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Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development. Nat Commun 2024; 15:2150. [PMID: 38459032 PMCID: PMC10923805 DOI: 10.1038/s41467-024-46457-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024] Open
Abstract
Fine-mapping and functional studies implicate rs117701653, a non-coding single nucleotide polymorphism in the CD28/CTLA4/ICOS locus, as a risk variant for rheumatoid arthritis and type 1 diabetes. Here, using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated risk allele is functional, reducing affinity for the inhibitory chromosomal regulator SMCHD1 to enhance expression of inducible T-cell costimulator (ICOS) in memory CD4+ T cells from healthy donors. Higher ICOS expression is paralleled by an increase in circulating T peripheral helper (Tph) cells and, in rheumatoid arthritis patients, of blood and joint fluid Tph cells as well as circulating plasmablasts. Correspondingly, ICOS ligation and carriage of the rs117701653 risk allele accelerate T cell differentiation into CXCR5-PD-1high Tph cells producing IL-21 and CXCL13. Thus, mechanistic dissection of a functional non-coding variant in human autoimmunity discloses a previously undefined pathway through which ICOS regulates Tph development and abundance.
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2
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Orthogonal inducible control of Cas13 circuits enables programmable RNA regulation in mammalian cells. Nat Commun 2024; 15:1572. [PMID: 38383558 PMCID: PMC10881482 DOI: 10.1038/s41467-024-45795-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
RNA plays an indispensable role in mammalian cell functions. Cas13, a class of RNA-guided ribonuclease, is a flexible tool for modifying and regulating coding and non-coding RNAs, with enormous potential for creating new cell functions. However, the lack of control over Cas13 activity has limited its cell engineering capability. Here, we present the CRISTAL (Control of RNA with Inducible SpliT CAs13 Orthologs and Exogenous Ligands) platform. CRISTAL is powered by a collection (10 total) of orthogonal split inducible Cas13 effectors that can be turned ON or OFF via small molecules in multiple cell types, providing precise temporal control. Also, we engineer Cas13 logic circuits that can respond to endogenous signaling and exogenous small molecule inputs. Furthermore, the orthogonality, low leakiness, and high dynamic range of our inducible Cas13d and Cas13b enable the design and construction of a robust incoherent feedforward loop, leading to near-perfect and tunable adaptation response. Finally, using our inducible Cas13 effectors, we achieve simultaneous multiplexed control of multiple genes in vitro and in mice. Together, our CRISTAL design represents a powerful platform for precisely regulating RNA dynamics to advance cell engineering and elucidate RNA biology.
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3
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Increased iron uptake by splenic hematopoietic stem cells promotes TET2-dependent erythroid regeneration. Nat Commun 2024; 15:538. [PMID: 38225226 PMCID: PMC10789814 DOI: 10.1038/s41467-024-44718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Hematopoietic stem cells (HSCs) are capable of regenerating the blood system, but the instructive cues that direct HSCs to regenerate particular lineages lost to the injury remain elusive. Here, we show that iron is increasingly taken up by HSCs during anemia and induces erythroid gene expression and regeneration in a Tet2-dependent manner. Lineage tracing of HSCs reveals that HSCs respond to hemolytic anemia by increasing erythroid output. The number of HSCs in the spleen, but not bone marrow, increases upon anemia and these HSCs exhibit enhanced proliferation, erythroid differentiation, iron uptake, and TET2 protein expression. Increased iron in HSCs promotes DNA demethylation and expression of erythroid genes. Suppressing iron uptake or TET2 expression impairs erythroid genes expression and erythroid differentiation of HSCs; iron supplementation, however, augments these processes. These results establish that the physiological level of iron taken up by HSCs has an instructive role in promoting erythroid-biased differentiation of HSCs.
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4
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OXR1 maintains the retromer to delay brain aging under dietary restriction. Nat Commun 2024; 15:467. [PMID: 38212606 PMCID: PMC10784588 DOI: 10.1038/s41467-023-44343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Dietary restriction (DR) delays aging, but the mechanism remains unclear. We identified polymorphisms in mtd, the fly homolog of OXR1, which influenced lifespan and mtd expression in response to DR. Knockdown in adulthood inhibited DR-mediated lifespan extension in female flies. We found that mtd/OXR1 expression declines with age and it interacts with the retromer, which regulates trafficking of proteins and lipids. Loss of mtd/OXR1 destabilized the retromer, causing improper protein trafficking and endolysosomal defects. Overexpression of retromer genes or pharmacological restabilization with R55 rescued lifespan and neurodegeneration in mtd-deficient flies and endolysosomal defects in fibroblasts from patients with lethal loss-of-function of OXR1 variants. Multi-omic analyses in flies and humans showed that decreased Mtd/OXR1 is associated with aging and neurological diseases. mtd/OXR1 overexpression rescued age-related visual decline and tauopathy in a fly model. Hence, OXR1 plays a conserved role in preserving retromer function and is critical for neuronal health and longevity.
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5
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Effectiveness of caffeine and blue-enriched light on cognitive performance and electroencephalography correlates of alertness in a spaceflight robotics simulation. NPJ Microgravity 2023; 9:93. [PMID: 38114500 PMCID: PMC10730879 DOI: 10.1038/s41526-023-00332-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/25/2023] [Indexed: 12/21/2023] Open
Abstract
Human cognitive impairment associated with sleep loss, circadian misalignment and work overload is a major concern in any high stress occupation but has potentially catastrophic consequences during spaceflight human robotic interactions. Two safe, wake-promoting countermeasures, caffeine and blue-enriched white light have been studied on Earth and are available on the International Space Station. We therefore conducted a randomized, placebo-controlled, cross-over trial examining the impact of regularly timed low-dose caffeine (0.3 mg per kg per h) and moderate illuminance blue-enriched white light (~90 lux, ~88 melEDI lux, 6300 K) as countermeasures, separately and combined, in a multi-night simulation of sleep-wake shifts experienced during spaceflight among 16 participants (7 F, ages 26-55). We find that chronic administration of low-dose caffeine improves subjective and objective correlates of alertness and performance during an overnight work schedule involving chronic sleep loss and circadian misalignment, although we also find that caffeine disrupts subsequent sleep. We further find that 90 lux of blue-enriched light moderately reduces electroencephalogram (EEG) power in the theta and delta regions, which are associated with sleepiness. These findings support the use of low-dose caffeine and potentially blue-enriched white light to enhance alertness and performance among astronauts and shiftworking populations.
