Publications by authors named "Ren Sun"

198 Publications

Inhibition of relaxin autocrine signaling confers therapeutic vulnerability in ovarian cancer.

J Clin Invest 2021 Feb 9. Epub 2021 Feb 9.

Department of Medical Biophysics, Department of Immunology, University of Toronto, Toronto, Canada.

Ovarian cancer (OC) is the most deadly gynaecological malignancy with unmet clinical need for new therapeutic approaches. The relaxin peptide is a pleiotropic hormone with reproductive functions in the ovary. Relaxin induces aggressive cell growth in several types of cancer, but the role of relaxin in OC is poorly understood. Here, we demonstrate that relaxin and its associated G-protein coupled receptor RXFP1 form an autocrine signaling loop essential for OC in vivo tumorigenesis, cell proliferation and viability. We have found that relaxin signaling activates expression of pro-oncogenic pathways including RHO, MAPK, Wnt, and Notch. We find that relaxin is detectable in OC tumors, ascites and serum. Further, inflammatory cytokines IL-6 and TNF-α activate transcription of relaxin via recruitment of STAT3 and NFκB to the proximal promoter initiating an autocrine feedback loop that potentiates expression. Inhibition of RXFP1 or relaxin increases cisplatin sensitivity of OC cell lines and abrogates in vivo tumor formation. Finally, we demonstrate that a relaxin neutralizing antibody reduces OC cell viability and sensitizes cells to cisplatin. Collectively, targeting relaxin-RXFP1 signaling offers a potential new therapeutic strategy for OC.
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http://dx.doi.org/10.1172/JCI142677DOI Listing
February 2021

Tracking HIV Rebound following Latency Reversal Using Barcoded HIV.

Cell Rep Med 2020 Dec 22;1(9):100162. Epub 2020 Dec 22.

Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.

HIV latency prevents cure of infection with antiretroviral therapy (ART) alone. One strategy for eliminating latently infected cells involves the induction of viral protein expression via latency-reversing agents (LRAs), allowing killing of host cells by viral cytopathic effects or immune effector mechanisms. Here, we combine a barcoded HIV approach and a humanized mouse model to study the effects of a designed, synthetic protein kinase C modulating LRA on HIV rebound. We show that administration of this compound during ART results in a delay in rebound once ART is stopped. Furthermore, the rebounding virus appears composed of a smaller number of unique barcoded viruses than occurs in control-treated animals, suggesting that some reservoir cells that would have contributed virus to the rebound process are eliminated by LRA administration. These data support the use of barcoded virus to study rebound and suggest that LRAs may be useful in HIV cure efforts.
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http://dx.doi.org/10.1016/j.xcrm.2020.100162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7762775PMC
December 2020

Deletion of immune evasion genes provides an effective vaccine design for tumor-associated herpesviruses.

NPJ Vaccines 2020 Nov 5;5(1):102. Epub 2020 Nov 5.

Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA.

Vaccines based on live attenuated viruses often induce broad, multifaceted immune responses. However, they also usually sacrifice immunogenicity for attenuation. It is particularly difficult to elicit an effective vaccine for herpesviruses due to an armament of immune evasion genes and a latent phase. Here, to overcome the limitation of attenuation, we developed a rational herpesvirus vaccine in which viral immune evasion genes were deleted to enhance immunogenicity while also attaining safety. To test this vaccine strategy, we utilized murine gammaherpesvirus-68 (MHV-68) as a proof-of-concept model for the cancer-associated human γ-herpesviruses, Epstein-Barr virus and Kaposi sarcoma-associated herpesvirus. We engineered a recombinant MHV-68 virus by targeted inactivation of viral antagonists of type I interferon (IFN-I) pathway and deletion of the latency locus responsible for persistent infection. This recombinant virus is highly attenuated with no measurable capacity for replication, latency, or persistence in immunocompetent hosts. It stimulates robust innate immunity, differentiates virus-specific memory T cells, and elicits neutralizing antibodies. A single vaccination affords durable protection that blocks the establishment of latency following challenge with the wild type MHV-68 for at least six months post-vaccination. These results provide a framework for effective vaccination against cancer-associated herpesviruses through the elimination of latency and key immune evasion mechanisms from the pathogen.
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http://dx.doi.org/10.1038/s41541-020-00251-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7644650PMC
November 2020

Maternal HBV Viremia and Association With Adverse Infant Outcomes in Women Living With HIV and HBV.

Pediatr Infect Dis J 2021 Feb;40(2):e56-e61

From the Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA.

Background: There is limited information on perinatal outcomes in HIV-hepatitis B virus (HBV) coinfection.

