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Wang S, Yao X, Ma S, Ping Y, Fan Y, Sun S, He Z, Shi Y, Sun L, Xiao S, Song M, Cai J, Li J, Tang R, Zhao L, Wang C, Wang Q, Zhao L, Hu H, Liu X, Sun G, Chen L, Pan G, Chen H, Li Q, Zhang P, Xu Y, Feng H, Zhao GG, Wen T, Yang Y, Huang X, Li W, Liu Z, Wang H, Wu H, Hu B, Ren Y, Zhou Q, Qu J, Zhang W, Liu GH, Bian XW. A single-cell transcriptomic landscape of the lungs of patients with COVID-19. Nat Cell Biol 2021; 23:1314-1328. [PMID: 34876692 PMCID: PMC8650955 DOI: 10.1038/s41556-021-00796-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 10/18/2021] [Indexed: 02/08/2023]
Abstract
The lung is the primary organ targeted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), making respiratory failure a leading coronavirus disease 2019 (COVID-19)-related mortality. However, our cellular and molecular understanding of how SARS-CoV-2 infection drives lung pathology is limited. Here we constructed multi-omics and single-nucleus transcriptomic atlases of the lungs of patients with COVID-19, which integrate histological, transcriptomic and proteomic analyses. Our work reveals the molecular basis of pathological hallmarks associated with SARS-CoV-2 infection in different lung and infiltrating immune cell populations. We report molecular fingerprints of hyperinflammation, alveolar epithelial cell exhaustion, vascular changes and fibrosis, and identify parenchymal lung senescence as a molecular state of COVID-19 pathology. Moreover, our data suggest that FOXO3A suppression is a potential mechanism underlying the fibroblast-to-myofibroblast transition associated with COVID-19 pulmonary fibrosis. Our work depicts a comprehensive cellular and molecular atlas of the lungs of patients with COVID-19 and provides insights into SARS-CoV-2-related pulmonary injury, facilitating the identification of biomarkers and development of symptomatic treatments.
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Wang S, Cheng F, Ji Q, Song M, Wu Z, Zhang Y, Ji Z, Feng H, Belmonte JCI, Zhou Q, Qu J, Li W, Liu GH, Zhang W. Hyperthermia differentially affects specific human stem cells and their differentiated derivatives. Protein Cell 2021; 13:615-622. [PMID: 34719769 PMCID: PMC9232687 DOI: 10.1007/s13238-021-00887-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Kang W, Jin T, Zhang T, Ma S, Yan H, Liu Z, Ji Z, Cai Y, Wang S, Song M, Ren J, Hu B, Zhou Q, Zhang W, Qu J, Bao Y, Liu GH. Regeneration Roadmap: database resources for regenerative biology. Nucleic Acids Res 2021; 50:D1085-D1090. [PMID: 34591960 PMCID: PMC8728239 DOI: 10.1093/nar/gkab870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
Regeneration plays an instrumental role in biological development and damage repair by constructing and replacing cells, tissues, and organs. Since regenerative capacity declines with age, promoting regeneration is heralded as a potential strategy for delaying aging. On this premise, mechanisms that regulate regeneration have been extensively studied across species and in different tissues. However, an open and comprehensive database collecting and standardizing the abundant data generated in regeneration research, such as high-throughput sequencing data, remains to be developed. In this work, we constructed Regeneration Roadmap to systematically and comprehensively collect such information over 2.38 million data entries across 11 species and 36 tissues, including regeneration-related genes, bulk and single-cell transcriptomics, epigenomics, and pharmacogenomics data. In this database, users can explore regulatory and expression changes of regeneration-associated genes in different species and tissues. Regeneration Roadmap provides the research community with a long-awaited and valuable data resource featuring convenient computing and visualizing tools, which is publicly available at https://ngdc.cncb.ac.cn/regeneration/index.
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Luo Q, Hofmann J, Song M, Pfeiffer R, Shiels M. Impact of overweight and obesity on U.S. renal cell carcinoma rates. Ann Epidemiol 2021. [DOI: 10.1016/j.annepidem.2021.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Li Z, Zhou Y, Tian G, Song M. Identification of Core Genes and Key Pathways in Gastric Cancer using Bioinformatics Analysis. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421080081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Diao Z, Ji Q, Wu Z, Zhang W, Cai Y, Wang Z, Hu J, Liu Z, Wang Q, Bi S, Huang D, Ji Z, Liu GH, Wang S, Song M, Qu J. Correction to 'SIRT3 consolidates heterochromatin and counteracts senescence'. Nucleic Acids Res 2021; 49:9004-9006. [PMID: 34370038 PMCID: PMC8421138 DOI: 10.1093/nar/gkab698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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Zhang X, Li MH, Chen SW, Yang ZY, Li QL, Yang AK, Zhang Q, Song M. [Transoral robotic surgery for parapharyngeal space neoplasm: a report of 7 cases]. ZHONGHUA ER BI YAN HOU TOU JING WAI KE ZA ZHI = CHINESE JOURNAL OF OTORHINOLARYNGOLOGY HEAD AND NECK SURGERY 2021; 56:730-735. [PMID: 34344100 DOI: 10.3760/cma.j.cn115330-20201101-00846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluate the safety, efficacy and feasibility of transoral robotic surgery (TORS) for parapharyngeal space (PPS) neoplasms. Methods: We collected data from 7 patients with PPS neoplasm who received TORS in Sun Yat-sen University Cancer Center between May 2017 and November 2020, and patients' clinical and pathological characteristics were analysed. There were 2 men and 5 women with age ranged from 35 to 76 years. Among them, 2 patients underwent secondary surgery, 2 patients required combined transcervical approach to complete surgery, and 1 patient was suspected of ipsilateral cervical lymph node metastasis and scheduled for diagnostic TORS. The preoperative tumor size, operation time, intraoperative blood loss, postoperative bleeding, dyspnea, neurological impairment, feeding time and postoperative hospital stay were analyzed. SPSS 24.0 was used to analyze the data. Results: TORS was performed successfully with complete removal of tumors in all 7 cases. Among 6 patients with curative TORS, 5 patients received TORS with postoperative diagnoses of neurogenic tumors and 1 patient underwent TORS combined transcervical approach with postoperative disgnosis of recurrent pleomorphic adenoma; no intraoperative tumor rupture occurred; the intraoperative blood loss was 20-200 ml with a median of 40 ml; the operation time was 65.0-238.0 min with a median of 77.5 min; the oral feeding time was 3-6 days with a median of 3 days; and the postoperative hospital stay was 4.2±1.6 days. One patient presented with neck swelling 3 days after surgery, but this symptom relieved 3 days later after treatments with antibiotic, hemostasis and detumescence. One patient received diagnostic TORS, as intraoperative pathology indicating a recurrent pleomorphic adenoma, then the neoplasm got completely resected through transcervical-transparotid approach. None of 7 patients manifested with airway obstruction, bleeding or nerve injury symptoms after operation. All patients were followed for 2 to 44 months, no local recurrence or distant metastasis was found. Conclusions: TORS is a safe, effective and feasible treatment for selected PPS neoplasms, with less cosmetic impact, less trauma and blood loss, few postoperative complications, enhanced postoperative recovery and short hospital stay.