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6
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Investigating genetically stratified subgroups to better understand the etiology of alcohol misuse. Mol Psychiatry 2023; 28:4225-4233. [PMID: 37488169 PMCID: PMC10827662 DOI: 10.1038/s41380-023-02174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 07/26/2023]
Abstract
Alcohol misuse (AM) is highly prevalent and harmful, with theorized subgroups differing on internalizing and externalizing dimensions. Despite known heterogeneity, genome-wide association studies (GWAS) are usually conducted on unidimensional phenotypes. These approaches have identified important genes related to AM but fail to capture a large part of the heritability, even with recent increases in sample sizes. This study aimed to address phenotypic heterogeneity in GWAS to aid gene finding and to uncover the etiology of different types of AM. Genetic and phenotypic data from 410,414 unrelated individuals of multiple ancestry groups (primarily European) in the UK Biobank were obtained. Mixture modeling was applied to measures of alcohol misuse and internalizing/externalizing psychopathology to uncover phenotypically homogenous subclasses, which were carried forward to GWAS and functional annotation. A four-class model emerged with "low risk", "internalizing-light/non-drinkers", "heavy alcohol use-low impairment", and "broad high risk" classes. SNP heritability ranged from 3 to 18% and both known AM signals and novel signals were captured by genomic risk loci. Class comparisons showed distinct patterns of regional brain tissue enrichment and genetic correlations with internalizing and externalizing phenotypes. Despite some limitations, this study demonstrated the utility of genetic research on homogenous subclasses. Not only were novel genetic signals identified that might be used for follow-up studies, but addressing phenotypic heterogeneity allows for the discovery and investigation of differential genetic vulnerabilities in the development of AM, which is an important step towards the goal of personalized medicine.
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7
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Author Correction: Single-nucleus multi-omics of human stem cell-derived islets identifies deficiencies in lineage specification. Nat Cell Biol 2023; 25:1546. [PMID: 37558893 PMCID: PMC10567556 DOI: 10.1038/s41556-023-01219-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
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8
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Brain mediators of negative affect-induced physical symptom reporting in patients with functional somatic syndromes. Transl Psychiatry 2023; 13:285. [PMID: 37604880 PMCID: PMC10442365 DOI: 10.1038/s41398-023-02567-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/23/2023] Open
Abstract
Functional somatic syndromes (FSS) include fibromyalgia, irritable bowel syndrome (IBS), and others. In FSS patients, merely viewing negative affective pictures can elicit increased physical symptoms. Our aim was to investigate the neural mechanisms underlying such negative affect-induced physical symptoms in FSS patients. Thirty patients with fibromyalgia and/or IBS and 30 healthy controls (all women) watched neutral, positive and negative affective picture blocks during functional MRI scanning and rated negative affect and physical symptoms after every block. We compared brain-wide activation during negative versus neutral picture viewing in FSS patients versus controls using robust general linear model analysis. Further, we compared neurologic pain signature (NPS), stimulus intensity-independent pain signature (SIIPS) and picture-induced negative emotion signature (PINES) responses to the negative versus neutral affect contrast and investigated whether they mediated between-group differences in affective picture-induced physical symptom reporting. More physical symptoms were reported after viewing negative compared to neutral pictures, and this effect was larger in patients than controls (p = 0.025). Accordingly, patients showed stronger activation in somatosensory regions during negative versus neutral picture viewing. NPS, but not SIIPS nor PINES, responses were higher in patients than controls during negative versus neutral pictures (p = 0.026). These differential NPS responses partially mediated between-group differences in physical symptoms. In conclusion, picture-induced negative affect elicits physical symptoms in FSS patients as a result of activation of somatosensory and nociceptive brain patterns, supporting the idea that affect-driven alterations in processing of somatic signals is a critical mechanism underlying FSS.
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9
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Deep-learning-enabled brain hemodynamic mapping using resting-state fMRI. NPJ Digit Med 2023; 6:116. [PMID: 37344684 PMCID: PMC10284915 DOI: 10.1038/s41746-023-00859-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/09/2023] [Indexed: 06/23/2023] Open
Abstract
Cerebrovascular disease is a leading cause of death globally. Prevention and early intervention are known to be the most effective forms of its management. Non-invasive imaging methods hold great promises for early stratification, but at present lack the sensitivity for personalized prognosis. Resting-state functional magnetic resonance imaging (rs-fMRI), a powerful tool previously used for mapping neural activity, is available in most hospitals. Here we show that rs-fMRI can be used to map cerebral hemodynamic function and delineate impairment. By exploiting time variations in breathing pattern during rs-fMRI, deep learning enables reproducible mapping of cerebrovascular reactivity (CVR) and bolus arrival time (BAT) of the human brain using resting-state CO2 fluctuations as a natural "contrast media". The deep-learning network is trained with CVR and BAT maps obtained with a reference method of CO2-inhalation MRI, which includes data from young and older healthy subjects and patients with Moyamoya disease and brain tumors. We demonstrate the performance of deep-learning cerebrovascular mapping in the detection of vascular abnormalities, evaluation of revascularization effects, and vascular alterations in normal aging. In addition, cerebrovascular maps obtained with the proposed method exhibit excellent reproducibility in both healthy volunteers and stroke patients. Deep-learning resting-state vascular imaging has the potential to become a useful tool in clinical cerebrovascular imaging.
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10
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Deep computational image analysis of immune cell niches reveals treatment-specific outcome associations in lung cancer. NPJ Precis Oncol 2023; 7:52. [PMID: 37264091 PMCID: PMC10235089 DOI: 10.1038/s41698-023-00403-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/19/2023] [Indexed: 06/03/2023] Open
Abstract
The tumor immune composition influences prognosis and treatment sensitivity in lung cancer. The presence of effective adaptive immune responses is associated with increased clinical benefit after immune checkpoint blockers. Conversely, immunotherapy resistance can occur as a consequence of local T-cell exhaustion/dysfunction and upregulation of immunosuppressive signals and regulatory cells. Consequently, merely measuring the amount of tumor-infiltrating lymphocytes (TILs) may not accurately reflect the complexity of tumor-immune interactions and T-cell functional states and may not be valuable as a treatment-specific biomarker. In this work, we investigate an immune-related biomarker (PhenoTIL) and its value in associating with treatment-specific outcomes in non-small cell lung cancer (NSCLC). PhenoTIL is a novel computational pathology approach that uses machine learning to capture spatial interplay and infer functional features of immune cell niches associated with tumor rejection and patient outcomes. PhenoTIL's advantage is the computational characterization of the tumor immune microenvironment extracted from H&E-stained preparations. Association with clinical outcome and major non-small cell lung cancer (NSCLC) histology variants was studied in baseline tumor specimens from 1,774 lung cancer patients treated with immunotherapy and/or chemotherapy, including the clinical trial Checkmate 057 (NCT01673867).
