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Brown M, Jensen A, Rochon P, Ryu R, Trivedi P. 3:54 PM Abstract No. 58 Racial disparity in survival following transjugular intrahepatic portosystemic shunt creation for acute variceal bleeding: a nationwide analysis. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Wadhwa V, DeWitt P, Lindquist J, Trivedi P. Abstract No. 665 Association of inferior vena cava filter placement and mortality among in-patients with pulmonary embolism after adjusting for immortal time bias. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Magnowski A, Schramm K, DeWitt P, Rochon P, Hieb R, Patel P, Ryu R, Rogers K, Dybul S, Trivedi P. 3:27 PM Abstract No. 45 Evolution in national endovascular management of femoral-popliteal artery disease: an analysis of the 2011 to 2017 Medicare data. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Lindquist J, Jensen A, Brown M, Rochon P, Ryu R, Trivedi P. 3:45 PM Abstract No. 57 Racial disparity in access to endoscopy and transjugular intrahepatic portosystemic shunt creation for acute variceal bleeding in the United States. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Magnowski A, Schramm K, DeWitt P, Rochon P, Hieb R, Patel P, Ryu R, Rogers K, Dybul S, Trivedi P. 4:12 PM Abstract No. 316 Variations in endovascular management of infrapopliteal arterial disease: national trends from the Medicare procedure database. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Schramm K, Yule A, DeWitt P, Rochon P, Hieb R, Patel P, Dybul S, Rogers K, Trivedi P. 3:54 PM Abstract No. 48 National trends in endovascular management of iliac arterial disease: insights from the Medicare population. J Vasc Interv Radiol 2020. [DOI: 10.1016/j.jvir.2019.12.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Delgado-Baquerizo M, Reich PB, Trivedi C, Eldridge DJ, Abades S, Alfaro FD, Bastida F, Berhe AA, Cutler NA, Gallardo A, García-Velázquez L, Hart SC, Hayes PE, He JZ, Hseu ZY, Hu HW, Kirchmair M, Neuhauser S, Pérez CA, Reed SC, Santos F, Sullivan BW, Trivedi P, Wang JT, Weber-Grullon L, Williams MA, Singh BK. Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat Ecol Evol 2020; 4:210-220. [PMID: 32015427 DOI: 10.1038/s41559-019-1084-y] [Citation(s) in RCA: 268] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 12/17/2019] [Indexed: 11/08/2022]
Abstract
The role of soil biodiversity in regulating multiple ecosystem functions is poorly understood, limiting our ability to predict how soil biodiversity loss might affect human wellbeing and ecosystem sustainability. Here, combining a global observational study with an experimental microcosm study, we provide evidence that soil biodiversity (bacteria, fungi, protists and invertebrates) is significantly and positively associated with multiple ecosystem functions. These functions include nutrient cycling, decomposition, plant production, and reduced potential for pathogenicity and belowground biological warfare. Our findings also reveal the context dependency of such relationships and the importance of the connectedness, biodiversity and nature of the globally distributed dominant phylotypes within the soil network in maintaining multiple functions. Moreover, our results suggest that the positive association between plant diversity and multifunctionality across biomes is indirectly driven by soil biodiversity. Together, our results provide insights into the importance of soil biodiversity for maintaining soil functionality locally and across biomes, as well as providing strong support for the inclusion of soil biodiversity in conservation and management programmes.
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Singh BK, Liu H, Trivedi P. Eco-holobiont: A new concept to identify drivers of host-associated microorganisms. Environ Microbiol 2019; 22:564-567. [PMID: 31849163 DOI: 10.1111/1462-2920.14900] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 11/28/2022]
Abstract
Host microbiomes play a critical role in host fitness and health. Whilst the current 'holobiont' concept framework has greatly expanded eco-evolutionary and functional understanding of host-microbiome interactions, the important role of biotic interactions and microbial loop (compositional linkage between soil, plant and animal) in shaping host-microbiome are poorly understood. We proposed an 'eco-holobiont' concept to fill the knowledge gap.
