND There is a need to identify and quantify mesenchymal stromal cells (MSCs) in human bone marrow aspirate concentrate (BMAC) source tissues, but current methods to do so were established in cultured cell populations. Given that surface marker and gene expression change in cultured cells, it is doubtful that these strategies are valid to quantify MSCs in fresh BMAC. PURPOSE To establish the presence, quantity, and heterogeneity of BMAC-derived MSCs in minimally manipulated BMAC using currently available strategies. STUDY DESIGN Descriptive laboratory study. METHODS Five published strategies to identify MSCs were compared for suitability and efficiency to quantify clinical-grade BMAC-MSCs and cultured MSCs at the single cell transcriptome level on BMAC samples being used clinically from 15 orthopaedic patients and on 1 cultured MSC sample. Strategies included (1) the guidelines by the International Society for Cellular Therapy (ISCT), (2) CD271 expression, (3) the Ghazanfari et al transcriptional profile, (4) the Jia et al transcriptional profile, and (5) the Silva et al transcriptional profile. RESULTS ISCT guidelines did not identify any MSCs in BMAC at the transcriptional level and only 1 in 9 million cells at the protein level. Of 12,850 BMAC cells, 9 expressed the CD271 gene. Only 116 of 396 Ghazanfari genes were detected in BMAC, whereas no cells expressed all of them. No cells expressed all Jia genes, but 25 cells expressed at least 13 of 22. No cells expressed all Silva genes, but 19 cells expressed at least 8 of 23. Most importantly, the liberalized strategies tended to identify different cells and most of them clustered with immune cells. CONCLUSION Currently available methods need to be liberalized to identify any MSCs in fresh human BMAC and lack consensus at the single cell transcriptome and protein expression levels. These different cells should be isolated and challenged to establish phenotypic differences. CLINICAL RELEVANCE This study demonstrated that improved strategies to quantify MSC concentrations in BMAC for clinical applications are urgently needed. Until then, injected minimally manipulated MSC doses should be reported as rough estimates or as unknown.
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Affiliation(s)
- Severin Ruoss
- Department of Orthopaedic Surgery, UC San Diego, La Jolla CA, USA
| | - J. Todd Walker
- Department of Orthopaedic Surgery, UC San Diego, La Jolla CA, USA
| | - Chanond A. Nasamran
- Center for Computational Biology and Bioinformatics, Department of Medicine, UC San Diego, La Jolla CA, USA
| | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, Department of Medicine, UC San Diego, La Jolla CA, USA
| | - Conner Paez
- Department of Orthopaedic Surgery, UC San Diego, La Jolla CA, USA
| | - Jesal N. Parekh
- Department of Orthopaedic Surgery, UC San Diego, La Jolla CA, USA
| | - Scott T. Ball
- Department of Orthopaedic Surgery, UC San Diego, La Jolla CA, USA
| | - Jeffrey L. Chen
- Department of Orthopaedic Surgery, UC San Diego, La Jolla CA, USA
| | - Sonya S. Ahmed
- Department of Orthopaedic Surgery, UC San Diego, La Jolla CA, USA
| | - Samuel R. Ward
- Department of Orthopaedic Surgery, UC San Diego, La Jolla CA, USA
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16
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Nasamran CA, Sachan ANS, Mott J, Kuras YI, Scherzer CR, Study HB, Ricciardelli E, Jepsen K, Edland SD, Fisch KM, Desplats P. Differential blood DNA methylation across Lewy body dementias. Alzheimers Dement (Amst) 2021; 13:e12156. [PMID: 33665346 PMCID: PMC7896631 DOI: 10.1002/dad2.12156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are characterized by cognitive alterations, visual hallucinations, and motor impairment. Diagnosis is based on type and timing of clinical manifestations; however, determination of clinical subtypes is challenging. The utility of blood DNA methylation as a biomarker for Lewy body disorders (LBD) is mostly unexplored. METHODS We performed a cross-sectional analysis of blood methylation in 42 DLB and 50 PDD cases applying linear models to compare groups and logistic least absolute shrinkage and selection operator regression to explore the discriminant power of methylation signals. RESULTS DLB blood shows differential methylation compared to PDD. Some methylation changes associate with core features of LBD. Sets of probes show high predictive value to discriminate between variants. DISCUSSION Our study is the first to explore LBD blood methylation. Despite overlapping clinical presentation, we detected differential epigenetic signatures that, if confirmed in independent cohorts, could be developed into useful biomarkers.