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Wang W, Zheng Y, Sun S, Li W, Song M, Ji Q, Wu Z, Liu Z, Fan Y, Liu F, Li J, Esteban CR, Wang S, Zhou Q, Belmonte JCI, Zhang W, Qu J, Tang F, Liu GH. A genome-wide CRISPR-based screen identifies KAT7 as a driver of cellular senescence. Sci Transl Med 2021; 13:13/575/eabd2655. [PMID: 33408182 DOI: 10.1126/scitranslmed.abd2655] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022]
Abstract
Understanding the genetic and epigenetic bases of cellular senescence is instrumental in developing interventions to slow aging. We performed genome-wide CRISPR-Cas9-based screens using two types of human mesenchymal precursor cells (hMPCs) exhibiting accelerated senescence. The hMPCs were derived from human embryonic stem cells carrying the pathogenic mutations that cause the accelerated aging diseases Werner syndrome and Hutchinson-Gilford progeria syndrome. Genes whose deficiency alleviated cellular senescence were identified, including KAT7, a histone acetyltransferase, which ranked as a top hit in both progeroid hMPC models. Inactivation of KAT7 decreased histone H3 lysine 14 acetylation, repressed p15INK4b transcription, and alleviated hMPC senescence. Moreover, lentiviral vectors encoding Cas9/sg-Kat7, given intravenously, alleviated hepatocyte senescence and liver aging and extended life span in physiologically aged mice as well as progeroid Zmpste24-/- mice that exhibit a premature aging phenotype. CRISPR-Cas9-based genetic screening is a robust method for systematically uncovering senescence genes such as KAT7, which may represent a therapeutic target for developing aging interventions.
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Wang Y, Han D, Zhou T, Chen C, Cao H, Zhang JZ, Ma N, Liu C, Song M, Shi J, Jin X, Cao F, Dong N. DUSP26 induces aortic valve calcification by antagonizing MDM2-mediated ubiquitination of DPP4 in human valvular interstitial cells. Eur Heart J 2021; 42:2935-2951. [PMID: 34179958 DOI: 10.1093/eurheartj/ehab316] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/21/2021] [Accepted: 05/07/2021] [Indexed: 12/21/2022] Open
Abstract
AIMS The morbidity and mortality rates of calcific aortic valve disease (CAVD) remain high while treatment options are limited. Here, we evaluated the role and therapeutic value of dual-specificity phosphatase 26 (DUSP26) in CAVD. METHODS AND RESULTS Microarray profiling of human calcific aortic valves and normal controls demonstrated that DUSP26 was significantly up-regulated in calcific aortic valves. ApoE-/- mice fed a normal diet or a high cholesterol diet (HCD) were infected with adeno-associated virus serotype 2 carrying DUSP26 short-hairpin RNA to examine the effects of DUSP26 silencing on aortic valve calcification. DUSP26 silencing ameliorated aortic valve calcification in HCD-treated ApoE-/- mice, as evidenced by reduced thickness and calcium deposition in the aortic valve leaflets, improved echocardiographic parameters (decreased peak transvalvular jet velocity and mean transvalvular pressure gradient, as well as increased aortic valve area), and decreased levels of osteogenic markers (Runx2, osterix, and osteocalcin) in the aortic valves. These results were confirmed in osteogenic medium-induced human valvular interstitial cells. Immunoprecipitation, liquid chromatography-tandem mass spectrometry, and functional assays revealed that dipeptidyl peptidase-4 (DPP4) interacted with DUSP26 to mediate the procalcific effects of DUSP26. High N6-methyladenosine levels up-regulated DUSP26 in CAVD; in turn, DUSP26 activated DPP4 by antagonizing mouse double minute 2-mediated ubiquitination and degradation of DPP4, thereby promoting CAVD progression. CONCLUSION DUSP26 promotes aortic valve calcification by inhibiting DPP4 degradation. Our findings identify a previously unrecognized mechanism of DPP4 up-regulation in CAVD, suggesting that DUSP26 silencing or inhibition is a viable therapeutic strategy to impede CAVD progression.
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Griffiths CEM, Papp K, Song M, Miller M, You Y, Shen YK, Blauvelt A. AB0532 MAINTENANCE OF RESPONSE THROUGH 5 YEARS OF CONTINUOUS GUSELKUMAB TREATMENT: RESULTS FROM THE PHASE-3 VOYAGE 1 TRIAL. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:VOYAGE 1, a phase-3, double-blinded, placebo- and active comparator-controlled study evaluated the efficacy and safety of guselkumab (GUS; a fully human anti-interleukin-23 monoclonal antibody) in patients with moderate-to-severe plaque psoriasis.1,2,3Objectives:To assess the efficacy and safety through 5 years of continuous GUS treatment.Methods:In VOYAGE 1, patients were randomized to GUS 100 mg at Weeks 0, 4, 12, then every 8 weeks (q8w); placebo at Weeks 0, 4, 12 followed by GUS 100 mg at Weeks 16, 20 then q8w; or adalimumab 80 mg at Week 0, 40 mg at Week 1, then 40 mg every 2 weeks (q2w) through Week 47. At Week 52, all patients continued open-label GUS through Week 252. Efficacy assessments included proportions of patients achieving ≥90% or 100% improvement in Psoriasis Area and Severity Index (PASI 90, PASI 100), and Investigator’s Global Assessment scores of cleared/minimal or cleared (IGA 0/1, IGA 0). Three statistical methods were used to analyze efficacy: prespecified Treatment Failure Rules (TFR), Nonresponder Imputation (NRI), and As Observed (OBS). For TFR analyses, patients who discontinued study agent due to lack of efficacy, worsening of psoriasis, or use of a protocol-prohibited psoriasis treatment were considered nonresponders. For NRI analyses, patients with missing efficacy data (regardless of the reason) after application of TFR were counted as nonresponders. For OBS analyses, missing data were not imputed. Safety was assessed through Week 264.Results:Among a total of 494 patients randomized to GUS at Week 0 (N=329) and placebo patients who crossed over to GUS at Week 16 (N=165), 76.9% (380/494) continued study agent through Week 252. PASI 90 responses were well-maintained with up to 5 years of continuous GUS use. At Week 52, PASI 90 response rates were 79.7%, 75.5%, and 80.6% based on TFR, NRI, and OBS analyses, respectively; corresponding rates at Week 252 were 84.1%, 66.6%, and 86.6%. Likewise, PASI 100, IGA 0/1, and IGA 0 responses were maintained from Week 52 through Week 252 (Table 1). Efficacy was also maintained through Week 252 in patients randomized to GUS at Week 0 (N=329). Through the end of the study for all patients (GUS group and adalimumab→GUS crossover group; N=774), the proportion of patients reporting at least one adverse event (AE), serious AE, or discontinuation due to AEs were 87.7%, 16.4%, and 6.1%, respectively. Rates of AEs of interest through Week 264 were as follows: serious infections (2.8%), malignancies (nonmelanoma skin cancer [1.7%]; cancer other than nonmelanoma skin cancer [2.3%]), major adverse cardiovascular events (1.0%), and suicidal ideation and behavior (0.6%).Conclusion:High efficacy response rates were maintained (regardless of the method used to analyze data) and no new safety concerns were identified through 5 years of continuous GUS treatment in VOYAGE 1.References:[1]Blauvelt A et al. J Am Acad Derm 2017;76:405-417[2]Griffiths CEM et al. J Drugs Dermatol 2018;17:826-832[3]Griffiths CEM et al. J Dermatol Treat 2020;13:1-9Table 1.Proportion of Patients in the GUS Groupa Achieving Clinical Responses by Analysis Type at Week 52 and Week 252Week 52Week 252TFR (N=468)(%)NRI (N=494)(%)OBS (N=463)(%)TFR (N=391)(%)NRI (N=494)(%)OBS (N=380)(%) PASI 90 77.9 75.5 80.6 84.1 66.686.6 PASI 100 49.7 46.6 49.7 52.741.7 54.2 IGA 0 84.6 80.2 85.582.4 65.2 84.7IGA 0 53.3 50.854.254.743.356.3GUS, guselkumab; IGA, Investigator’s Global Assessment; NRI, nonresponder imputation method; OBS, As Observed method; PASI, Psoriasis Area and Severity Index; TFR, treatment failure rules methodaIncludes patients randomized to GUS and placebo patients who crossed over to GUS at Week 16Disclosure of Interests:Christopher E.M. Griffiths Speakers bureau: AbbVie, Eli Lilly, Janssen, Leo, Novartis, Pfizer, Sandoz, and Sun Pharma, Consultant of: AbbVie, Eli Lilly, Janssen, Leo, Novartis, Pfizer, Sandoz, and Sun Pharma, Grant/research support from: AbbVie, Eli Lilly, Janssen, Leo, Novartis, Pfizer, Sandoz, and Sun Pharma, Kim Papp Speakers bureau: AbbVie, Amgen, Astellas, Baxalta, Baxter, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Centocor, Dermira, Eli Lilly, Forward Pharma, Galderma, Genentech, GlaxoSmithKline, Janssen, Kyowa-Hakko Kirin, Leo Pharma, MedImmune, Merck-Serono, Merck Sharp & Dohme, Novartis, Pfizer, Regeneron, Roche, Sanofi-Genzyme, Stiefel, Sun Pharma, Takeda, UCB, and Valeant, Consultant of: AbbVie, Amgen, Astellas, Baxalta, Baxter, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Centocor, Dermira, Eli Lilly, Forward Pharma, Galderma, Genentech, GlaxoSmithKline, Janssen, Kyowa-Hakko Kirin, Leo Pharma, MedImmune, Merck-Serono, Merck Sharp & Dohme, Novartis, Pfizer, Regeneron, Roche, Sanofi-Genzyme, Stiefel, Sun Pharma, Takeda, UCB, and Valeant, Grant/research support from: AbbVie, Amgen, Astellas, Baxalta, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Centocor, Dermira, Eli Lilly, Galderma, Genentech, GlaxoSmithKline, Janssen, Kyowa-Hakko Kirin, Leo Pharma, MedImmune, Merck-Serono, Merck Sharp & Dohme, Novartis, Pfizer, Regeneron, Roche, Sanofi-Genzyme, Stiefel, Takeda, UCB, and Valeant, Michael Song Shareholder of: Johnson and Johnson, Employee of: Janssen Research & Development, LLC, Megan Miller Shareholder of: Johnson and Johnson, Employee of: Janssen Research & Development, LLC, Yin You Shareholder of: Johnson and Johnson, Employee of: Janssen Research & Development, LLC, Yaung-Kaung Shen Shareholder of: Johnson and Johnson, Employee of: Janssen Research & Development, LLC, Andrew Blauvelt Speakers bureau: AbbVie, Consultant of: AbbVie, Aclaris, Almirall, Arena, Athenex, Boehringer Ingelheim, Bristol-Myers Squibb, Dermavant, Dermira, Eli Lilly, FLX Bio, Forte, Galderma, Janssen, Leo, Novartis, Ortho, Pfizer, Regeneron, Sandoz, Sanofi Genzyme, Sun Pharma, and UCB Pharma.
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Diao Z, Ji Q, Wu Z, Zhang W, Cai Y, Wang Z, Hu J, Liu Z, Wang Q, Bi S, Huang D, Ji Z, Liu GH, Wang S, Song M, Qu J. SIRT3 consolidates heterochromatin and counteracts senescence. Nucleic Acids Res 2021; 49:4203-4219. [PMID: 33706382 PMCID: PMC8096253 DOI: 10.1093/nar/gkab161] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/09/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Sirtuin 3 (SIRT3) is an NAD+-dependent deacetylase linked to a broad range of physiological and pathological processes, including aging and aging-related diseases. However, the role of SIRT3 in regulating human stem cell homeostasis remains unclear. Here we found that SIRT3 expression was downregulated in senescent human mesenchymal stem cells (hMSCs). CRISPR/Cas9-mediated depletion of SIRT3 led to compromised nuclear integrity, loss of heterochromatin and accelerated senescence in hMSCs. Further analysis indicated that SIRT3 interacted with nuclear envelope proteins and heterochromatin-associated proteins. SIRT3 deficiency resulted in the detachment of genomic lamina-associated domains (LADs) from the nuclear lamina, increased chromatin accessibility and aberrant repetitive sequence transcription. The re-introduction of SIRT3 rescued the disorganized heterochromatin and the senescence phenotypes. Taken together, our study reveals a novel role for SIRT3 in stabilizing heterochromatin and counteracting hMSC senescence, providing new potential therapeutic targets to ameliorate aging-related diseases.
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Yan P, Liu Z, Song M, Wu Z, Xu W, Li K, Ji Q, Wang S, Liu X, Yan K, Esteban CR, Ci W, Belmonte JCI, Xie W, Ren J, Zhang W, Sun Q, Qu J, Liu GH. Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming. Cell Rep 2021; 32:107870. [PMID: 32640235 DOI: 10.1016/j.celrep.2020.107870] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/01/2020] [Accepted: 06/15/2020] [Indexed: 12/14/2022] Open
Abstract
DNA:RNA hybrids play key roles in both physiological and disease states by regulating chromatin and genome organization. Their homeostasis during cell differentiation and cell plasticity remains elusive. Using an isogenic human stem cell platform, we systematically characterize R-loops, DNA methylation, histone modifications, and chromatin accessibility in pluripotent cells and their lineage-differentiated derivatives. We confirm that a portion of R-loops formed co-transcriptionally at pluripotency genes in pluripotent stem cells and at lineage-controlling genes in differentiated lineages. Notably, a subset of R-loops maintained after differentiation are associated with repressive chromatin marks on silent pluripotency genes and undesired lineage genes. Moreover, in reprogrammed pluripotent cells, cell-of-origin-specific R-loops are initially present but are resolved with serial passaging. Our analysis suggests a multifaceted role of R-loops in cell fate determination that may serve as an additional layer of modulation on cell fate memory and cell plasticity.