Methods: HIV Prevention Trials Network (HPTN) 046 was a randomized double-blind placebo-controlled trial of perinatal transmission that evaluated 6 months of infant nevirapine versus placebo among breast-fed infants. Women living with HIV and their infants enrolled in sub-Saharan Africa from 2007 to 2010; 78% received antiretroviral therapy (ART). Maternal samples were tested for hepatitis B surface antigen (HBsAg). High and low HBV viral load (VL) was defined as ≥106 IU/mL and <106 IU/mL. The association between HIV-HBV coinfection and maternal and infant outcomes was assessed using multivariate (MV) logistic and Cox regression.

Results: Among 2025 women, 88 (4.3%) had HBV. HIV-HBV women with high HBV VL had lower median CD4, versus HIV alone or HIV-HBV women with low HBV VL [320, 490 and 434 cells/mm3, respectively (P < 0.007)]. In MV analysis, adjusted for maternal CD4, age and maternal ART, infants born to women with high HBV VL were more likely to be low birth weight (LBW), versus HIV+/HBV- and low HBV VL women: [30% (3/10) vs. 10% (194/1953) vs. 6% (5/78), respectively, P = 0.03). High HBV VL was associated with HIV perinatal transmission [(hazard ratio 6.75 (95% confidence interval (CI): 1.86 - 24.50)]. There was no impact on infant mortality or maternal outcomes at 18 months.

Conclusions: In HIV-HBV women, high HBV viral loads increase the risk of LBW and potentially HIV perinatal transmission. Reduction of antepartum HBV viremia may have beneficial effects beyond the prevention of HBV perinatal transmission.
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http://dx.doi.org/10.1097/INF.0000000000002980DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7855346PMC
February 2021

Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease.

PLoS Genet 2020 10 21;16(10):e1009009. Epub 2020 Oct 21.

Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.

Drug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies or in vitro selection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance.
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http://dx.doi.org/10.1371/journal.pgen.1009009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605711PMC
October 2020

Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters.

Res Sq 2020 Oct 7. Epub 2020 Oct 7.

COVID-19 pandemic is the third zoonotic coronavirus (CoV) outbreak of the century after severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) since 2012. Treatment options for CoVs are largely lacking. Here, we show that clofazimine, an anti-leprosy drug with a favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple systems, including the human embryonic stem cell-derived cardiomyocytes and lung cultures. The FDA-approved molecule was found to inhibit multiple steps of viral replication, suggesting multiple underlying antiviral mechanisms. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic or therapeutic administration of clofazimine significantly reduced viral load in the lung and fecal viral shedding, and also prevented cytokine storm associated with viral infection. Additionally, clofazimine exhibited synergy when administered with remdesivir. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. Taken together, our data provide evidence that clofazimine may have a role in the control of the current pandemic SARS-CoV-2, endemic MERS-CoV in the Middle East, and, possibly most importantly, emerging CoVs of the future.
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http://dx.doi.org/10.21203/rs.3.rs-86169/v1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7553155PMC
October 2020

Haploinsufficiency of RREB1 causes a Noonan-like RASopathy via epigenetic reprogramming of RAS-MAPK pathway genes.

Nat Commun 2020 09 16;11(1):4673. Epub 2020 Sep 16.

Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, M5G 1×5, Canada.

RAS-MAPK signaling mediates processes critical to normal development including cell proliferation, survival, and differentiation. Germline mutation of RAS-MAPK genes lead to the Noonan-spectrum of syndromes. Here, we present a patient affected by a 6p-interstitial microdeletion with unknown underlying molecular etiology. Examination of 6p-interstitial microdeletion cases reveals shared clinical features consistent with Noonan-spectrum disorders including short stature, facial dysmorphia and cardiovascular abnormalities. We find the RAS-responsive element binding protein-1 (RREB1) is the common deleted gene in multiple 6p-interstitial microdeletion cases. Rreb1 hemizygous mice display orbital hypertelorism and cardiac hypertrophy phenocopying the human syndrome. Rreb1 haploinsufficiency leads to sensitization of MAPK signaling. Rreb1 recruits Sin3a and Kdm1a to control H3K4 methylation at MAPK pathway gene promoters. Haploinsufficiency of SIN3A and mutations in KDM1A cause syndromes similar to RREB1 haploinsufficiency suggesting genetic perturbation of the RREB1-SIN3A-KDM1A complex represents a new category of RASopathy-like syndromes arising through epigenetic reprogramming of MAPK pathway genes.
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http://dx.doi.org/10.1038/s41467-020-18483-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7495420PMC
September 2020

Sex differences in oncogenic mutational processes.

Nat Commun 2020 08 28;11(1):4330. Epub 2020 Aug 28.

Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
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http://dx.doi.org/10.1038/s41467-020-17359-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455744PMC
August 2020

Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus.