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Bastida F, Eldridge DJ, Abades S, Alfaro FD, Gallardo A, García‐Velázquez L, García C, Hart SC, Pérez CA, Santos F, Trivedi P, Williams MA, Delgado‐Baquerizo M. Climatic vulnerabilities and ecological preferences of soil invertebrates across biomes. Mol Ecol 2019; 29:752-761. [DOI: 10.1111/mec.15299] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/28/2019] [Accepted: 11/01/2019] [Indexed: 01/01/2023]
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Pinato DJ, Kythreotou A, Mauri FA, Suardi E, Allara E, Shiner RJ, Akarca AU, Trivedi P, Gupta N, Dalla Pria A, Marafioti T, Oliveri P, Newsom-Davis T, Bower M. Functional immune characterization of HIV-associated non-small-cell lung cancer. Ann Oncol 2019; 29:1486-1488. [PMID: 29897389 DOI: 10.1093/annonc/mdy125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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61
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Manchala NR, Dungdung R, Trivedi P, Unniyampurath U, Pilankatta R. Mycophenolic acid (MPA) modulates host cellular autophagy progression in sub genomic dengue virus-2 replicon cells. Microb Pathog 2019; 137:103762. [PMID: 31560972 DOI: 10.1016/j.micpath.2019.103762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/10/2019] [Accepted: 09/24/2019] [Indexed: 10/26/2022]
Abstract
Cellular autophagy (Macrophagy) is a self-degradative process, executed through the network of autophagy associated genes (ATGs) encoded proteins. Both in vitro and in vivo studies suggest that dengue virus (DENV) induces autophagy and supports the viral genome replication and translation. Therefore, the cellular autophagy induced by dengue virus can be a good target for antiviral drug development. The action of mycophenolic acid (MPA), a specific inhibitor of DENV replication, was investigated in the stable BHK-21/DENV2 replicon cells. The inhibition was mediated by enhanced degradation of autophagic substrates in stable BHK-21/DENV2 replicon cells as evidenced by a decrease in lapidated LC3 (LC3II) and p62 expression in the presence of MPA. In contrast, the results indicated that four gene sets, namely Transmembrane protein 74 (TMEM74), Unc-51-like kinase 2 (ULK2), Cathepsin D (CTSD) and Estrogen receptor 1 (ESR1) were upregulated in stable BHK-21/DENV2 replicon cells, due to the sustained dynamic replication of DENV2 genome. These ATGs involved in the pre-autophagosomal structure (PAS) formation, were suppressed in the presence MPA. Instead, MPA induced the expression of different set of autophagy genes such as ATG4, AKT1, APP, ATG16L1, ATG16L2, B2M and HPRT1. An enzyme involved in the nucleotide salvage pathway, HPRT1, was highly expressed in the presence of MPA. The study shows that DENV2 replication is dependent on PAS formation and is inhibited in the presence of MPA by enhancing the degradation of autophagic substrates and suppression of PAS formation. This study provides impetus in designing MPA analogues to effectively inhibit dengue viral replication.
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Foschi V, Bortolotti D, Doyle AF, Stratigou V, Stephens L, Trivedi P, Rinaldi R, Padovan M, Bortoluzzi A, Lightstone L, Cairns TD, Botto M, Cook TH, Rizzo R, Govoni M, Pickering MC. Analysis of HLA-G expression in renal tissue in lupus nephritis: a pilot study. Lupus 2019; 28:1091-1100. [PMID: 31291846 DOI: 10.1177/0961203319860582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND The study aimed to investigate whether HLA-G antigen is expressed in the kidneys of patients affected by lupus nephritis (LN) and whether its detection in renal biopsies could be adopted as a marker of treatment response and prognosis. METHODS Thirty renal biopsies from patients with LN were selected and analyzed through immunohistochemistry. Laboratory and clinical data were retrospectively collected at baseline, 6 and 12 months and at the latest clinical appointment. A number of patients (63.3%) were treated with rituximab (RTX) +/- methylprednisolone in the induction phase. The expression of HLA-G in glomeruli, tubules and infiltrating cells was examined and compared between lupus patients who achieved either complete or partial renal response and those who did not respond to treatment. RESULTS HLA-G staining was observed in the glomeruli of 20 of 30 samples from patients with LN. The expression of the antigen was detected in podocytes, along glomerular capillary walls, on parietal glomerular epithelial cells and within the juxtaglomerular apparatus. Seventy per cent of patients whose glomeruli expressed HLA-G achieved partial or complete response at 6 months and 75% at the latest available follow up compared with 30% and 40%, respectively, of those who did not show any expression. The pattern of staining in tubules and infiltrating cells was highly variable precluding any clinical correlation. CONCLUSION This study demonstrates that HLA-G is expressed in renal tissue in LN. Our retrospective data suggest that its expression could correlate with response to treatment.
