PLoS Pathog Research Articles

The master antioxidant defense is activated during EBV latent infection.

To our knowledge, this is the first report delineating the activation of the master antioxidant defense during EBV latency. We show that EBV-triggered reactive oxygen species production activates the Keap1-NRF2 pathway in EBV-transformed cells, and LMP1 plays a major role in this event, and the stress-related kinase TBK1 is required for NRF2 activation. Moreover, we show that the Keap1-NRF2 pathway is important for cell proliferation and EBV latency maintenance. Our findings disclose how EBV controls the balance between oxidative stress and antioxidant defense, which greatly improve our understanding of EBV latency and pathogenesis and may be leveraged to opportunities toward the improvement of therapeutic outcomes in EBV-associated diseases.

Immunomodulatory AVM0703 enhances R-CHOP anti-lymphoma effect with reduced toxicity: Immune-resistant, aggressive A20 lymphoma model.

e14583 Background: Rituximab-cyclophosphamide-doxorubicin-vincristine-prednisone (RCHOP) is the standard of care for most aggressive B-cell lymphomas. RCHOP requires numerous treatment cycles, typically 6, with challenging side effects, including toxicity and long-term secondary malignancies. Trials have demonstrated that 4 cycles of RCHOP was non-inferior to 6 with similar secondary malignancies, however, real world experience has demonstrated that long term outcomes are superior when patients achieve minimal residual disease negative (MRD-) status after the 3rd cycle (1,2). Addition of a novel agent to RCHOP that could reduce the number of cycles to 3 while maintaining response, could overcome the long-term side-effects and allow frail and elderly patients to receive full dose RCHOP in each cycle to improve outcomes. For example, addition of Lenalidomide with RCHOP improved outcomes in ABC-DLBCL patients (3), but leads to therapy related myeloid neoplasm in recent studies (4). AVM0703, an immunomodulatory drug, mobilizes bispecific and i-TCR double-positive NKT cells (AVM_NKT). In the aggressive, immune resistant A20 mouse lymphoma model, neoadjuvant AVM0703 was additive/synergistic, when cyclophosphamide/fludarabine (CyFlu) was dosed 3 + 24 hours later, with no additional toxicities. Therefore, we hypothesized that combining AVM0703 with RCHOP would be an effective and well tolerated treatment of DLBCL. Methods: Tumor-bearing mice were made by sc flank injection of 2x106 murine A20 B-cells in 10-week-old Balb/c mice. When tumor size reached established ~100 mm3, 48 mice (1:1 male: female) were randomized (12 mice each cohort) 1) Placebo 2) 1 cycle RCHOP 3) AVM0703 (18mg/kg HED) 4) AVM0703+1 cycle RCHOP combination treated as described previously (5,6). When Placebo tumors reached ~ 2000 mm3, all mice were sacrificed and tumors, blood, spleen, bone marrow were analyzed for the presence of remnant A20, and immune cell state by flow cytometer. Results: One RCHOP only mouse died from the chemo. There were no deaths in AVM0703+RCHOP group. Tumor remnant live A20 were significantly reduced in all 3 treatment groups compared to Placebo. Interestingly, AVM0703+RCHOP significantly increased the number of MRD- A20 tumors compared to RCHOP alone. Conclusions: Based on this study we plan to determine whether 3 cycles of AVM0703+RCHOP can induce long term CR and if AVM0703 could replace R and reduce long term side effects. 1) Poeschel Lancet 2019. 2) Spurgeon J Natl Canc Inst 2016. 3) Nowakowski JCO 2021. 4) Sperling Blood 2022. 5) Bascuas J Transl Med 2016. 6) Bongard PLoS Pathog 2019. [Table: see text]

Experimental Support for Human Papillomavirus Genome Amplification Early after Infectious Delivery.