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Yue Y, Hur J, Cao Y, Tabung FK, Wang M, Wu K, Song M, Zhang X, Liu Y, Meyerhardt JA, Ng K, Smith-Warner SA, Willett WC, Giovannucci E. Prospective evaluation of dietary and lifestyle pattern indices with risk of colorectal cancer in a cohort of younger women. Ann Oncol 2021; 32:778-786. [PMID: 33812017 DOI: 10.1016/j.annonc.2021.03.200] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Although colorectal cancer (CRC) incidence in the USA is declining overall, its incidence is increasing among those younger than 50 years of age. The reasons underlying the increasing trend are largely unknown, although behavioral changes, such as unhealthy diet and lifestyle factors, may be partially responsible. DESIGN A prospective cohort study included 94 217 women aged 26-45 years at baseline. Validated anthropometric measures and lifestyle information were self-reported biennially. Exposures were four recommendation-based dietary indices-the prime diet quality score and three plant-based dietary indices; and two mechanism-based indices-the empirical dietary and lifestyle index for hyperinsulinemia (EDIH and ELIH). We calculated hazard ratios (HRs) and 95% confidence intervals (CIs) for overall CRC and for early-onset (before age 50) and after age 50 CRC separately. RESULTS We documented 332 cases of CRC during 24 years of follow-up (2 113 655 person-years), with an average age of 52 ± 7 years at diagnosis. Hyperinsulinemic dietary and lifestyle patterns were associated with a higher risk of CRC. Multivariable-adjusted HRs (95% CIs) comparing participants in the highest versus lowest quartile were: 1.67 for EDIH (95% CI: 1.15-2.44, P-trend = 0.01) and 1.51 for ELIH (95% CI: 1.10-2.08, P-trend = 0.01). Moreover, per 75% increment in rank, ELIH appeared to be a stronger risk factor for early-onset CRC (HR = 1.86, 95% CI: 1.12-3.07) than after age 50 CRC (HR = 1.20, 95% CI: 0.83-1.73, P-heterogeneity = 0.16). The four recommendation-based indices were not significantly associated with overall, early-onset, or after age 50 CRC risk (per 75% increment in rank, HRs ranged from 0.75 to 1.28). CONCLUSION Dietary and lifestyle patterns contributing to hyperinsulinemia were associated with greater CRC risk in younger women. Moreover, the hyperinsulinemic lifestyle showed a suggestively stronger positive association with early-onset CRC risk, compared with after age 50 CRC. Our findings suggest that dietary and lifestyle interventions to reduce insulinemic potential may be effective for CRC prevention among younger women.
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Zhou H, Zhang Y, Zhao Y, Ji L, Song M, Li P, Guan Y, Xia X, Zhou N. FP10.03 Multi-Region Exome Sequencing Reveals the Intratumoral Heterogeneity of Surgically Resected Small Cell Lung Cancer. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Li H, Wu Z, Liu X, Zhang S, Ji Q, Jiang X, Liu Z, Wang S, Qu J, Zhang W, Song M, Song E, Liu GH. ALKBH1 deficiency leads to loss of homeostasis in human diploid somatic cells. Protein Cell 2021; 11:688-695. [PMID: 32661925 PMCID: PMC7452965 DOI: 10.1007/s13238-020-00744-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Liu GH, Bao Y, Qu J, Zhang W, Zhang T, Kang W, Yang F, Ji Q, Jiang X, Ma Y, Ma S, Liu Z, Chen S, Wang S, Sun S, Geng L, Yan K, Yan P, Fan Y, Song M, Ren J, Wang Q, Yang S, Yang Y, Xiong M, Liang C, Li LZ, Cao T, Hu J, Yang P, Ping J, Hu H, Zheng Y, Sun G, Li J, Liu L, Zou Z, Ding Y, Li M, Liu D, Wang M, Ji Q, Sun X, Wang C, Bi S, Shan H, Zhuo X. Aging Atlas: a multi-omics database for aging biology. Nucleic Acids Res 2021; 49:D825-D830. [PMID: 33119753 PMCID: PMC7779027 DOI: 10.1093/nar/gkaa894] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022] Open
Abstract
Organismal aging is driven by interconnected molecular changes encompassing internal and extracellular factors. Combinational analysis of high-throughput 'multi-omics' datasets (gathering information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and pharmacogenomics), at either populational or single-cell levels, can provide a multi-dimensional, integrated profile of the heterogeneous aging process with unprecedented throughput and detail. These new strategies allow for the exploration of the molecular profile and regulatory status of gene expression during aging, and in turn, facilitate the development of new aging interventions. With a continually growing volume of valuable aging-related data, it is necessary to establish an open and integrated database to support a wide spectrum of aging research. The Aging Atlas database aims to provide a wide range of life science researchers with valuable resources that allow access to a large-scale of gene expression and regulation datasets created by various high-throughput omics technologies. The current implementation includes five modules: transcriptomics (RNA-seq), single-cell transcriptomics (scRNA-seq), epigenomics (ChIP-seq), proteomics (protein-protein interaction), and pharmacogenomics (geroprotective compounds). Aging Atlas provides user-friendly functionalities to explore age-related changes in gene expression, as well as raw data download services. Aging Atlas is freely available at https://bigd.big.ac.cn/aging/index.
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Song M, Zhang Q, Xu H, Li W, Shi H, Song C. Development of nomograms predicting overall survival of breast cancer based on indicators of nutritional status: An observational prospective study. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2020.09.267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zou Z, Long X, Zhao Q, Zheng Y, Song M, Ma S, Jing Y, Wang S, He Y, Esteban CR, Yu N, Huang J, Chan P, Chen T, Izpisua Belmonte JC, Zhang W, Qu J, Liu GH. A Single-Cell Transcriptomic Atlas of Human Skin Aging. Dev Cell 2020; 56:383-397.e8. [PMID: 33238152 DOI: 10.1016/j.devcel.2020.11.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/26/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022]
Abstract
Skin undergoes constant self-renewal, and its functional decline is a visible consequence of aging. Understanding human skin aging requires in-depth knowledge of the molecular and functional properties of various skin cell types. We performed single-cell RNA sequencing of human eyelid skin from healthy individuals across different ages and identified eleven canonical cell types, as well as six subpopulations of basal cells. Further analysis revealed progressive accumulation of photoaging-related changes and increased chronic inflammation with age. Transcriptional factors involved in the developmental process underwent early-onset decline during aging. Furthermore, inhibition of key transcription factors HES1 in fibroblasts and KLF6 in keratinocytes not only compromised cell proliferation, but also increased inflammation and cellular senescence during aging. Lastly, we found that genetic activation of HES1 or pharmacological treatment with quercetin alleviated cellular senescence of dermal fibroblasts. These findings provide a single-cell molecular framework of human skin aging, providing a rich resource for developing therapeutic strategies against aging-related skin disorders.