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Severa M, Rizzo F, Srinivasan S, Di Dario M, Giacomini E, Buscarinu MC, Cruciani M, Etna MP, Sandini S, Mechelli R, Farina A, Trivedi P, Hertzog PJ, Salvetti M, Farina C, Coccia EM. A cell type-specific transcriptomic approach to map B cell and monocyte type I interferon-linked pathogenic signatures in Multiple Sclerosis. J Autoimmun 2019; 101:1-16. [PMID: 31047767 DOI: 10.1016/j.jaut.2019.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 12/15/2022]
Abstract
Alteration in endogenous Interferon (IFN) system may profoundly impact immune cell function in autoimmune diseases. Here, we provide evidence that dysregulation in IFN-regulated genes and pathways are involved in B cell- and monocyte-driven pathogenic contribution to Multiple Sclerosis (MS) development and maintenance. In particular, by using an Interferome-based cell type-specific approach, we characterized an increased susceptibility to an IFN-linked caspase-3 dependent apoptotic cell death in both B cells and monocytes of MS patients that may arise from their chronic activation and persistent stimulation by activated T cells. Ongoing caspase-3 activation functionally impacts on MS monocyte properties influencing the STAT-3/IL-16 axis, thus, driving increased expression and massive release of the bio-active IL-16 triggering and perpetuating CD4+ T cell migration. Importantly, our analysis also identified a previously unknown multi-component defect in type I IFN-mediated signaling and response to virus pathways specific of MS B cells, impacting on induction of anti-viral responses and Epstein-barr virus infection control in patients. Taking advantage of cell type-specific transcriptomics and in-depth functional validation, this study revealed pathogenic contribution of endogenous IFN signaling and IFN-regulated cell processes to MS pathogenesis with implications on fate and functions of B cells and monocytes that may hold therapeutic potential.
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Brice KL, Trivedi P, Jeffries TC, Blyton MDJ, Mitchell C, Singh BK, Moore BD. The Koala ( Phascolarctos cinereus) faecal microbiome differs with diet in a wild population. PeerJ 2019; 7:e6534. [PMID: 30972242 PMCID: PMC6448554 DOI: 10.7717/peerj.6534] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/28/2019] [Indexed: 12/25/2022] Open
Abstract
Background The diet of the koala (Phascolarctos cinereus) is comprised almost exclusively of foliage from the genus Eucalyptus (family Myrtaceae). Eucalyptus produces a wide variety of potentially toxic plant secondary metabolites which have evolved as chemical defences against herbivory. The koala is classified as an obligate dietary specialist, and although dietary specialisation is rare in mammalian herbivores, it has been found elsewhere to promote a highly-conserved but low-diversity gut microbiome. The gut microbes of dietary specialists have been found sometimes to enhance tolerance of dietary PSMs, facilitating competition-free access to food. Although the koala and its gut microbes have evolved together to utilise a low nutrient, potentially toxic diet, their gut microbiome has not previously been assessed in conjunction with diet quality. Thus, linking the two may provide new insights in to the ability of the koala to extract nutrients and detoxify their potentially toxic diet. Method The 16S rRNA gene was used to characterise the composition and diversity of faecal bacterial communities from a wild koala population (n = 32) comprising individuals that predominately eat either one of two different food species, one the strongly preferred and relatively nutritious species Eucalyptus viminalis, the other comprising the less preferred and less digestible species Eucalyptus obliqua. Results Alpha diversity indices indicated consistently and significantly lower diversity and richness in koalas eating E. viminalis. Assessment of beta diversity using both weighted and unweighted UniFrac matrices indicated that diet was a strong driver of both microbial community structure, and of microbial presence/absence across the combined koala population and when assessed independently. Further, principal coordinates analysis based on both the weighted and unweighted UniFrac matrices for the combined and separated populations, also revealed a separation linked to diet. During our analysis of the OTU tables we also detected a strong association between microbial community composition and host diet. We found that the phyla Bacteroidetes and Firmicutes were co-dominant in all faecal microbiomes, with Cyanobacteria also co-dominant in some individuals; however, the E. viminalis diet produced communities dominated by the genera Parabacteroides and/or Bacteroides, whereas the E. obliqua-associated diets were dominated by unidentified genera from the family Ruminococcaceae. Discussion We show that diet differences, even those caused by differential consumption of the foliage of two species from the same plant genus, can profoundly affect the gut microbiome of a specialist folivorous mammal, even amongst individuals in the same population. We identify key microbiota associated with each diet type and predict functions within the microbial community based on 80 previously identified Parabacteroides and Ruminococcaceae genomes.