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11
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Single-nucleus multi-omics of human stem cell-derived islets identifies deficiencies in lineage specification. Nat Cell Biol 2023; 25:904-916. [PMID: 37188763 PMCID: PMC10264244 DOI: 10.1038/s41556-023-01150-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023]
Abstract
Insulin-producing β cells created from human pluripotent stem cells have potential as a therapy for insulin-dependent diabetes, but human pluripotent stem cell-derived islets (SC-islets) still differ from their in vivo counterparts. To better understand the state of cell types within SC-islets and identify lineage specification deficiencies, we used single-nucleus multi-omic sequencing to analyse chromatin accessibility and transcriptional profiles of SC-islets and primary human islets. Here we provide an analysis that enabled the derivation of gene lists and activity for identifying each SC-islet cell type compared with primary islets. Within SC-islets, we found that the difference between β cells and awry enterochromaffin-like cells is a gradient of cell states rather than a stark difference in identity. Furthermore, transplantation of SC-islets in vivo improved cellular identities overtime, while long-term in vitro culture did not. Collectively, our results highlight the importance of chromatin and transcriptional landscapes during islet cell specification and maturation.
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12
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Elucidating the molecular programming of a nonlinear non-ribosomal peptide synthetase responsible for fungal siderophore biosynthesis. Nat Commun 2023; 14:2832. [PMID: 37198174 PMCID: PMC10192304 DOI: 10.1038/s41467-023-38484-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/25/2023] [Indexed: 05/19/2023] Open
Abstract
Siderophores belonging to the ferrichrome family are essential for the viability of fungal species and play a key role for virulence of numerous pathogenic fungi. Despite their biological significance, our understanding of how these iron-chelating cyclic hexapeptides are assembled by non-ribosomal peptide synthetase (NRPS) enzymes remains poorly understood, primarily due to the nonlinearity exhibited by the domain architecture. Herein, we report the biochemical characterization of the SidC NRPS, responsible for construction of the intracellular siderophore ferricrocin. In vitro reconstitution of purified SidC reveals its ability to produce ferricrocin and its structural variant, ferrichrome. Application of intact protein mass spectrometry uncovers several non-canonical events during peptidyl siderophore biosynthesis, including inter-modular loading of amino acid substrates and an adenylation domain capable of poly-amide bond formation. This work expands the scope of NRPS programming, allows biosynthetic assignment of ferrichrome NRPSs, and sets the stage for reprogramming towards novel hydroxamate scaffolds.
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13
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A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. Nat Methods 2022; 19:1599-1611. [PMID: 36303018 PMCID: PMC10008172 DOI: 10.1038/s41592-022-01640-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 09/06/2022] [Indexed: 02/07/2023]
Abstract
Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 TOPMed samples. We also analyze five non-lipid TOPMed traits.
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Grants
- R01 DK078616 NIDDK NIH HHS
- U01 HG007417 NHGRI NIH HHS
- KL2 TR001100 NCATS NIH HHS
- R01 HL112064 NHLBI NIH HHS
- N01-HC-95160 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R35 HG010692 NHGRI NIH HHS
- U01-HL054472 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01-HL142711 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01-DK071891 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- F30 HL149180 NHLBI NIH HHS
- R01 NR019628 NINR NIH HHS
- R01 HL113323 NHLBI NIH HHS
- N01-HC-95166 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UL1RR033176 U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)
- R01 HL132947 NHLBI NIH HHS
- P30 DK040561 NIDDK NIH HHS
- U01 HL137183 NHLBI NIH HHS
- R01-HL127564 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P30 CA016672 NCI NIH HHS
- R01-HL071051 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL104135 NHLBI NIH HHS
- T32 HL144442 NHLBI NIH HHS
- R35 CA197449 NCI NIH HHS
- P30 ES010126 NIEHS NIH HHS
- DP5 OD029586 NIH HHS
- R01-NS058700 U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)
- R01 HL123915 NHLBI NIH HHS
- R01 HL120393 NHLBI NIH HHS
- R01HL071259 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL046380 NHLBI NIH HHS
- R01HL071251, R01HL071258, R01HL071259 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U54 HG003067 NHGRI NIH HHS
- 75N92020D00003 NHLBI NIH HHS
- K01 AG059898 NIA NIH HHS
- U01 DK085524 NIDDK NIH HHS
- KL2 TR002542 NCATS NIH HHS
- R01-HL055673-18S1 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R03 HL141439 NHLBI NIH HHS
- HHSN268201500001I NHLBI NIH HHS
- R01-MH078143, R01-MH078111, R01-MH083824 U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)
- U01 DK062413 NIDDK NIH HHS
- R01 HL109946 NHLBI NIH HHS
- U01-HL054495 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- K01 HL136700 NHLBI NIH HHS
- U19 CA203654 NCI NIH HHS
- R01-DK078616 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- U01 HL080295 NHLBI NIH HHS
- NO1-HC-25195 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HG006703 NHGRI NIH HHS
- UL1-TR-001420 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- U01 HG012064 NHGRI NIH HHS
- R35-CA197449 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- P30 ES005605 NIEHS NIH HHS
- R01 AR042742 NIAMS NIH HHS
- R21 HL140385 NHLBI NIH HHS
- HHSN268201800015I NHLBI NIH HHS
- U01 HL130114 NHLBI NIH HHS
- R01 HL117191 NHLBI NIH HHS
- R01 HG009974 NHGRI NIH HHS
- U01-HL054473 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 DK113003 NIDDK NIH HHS
- UL1RR033176 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL059367 NHLBI NIH HHS
- R24 AG047115 NIA NIH HHS
- U01-HL137181 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P01 HL107202 NHLBI NIH HHS
- NR0224103 U.S. Department of Health & Human Services | NIH | National Institute of Nursing Research (NINR)
- P50 HL118006 NHLBI NIH HHS
- U01-HL72518, HL087698, HL49762, HL59684, HL58625, HL071025, HL112064 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01 HL120393 NHLBI NIH HHS
- R01 DK117445 NIDDK NIH HHS
- R01-AG058921 U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- R03-HL154284 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UL1-TR-000040, UL1-TR-001079, UL1-TR-001420, UL1-TR-001881 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- R01 AG058921 NIA NIH HHS
- R01 HL129132 NHLBI NIH HHS
- R01 HL113338 NHLBI NIH HHS
- HHSN268201800012I NHLBI NIH HHS
- R01 HL153805 NHLBI NIH HHS
- R01 DK072193 NIDDK NIH HHS
- R01 HL137922 NHLBI NIH HHS
- R01 AI079139 NIAID NIH HHS
- N01-HC-95164 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01-DK085524 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- U19 AI111224 NIAID NIH HHS
- R35 HL135824 NHLBI NIH HHS
- 75N92019D00031 NHLBI NIH HHS
- R01 DK110113 NIDDK NIH HHS
- N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- N01-HC-95165 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL138737 NHLBI NIH HHS
- P30 DK079626 NIDDK NIH HHS
- R01 NS058700 NINDS NIH HHS
- R01 HL127564 NHLBI NIH HHS
- T32 HG000040 NHGRI NIH HHS
- DK063491 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01 HL141845 NHLBI NIH HHS
- R01 DK075787 NIDDK NIH HHS
- R01 AR072199 NIAMS NIH HHS
- R01 HL120854 NHLBI NIH HHS
- R01 HL163560 NHLBI NIH HHS