Even though replication and transcription of human papillomavirus type 16 (HPV16) has been intensively studied, little is known about immediate-early events of the viral life cycle due to the lack of an efficient infection model allowing genetic dissection of viral factors. We employed the recently developed infection model (Bienkowska-Haba M, Luszczek W, Myers JE, Keiffer TR, et al. 2018. PLoS Pathog 14:e1006846) to investigate genome amplification and transcription immediately after infectious delivery of viral genome to nuclei of primary keratinocytes. Using 5-ethynyl-2'-deoxyuridine (EdU) pulse-labeling and highly sensitive fluorescence in situ hybridization, we observed that the HPV16 genome is replicated and amplified in an E1- and E2-dependent manner. Knockout of E1 resulted in failure of the viral genome to replicate and amplify. In contrast, knockout of the E8^E2 repressor led to increased viral genome copy number, confirming previous reports. Genome copy control by E8^E2 was confirmed for differentiation-induced genome amplification. Lack of functional E1 had no effect on transcription from the early promoter, suggesting that viral genome replication is not required for p97 promoter activity. However, infection with an HPV16 mutant virus defective for E2 transcriptional function revealed a requirement of E2 for efficient transcription from the early promoter. In the absence of the E8^E2 protein, early transcript levels are unaltered and even decreased when normalized to genome copy number. Surprisingly, a lack of functional E8^E2 repressor did not affect E8^E2 transcript levels when normalized to genome copy number. These data suggest that the main function of E8^E2 in the viral life cycle is to control genome copy number. IMPORTANCE It is being assumed that human papillomavirus (HPV) utilizes three different modes of replication during its life cycle: initial amplification during the establishment phase, genome maintenance, and differentiation-induced amplification. However, HPV16 initial amplification was never formally proven due to a lack of an infection model. Using our recently established infection model (Bienkowska-Haba M, Luszczek W, Myers JE, Keiffer TR, et al. 2018. PLoS Pathog 14:e1006846), we demonstrate herein that viral genome is indeed amplified in an E1- and E2-dependent manner. Furthermore, we find that the main function of the viral repressor E8^E2 is to control viral genome copy number. We did not find evidence that it regulates its own promoter in a negative feedback loop. Our data also suggest that the E2 transactivator function is required for stimulation of early promoter activity, which has been debated in the literature. Overall, this report confirms the usefulness of the infection model for studying early events of the HPV life cycle using mutational approaches.

Genome and Transcriptome Sequence Resources and Effector Repertoire of Pythium myriotylum Drechsler.

Genome and Transcriptome Sequence Resources and Effector Repertoire of Pythium myriotylum Drechsler.

An anti-picornaviral strategy based on the crystal structure of foot-and-mouth disease virus 2C protein.

The foot-and-mouth disease virus (FMDV) 2C protein shares conserved motifs with enterovirus 2Cs despite low sequence identity. Here, we determine the crystal structure of an FMDV 2C fragment to 1.83Å resolution, which comprises an ATPase domain, a region equivalent to the enterovirus 2C zinc-finger (ZFER), and a C-terminal domain harboring a loop (PBL) that occupies a hydrophobic cleft (Pocket) in an adjacent 2C molecule. Mutations at ZFER, PBL, and Pocket affect FMDV 2C ATPase activity and are lethal to FMDV infectious clones. Because the PBL-Pocket interaction between FMDV 2C molecules is essential for its functions, we design an anti-FMDV peptide derived from PBL (PBL-peptide). PBL-peptide inhibits FMDV 2C ATPase activity, binds FMDV 2C with nanomolar affinity, and disrupts FMDV 2C oligomerization. FMDV 2C targets lipid droplets (LDs) and induces LD clustering in cells, and PBL-peptide disrupts FMDV 2C-induced LD clustering. Finally, we demonstrate that PBL-peptide exhibits anti-FMDV activity in cells.

Retraction of: miR-142 Suppresses Endometrial Cancer Proliferation In Vitro and In Vivo by Targeting Cyclin D1 (10.1089/dna.2018.4441)