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Affiliation(s)
- Chanond A. Nasamran
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Anubhav Nikunj Singh Sachan
- Division of Biostatistics, Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Jennifer Mott
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Yuliya I. Kuras
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | - Clemens R. Scherzer
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | | | - Eugenia Ricciardelli
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kristen Jepsen
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Steven D. Edland
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kathleen M. Fisch
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Paula Desplats
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Pathology, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
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17
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Espanola SG, Song H, Ryu E, Saxena A, Kim ES, Manegold JE, Nasamran CA, Sahoo D, Oh CK, Bickers C, Shin U, Grainger S, Park YH, Pandolfo L, Kang MS, Kang S, Myung K, Cooper KL, Yelon D, Traver D, Lee Y. Haematopoietic stem cell-dependent Notch transcription is mediated by p53 through the Histone chaperone Supt16h. Nat Cell Biol 2020; 22:1411-1422. [PMID: 33230303 PMCID: PMC8092813 DOI: 10.1038/s41556-020-00604-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/21/2020] [Indexed: 02/07/2023]
Abstract
Haematopoietic stem and progenitor cells (HSPCs) have been the focus of developmental and regenerative studies, yet our understanding of the signalling events regulating their specification remains incomplete. We demonstrate that supt16h, a component of the Facilitates chromatin transcription (FACT) complex, is required for HSPC formation. Zebrafish supt16h mutants express reduced levels of Notch-signalling components, genes essential for HSPC development, due to abrogated transcription. Whereas global chromatin accessibility in supt16h mutants is not substantially altered, we observe a specific increase in p53 accessibility, causing an accumulation of p53. We further demonstrate that p53 influences expression of the Polycomb-group protein PHC1, which functions as a transcriptional repressor of Notch genes. Suppression of phc1 or its upstream regulator, p53, rescues the loss of both Notch and HSPC phenotypes in supt16h mutants. Our results highlight a relationship between supt16h, p53 and phc1 to specify HSPCs via modulation of Notch signalling.
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Affiliation(s)
- Sophia G Espanola
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Hyemin Song
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Eunjin Ryu
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Aditya Saxena
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Eun-Sun Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Jennifer E Manegold
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Debashis Sahoo
- Department of Pediatrics and Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Chang-Kyu Oh
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Cara Bickers
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Unbeom Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Stephanie Grainger
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Yong Hwan Park
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Lauren Pandolfo
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Kimberly L Cooper
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Deborah Yelon
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - David Traver
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.
| | - Yoonsung Lee
- Department of Cellular and Molecular Medicine and Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea.