Nat Microbiol 2020 10 27;5(10):1285-1298. Epub 2020 Jul 27.

California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.

As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies.
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http://dx.doi.org/10.1038/s41564-020-0758-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7546529PMC
October 2020

Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing.

Nature 2020 10 24;586(7827):113-119. Epub 2020 Jul 24.

Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 has triggered an ongoing global pandemic of the severe pneumonia-like disease coronavirus disease 2019 (COVID-19). The development of a vaccine is likely to take at least 12-18 months, and the typical timeline for approval of a new antiviral therapeutic agent can exceed 10 years. Thus, repurposing of known drugs could substantially accelerate the deployment of new therapies for COVID-19. Here we profiled a library of drugs encompassing approximately 12,000 clinical-stage or Food and Drug Administration (FDA)-approved small molecules to identify candidate therapeutic drugs for COVID-19. We report the identification of 100 molecules that inhibit viral replication of SARS-CoV-2, including 21 drugs that exhibit dose-response relationships. Of these, thirteen were found to harbour effective concentrations commensurate with probable achievable therapeutic doses in patients, including the PIKfyve kinase inhibitor apilimod and the cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825 and ONO 5334. Notably, MDL-28170, ONO 5334 and apilimod were found to antagonize viral replication in human pneumocyte-like cells derived from induced pluripotent stem cells, and apilimod also demonstrated antiviral efficacy in a primary human lung explant model. Since most of the molecules identified in this study have already advanced into the clinic, their known pharmacological and human safety profiles will enable accelerated preclinical and clinical evaluation of these drugs for the treatment of COVID-19.
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http://dx.doi.org/10.1038/s41586-020-2577-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603405PMC
October 2020

A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals.

bioRxiv 2020 Apr 17. Epub 2020 Apr 17.

The emergence of novel SARS coronavirus 2 (SARS-CoV-2) in 2019 has triggered an ongoing global pandemic of severe pneumonia-like disease designated as coronavirus disease 2019 (COVID-19). To date, more than 2.1 million confirmed cases and 139,500 deaths have been reported worldwide, and there are currently no medical countermeasures available to prevent or treat the disease. As the development of a vaccine could require at least 12-18 months, and the typical timeline from hit finding to drug registration of an antiviral is >10 years, repositioning of known drugs can significantly accelerate the development and deployment of therapies for COVID-19. To identify therapeutics that can be repurposed as SARS-CoV-2 antivirals, we profiled a library of known drugs encompassing approximately 12,000 clinical-stage or FDA-approved small molecules. Here, we report the identification of 30 known drugs that inhibit viral replication. Of these, six were characterized for cellular dose-activity relationships, and showed effective concentrations likely to be commensurate with therapeutic doses in patients. These include the PIKfyve kinase inhibitor Apilimod, cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825, and ONO 5334, and the CCR1 antagonist MLN-3897. Since many of these molecules have advanced into the clinic, the known pharmacological and human safety profiles of these compounds will accelerate their preclinical and clinical evaluation for COVID-19 treatment.
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http://dx.doi.org/10.1101/2020.04.16.044016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7263415PMC
April 2020

Anti-EGFR Therapy Induces EGF Secretion by Cancer-Associated Fibroblasts to Confer Colorectal Cancer Chemoresistance.

Cancers (Basel) 2020 May 28;12(6). Epub 2020 May 28.

Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA 90033, USA.

Targeted agents have improved the efficacy of chemotherapy for cancer patients, however, there remains a lack of understanding of how these therapies affect the unsuspecting bystanders of the stromal microenvironment. Cetuximab, a monoclonal antibody therapy targeting the epidermal growth factor receptor (EGFR), is given in combination with chemotherapy as the standard of care for a subset of metastatic colorectal cancer patients. The overall response to this treatment is underwhelming and, while genetic mutations that confer resistance have been identified, it is still not known why this drug is ineffective for some patients. We discovered that cancer-associated fibroblasts (CAFs), a major cellular subset of the tumor stroma, can provide a source of cancer cell resistance. Specifically, we observed that upon treatment with cetuximab, CAFs increased their secretion of EGF, which was sufficient to render neighboring cancer cells resistant to cetuximab treatment through sustained mitogen-activated protein kinases (MAPK) signaling. Furthermore, we show the cetuximab-induced EGF secretion to be specific to CAFs and not to cancer cells or normal fibroblasts. Altogether, this work emphasizes the importance of the tumor microenvironment and considering the potential unintended consequences of therapeutically targeting cancer-driving proteins on non-tumorigenic cell types.
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http://dx.doi.org/10.3390/cancers12061393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7352975PMC
May 2020

mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1.