- R01HL071258 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01-HG009088 U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)
- R01 HL163972 NHLBI NIH HHS
- K23 HL123778 NHLBI NIH HHS
- U01 HL137181 NHLBI NIH HHS
- R01 MH078111 NIMH NIH HHS
- HHSN268201700005I NHLBI NIH HHS
- N01-HC-95159 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01-HL113323 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL141944 NHLBI NIH HHS
- R01 HL119443 NHLBI NIH HHS
- R01-HL071051, R01-HL071205, R01HL071250 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P60-AG10484 U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- 75N92020D00007 NHLBI NIH HHS
- UM1 AI068634 NIAID NIH HHS
- HHSN268201500003I NHLBI NIH HHS
- HHSN268201700004I NHLBI NIH HHS
- N01-HC-95163 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01-HL071205 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- F30 HL107066 NHLBI NIH HHS
- R01-HL153805 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL105756 NHLBI NIH HHS
- K01 HL125751 NHLBI NIH HHS
- R01 HL067348 NHLBI NIH HHS
- T32 HL007208 NHLBI NIH HHS
- R01 HL142711 NHLBI NIH HHS
- R35 HL135818 NHLBI NIH HHS
- R01-HL92301 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- T32 GM074897 NIGMS NIH HHS
- I01 BX005295 BLRD VA
- 75N92020D00001 NHLBI NIH HHS
- R01 HL113326 NHLBI NIH HHS
- R00 HL129045 NHLBI NIH HHS
- UL1-TR-000040 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- UL1-TR-001079 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- U01 HL072524 NHLBI NIH HHS
- R35-HL135818 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- K08 HL140203 NHLBI NIH HHS
- N01-HC-95162 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- K08 HL141601 NHLBI NIH HHS
- 75N92020D00005 NHLBI NIH HHS
- R01-DK117445 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01-AR48797 U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
- R56 AG058543 NIA NIH HHS
- U19 AI077439 NIAID NIH HHS
- R01 HL142028 NHLBI NIH HHS
- 75N92020D00004 NHLBI NIH HHS
- HHSN268201800011I NHLBI NIH HHS
- R35 GM127131 NIGMS NIH HHS
- U01 HL137880 NHLBI NIH HHS
- R01 HG010869 NHGRI NIH HHS
- R01-HL133040 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HHSN268201700003I NHLBI NIH HHS
- R01HL071250 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- N01-HC-95168 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL148239 NHLBI NIH HHS
- U01-HL137162 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 AI132476 NIAID NIH HHS
- T32 GM007205 NIGMS NIH HHS
- HHSN268201800010I NHLBI NIH HHS
- R01-HL092577-06S1 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UL1-TR-001881 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- R01-HL104135-04S1 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL132320 NHLBI NIH HHS
- U01 DK078616 NIDDK NIH HHS
- HHSN268201700001I NHLBI NIH HHS
- R01-HL141944 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01 HL137162 NHLBI NIH HHS
- R01 HG005701 NHGRI NIH HHS
- 75N92020D00001, 75N92020D00002, 75N92020D00003, 75N92020D00004 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01 HL143221 NHLBI NIH HHS
- R01 HL142992 NHLBI NIH HHS
- K01 HL129039 NHLBI NIH HHS
- R01 HL133870 NHLBI NIH HHS
- R01 DA037904 NIDA NIH HHS
- R21 HL123677 NHLBI NIH HHS
- R01 DK071891 NIDDK NIH HHS
- HHSN268201800001I U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- 75N92020D00002 NHLBI NIH HHS
- K01 HL130609 NHLBI NIH HHS
- N01-HC-95167 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- T32 HL007374 NHLBI NIH HHS
- N01-HC-95169 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01-DK078616 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01 AR063611 NIAMS NIH HHS
- KL2TR002490 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- R03 HL154284 NHLBI NIH HHS
- M01-RR000052 U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)
- 75N92020D00006 NHLBI NIH HHS
- S10 OD020069 NIH HHS
- R01 MD012765 NIMHD NIH HHS
- N01-HC-95161 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HHSN268201700002I NHLBI NIH HHS
- R01 HL151855 NHLBI NIH HHS
- K23 HL138461 NHLBI NIH HHS
- U01 CA182913 NCI NIH HHS
- UG3 HL151865 NHLBI NIH HHS
- F32 HL150992 NHLBI NIH HHS
- R01-MD012765 U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)
- 75N92020D00005, 75N92020D00006, 75N92020D00007 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01 MH101244 NIMH NIH HHS
- U01 HG009088 NHGRI NIH HHS
- N01-HC-95163, N01-HC-95164, N01-HC-95165, N01-HC-95166 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P42 ES016454 NIEHS NIH HHS
- UM1 DK078616 NIDDK NIH HHS
- U01-HL054509 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R35-HL135824 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- M01-RR07122 U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)
- U01 DK105561 NIDDK NIH HHS
- U01-HL072524 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P20 GM121334 NIGMS NIH HHS
- N01-HC-95167, N01-HC-95168, N01-HC-95169 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL131565 NHLBI NIH HHS
- R01HL071251 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R13 CA124365 NCI NIH HHS
- R01-HL045522 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P01 HL132825 NHLBI NIH HHS
- R01 HL118267 NHLBI NIH HHS
- HHSN268201800013I NIMHD NIH HHS
- R01-HL67348 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U54 GM115428 NIGMS NIH HHS
- R01 HL055673 NHLBI NIH HHS
- HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UM1-DK078616 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01 HL149683 NHLBI NIH HHS
- R01 HL092301 NHLBI NIH HHS
- P30 DK020595 NIDDK NIH HHS
- R01 HL149836 NHLBI NIH HHS
- K08 HL145095 NHLBI NIH HHS
- K01 HL135405 NHLBI NIH HHS
- R03 OD030608 NIH HHS
- HHSN268201800014I NHLBI NIH HHS
- R01-HL113338 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- F32-HL085989 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UM1 AI068636 NIAID NIH HHS
- R01 AG057381 NIA NIH HHS
- U19-CA203654 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
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14
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Enterotoxigenic Escherichia coli heat-labile toxin drives enteropathic changes in small intestinal epithelia. Nat Commun 2022; 13:6886. [PMID: 36371425 PMCID: PMC9653437 DOI: 10.1038/s41467-022-34687-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/01/2022] [Indexed: 11/14/2022] Open
Abstract
Enterotoxigenic E. coli (ETEC) produce heat-labile (LT) and/or heat-stable (ST) enterotoxins, and commonly cause diarrhea in resource-poor regions. ETEC have been linked repeatedly to sequelae in children including enteropathy, malnutrition, and growth impairment. Although cellular actions of ETEC enterotoxins leading to diarrhea are well-established, their contributions to sequelae remain unclear. LT increases cellular cAMP to activate protein kinase A (PKA) that phosphorylates ion channels driving intestinal export of salt and water resulting in diarrhea. As PKA also modulates transcription of many genes, we interrogated transcriptional profiles of LT-treated intestinal epithelia. Here we show that LT significantly alters intestinal epithelial gene expression directing biogenesis of the brush border, the major site for nutrient absorption, suppresses transcription factors HNF4 and SMAD4 critical to enterocyte differentiation, and profoundly disrupts microvillus architecture and essential nutrient transport. In addition, ETEC-challenged neonatal mice exhibit substantial brush border derangement that is prevented by maternal vaccination with LT. Finally, mice repeatedly challenged with toxigenic ETEC exhibit impaired growth recapitulating the multiplicative impact of recurring ETEC infections in children. These findings highlight impacts of ETEC enterotoxins beyond acute diarrheal illness and may inform approaches to prevent major sequelae of these common infections including malnutrition that impact millions of children.