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
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18
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Ryan AF, Nasamran CA, Pak K, Draf C, Fisch KM, Webster N, Kurabi A. Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection. Front Genet 2020; 11:358. [PMID: 32351546 PMCID: PMC7174727 DOI: 10.3389/fgene.2020.00358] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 08/09/2019] [Accepted: 03/24/2020] [Indexed: 12/30/2022] Open
Abstract
Single-cell transcriptomics was used to profile cells of the normal murine middle ear. Clustering analysis of 6770 transcriptomes identified 17 cell clusters corresponding to distinct cell types: five epithelial, three stromal, three lymphocyte, two monocyte, two endothelial, one pericyte and one melanocyte cluster. Within some clusters, cell subtypes were identified. While many corresponded to those cell types known from prior studies, several novel types or subtypes were noted. The results indicate unexpected cellular diversity within the resting middle ear mucosa. The resolution of uncomplicated, acute, otitis media is too rapid for cognate immunity to play a major role. Thus innate immunity is likely responsible for normal recovery from middle ear infection. The need for rapid response to pathogens suggests that innate immune genes may be constitutively expressed by middle ear cells. We therefore assessed expression of innate immune genes across all cell types, to evaluate potential for rapid responses to middle ear infection. Resident monocytes/macrophages expressed the most such genes, including pathogen receptors, cytokines, chemokines and chemokine receptors. Other cell types displayed distinct innate immune gene profiles. Epithelial cells preferentially expressed pathogen receptors, bactericidal peptides and mucins. Stromal and endothelial cells expressed pathogen receptors. Pericytes expressed pro-inflammatory cytokines. Lymphocytes expressed chemokine receptors and antimicrobials. The results suggest that tissue monocytes, including macrophages, are the master regulators of the immediate middle ear response to infection, but that virtually all cell types act in concert to mount a defense against pathogens.
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Affiliation(s)
- Allen F. Ryan
- Departments of Surgery/Otolaryngology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States
| | - Chanond A. Nasamran
- Medicine/Center for Computational Biology & Bioinformatics, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States
| | - Kwang Pak
- Departments of Surgery/Otolaryngology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States
| | - Clara Draf
- Departments of Surgery/Otolaryngology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States
| | - Kathleen M. Fisch
- Medicine/Center for Computational Biology & Bioinformatics, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States
| | - Nicholas Webster
- Medicine/Endocrinology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States
| | - Arwa Kurabi
- Departments of Surgery/Otolaryngology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States
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19
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Cooke EJ, Wyseure T, Zhou JY, Gopal S, Nasamran CA, Fisch KM, Manon-Jensen T, Karsdal MA, Mosnier LO, von Drygalski A. Mechanisms of vascular permeability and remodeling associated with hemarthrosis in factor VIII-deficient mice. J Thromb Haemost 2019; 17:1815-1826. [PMID: 31301687 PMCID: PMC6824926 DOI: 10.1111/jth.14567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/19/2019] [Accepted: 07/06/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Vascular remodeling associated with hemophilic arthropathy (HA) may contribute to bleed propagation, but the mechanisms remain poorly understood. OBJECTIVES To explore molecular mechanisms of HA and the effects of hemostasis correction on synovial vascular remodeling after joint injury in hypocoagulable mice. METHODS Factor VIII (FVIII)-deficient mice +/- FVIII treatment and hypocoagulable wild-type mice (Hypo BALB/c) were subjected to subpatellar puncture. Hypo BALB/c mice were treated with warfarin and anti-FVIII before injury, after which warfarin was continued for 2 weeks or reversed +/- continuous anti-FVIII until harvest. Synovial vascularity was analyzed at baseline and 2 to 4 weeks post injury by histology, musculoskeletal ultrasound with power Doppler (microvascular flow), and Evans blue extravasation (vascular permeability). Synovial gene expression and systemic markers of vascular collagen turnover were studied in FVIII-deficient mice by RNA sequencing and enzyme-linked immunosorbent assay. RESULTS Vascular changes occurred in FVIII-deficient and Hypo BALB/c mice after injury with minimal effect of hemostasis correction. Increased vascular permeability was only significant in FVIII-deficient mice, who exhibited more pronounced vascular remodeling than Hypo BALB/c mice despite similar bleed volumes. FVIII-deficient mice exhibited a strong transcriptional response in synovium that was only partially affected by FVIII treatment and involved genes relating to angiogenesis and extracellular matrix remodeling, with vascular collagen turnover markers detected systemically. CONCLUSIONS Intact hemostasis at the time of hemarthrosis and during healing are both critical to prevent vascular remodeling, which appears worse with severe and prolonged FVIII deficiency. Unbiased RNA sequencing revealed potential targets for intervention and biomarker development to improve management of HA.