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Wu Z, Shi Y, Lu M, Song M, Yu Z, Wang J, Wang S, Ren J, Yang YG, Liu GH, Zhang W, Ci W, Qu J. METTL3 counteracts premature aging via m6A-dependent stabilization of MIS12 mRNA. Nucleic Acids Res 2020; 48:11083-11096. [PMID: 33035345 PMCID: PMC7641765 DOI: 10.1093/nar/gkaa816] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/31/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
N6-Methyladenosine (m6A) messenger RNA methylation is a well-known epitranscriptional regulatory mechanism affecting central biological processes, but its function in human cellular senescence remains uninvestigated. Here, we found that levels of both m6A RNA methylation and the methyltransferase METTL3 were reduced in prematurely senescent human mesenchymal stem cell (hMSC) models of progeroid syndromes. Transcriptional profiling of m6A modifications further identified MIS12, for which m6A modifications were reduced in both prematurely senescent hMSCs and METTL3-deficient hMSCs. Knockout of METTL3 accelerated hMSC senescence whereas overexpression of METTL3 rescued the senescent phenotypes. Mechanistically, loss of m6A modifications accelerated the turnover and decreased the expression of MIS12 mRNA while knockout of MIS12 accelerated cellular senescence. Furthermore, m6A reader IGF2BP2 was identified as a key player in recognizing and stabilizing m6A-modified MIS12 mRNA. Taken together, we discovered that METTL3 alleviates hMSC senescence through m6A modification-dependent stabilization of the MIS12 transcript, representing a novel epitranscriptional mechanism in premature stem cell senescence.
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Aartsen MG, Abbasi R, Ackermann M, Adams J, Aguilar JA, Ahlers M, Ahrens M, Alispach C, Amin NM, Andeen K, Anderson T, Ansseau I, Anton G, Argüelles C, Auffenberg J, Axani S, Bagherpour H, Bai X, Balagopal A, Barbano A, Barwick SW, Bastian B, Basu V, Baum V, Baur S, Bay R, Beatty JJ, Becker KH, Becker Tjus J, BenZvi S, Berley D, Bernardini E, Besson DZ, Binder G, Bindig D, Blaufuss E, Blot S, Bohm C, Böser S, Botner O, Böttcher J, Bourbeau E, Bourbeau J, Bradascio F, Braun J, Bron S, Brostean-Kaiser J, Burgman A, Buscher J, Busse RS, Carver T, Chen C, Cheung E, Chirkin D, Choi S, Clark BA, Clark K, Classen L, Coleman A, Collin GH, Conrad JM, Coppin P, Correa P, Cowen DF, Cross R, Dave P, De Clercq C, DeLaunay JJ, Dembinski H, Deoskar K, De Ridder S, Desai A, Desiati P, de Vries KD, de Wasseige G, de With M, DeYoung T, Dharani S, Diaz A, Díaz-Vélez JC, Dujmovic H, Dunkman M, DuVernois MA, Dvorak E, Ehrhardt T, Eller P, Engel R, Evenson PA, Fahey S, Fazely AR, Fedynitch A, Felde J, Fienberg AT, Filimonov K, Finley C, Fox D, Franckowiak A, Friedman E, Fritz A, Gaisser TK, Gallagher J, Ganster E, Garrappa S, Gerhardt L, Glauch T, Glüsenkamp T, Goldschmidt A, Gonzalez JG, Grant D, Grégoire T, Griffith Z, Griswold S, Günder M, Gündüz M, Haack C, Hallgren A, Halliday R, Halve L, Halzen F, Hanson K, Hardin J, Haungs A, Hauser S, Hebecker D, Heereman D, Heix P, Helbing K, Hellauer R, Henningsen F, Hickford S, Hignight J, Hill GC, Hoffman KD, Hoffmann R, Hoinka T, Hokanson-Fasig B, Hoshina K, Huang F, Huber M, Huber T, Hultqvist K, Hünnefeld M, Hussain R, In S, Iovine N, Ishihara A, Jansson M, Japaridze GS, Jeong M, Jones BJP, Jonske F, Joppe R, Kang D, Kang W, Kappes A, Kappesser D, Karg T, Karl M, Karle A, Katz U, Kauer M, Kellermann M, Kelley JL, Kheirandish A, Kim J, Kintscher T, Kiryluk J, Kittler T, Klein SR, Koirala R, Kolanoski H, Köpke L, Kopper C, Kopper S, Koskinen DJ, Koundal P, Kowalski M, Krings K, Krückl G, Kulacz N, Kurahashi N, Kyriacou A, Lanfranchi JL, Larson MJ, Lauber F, Lazar JP, Leonard K, Leszczyńska A, Li Y, Liu QR, Lohfink E, Lozano Mariscal CJ, Lu L, Lucarelli F, Ludwig A, Lünemann J, Luszczak W, Lyu Y, Ma WY, Madsen J, Maggi G, Mahn KBM, Makino Y, Mallik P, Mancina S, Mariş IC, Maruyama R, Mase K, Maunu R, McNally F, Meagher K, Medici M, Medina A, Meier M, Meighen-Berger S, Merz J, Meures T, Micallef J, Mockler D, Momenté G, Montaruli T, Moore RW, Morse R, Moulai M, Muth P, Nagai R, Naumann U, Neer G, Nguyen LV, Niederhausen H, Nisa MU, Nowicki SC, Nygren DR, Obertacke Pollmann A, Oehler M, Olivas A, O'Murchadha A, O'Sullivan E, Palczewski T, Pandya H, Pankova DV, Park N, Parker GK, Paudel EN, Peiffer P, Pérez de Los Heros C, Philippen S, Pieloth D, Pieper S, Pinat E, Pizzuto A, Plum M, Popovych Y, Porcelli A, Prado Rodriguez M, Price PB, Przybylski GT, Raab C, Raissi A, Rameez M, Rauch L, Rawlins K, Rea IC, Rehman A, Reimann R, Relethford B, Renschler M, Renzi G, Resconi E, Rhode W, Richman M, Riedel B, Robertson S, Rongen M, Rott C, Ruhe T, Ryckbosch D, Rysewyk Cantu D, Safa I, Sanchez Herrera SE, Sandrock A, Sandroos J, Santander M, Sarkar S, Sarkar S, Satalecka K, Scharf M, Schaufel M, Schieler H, Schlunder P, Schmidt T, Schneider A, Schneider J, Schröder FG, Schumacher L, Sclafani S, Seckel D, Seunarine S, Shefali S, Silva M, Smithers B, Snihur R, Soedingrekso J, Soldin D, Song M, Spiczak GM, Spiering C, Stachurska J, Stamatikos M, Stanev T, Stein R, Stettner J, Steuer A, Stezelberger T, Stokstad RG, Stößl A, Strotjohann NL, Stürwald T, Stuttard T, Sullivan GW, Taboada I, Tenholt F, Ter-Antonyan S, Terliuk A, Tilav S, Tollefson K, Tomankova L, Tönnis C, Toscano S, Tosi D, Trettin A, Tselengidou M, Tung CF, Turcati A, Turcotte R, Turley CF, Ty B, Unger E, Unland Elorrieta MA, Usner M, Vandenbroucke J, Van Driessche W, van Eijk D, van Eijndhoven N, Vannerom D, van Santen J, Verpoest S, Vraeghe M, Walck C, Wallace A, Wallraff M, Watson TB, Weaver C, Weindl A, Weiss MJ, Weldert J, Wendt C, Werthebach J, Whelan BJ, Whitehorn N, Wiebe K, Wiebusch CH, Williams DR, Wills L, Wolf M, Wood TR, Woschnagg K, Wrede G, Wulff J, Xu XW, Xu Y, Yanez JP, Yodh G, Yoshida S, Yuan T, Zhang Z, Zöcklein M. eV-Scale Sterile Neutrino Search Using Eight Years of Atmospheric Muon Neutrino Data from the IceCube Neutrino Observatory. PHYSICAL REVIEW LETTERS 2020; 125:141801. [PMID: 33064514 DOI: 10.1103/physrevlett.125.141801] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
The results of a 3+1 sterile neutrino search using eight years of data from the IceCube Neutrino Observatory are presented. A total of 305 735 muon neutrino events are analyzed in reconstructed energy-zenith space to test for signatures of a matter-enhanced oscillation that would occur given a sterile neutrino state with a mass-squared differences between 0.01 and 100 eV^{2}. The best-fit point is found to be at sin^{2}(2θ_{24})=0.10 and Δm_{41}^{2}=4.5 eV^{2}, which is consistent with the no sterile neutrino hypothesis with a p value of 8.0%.