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15
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Prostaglandin-based rAAV-mediated glaucoma gene therapy in Brown Norway rats. Commun Biol 2022; 5:1169. [PMID: 36329259 PMCID: PMC9633612 DOI: 10.1038/s42003-022-04134-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Prostaglandin analogs are first-line treatments for open angle glaucoma and while effective at lowering intraocular pressure, they are undermined by patient non-compliance, causing atrophy of the optic nerve and severe visual impairment. Herein, we evaluate the safety and efficacy of a recombinant adeno-associated viral vector-mediated gene therapy aimed at permanently lowering intraocular pressure through de novo biosynthesis of prostaglandin F2α within the anterior chamber. This study demonstrated a dose dependent reduction in intraocular pressure in normotensive Brown Norway rats maintained over 12-months. Crucially, therapy could be temporarily halted through off-type riboswitch activation, reverting intraocular pressure to normal. Longitudinal multimodal imaging, electrophysiology, and post-mortem histology revealed the therapy was well tolerated at low and medium doses, with no major adverse effects to anterior chamber health, offering a promising alternative to current treatment strategies leading to clinically relevant reductions in intraocular pressure without the need for adherence to a daily treatment regimen.
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16
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Structural characterization of a soil viral auxiliary metabolic gene product - a functional chitosanase. Nat Commun 2022; 13:5485. [PMID: 36123347 PMCID: PMC9485262 DOI: 10.1038/s41467-022-32993-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/26/2022] [Indexed: 11/12/2022] Open
Abstract
Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin - a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.
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17
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Age estimation from sleep studies using deep learning predicts life expectancy. NPJ Digit Med 2022; 5:103. [PMID: 35869169 PMCID: PMC9307657 DOI: 10.1038/s41746-022-00630-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/10/2022] [Indexed: 11/11/2022] Open
Abstract
Sleep disturbances increase with age and are predictors of mortality. Here, we present deep neural networks that estimate age and mortality risk through polysomnograms (PSGs). Aging was modeled using 2500 PSGs and tested in 10,699 PSGs from men and women in seven different cohorts aged between 20 and 90. Ages were estimated with a mean absolute error of 5.8 ± 1.6 years, while basic sleep scoring measures had an error of 14.9 ± 6.29 years. After controlling for demographics, sleep, and health covariates, each 10-year increment in age estimate error (AEE) was associated with increased all-cause mortality rate of 29% (95% confidence interval: 20-39%). An increase from -10 to +10 years in AEE translates to an estimated decreased life expectancy of 8.7 years (95% confidence interval: 6.1-11.4 years). Greater AEE was mostly reflected in increased sleep fragmentation, suggesting this is an important biomarker of future health independent of sleep apnea.
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18
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Insulin-like growth factor 1 receptor mediates photoreceptor neuroprotection. Cell Death Dis 2022; 13:613. [PMID: 35840554 PMCID: PMC9287313 DOI: 10.1038/s41419-022-05074-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 01/21/2023]
Abstract
Insulin-like growth factor I (IGF-1) is a neurotrophic factor and is the ligand for insulin-like growth factor 1 receptor (IGF-1R). Reduced expression of IGF-1 has been reported to cause deafness, mental retardation, postnatal growth failure, and microcephaly. IGF-1R is expressed in the retina and photoreceptor neurons; however, its functional role is not known. Global IGF-1 KO mice have age-related vision loss. We determined that conditional deletion of IGF-1R in photoreceptors and pan-retinal cells produces age-related visual function loss and retinal degeneration. Retinal pigment epithelial cell-secreted IGF-1 may be a source for IGF-1R activation in the retina. Altered retinal, fatty acid, and phosphoinositide metabolism are observed in photoreceptor and retinal cells lacking IGF-1R. Our results suggest that the IGF-1R pathway is indispensable for photoreceptor survival, and activation of IGF-1R may be an essential element of photoreceptor and retinal neuroprotection.
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19
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SARS-CoV-2 RBD trimer protein adjuvanted with Alum-3M-052 protects from SARS-CoV-2 infection and immune pathology in the lung. Nat Commun 2021; 12:3587. [PMID: 34117252 PMCID: PMC8196016 DOI: 10.1038/s41467-021-23942-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
There is a great need for the development of vaccines that induce potent and long-lasting protective immunity against SARS-CoV-2. Multimeric display of the antigen combined with potent adjuvant can enhance the potency and longevity of the antibody response. The receptor binding domain (RBD) of the spike protein is a primary target of neutralizing antibodies. Here, we developed a trimeric form of the RBD and show that it induces a potent neutralizing antibody response against live virus with diverse effector functions and provides protection against SARS-CoV-2 challenge in mice and rhesus macaques. The trimeric form induces higher neutralizing antibody titer compared to monomer with as low as 1μg antigen dose. In mice, adjuvanting the protein with a TLR7/8 agonist formulation alum-3M-052 induces 100-fold higher neutralizing antibody titer and superior protection from infection compared to alum. SARS-CoV-2 infection causes significant loss of innate cells and pathology in the lung, and vaccination protects from changes in innate cells and lung pathology. These results demonstrate RBD trimer protein as a suitable candidate for vaccine against SARS-CoV-2.