DNA and Cell BiologyVol. 41, No. 6 Retraction NoticeFree AccessRetraction of: miR-142 Suppresses Endometrial Cancer Proliferation In Vitro and In Vivo by Targeting Cyclin D1 (10.1089/dna.2018.4441)This article retracts the following:Retracted: miR-142 Suppresses Endometrial Cancer Proliferation In Vitro and In Vivo by Targeting Cyclin D1Published Online:10 Jun 2022https://doi.org/10.1089/dna.2018.4441.retractAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail The Editor-in-Chief of DNA and Cell Biology officially retracts the article entitled, “miR-142 Suppresses Endometrial Cancer Proliferation In Vitro and In Vivo by Targeting Cyclin D1” by Su Y, Wang J, Ma Z, Gong W, Yu L. (DNA Cell Biol. 2019;38(2):144–150; 10.1089/dna.2018.4441) due to apparent duplication of images published in another journal1 and after receiving a report by the PRIMeR group out of the University of Sydney (Australia) led by Professor Jennifer Byrne, identifying that the ACTB forward and reverse primers provided under the section quantitative real-time PCR are primers targeting ACTB within Rattus rattus, not humans. Within the human transcriptome, they would be expected to also target two separate genes (forward: ACTG1, reverse: ACTC1). The Editor agrees with the report.The authors were contacted via email of the reported issues utilizing the email addresses provided to the journal at the time of submission in 2018, though no response was received.The Editor and Publisher of DNA and Cell Biology are committed to preserving the veracity of scientific literature and the community it serves.Reference1. Ono C, Fukuhara T, Motooka D, et al. Characterization of miR-122-independent propagation of HCV. PLoS Pathog. Epub May 11, 2017; https://doi.org/10.1371/journal.ppat.1006374 Google ScholarFiguresReferencesRelatedDetailsRelated articlesRetracted: miR-142 Suppresses Endometrial Cancer Proliferation In Vitro and In Vivo by Targeting Cyclin D16 Feb 2019DNA and Cell Biology Volume 41Issue 6Jun 2022 InformationCopyright 2022, Mary Ann Liebert, Inc., publishersTo cite this article:Retraction of: miR-142 Suppresses Endometrial Cancer Proliferation In Vitro and In Vivo by Targeting Cyclin D1 (10.1089/dna.2018.4441).DNA and Cell Biology.Jun 2022.641-641.http://doi.org/10.1089/dna.2018.4441.retractPublished in Volume: 41 Issue 6: June 10, 2022PDF download

An Improved Genome Sequence Resource of Bipolaris maydis, Causal Agent of Southern Corn Leaf Blight.

An Improved Genome Sequence Resource of Bipolaris maydis, Causal Agent of Southern Corn Leaf Blight.

Genome Sequence Resource of Sarocladium terricola TR, an Endophytic Fungus as a Potential Biocontrol Agent Against Meloidogyne incognita.

Genome Sequence Resource of Sarocladium terricola TR, an Endophytic Fungus as a Potential Biocontrol Agent Against Meloidogyne incognita.

Whole-Genome Sequence Resource of Fusarium oxysporum Strain TH15, a Plant Growth Promoting Endophytic Fungus Isolated from Tetrastigma hemsleyanum

Whole-Genome Sequence Resource of <i>Fusarium oxysporum</i> Strain TH15, a Plant Growth Promoting Endophytic Fungus Isolated from <i>Tetrastigma hemsleyanum</i>

Stimulation of Human Periodontal Ligament Fibroblasts Using Purified Dentilisin Extracted from Treponema denticola.

Periodontal disease is a chronic multifactorial disease triggered by a complex of bacterial species. These interact with host tissues to cause the release of a broad array of pro-inflammatory cytokines, chemokines, and tissue remodelers, such as matrix metalloproteinases (MMPs), which lead to the destruction of periodontal tissues. Patients with severe forms of periodontitis are left with a persistent pro-inflammatory transcriptional profile throughout the periodontium, even after clinical intervention, leading to the destruction of teeth-supporting tissues. The oral spirochete, Treponema denticola , is consistently found at significantly elevated levels at sites with advanced periodontal disease. Of all T. denticola virulence factors that have been described, its chymotrypsin-like protease complex, also called dentilisin, has demonstrated a multitude of cytopathic effects consistent with periodontal disease pathogenesis, including alterations in cellular adhesion activity, degradation of various endogenous extracellular matrix-substrates, degradation of host chemokines and cytokines, and ectopic activation of host MMPs. Thus, the following model of T. denticola -human periodontal ligament cell interactions may provide new knowledge about the mechanisms that drive the chronicity of periodontal disease at the protein, transcriptional, and epigenetic levels, which could afford new putative therapeutic targets. This protocol was validated in: PLOS Pathog (2021), DOI: 10.1371/journal.ppat.1009311.