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Lindquist J, Reghunathan A, Brown M, Schramm K, Trivedi P, Ryu R, Lindquist J. 04:21 PM Abstract No. 198 Comparison of the Captus device versus conventional snare for IVC filter retrieval. J Vasc Interv Radiol 2019. [DOI: 10.1016/j.jvir.2018.12.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Trivedi P, Lind K, Borgstede J, Rochon P, Hong K, Duszak R, Ryu R. 03:09 PM Abstract No. 259 Comparative cost-effectiveness analysis of dialysis access maintenance interventions by provider specialty. J Vasc Interv Radiol 2019. [DOI: 10.1016/j.jvir.2018.12.321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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67
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Trivedi P, Slack FJ, Anastasiadou E. Epstein-Barr virus: From kisses to cancer, an ingenious immune evader. Oncotarget 2018; 9:36411-36412. [PMID: 30559926 PMCID: PMC6284857 DOI: 10.18632/oncotarget.26381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/13/2018] [Indexed: 12/28/2022] Open
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Xu J, Zhang Y, Zhang P, Trivedi P, Riera N, Wang Y, Liu X, Fan G, Tang J, Coletta-Filho HD, Cubero J, Deng X, Ancona V, Lu Z, Zhong B, Roper MC, Capote N, Catara V, Pietersen G, Vernière C, Al-Sadi AM, Li L, Yang F, Xu X, Wang J, Yang H, Jin T, Wang N. The structure and function of the global citrus rhizosphere microbiome. Nat Commun 2018; 9:4894. [PMID: 30459421 PMCID: PMC6244077 DOI: 10.1038/s41467-018-07343-2] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 10/25/2018] [Indexed: 11/23/2022] Open
Abstract
Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome is thought to play an important role in promoting citrus growth and health. Here, we report a comprehensive analysis of the structural and functional composition of the citrus rhizosphere microbiome. We use both amplicon and deep shotgun metagenomic sequencing of bulk soil and rhizosphere samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes. The core citrus rhizosphere microbiome comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax and Paraburkholderia, some of which are potential plant beneficial microbes. We also identify over-represented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition and plant growth promotion in citrus rhizosphere. The results provide valuable information to guide microbial isolation and culturing and, potentially, to harness the power of the microbiome to improve plant production and health.
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Eleni A, Dina S, Alimperti S, Jiao A, Pyzer A, Cipitelli C, Severa M, Chen CS, Uccini S, Avigan D, Faggioni A, Trivedi P, Slack FJ. Abstract A16: Epstein-Barr virus encoded EBNA2 alters immune checkpoint PD-L1 expression by downregulating miR-34a in B cell lymphomas. Cancer Immunol Res 2018. [DOI: 10.1158/2326-6074.tumimm17-a16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer cells subvert host immune surveillance by altering immune checkpoint (IC) proteins. Indeed, Epstein-Barr virus (EBV) positive Hodgkin’s lymphoma and gastric adenocarcinomas have higher Programmed Cell Death Ligand, PD-L1, expression. However, how EBV alters ICs in the context of its preferred host, the B lymphocyte and lymphomas, is unknown. Here, we used Burkitt lymphoma (BL), diffuse large B cell lymphomas (DLBCL) and their EBV infected or EBNA2 transfected derivatives to address this question. EBV latency III cells expressed high levels of PD-L1. In a DLBCL model, we found that EBNA2 but not LMP1 is sufficient to induce PD-L1. The upregulation of PD-L1 was confirmed in estrogen inducible EBNA2 carrying B lymphoma cells. Clinical samples from DLBCL patients showed that EBV infected, latency III cases expressed high levels of PD-L1. The PD-L1 targeting oncosuppressor miR-34a was downregulated in EBNA2 transfected cells. miR-34a reconstitution in EBNA2 expressing DLBCL reduced PD-L1 expression and increased their immunogenicity in 2D mixed lymphocyte reactions (MLR) and 3D microfluidic chip based MLRs. Given the importance of PD-L1 inhibition in immunotherapy and miR-34a dysregulation in cancers, our findings may have important implications for diagnosis and combinatorial immunotherapy approaches which include IC inhibiting antibodies and miR-34a, for EBV-associated cancers.