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Zheng Y, Liu X, Le W, Xie L, Li H, Wen W, Wang S, Ma S, Huang Z, Ye J, Shi W, Ye Y, Liu Z, Song M, Zhang W, Han JDJ, Belmonte JCI, Xiao C, Qu J, Wang H, Liu GH, Su W. A human circulating immune cell landscape in aging and COVID-19. Protein Cell 2020; 11:740-770. [PMID: 32780218 PMCID: PMC7417788 DOI: 10.1007/s13238-020-00762-2] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/01/2020] [Indexed: 12/21/2022] Open
Abstract
Age-associated changes in immune cells have been linked to an increased risk for infection. However, a global and detailed characterization of the changes that human circulating immune cells undergo with age is lacking. Here, we combined scRNA-seq, mass cytometry and scATAC-seq to compare immune cell types in peripheral blood collected from young and old subjects and patients with COVID-19. We found that the immune cell landscape was reprogrammed with age and was characterized by T cell polarization from naive and memory cells to effector, cytotoxic, exhausted and regulatory cells, along with increased late natural killer cells, age-associated B cells, inflammatory monocytes and age-associated dendritic cells. In addition, the expression of genes, which were implicated in coronavirus susceptibility, was upregulated in a cell subtype-specific manner with age. Notably, COVID-19 promoted age-induced immune cell polarization and gene expression related to inflammation and cellular senescence. Therefore, these findings suggest that a dysregulated immune system and increased gene expression associated with SARS-CoV-2 susceptibility may at least partially account for COVID-19 vulnerability in the elderly.
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Tian G, Wang SW, Song M, Hu YF, Cao XN, Ge JW. MicroRNA-16 inhibits the proliferation, migration and invasion of non-small cell lung carcinoma cells by down-regulating matrix metalloproteinase-19 expression. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2020; 23:5260-5269. [PMID: 31298377 DOI: 10.26355/eurrev_201906_18192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE This study aims to investigate the expression of microRNA (miR)-16 in non-small cell lung carcinoma (NSCLC) and to identify its potential mechanism. PATIENTS AND METHODS A total of 45 NSCLC patients were included in the present work. NSCLC tissues and adjacent normal tissues were resected and collected. The Reverse Transcription-quantitative Polymerase Chain Reaction was used to determine miR-16 expression. Regulatory effects of miR-16 on proliferation, migration and invasion, and cell cycle of A549 cells were determined by Cell-Counting Kit 8 assay, transwell assay, and flow cytometry, respectively. Western blotting was performed to measure the protein expression of matrix metalloproteinase (MMP)-19 in cells overexpressing miR-16. Dual-luciferase reporter gene assay was conducted to identify the interaction between miR-16 and MMP-19. RESULTS MiR-16 expression in NSCLC significantly decreased compared with that in healthy tissue (p<0.05). The expression level of miR-16 was negatively correlated to the clinical staging of NSCLC. In addition, the expression of miR-16 in NSCLC patients with lymph node metastasis was significantly lower than that in patients without lymph node metastasis (p<0.05). In vitro studies demonstrated that miR-16 inhibited the proliferation, migration, and invasion of A549 cells. Western blotting analyses indicated that overexpression of miR-16 down-regulated the expression of MMP-19. Additionally, the dual-luciferase reporter gene assay determined that miR-16 directly regulated the expression of MMP-16. CONCLUSIONS The present study demonstrates that miR-16 acts as a tumor-suppressor gene by inhibiting the proliferation, migration, and invasion of NSCLC cells via downregulating MMP-19 expression.