Distinct conformers of amyloid beta accumulate in the neocortex of patients with rapidly progressive Alzheimer's disease

Amyloid beta (Aβ) deposition in the neocortex is a major hallmark of Alzheimer's disease (AD), but the extent of deposition does not readily explain phenotypic diversity and rate of disease progression. The prion strain–like model of disease heterogeneity suggests the existence of different conformers of Aβ. We explored this paradigm using conformation-dependent immunoassay (CDI) for Aβ and conformation-sensitive luminescent conjugated oligothiophenes (LCOs) in AD cases with variable progression rates. Mapping the Aβ conformations in the frontal, occipital, and temporal regions in 20 AD patients with CDI revealed extensive interindividual and anatomical diversity in the structural organization of Aβ with the most significant differences in the temporal cortex of rapidly progressive AD. The fluorescence emission spectra collected in situ from Aβ plaques in the same regions demonstrated considerable diversity of spectral characteristics of two LCOs—quatroformylthiophene acetic acid and heptaformylthiophene acetic acid. Heptaformylthiophene acetic acid detected a wider range of Aβ deposits, and both LCOs revealed distinct spectral attributes of diffuse and cored plaques in the temporal cortex of rapidly and slowly progressive AD and less frequent and discernible differences in the frontal and occipital cortex. These and CDI findings indicate a major conformational diversity of Aβ accumulating in the neocortex, with the most notable differences in temporal cortex of cases with shorter disease duration, and implicate distinct Aβ conformers (strains) in the rapid progression of AD.

Traces of SARS-CoV-2 RNA in Peripheral Blood Cells of Patients with COVID-19.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third virus that caused coronavirus-related outbreaks over the past 20 years. The outbreak was first reported in December 2019 in Wuhan, China, but rapidly progressed into a pandemic of an unprecedented scale since the 1918 flu pandemic. Besides respiratory complications in patients with COVID-19, clinical characterization of severe infection cases showed several other comorbidities, including multiple organ failure, and septic shock. To better understand the systemic pathogenesis of COVID-19, we interrogated the virus's presence in the peripheral blood cells, which might provide a form of trafficking or hiding to the virus. By analyzing >2 billion sequence reads of high-throughput transcriptome sequence data from 180 samples of patients with active SARS-CoV-2 infection or healthy controls collected from 6 studies, we found evidence of traces of SARS-CoV-2 RNA in peripheral blood mononuclear cells in two samples from two independent studies. In contrast, the viral RNA was abundant in bronchoalveolar lavage specimens from the same patients. We also devised a “viral spike-to-actin” RNA normalization as a metric to compare across various samples and minimize errors caused by intersample variability in total human RNA abundance. Our observation suggests immune presentation and discounts the possibility of extensive viral infection of lymphocytes or monocytes.

Gp130 Signaling in NOD2-Driven Crohn’s Disease: A Key Player in Fibrosis and a Novel Target for Refractory Patients

Gp130 Signaling in NOD2-Driven Crohn’s Disease: A Key Player in Fibrosis and a Novel Target for Refractory Patients

Using a Phosphoproteomic Screen to Profile Early Changes During HCMV Infection of Human Monocytes.

During the binding and infection of monocytes, HCMV binds to at least two major cell surface receptors/receptor families: the epidermal growth factor receptor (EGFR) to initiate downstream signaling through the EGFR-PI3K pathway, and to β1- and β3-integrins to initiate downstream signaling through the integrin-c-Src pathway (Nogalski et al. PLoS Pathog 9:e1003463, 2013; Chan et al. Proc Natl Acad Sci U S A 106:22369-22374, 2009; Kim et al. Proc Natl Acad Sci U S A 113:8819-8824, 2016; Wang et al. Nature 424:456-461, 2003; Wang et al. Nat Med 11:515-521, 2005; Yurochko et al. Proc Natl Acad Sci U S A 89:9034-9038, 1992). Signaling through these receptors can occur rapidly with phosphorylation observed as early as 15s after EGF-EGFR interaction, for example (Alvarez-Salamero et al. Front Immunol 8:938, 2017). The ability to detect signaling and the consequences of that signaling are critical for our understanding of how HCMV-receptor engagement promotes infection and modulates the biology of different target cells. In this chapter we describe how we used an ELISA-based antibody platform to perform an assessment of the rapid phosphorylation events that occur in monocytes following infection. This assay can be adapted to other infection systems, time points and cell types as needed. Together, we examined via an ELISA-based antibody array a phosphoproteomic screen to search for potential phosphorylated proteins that might influence HCMV infection.