Citation Format: Anastasiadou Eleni, Stroopinsky Dina, Stella Alimperti, Alan Jiao, Athalia Pyzer, Claudia Cipitelli, Martina Severa, Christopher S. Chen, Stefania Uccini, David Avigan, Alberto Faggioni, Pankaj Trivedi, Frank J. Slack. Epstein-Barr virus encoded EBNA2 alters immune checkpoint PD-L1 expression by downregulating miR-34a in B cell lymphomas [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr A16.
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Anastasiadou E, Stroopinsky D, Alimperti S, Jiao AL, Pyzer AR, Cippitelli C, Pepe G, Severa M, Rosenblatt J, Etna MP, Rieger S, Kempkes B, Coccia EM, Sui SJH, Chen CS, Uccini S, Avigan D, Faggioni A, Trivedi P, Slack FJ. Epstein-Barr virus-encoded EBNA2 alters immune checkpoint PD-L1 expression by downregulating miR-34a in B-cell lymphomas. Leukemia 2018; 33:132-147. [PMID: 29946193 PMCID: PMC6327052 DOI: 10.1038/s41375-018-0178-x] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 04/27/2018] [Accepted: 05/11/2018] [Indexed: 12/13/2022]
Abstract
Cancer cells subvert host immune surveillance by altering immune checkpoint (IC) proteins. Some Epstein−Barr virus (EBV)-associated tumors have higher Programmed Cell Death Ligand, PD-L1 expression. However, it is not known how EBV alters ICs in the context of its preferred host, the B lymphocyte and in derived lymphomas. Here, we found that latency III-expressing Burkitt lymphoma (BL), diffuse large B-cell lymphomas (DLBCL) or their EBNA2-transfected derivatives express high PD-L1. In a DLBCL model, EBNA2 but not LMP1 is sufficient to induce PD-L1. Latency III-expressing DLBCL biopsies showed high levels of PD-L1. The PD-L1 targeting oncosuppressor microRNA miR-34a was downregulated in EBNA2-transfected lymphoma cells. We identified early B-cell factor 1 (EBF1) as a repressor of miR-34a transcription. Short hairpin RNA (shRNA)-mediated knockdown of EBF1 was sufficient to induce miR-34a transcription, which in turn reduced PD-L1. MiR-34a reconstitution in EBNA2-transfected DLBCL reduced PD-L1 expression and increased its immunogenicity in mixed lymphocyte reactions (MLR) and in three-dimensional biomimetic microfluidic chips. Given the importance of PD-L1 inhibition in immunotherapy and miR-34a dysregulation in cancers, our findings may have important implications for combinatorial immunotherapy, which include IC inhibiting antibodies and miR-34a, for EBV-associated cancers.
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Delgado-Baquerizo M, Eldridge DJ, Maestre FT, Karunaratne SB, Trivedi P, Reich PB, Singh BK. Response to comment on "Climate legacies drive global soil carbon stocks in terrestrial ecosystem". SCIENCE ADVANCES 2018; 4:eaat1296. [PMID: 29546246 PMCID: PMC5851665 DOI: 10.1126/sciadv.aat1296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
The technical comment from Sanderman provides a unique opportunity to deepen our understanding of the mechanisms explaining the role of paleoclimate in the contemporary distribution of global soil C content, as reported in our article. Sanderman argues that the role of paleoclimate in predicting soil C content might be accounted for by using slowly changing soil properties as predictors. This is a key point that we highlighted in the supplementary materials of our article, which demonstrated, to the degree possible given available data, that soil properties alone cannot account for the unique portion of the variation in soil C explained by paleoclimate. Sanderman also raised an interesting question about how paleoclimate might explain the contemporary amount of C in our soils if such a C is relatively new, particularly in the topsoil layer. There is one relatively simple, yet plausible, reason. A soil with a higher amount of C, a consequence of accumulation over millennia, might promote higher contemporary C fixation rates, leading to a higher amount of new C in our soils. Thus, paleoclimate can be a good predictor of the amount of soil C in soil, but not necessarily of its age. In summary, Sanderman did not question the validity of our results but rather provides an alternative potential mechanistic explanation for the conclusion of our original article, that is, that paleoclimate explains a unique portion of the global variation of soil C content that cannot be accounted for by current climate, vegetation attributes, or soil properties.