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20
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In vivo human whole-brain Connectom diffusion MRI dataset at 760 µm isotropic resolution. Sci Data 2021; 8:122. [PMID: 33927203 PMCID: PMC8084962 DOI: 10.1038/s41597-021-00904-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/26/2021] [Indexed: 01/18/2023] Open
Abstract
We present a whole-brain in vivo diffusion MRI (dMRI) dataset acquired at 760 μm isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy participant. The creation of this benchmark dataset is possible through the synergistic use of advanced acquisition hardware and software including the high-gradient-strength Connectom scanner, a custom-built 64-channel phased-array coil, a personalized motion-robust head stabilizer, a recently developed SNR-efficient dMRI acquisition method, and parallel imaging reconstruction with advanced ghost reduction algorithm. With its unprecedented resolution, SNR and image quality, we envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance the understanding of human brain structures and connectivity. This comprehensive dataset can also be used as a test bed for new modeling, sub-sampling strategies, denoising and processing algorithms, potentially providing a common testing platform for further development of in vivo high resolution dMRI techniques. Whole brain anatomical T1-weighted and T2-weighted images at submillimeter scale along with field maps are also made available.
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21
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Abstract
Prokaryotic cell transcriptomics has been limited to mixed or sub-population dynamics and individual cells within heterogeneous populations, which has hampered further understanding of spatiotemporal and stage-specific processes of prokaryotic cells within complex environments. Here we develop a 'TRANSITomic' approach to profile transcriptomes of single Burkholderia pseudomallei cells as they transit through host cell infection at defined stages, yielding pathophysiological insights. We find that B. pseudomallei transits through host cells during infection in three observable stages: vacuole entry; cytoplasmic escape and replication; and membrane protrusion, promoting cell-to-cell spread. The B. pseudomallei 'TRANSITome' reveals dynamic gene-expression flux during transit in host cells and identifies genes that are required for pathogenesis. We find several hypothetical proteins and assign them to virulence mechanisms, including attachment, cytoskeletal modulation, and autophagy evasion. The B. pseudomallei 'TRANSITome' provides prokaryotic single-cell transcriptomics information enabling high-resolution understanding of host-pathogen interactions.
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PD-1 pathway regulates ILC2 metabolism and PD-1 agonist treatment ameliorates airway hyperreactivity. Nat Commun 2020; 11:3998. [PMID: 32778730 PMCID: PMC7417739 DOI: 10.1038/s41467-020-17813-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023] Open
Abstract
Allergic asthma is a leading chronic disease associated with airway hyperreactivity (AHR). Type-2 innate lymphoid cells (ILC2s) are a potent source of T-helper 2 (Th2) cytokines that promote AHR and lung inflammation. As the programmed cell death protein-1 (PD-1) inhibitory axis regulates a variety of immune responses, here we investigate PD-1 function in pulmonary ILC2s during IL-33-induced airway inflammation. PD-1 limits the viability of ILC2s and downregulates their effector functions. Additionally, PD-1 deficiency shifts ILC2 metabolism toward glycolysis, glutaminolysis and methionine catabolism. PD-1 thus acts as a metabolic checkpoint in ILC2s, affecting cellular activation and proliferation. As the blockade of PD-1 exacerbates AHR, we also develop a human PD-1 agonist and show that it can ameliorate AHR and suppresses lung inflammation in a humanized mouse model. Together, these results highlight the importance of PD-1 agonistic treatment in allergic asthma and underscore its therapeutic potential.
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23
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Basement membrane damage by ROS- and JNK-mediated Mmp2 activation drives macrophage recruitment to overgrown tissue. Nat Commun 2020; 11:3631. [PMID: 32686670 PMCID: PMC7371875 DOI: 10.1038/s41467-020-17399-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 06/25/2020] [Indexed: 01/25/2023] Open
Abstract
Macrophages are a major immune cell type infiltrating tumors and promoting tumor growth and metastasis. To elucidate the mechanism of macrophage recruitment, we utilize an overgrowth tumor model ("undead" model) in larval Drosophila imaginal discs that are attached by numerous macrophages. Here we report that changes to the microenvironment of the overgrown tissue are important for recruiting macrophages. First, we describe a correlation between generation of reactive oxygen species (ROS) and damage of the basement membrane (BM) in all neoplastic, but not hyperplastic, models examined. ROS and the stress kinase JNK mediate the accumulation of matrix metalloproteinase 2 (Mmp2), damaging the BM, which recruits macrophages to the tissue. We propose a model where macrophage recruitment to and activation at overgrowing tissue is a multi-step process requiring ROS- and JNK-mediated Mmp2 upregulation and BM damage. These findings have implications for understanding the role of the tumor microenvironment for macrophage activation.
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Neural responsivity to social rewards in autistic female youth. Transl Psychiatry 2020; 10:178. [PMID: 32488083 PMCID: PMC7266816 DOI: 10.1038/s41398-020-0824-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 01/25/2023] Open
Abstract
Autism is hypothesized to be in part driven by a reduced sensitivity to the inherently rewarding nature of social stimuli. Previous neuroimaging studies have indicated that autistic males do indeed display reduced neural activity to social rewards, but it is unknown whether this finding extends to autistic females, particularly as behavioral evidence suggests that affected females may not exhibit the same reduction in social motivation as their male peers. We therefore used functional magnetic resonance imaging to examine social reward processing during an instrumental implicit learning task in 154 children and adolescents (ages 8-17): 39 autistic girls, 43 autistic boys, 33 typically developing girls, and 39 typically developing boys. We found that autistic girls displayed increased activity to socially rewarding stimuli, including greater activity in the nucleus accumbens relative to autistic boys, as well as greater activity in lateral frontal cortices and the anterior insula compared with typically developing girls. These results demonstrate for the first time that autistic girls do not exhibit the same reduction in activity within social reward systems as autistic boys. Instead, autistic girls display increased neural activation to such stimuli in areas related to reward processing and salience detection. Our findings indicate that a reduced sensitivity to social rewards, as assessed with a rewarded instrumental implicit learning task, does not generalize to affected female youth and highlight the importance of studying potential sex differences in autism to improve our understanding of the condition and its heterogeneity.