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Aartsen M, Abbasi R, Ackermann M, Adams J, Aguilar J, Ahlers M, Ahrens M, Alispach C, Amin N, Andeen K, Anderson T, Ansseau I, Anton G, Argüelles C, Auffenberg J, Axani S, Bagherpour H, Bai X, Balagopal V. A, Barbano A, Barwick S, Bastian B, Basu V, Baum V, Baur S, Bay R, Beatty J, Becker KH, Becker Tjus J, BenZvi S, Berley D, Bernardini E, Besson D, Binder G, Bindig D, Blaufuss E, Blot S, Bohm C, Böser S, Botner O, Böttcher J, Bourbeau E, Bourbeau J, Bradascio F, Braun J, Bron S, Brostean-Kaiser J, Burgman A, Buscher J, Busse R, Carver T, Chen C, Cheung E, Chirkin D, Choi S, Clark B, Clark K, Classen L, Coleman A, Collin G, Conrad J, Coppin P, Correa P, Cowen D, Cross R, Dave P, De Clercq C, DeLaunay J, Dembinski H, Deoskar K, De Ridder S, Desai A, Desiati P, de Vries K, de Wasseige G, de With M, DeYoung T, Dharani S, Diaz A, Díaz-Vélez J, Dujmovic H, Dunkman M, DuVernois M, Dvorak E, Ehrhardt T, Eller P, Engel R, Evenson P, Fahey S, Fazely A, Fedynitch A, Felde J, Fienberg A, Filimonov K, Finley C, Fox D, Franckowiak A, Friedman E, Fritz A, Gaisser T, Gallagher J, Ganster E, Garrappa S, Gerhardt L, Glauch T, Glüsenkamp T, Goldschmidt A, Gonzalez J, Grant D, Grégoire T, Griffith Z, Griswold S, Günder M, Gündüz M, Haack C, Hallgren A, Halliday R, Halve L, Halzen F, Hanson K, Hardin J, Haungs A, Hauser S, Hebecker D, Heereman D, Heix P, Helbing K, Hellauer R, Henningsen F, Hickford S, Hignight J, Hill G, Hoffman K, Hoffmann R, Hoinka T, Hokanson-Fasig B, Hoshina K, Huang F, Huber M, Huber T, Hultqvist K, Hünnefeld M, Hussain R, In S, Iovine N, Ishihara A, Jansson M, Japaridze G, Jeong M, Jones B, Jonske F, Joppe R, Kang D, Kang W, Kappes A, Kappesser D, Karg T, Karl M, Karle A, Katz U, Kauer M, Kellermann M, Kelley J, Kheirandish A, Kim J, Kintscher T, Kiryluk J, Kittler T, Klein S, Koirala R, Kolanoski H, Köpke L, Kopper C, Kopper S, Koskinen D, Koundal P, Kowalski M, Krings K, Krückl G, Kulacz N, Kurahashi N, Kyriacou A, Lanfranchi J, Larson M, Lauber F, Lazar J, Leonard K, Leszczyńska A, Li Y, Liu Q, Lohfink E, Lozano Mariscal C, Lu L, Lucarelli F, Ludwig A, Lünemann J, Luszczak W, Lyu Y, Ma W, Madsen J, Maggi G, Mahn K, Makino Y, Mallik P, Mancina S, Mariş I, Maruyama R, Mase K, Maunu R, McNally F, Meagher K, Medici M, Medina A, Meier M, Meighen-Berger S, Merz J, Meures T, Micallef J, Mockler D, Momenté G, Montaruli T, Moore R, Morse R, Moulai M, Muth P, Nagai R, Naumann U, Neer G, Nguyen L, Niederhausen H, Nisa M, Nowicki S, Nygren D, Obertacke Pollmann A, Oehler M, Olivas A, O’Murchadha A, O’Sullivan E, Palczewski T, Pandya H, Pankova D, Park N, Parker G, Paudel E, Peiffer P, Pérez de los Heros C, Philippen S, Pieloth D, Pieper S, Pinat E, Pizzuto A, Plum M, Popovych Y, Porcelli A, Prado Rodriguez M, Price P, Przybylski G, Raab C, Raissi A, Rameez M, Rauch L, Rawlins K, Rea I, Rehman A, Reimann R, Relethford B, Renschler M, Renzi G, Resconi E, Rhode W, Richman M, Riedel B, Robertson S, Rongen M, Rott C, Ruhe T, Ryckbosch D, Rysewyk Cantu D, Safa I, Sanchez Herrera S, Sandrock A, Sandroos J, Santander M, Sarkar S, Sarkar S, Satalecka K, Scharf M, Schaufel M, Schieler H, Schlunder P, Schmidt T, Schneider A, Schneider J, Schröder F, Schumacher L, Sclafani S, Seckel D, Seunarine S, Shefali S, Silva M, Smithers B, Snihur R, Soedingrekso J, Soldin D, Song M, Spiczak G, Spiering C, Stachurska J, Stamatikos M, Stanev T, Stein R, Stettner J, Steuer A, Stezelberger T, Stokstad R, Stößl A, Strotjohann N, Stürwald T, Stuttard T, Sullivan G, Taboada I, Tenholt F, Ter-Antonyan S, Terliuk A, Tilav S, Tollefson K, Tomankova L, Tönnis C, Toscano S, Tosi D, Trettin A, Tselengidou M, Tung C, Turcati A, Turcotte R, Turley C, Ty B, Unger E, Unland Elorrieta M, Usner M, Vandenbroucke J, Van Driessche W, van Eijk D, van Eijndhoven N, Vannerom D, van Santen J, Verpoest S, Vraeghe M, Walck C, Wallace A, Wallraff M, Watson T, Weaver C, Weindl A, Weiss M, Weldert J, Wendt C, Werthebach J, Whelan B, Whitehorn N, Wiebe K, Wiebusch C, Williams D, Wills L, Wolf M, Wood T, Woschnagg K, Wrede G, Wulff J, Xu X, Xu Y, Yanez J, Yodh G, Yoshida S, Yuan T, Zhang Z, Zöcklein M. Searching for eV-scale sterile neutrinos with eight years of atmospheric neutrinos at the IceCube Neutrino Telescope. Int J Clin Exp Med 2020. [DOI: 10.1103/physrevd.102.052009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Aartsen MG, Ackermann M, Adams J, Aguilar JA, Ahlers M, Ahrens M, Alispach C, Andeen K, Anderson T, Ansseau I, Anton G, Argüelles C, Auffenberg J, Axani S, Backes P, Bagherpour H, Bai X, Balagopal V A, Barbano A, Barwick SW, Bastian B, Baum V, Baur S, Bay R, Beatty JJ, Becker KH, Becker Tjus J, BenZvi S, Berley D, Bernardini E, Besson DZ, Binder G, Bindig D, Blaufuss E, Blot S, Bohm C, Böser S, Botner O, Böttcher J, Bourbeau E, Bourbeau J, Bradascio F, Braun J, Bron S, Brostean-Kaiser J, Burgman A, Buscher J, Busse RS, Carver T, Chen C, Cheung E, Chirkin D, Choi S, Clark K, Classen L, Coleman A, Collin GH, Conrad JM, Coppin P, Correa P, Cowen DF, Cross R, Dave P, De Clercq C, DeLaunay JJ, Dembinski H, Deoskar K, De Ridder S, Desiati P, de Vries KD, de Wasseige G, de With M, DeYoung T, Diaz A, Díaz-Vélez JC, Dujmovic H, Dunkman M, Dvorak E, Eberhardt B, Ehrhardt T, Eller P, Engel R, Evenson PA, Fahey S, Fazely AR, Felde J, Filimonov K, Finley C, Fox D, Franckowiak A, Friedman E, Fritz A, Gaisser TK, Gallagher J, Ganster E, Garrappa S, Gerhardt L, Ghorbani K, Glauch T, Glüsenkamp T, Goldschmidt A, Gonzalez JG, Grant D, Grégoire T, Griffith Z, Griswold S, Günder M, Gündüz M, Haack C, Hallgren A, Halliday R, Halve L, Halzen F, Hanson K, Haungs A, Hebecker D, Heereman D, Heix P, Helbing K, Hellauer R, Henningsen F, Hickford S, Hignight J, Hill GC, Hoffman KD, Hoffmann R, Hoinka T, Hokanson-Fasig B, Hoshina K, Huang F, Huber M, Huber T, Hultqvist K, Hünnefeld M, Hussain R, In S, Iovine N, Ishihara A, Jansson M, Japaridze GS, Jeong M, Jero K, Jones BJP, Jonske F, Joppe R, Kang D, Kang W, Kappes A, Kappesser D, Karg T, Karl M, Karle A, Katz