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Affiliation(s)
- Esther J Cooke
- University of California San Diego, Department of Medicine,
Division of Hematology/Oncology, La Jolla, CA, USA
- The Scripps Research Institute, Department of Molecular
Medicine, La Jolla, CA, USA
| | - Tine Wyseure
- The Scripps Research Institute, Department of Molecular
Medicine, La Jolla, CA, USA
| | - Jenny Y Zhou
- University of California San Diego, Department of Medicine,
Division of Hematology/Oncology, La Jolla, CA, USA
| | - Srila Gopal
- University of California San Diego, Department of Medicine,
Division of Hematology/Oncology, La Jolla, CA, USA
| | - Chanond A Nasamran
- University of California San Diego, Center for
Computational Biology and Bioinformatics, La Jolla, CA, USA
| | - Kathleen M Fisch
- University of California San Diego, Center for
Computational Biology and Bioinformatics, La Jolla, CA, USA
| | | | | | - Laurent O Mosnier
- The Scripps Research Institute, Department of Molecular
Medicine, La Jolla, CA, USA
| | - Annette von Drygalski
- University of California San Diego, Department of Medicine,
Division of Hematology/Oncology, La Jolla, CA, USA
- The Scripps Research Institute, Department of Molecular
Medicine, La Jolla, CA, USA
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20
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Jahedi A, Nasamran CA, Faires B, Fan J, Müller RA. Distributed Intrinsic Functional Connectivity Patterns Predict Diagnostic Status in Large Autism Cohort. Brain Connect 2018; 7:515-525. [PMID: 28825309 DOI: 10.1089/brain.2017.0496] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Diagnosis of autism spectrum disorder (ASD) currently relies on behavioral observations because brain markers are unknown. Machine learning approaches can identify patterns in imaging data that predict diagnostic status, but most studies using functional connectivity MRI (fcMRI) data achieved only modest accuracies of 60-80%. We used conditional random forest (CRF), an ensemble learning technique protected against bias from feature correlation (which exists in fcMRI matrices). We selected 252 low-motion resting-state functional MRI scans from the Autism Brain Imaging Data Exchange, including 126 typically developing (TD) and 126 ASD participants, matched for age, nonverbal IQ, and head motion. A matrix of functional connectivities between 220 functionally defined regions of interest was used for diagnostic classification. In several runs, we achieved accuracies of 92-99% for classifiers with >300 features (most informative connections). Features, including pericentral somatosensory and motor regions, were disproportionately informative. Findings differed partially from a previous study in the same sample that used feature selection with random forest (which is biased by feature correlations). External validation in a smaller in-house data set, however, achieved only 67-71% accuracy. The large number of features in optimal models can be attributed to etiological heterogeneity under the clinical ASD umbrella. Lower accuracy in external validation is expected due to differences in unknown composition of ASD variants across samples. High accuracy in the main data set is unlikely due to noise overfitting, but rather indicates optimized characterization of a given cohort.
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Affiliation(s)
- Afrooz Jahedi
- 1 Brain Development Imaging Laboratories, Department of Psychology, San Diego State University , San Diego, California.,2 Computational Science Research Center, San Diego State University , San Diego, California.,3 Department of Mathematics and Statistics, San Diego State University , San Diego, California
| | - Chanond A Nasamran
- 1 Brain Development Imaging Laboratories, Department of Psychology, San Diego State University , San Diego, California.,4 Department of Bioinformatics and Medical Informatics, San Diego State University , San Diego, California
| | - Brian Faires
- 1 Brain Development Imaging Laboratories, Department of Psychology, San Diego State University , San Diego, California.,4 Department of Bioinformatics and Medical Informatics, San Diego State University , San Diego, California
| | - Juanjuan Fan
- 3 Department of Mathematics and Statistics, San Diego State University , San Diego, California
| | - Ralph-Axel Müller
- 1 Brain Development Imaging Laboratories, Department of Psychology, San Diego State University , San Diego, California
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