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25
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Short Report: Circulating microRNAs are associated with incident diabetes over 10 years in Japanese Americans. Sci Rep 2020; 10:6509. [PMID: 32300167 PMCID: PMC7162904 DOI: 10.1038/s41598-020-63606-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/02/2020] [Indexed: 02/07/2023] Open
Abstract
Epigenetic changes precede the development of diabetes by many years, providing clues to its pathogenesis. We explored whether the epigenetic markers, circulating microRNAs (miRNAs), were associated with incident diabetes in Japanese Americans. We conducted a pilot study (n = 10) using plasma from age- and sex-matched participants who did or did not develop diabetes in the Japanese American Community Diabetes Study, an observational study of diabetes risk factors. Extraction and high-throughput sequencing of miRNAs were performed using samples collected at baseline. Regression models were fit comparing circulating miRNAs (N = 1640) among individuals who did or did not develop incident diabetes at 10-year follow-up. Participants averaged 51.7 years of age at baseline; 60% were male. We identified 36 miRNAs present at different (10 higher and 26 lower) levels in individuals who developed diabetes compared to those who did not (log2fold change ≥1.25 and false discovery rate ≤5%). These included miRNAs with functions in skeletal muscle insulin metabolism (miR-106b and miR-20b-5p) and miRNAs with functions in both skeletal muscle insulin metabolism and cell cycle regulation in endocrine pancreas (miR-15a and miR-17). Circulating miRNAs were associated with subsequent development of diabetes among Japanese Americans over 10 years of follow-up. Results are preliminary. Large-scale miRNA sequencing studies could inform our understanding of diabetes pathogenesis and development of therapies, based on gene expression regulation, that target diabetes.
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26
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Abstract
The majority of circular RNAs (circRNAs) spliced from coding genes contain open reading frames (ORFs) and thus, have protein coding potential. However, it remains unknown what regulates the biogenesis of these ORF-containing circRNAs, whether they are actually translated into proteins and what functions they play in specific physiological contexts. Here, we report that a large number of circRNAs are synthesized with increasing abundance when late pachytene spermatocytes develop into round and then elongating spermatids during murine spermatogenesis. For a subset of circRNAs, the back splicing appears to occur mostly at m6A-enriched sites, which are usually located around the start and stop codons in linear mRNAs. Consequently, approximately a half of these male germ cell circRNAs contain large ORFs with m6A-modified start codons in their junctions, features that have been recently shown to be associated with protein-coding potential. Hundreds of peptides encoded by the junction sequences of these circRNAs were detected using liquid chromatography coupled with mass spectrometry, suggesting that these circRNAs can indeed be translated into proteins in both developing (spermatocytes and spermatids) and mature (spermatozoa) male germ cells. The present study discovered not only a novel role of m6A in the biogenesis of coding circRNAs, but also a potential mechanism to ensure stable and long-lasting protein production in the absence of linear mRNAs, i.e., through production of circRNAs containing large ORFs and m6A-modified start codons in junction sequences.
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27
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Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum. Nat Commun 2019; 10:5612. [PMID: 31819058 PMCID: PMC6901522 DOI: 10.1038/s41467-019-13577-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
Abstract
Human myeloid-derived growth factor (hMYDGF) is a 142-residue protein with a C-terminal endoplasmic reticulum (ER) retention sequence (ERS). Extracellular MYDGF mediates cardiac repair in mice after anoxic injury. Although homologs of hMYDGF are found in eukaryotes as distant as protozoans, its structure and function are unknown. Here we present the NMR solution structure of hMYDGF, which consists of a short α-helix and ten β-strands distributed in three β-sheets. Conserved residues map to the unstructured ERS, loops on the face opposite the ERS, and the surface of a cavity underneath the conserved loops. The only protein or portion of a protein known to have a similar fold is the base domain of VNN1. We suggest, in analogy to the tethering of the VNN1 nitrilase domain to the plasma membrane via its base domain, that MYDGF complexed to the KDEL receptor binds cargo via its conserved residues for transport to the ER.
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7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat Commun 2019; 10:5442. [PMID: 31784519 PMCID: PMC6884629 DOI: 10.1038/s41467-019-13384-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, was recently detected in genomic DNA of Enterobacteria phage 9g and was proposed to protect phage DNA from a wide variety of restriction enzymes. In this study, we identify three additional 2'-deoxy-7-deazaguanine modifications, which are all intermediates of the same pathway, in viruses: 2'-deoxy-7-amido-7-deazaguanine (dADG), 2'-deoxy-7-cyano-7-deazaguanine (dPreQ0) and 2'-deoxy-7- aminomethyl-7-deazaguanine (dPreQ1). We identify 180 phages or archaeal viruses that encode at least one of the enzymes of this pathway with an overrepresentation (60%) of viruses potentially infecting pathogenic microbial hosts. Genetic studies with the Escherichia phage CAjan show that DpdA is essential to insert the 7-deazaguanine base in phage genomic DNA and that 2'-deoxy-7-deazaguanine modifications protect phage DNA from host restriction enzymes.
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29
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Using a Single Daytime Performance Test to Identify Most Individuals at High-Risk for Performance Impairment during Extended Wake. Sci Rep 2019; 9:16681. [PMID: 31723161 PMCID: PMC6853981 DOI: 10.1038/s41598-019-52930-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/25/2019] [Indexed: 12/20/2022] Open
Abstract
We explored the predictive value of a neurobehavioral performance assessment under rested baseline conditions (evaluated at 8 hours awake following 8 hours of sleep) on neurobehavioral response to moderate sleep loss (evaluated at 20 hours awake two days later) in 151 healthy young participants (18-30 years). We defined each participant's response-to-sleep-loss phenotype based on the number of attentional failures on a 10-min visual psychomotor vigilance task taken at 20 hours awake (resilient: less than 6 attentional failures, n = 26 participants; non-resilient: 6 or more attentional failures, n = 125 participants). We observed that 97% of rested participants with 2 or more attentional failures (n = 73 of 151) and 100% of rested participants with 3 or more attentional failures (n = 57 of 151) were non-resilient after moderate sleep loss. Our approach can accurately identify a significant proportion of individuals who are at high risk for neurobehavioral performance impairment from staying up late with a single neurobehavioral performance assessment conducted during rested conditions. Additional methods are needed to predict the future performance of individuals who are not identified as high risk during baseline.
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30
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Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics. NPJ Biofilms Microbiomes 2019; 5:31. [PMID: 31666981 PMCID: PMC6814747 DOI: 10.1038/s41522-019-0104-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/25/2019] [Indexed: 12/17/2022] Open
Abstract
Microorganisms enhance fitness by prioritizing catabolism of available carbon sources using a process known as carbon catabolite repression (CCR). Planktonically grown Pseudomonas aeruginosa is known to prioritize the consumption of organic acids including lactic acid over catabolism of glucose using a CCR strategy termed "reverse diauxie." P. aeruginosa is an opportunistic pathogen with well-documented biofilm phenotypes that are distinct from its planktonic phenotypes. Reverse diauxie has been described in planktonic cultures, but it has not been documented explicitly in P. aeruginosa biofilms. Here a combination of exometabolomics and label-free proteomics was used to analyze planktonic and biofilm phenotypes for reverse diauxie. P. aeruginosa biofilm cultures preferentially consumed lactic acid over glucose, and in addition, the cultures catabolized the substrates completely and did not exhibit the acetate secreting "overflow" metabolism that is typical of many model microorganisms. The biofilm phenotype was enabled by changes in protein abundances, including lactate dehydrogenase, fumarate hydratase, GTP cyclohydrolase, L-ornithine N(5)-monooxygenase, and superoxide dismutase. These results are noteworthy because reverse diauxie-mediated catabolism of organic acids necessitates a terminal electron acceptor like O2, which is typically in low supply in biofilms due to diffusion limitation. Label-free proteomics identified dozens of proteins associated with biofilm formation including 16 that have not been previously reported, highlighting both the advantages of the methodology utilized here and the complexity of the proteomic adaptation for P. aeruginosa biofilms. Documenting the reverse diauxic phenotype in P. aeruginosa biofilms is foundational for understanding cellular nutrient and energy fluxes, which ultimately control growth and virulence.