Antagonism of Type I Interferon by Severe Acute Respiratory Syndrome Coronavirus 2.

The coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), warranting urgent study of the molecular mechanisms of SARS-CoV-2 infection and host immune response. Type I interferon (IFN-I) is a key component of host innate immune system responsible for eliminating the virus at the early stage of infection. In contrast, SARS-CoV-2 has evolved multiple strategies to evade innate immune response to facilitate viral replication, transmission, and pathogenesis. This review summarizes the recent progresses on SARS-CoV-2 proteins that antagonize host IFN-I production and/or signaling. These progresses have provided knowledge for new vaccine and antiviral development to prevent and control COVID-19.

Associations of NOD2 polymorphisms with Erysipelotrichaceae in stool of in healthy first degree relatives of Crohn\u2019s disease subjects

BackgroundGenetic analyses have identified many variants associated with the risk of inflammatory bowel disease (IBD) development. Among these variants, the ones located within the NOD2 gene have the highest odds ratio of all IBD genetic risk variants. Also, patients with Crohn’s disease (CD) have been shown to have an altered gut microbiome, which might be a reflection of inflammation itself or an effect of other parameters that contribute to the risk of the disease. Since NOD2 is an intracellular pattern recognition receptor that senses bacterial peptidoglycan in the cytosol and stimulates the host immune response (Al Nabhani et al., PLoS Pathog 13:e1006177, 2017), it is hypothesized that NOD2 variants represent perfect candidates for influencing host-microbiome interactions. We hypothesized that NOD2 risk variants affect the microbiome composition of healthy first degree relative (FDR) of CD patients and thus potentially contribute to an altered microbiome state before disease onset.MethodsBased on this, we studied a large cohort of 1546 healthy FDR of CD patients and performed a focused analysis of the association of three major CD SNPs in the coding region of the NOD2 gene, which are known to confer a 15–40-fold increased risk of developing CD in homozygous or compound heterozygous individuals.ResultsOur results show that carriers of the C allele at rs2066845 was significantly associated with an increase in relative abundance in the fecal bacterial family Erysipelotrichaceae.ConclusionsThis result suggests that NOD2 polymorphisms contribute to fecal microbiome composition in asymptomatic individuals. Whether this modulation of the microbiome influences the future development of CD remains to be assessed.

Sperm associated antigen 9 promotes oncogenic KSHV-encoded interferon regulatory factor-induced cellular transformation and angiogenesis by activating the JNK/VEGFA pathway

Kaposi’s sarcoma (KS), caused by Kaposi’s sarcoma-associated herpesvirus (KSHV), is a highly angioproliferative disseminated tumor of endothelial cells commonly found in AIDS patients. We have recently shown that KSHV-encoded viral interferon regulatory factor 1 (vIRF1) mediates KSHV-induced cell motility (PLoS Pathog. 2019 Jan 30;15(1):e1007578). However, the role of vIRF1 in KSHV-induced cellular transformation and angiogenesis remains unknown. Here, we show that vIRF1 promotes angiogenesis by upregulating sperm associated antigen 9 (SPAG9) using two in vivo angiogenesis models including the chick chorioallantoic membrane assay (CAM) and the matrigel plug angiogenesis assay in mice. Mechanistically, vIRF1 interacts with transcription factor Lef1 to promote SPAG9 transcription. vIRF1-induced SPAG9 promotes the interaction of mitogen-activated protein kinase kinase 4 (MKK4) with JNK1/2 to increase their phosphorylation, resulting in enhanced VEGFA expression, angiogenesis, cell proliferation and migration. Finally, genetic deletion of ORF-K9 from KSHV genome abolishes KSHV-induced cellular transformation and impairs angiogenesis. Our results reveal that vIRF1 transcriptionally activates SPAG9 expression to promote angiogenesis and tumorigenesis via activating JNK/VEGFA signaling. These novel findings define the mechanism of KSHV induction of the SPAG9/JNK/VEGFA pathway and establish the scientific basis for targeting this pathway for treating KSHV-associated cancers.