U, Kauer M, Kelley JL, Kheirandish A, Kim J, Kintscher T, Kiryluk J, Kittler T, Klein SR, Koirala R, Kolanoski H, Köpke L, Kopper C, Kopper S, Koskinen DJ, Kowalski M, Krings K, Krückl G, Kulacz N, Kurahashi N, Kyriacou A, Lanfranchi JL, Larson MJ, Lauber F, Lazar JP, Leonard K, Lesiak-Bzdak M, Leszczyńska A, Leuermann M, Liu QR, Lohfink E, Lozano Mariscal CJ, Lu L, Lucarelli F, Lünemann J, Luszczak W, Lyu Y, Ma WY, Madsen J, Maggi G, Mahn KBM, Makino Y, Mallik P, Mallot K, Mancina S, Mariş IC, Maruyama R, Mase K, Maunu R, McNally F, Meagher K, Medici M, Medina A, Meier M, Meighen-Berger S, Merino G, Meures T, Micallef J, Mockler D, Momenté G, Montaruli T, Moore RW, Morse R, Moulai M, Muth P, Nagai R, Naumann U, Neer G, Niederhausen H, Nisa MU, Nowicki SC, Nygren DR, Obertacke Pollmann A, Oehler M, Olivas A, O'Murchadha A, O'Sullivan E, Palczewski T, Pandya H, Pankova DV, Park N, Peiffer P, Pérez de Los Heros C, Philippen S, Pieloth D, Pieper S, Pinat E, Pizzuto A, Plum M, Porcelli A, Price PB, Przybylski GT, Raab C, Raissi A, Rameez M, Rauch L, Rawlins K, Rea IC, Rehman A, Reimann R, Relethford B, Renschler M, Renzi G, Resconi E, Rhode W, Richman M, Robertson S, Rongen M, Rott C, Ruhe T, Ryckbosch D, Rysewyk D, Safa I, Sanchez Herrera SE, Sandrock A, Sandroos J, Santander M, Sarkar S, Sarkar S, Satalecka K, Schaufel M, Schieler H, Schlunder P, Schmidt T, Schneider A, Schneider J, Schröder FG, Schumacher L, Sclafani S, Seckel D, Seunarine S, Shefali S, Silva M, Snihur R, Soedingrekso J, Soldin D, Song M, Spiczak GM, Spiering C, Stachurska J, Stamatikos M, Stanev T, Stein R, Stettner J, Steuer A, Stezelberger T, Stokstad RG, Stößl A, Strotjohann NL, Stürwald T, Stuttard T, Sullivan GW, Taboada I, Tenholt F, Ter-Antonyan S, Terliuk A, Tilav S, Tollefson K, Tomankova L, Tönnis C, Toscano S, Tosi D, Trettin A, Tselengidou M, Tung CF, Turcati A, Turcotte R, Turley CF, Ty B, Unger E, Unland Elorrieta MA, Usner M, Vandenbroucke J, Van Driessche W, van Eijk D, van Eijndhoven N, van Santen J, Verpoest S, Vraeghe M, Walck C, Wallace A, Wallraff M, Wandkowsky N, Watson TB, Weaver C, Weindl A, Weiss MJ, Weldert J, Wendt C, Werthebach J, Whelan BJ, Whitehorn N, Wiebe K, Wiebusch CH, Wille L, Williams DR, Wills L, Wolf M, Wood J, Wood TR, Woschnagg K, Wrede G, Xu DL, Xu XW, Xu Y, Yanez JP, Yodh G, Yoshida S, Yuan T, Zöcklein M. Characteristics of the Diffuse Astrophysical Electron and Tau Neutrino Flux with Six Years of IceCube High Energy Cascade Data. PHYSICAL REVIEW LETTERS 2020; 125:121104. [PMID: 33016752 DOI: 10.1103/physrevlett.125.121104] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 06/02/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
We report on the first measurement of the astrophysical neutrino flux using particle showers (cascades) in IceCube data from 2010-2015. Assuming standard oscillations, the astrophysical neutrinos in this dedicated cascade sample are dominated (∼90%) by electron and tau flavors. The flux, observed in the sensitive energy range from 16 TeV to 2.6 PeV, is consistent with a single power-law model as expected from Fermi-type acceleration of high energy particles at astrophysical sources. We find the flux spectral index to be γ=2.53±0.07 and a flux normalization for each neutrino flavor of ϕ_{astro}=1.66_{-0.27}^{+0.25} at E_{0}=100 TeV, in agreement with IceCube's complementary muon neutrino results and with all-neutrino flavor fit results. In the measured energy range we reject spectral indices γ≤2.28 at ≥3σ significance level. Because of high neutrino energy resolution and low atmospheric neutrino backgrounds, this analysis provides the most detailed characterization of the neutrino flux at energies below ∼100 TeV compared to previous IceCube results. Results from fits assuming more complex neutrino flux models suggest a flux softening at high energies and a flux hardening at low energies (p value ≥0.06). The sizable and smooth flux measured below ∼100 TeV remains a puzzle. In order to not violate the isotropic diffuse gamma-ray background as measured by the Fermi Large Area Telescope, it suggests the existence of astrophysical neutrino sources characterized by dense environments which are opaque to gamma rays.
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Ma S, Sun S, Li J, Fan Y, Qu J, Sun L, Wang S, Zhang Y, Yang S, Liu Z, Wu Z, Zhang S, Wang Q, Zheng A, Duo S, Yu Y, Belmonte JCI, Chan P, Zhou Q, Song M, Zhang W, Liu GH. Single-cell transcriptomic atlas of primate cardiopulmonary aging. Cell Res 2020; 31:415-432. [PMID: 32913304 PMCID: PMC7483052 DOI: 10.1038/s41422-020-00412-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023] Open
Abstract
Aging is a major risk factor for many diseases, especially in highly prevalent cardiopulmonary comorbidities and infectious diseases including Coronavirus Disease 2019 (COVID-19). Resolving cellular and molecular mechanisms associated with aging in higher mammals is therefore urgently needed. Here, we created young and old non-human primate single-nucleus/cell transcriptomic atlases of lung, heart and artery, the top tissues targeted by SARS-CoV-2. Analysis of cell type-specific aging-associated transcriptional changes revealed increased systemic inflammation and compromised virus defense as a hallmark of cardiopulmonary aging. With age, expression of the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) was increased in the pulmonary alveolar epithelial barrier, cardiomyocytes, and vascular endothelial cells. We found that interleukin 7 (IL7) accumulated in aged cardiopulmonary tissues and induced ACE2 expression in human vascular endothelial cells in an NF-κB-dependent manner. Furthermore, treatment with vitamin C blocked IL7-induced ACE2 expression. Altogether, our findings depict the first transcriptomic atlas of the aged primate cardiopulmonary system and provide vital insights into age-linked susceptibility to SARS-CoV-2, suggesting that geroprotective strategies may reduce COVID-19 severity in the elderly.
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