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31
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In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release. Nat Commun 2019; 10:2216. [PMID: 31101900 PMCID: PMC6525196 DOI: 10.1038/s41467-019-10236-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/25/2019] [Indexed: 01/11/2023] Open
Abstract
Transcribing and replicating a double-stranded genome require protein modules to unwind, transcribe/replicate nucleic acid substrates, and release products. Here we present in situ cryo-electron microscopy structures of rotavirus dsRNA-dependent RNA polymerase (RdRp) in two states pertaining to transcription. In addition to the previously discovered universal "hand-shaped" polymerase core domain shared by DNA polymerases and telomerases, our results show the function of N- and C-terminal domains of RdRp: the former opens the genome duplex to isolate the template strand; the latter splits the emerging template-transcript hybrid, guides genome reannealing to form a transcription bubble, and opens a capsid shell protein (CSP) to release the transcript. These two "helicase" domains also extensively interact with CSP, which has a switchable N-terminal helix that, like cellular transcriptional factors, either inhibits or promotes RdRp activity. The in situ structures of RdRp, CSP, and RNA in action inform mechanisms of not only transcription, but also replication.
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32
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Time resolved quantitative phospho-tyrosine analysis reveals Bruton's Tyrosine kinase mediated signaling downstream of the mutated granulocyte-colony stimulating factor receptors. Leukemia 2019; 33:75-87. [PMID: 29977015 PMCID: PMC6320735 DOI: 10.1038/s41375-018-0188-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022]
Abstract
Granulocyte-colony stimulating factor receptor (G-CSFR) controls myeloid progenitor proliferation and differentiation to neutrophils. Mutations in CSF3R (encoding G-CSFR) have been reported in patients with chronic neutrophilic leukemia (CNL) and acute myeloid leukemia (AML); however, despite years of research, the malignant downstream signaling of the mutated G-CSFRs is not well understood. Here, we used a quantitative phospho-tyrosine analysis to generate a comprehensive signaling map of G-CSF induced tyrosine phosphorylation in the normal versus mutated (proximal: T618I and truncated: Q741x) G-CSFRs. Unbiased clustering and kinase enrichment analysis identified rapid induction of phospho-proteins associated with endocytosis by the wild type G-CSFR only; while G-CSFR mutants showed abnormal kinetics of canonical Stat3, Stat5, and Mapk phosphorylation, and aberrant activation of Bruton's Tyrosine Kinase (Btk). Mutant-G-CSFR-expressing cells displayed enhanced sensitivity (3-5-fold lower IC50) for ibrutinib-based chemical inhibition of Btk. Primary murine progenitor cells from G-CSFR-Q741x knock-in mice validated activation of Btk by the mutant receptor and retrovirally transduced human CD34+ umbilical cord blood cells expressing mutant receptors displayed enhanced sensitivity to Ibrutinib. A significantly lower clonogenic potential was displayed by both murine and human primary cells expressing mutated receptors upon ibrutinib treatment. Finally, a dramatic synergy was observed between ibrutinib and ruxolinitib at lower dose of the individual drug. Altogether, these data demonstrate the strength of unsupervised proteomics analyses in dissecting oncogenic pathways, and suggest repositioning Ibrutinib for therapy of myeloid leukemia bearing CSF3R mutations. Phospho-tyrosine data are available via ProteomeXchange with identifier PXD009662.
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MESH Headings
- Adenine/analogs & derivatives
- Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors
- Agammaglobulinaemia Tyrosine Kinase/genetics
- Agammaglobulinaemia Tyrosine Kinase/metabolism
- Animals
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Humans
- Leukemia, Myeloid, Acute
- Leukemia, Neutrophilic, Chronic
- Mice
- Mutation
- Phosphoproteins/metabolism
- Phosphorylation
- Piperidines
- Precursor Cells, B-Lymphoid/metabolism
- Precursor Cells, B-Lymphoid/pathology
- Protein-Tyrosine Kinases/analysis
- Protein-Tyrosine Kinases/metabolism
- Proteome/analysis
- Pyrazoles/pharmacology
- Pyrimidines/pharmacology
- Receptors, Granulocyte Colony-Stimulating Factor/genetics
- Receptors, Granulocyte Colony-Stimulating Factor/metabolism
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33
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Regional Differences in mRNA and lncRNA Expression Profiles in Non-Failing Human Atria and Ventricles. Sci Rep 2018; 8:13919. [PMID: 30224797 PMCID: PMC6141608 DOI: 10.1038/s41598-018-32154-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/22/2018] [Indexed: 01/27/2023] Open
Abstract
The four chambers of the human heart play distinct roles in the maintenance of normal cardiac function, and are differentially affected by inherited/acquired cardiovascular disease. To probe the molecular determinants of these functional differences, we examined mRNA and lncRNA expression profiles in the left (LA) and right (RA) atria, the left (LV) and right (RV) ventricles, and the interventricular septum (IVS) of non-failing human hearts (N = 8). Analysis of paired atrial and ventricular samples (n = 40) identified 5,747 mRNAs and 2,794 lncRNAs that were differentially (>1.5 fold; FDR < 0.05) expressed. The largest differences were observed in comparisons between the atrial (RA/LA) and ventricular (RV/LV/IVS) samples. In every case (e.g., LA vs LV, LA vs RV, etc.), >2,300 mRNAs and >1,200 lncRNAs, corresponding to 17-28% of the total transcripts, were differentially expressed. Heterogeneities in mRNA/lncRNA expression profiles in the LA and RA, as well as in the LV, RV and IVS, were also revealed, although the numbers of differentially expressed transcripts were substantially smaller. Gender differences in mRNA and lncRNA expression profiles were also evident in non-failing human atria and ventricles. Gene ontology classification of differentially expressed gene sets revealed chamber-specific enrichment of numerous signaling pathways.
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