An oncogenic viral interferon regulatory factor upregulates CUB domain-containing protein 1 to promote angiogenesis by hijacking transcription factor lymphoid enhancer-binding factor 1 and metastasis suppressor CD82.

Kaposi's sarcoma (KS), a highly angiogenic and invasive vascular tumor, is the most common AIDS-associated cancer caused by KS-associated herpesvirus (KSHV) infection. We have recently shown that KSHV-encoded viral interferon regulatory factor 1 (vIRF1) contributes to KSHV-induced cell motility (PLoS Pathog. 15:e1007578, 2019). However, the role of vIRF1 in KSHV-induced angiogenesis remains unknown. Here, using two in vivo angiogenesis models including the chick chorioallantoic membrane assay (CAM) and the matrigel plug angiogenesis assay in mice, we show that vIRF1 promotes angiogenesis by upregulating CUB domain (for complement C1r/C1s, Uegf, Bmp1) containing protein 1 (CDCP1). Mechanistically, vIRF1 enhances the expression of transcription factor lymphoid enhancer-binding factor 1 (Lef1) and binds to Lef1 to promote CDCP1 transcription. Meanwhile, vIRF1 degrades metastasis suppressor CD82 through an ubiquitin-proteasome pathway by recruiting E3 ubiquitin ligase AMFR to CD82, which protects CDCP1 from CD82-mediated, palmitoylation-dependent degradation. CDCP1 activates AKT signaling, which is required for vIRF1-induced cell motility but not angiogenesis. Our results illustrate that, by hijacking Lef1 and CD82, vIRF1 upregulates CDCP1 to promote angiogenesis and cell invasion. These novel findings demonstrate the vIRF1 targets multiple cellular proteins and pathways to promote the pathogenesis of KS, which could be attractive therapeutic targets for KSHV-induced malignancies.

MSphere of Influence: Understanding Virus-Host Interactions Requires a Multifaceted Approach.

Rory de Vries works in the field of viral pathogenesis and focuses on interactions between respiratory viruses (or corresponding vaccines) and the host immune system. In this mSphere of Influence article, he reflects on how the articles "Predominant infection of CD150+ lymphocytes and dendritic cells during measles virus infection of macaques" by R. L. de Swart et al. (R. L. de Swart, M. Ludlow, L. de Witte, Y. Yanagi, et al., PLoS Pathog 3:e178, 2007, https://doi.org/10.1371/journal.ppat.0030178) and "Long-term measles-induced immunomodulation increases overall childhood infectious disease mortality" by M. J. Mina et al. (M. J. Mina, C. J. Metcalf, R. L. de Swart, A. D. M. E. Osterhaus, and B. T. Grenfell, Science 348:694-699, 2015, https://doi.org/10.1126/science.aaa3662) made an impact on him. These articles studied interactions between measles virus and the host and influenced him by making two important points. (i) It is crucial to use nonadapted (recombinant) viruses in disease-relevant model systems when studying virus-host interactions. (ii) Studying viral pathogenesis requires a combination of in vitro, ex vivo, and in vivo studies, and a group of researchers with multiple expertises. He learned that only when all these aspects are combined, can one truly answer the question: "How does a virus cause disease?"

MSphere of Influence: Positive Research Culture Enables Excellence and Innovation.

Elizabeth Ballou works in the field of medical mycology. In this mSphere of Influence article, she reflects on how two papers by Okagaki et al. (PLoS Pathog 6:e1000953, 2010, https://doi.org/10.1371/journal.ppat.1000953) and Zaragoza et al. (PLoS Pathog 6:e1000945, 2010, https://doi.org/10.1371/journal.ppat.1000945) made an impact on her career by demonstrating an alternative to destructive publication practices.