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Hamonts K, Trivedi P, Garg A, Janitz C, Grinyer J, Holford P, Botha FC, Anderson IC, Singh BK. Field study reveals core plant microbiota and relative importance of their drivers. Environ Microbiol 2018; 20:124-140. [PMID: 29266641 DOI: 10.1111/1462-2920.14031] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022]
Abstract
Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome-based approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop microbiome under relevant field conditions. We examined bacterial and fungal communities associated with both aerial (leaves, stalks) and belowground (roots, soil) compartments of four commercial sugarcane varieties (Saccharum spp.) grown in several growing regions in Australia. We identified drivers of the sugarcane microbiome under field conditions and evaluated whether the plants shared a core microbiome. Sugarcane-associated microbial assemblages were primarily determined by plant compartment, followed by growing region, crop age, variety and Yellow Canopy Syndrome (YCS). We detected a core set of microbiota and identified members of the core microbiome that were influenced by YCS incidence. Our study revealed key hub microorganisms in the core microbiome networks of sugarcane leaves, stalks, roots and rhizosphere soil despite location and time-associated shifts in the community assemblages. Elucidating their functional roles and identification of the keystone core microbiota that sustain plant health could provide a technological breakthrough for a sustainable increase in crop productivity.
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Kythreotou A, Mauri F, Shiner R, Suardi E, Dalla Pria A, Akarca A, Trivedi P, Gupta N, Marafioti T, Newsom-Davis T, Bower M, Pinato D. The influence of HIV status on programmed-death ligands expression in non-small cell lung cancer. Lung Cancer 2018. [DOI: 10.1016/s0169-5002(18)30036-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Singh BK, Trivedi P, Singh S, Macdonald CA, Verma JP. Emerging microbiome technologies for sustainable increase in farm productivity and environmental security. MICROBIOLOGY AUSTRALIA 2018. [DOI: 10.1071/ma18006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Farming systems are under pressure to sustainably increase productivity to meet demand for food and fibre for a growing global population under shrinking arable lands and changing climatic conditions. Furthermore, conventional farming has led to declines in soil fertility and, in some cases, inappropriate and excessive use of chemical fertilisers and pesticides has caused soil degradation, negatively impacting human and environmental health. The soil and plant microbiomes are significant determinants of plant fitness and productivity. Microbes are also the main drivers of global biogeochemical cycles and thus key to sustainable agriculture. There is increasing evidence that with development of appropriate technologies, the plant microbiome can be harnessed to potentially decrease the frequency of plant diseases, increase resource use efficiencies and ultimately enhance agricultural productivity, while simultaneously decreasing the input of chemical fertilisers and pesticides, resulting in reduced greenhouse gas emissions and promoting environmental sustainability. However, to successfully translate potential to practical outcomes, both fundamental and applied research are needed to overcome current constraints. Research efforts need to be embedded in industrial requirements and policy and social frameworks to expedite the process of innovation, commercialisation and adoption. We propose that learning from the advancement in the human microbiome can significantly expedite the discovery and innovation of effective microbial products for sustainable and productive farming. This article summarises the emergence of microbiome technologies for the agriculture industry and how to facilitate the development and adoption of environmentally friendly microbiome technologies for sustainable increase in farm productivity.
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Trivedi P, Schenk PM, Wallenstein MD, Singh BK. Tiny Microbes, Big Yields: enhancing food crop production with biological solutions. Microb Biotechnol 2017; 10:999-1003. [PMID: 28840959 PMCID: PMC5609239 DOI: 10.1111/1751-7915.12804] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/12/2017] [Indexed: 01/19/2023] Open
Abstract
Plant‐associated microbiomes have tremendous potential to improve plant resilience and yields in farming systems. There is increasing evidence that biological technologies that use microbes or their metabolites can enhance nutrient uptake and yield, control pests and mitigate plant stress responses. However, to fully realize the potential of microbial technology, their efficacy and consistency under the broad range of real‐world conditions need to be improved. While the optimization of microbial biofertilizers and biopesticides is advancing rapidly to enable use in various soils, crop varieties and environments, crop breeding programmes have yet to incorporate the selection of beneficial plant–microbe interactions to breed ‘microbe‐optimized plants’. Emerging efforts exploring microbiome engineering could lead to microbial consortia that are better suited to support plants. The combination of all three approaches could be integrated to achieve maximum benefits and significantly improved crop yields to address food security.
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