Nat Commun 2020 05 15;11(1):2449. Epub 2020 May 15.

Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA.

A comprehensive examination of protein-protein interactions (PPIs) is fundamental for the understanding of cellular machineries. However, limitations in current methodologies often prevent the detection of PPIs with low abundance proteins. To overcome this challenge, we develop a mRNA display with library of even-distribution (md-LED) method that facilitates the detection of low abundance binders with high specificity and sensitivity. As a proof-of-principle, we apply md-LED to IAV NS1 protein. Complementary to AP-MS, md-LED enables us to validate previously described PPIs as well as to identify novel NS1 interactors. We show that interacting with FASN allows NS1 to directly regulate the synthesis of cellular fatty acids. We also use md-LED to identify a mutant of NS1, D92Y, results in a loss of interaction with CPSF1. The use of high-throughput sequencing as the readout for md-LED enables sensitive quantification of interactions, ultimately enabling massively parallel experimentation for the investigation of PPIs.
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http://dx.doi.org/10.1038/s41467-020-16140-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229031PMC
May 2020

Comparison of Cell and Organoid-Level Analysis of Patient-Derived 3D Organoids to Evaluate Tumor Cell Growth Dynamics and Drug Response.

SLAS Discov 2020 08 30;25(7):744-754. Epub 2020 Apr 30.

Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA.

3D cell culture models have been developed to better mimic the physiological environments that exist in human diseases. As such, these models are advantageous over traditional 2D cultures for screening drug compounds. However, the practicalities of transitioning from 2D to 3D drug treatment studies pose challenges with respect to analysis methods. Patient-derived tumor organoids (PDTOs) possess unique features given their heterogeneity in size, shape, and growth patterns. A detailed assessment of the length scale at which PDTOs should be evaluated (i.e., individual cell or organoid-level analysis) has not been done to our knowledge. Therefore, using dynamic confocal live cell imaging and data analysis methods we examined tumor cell growth rates and drug response behaviors in colorectal cancer (CRC) PDTOs. High-resolution imaging of H2B-GFP-labeled organoids with DRAQ7 vital dye permitted tracking of cellular changes, such as cell birth and death events, in individual organoids. From these same images, we measured morphological features of the 3D objects, including volume, sphericity, and ellipticity. Sphericity and ellipticity were used to evaluate intra- and interpatient tumor organoid heterogeneity. We found a strong correlation between organoid live cell number and volume. Linear growth rate calculations based on volume or live cell counts were used to determine differential responses to therapeutic interventions. We showed that this approach can detect different types of drug effects (cytotoxic vs cytostatic) in PDTO cultures. Overall, our imaging-based quantification workflow results in multiple parameters that can provide patient- and drug-specific information for screening applications.
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http://dx.doi.org/10.1177/2472555220915827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7372585PMC
August 2020

Basic biochemical characterization of cytosolic enzymes in thymidine nucleotide synthesis in adult rat tissues: implications for tissue specific mitochondrial DNA depletion and deoxynucleoside-based therapy for TK2-deficiency.

BMC Mol Cell Biol 2020 Apr 28;21(1):33. Epub 2020 Apr 28.

Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.

Background: Deficiency in thymidine kinase 2 (TK2) or p53 inducible ribonucleotide reductase small subunit (p53R2) is associated with tissue specific mitochondrial DNA (mtDNA) depletion. To understand the mechanisms of the tissue specific mtDNA depletion we systematically studied key enzymes in dTMP synthesis in mitochondrial and cytosolic extracts prepared from adult rat tissues.

Results: In addition to mitochondrial TK2 a cytosolic isoform of TK2 was characterized, which showed similar substrate specificity to the mitochondrial TK2. Total TK activity was highest in spleen and lowest in skeletal muscle. Thymidylate synthase (TS) was detected in cytosols and its activity was high in spleen but low in other tissues. TS protein levels were high in heart, brain and skeletal muscle, which deviated from TS activity levels. The p53R2 proteins were at similar levels in all tissues except liver where it was ~ 6-fold lower. Our results strongly indicate that mitochondria in most tissues are capable of producing enough dTTP for mtDNA replication via mitochondrial TK2, but skeletal muscle mitochondria do not and are most likely dependent on both the salvage and de novo synthesis pathways.

Conclusion: These results provide important information concerning mechanisms for the tissue dependent variation of dTTP synthesis and explained why deficiency in TK2 or p53R2 leads to skeletal muscle dysfunctions. Furthermore, the presence of a putative cytosolic TK2-like enzyme may provide basic knowledge for the understanding of deoxynucleoside-based therapy for mitochondrial disorders.
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http://dx.doi.org/10.1186/s12860-020-00272-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189545PMC
April 2020

The expression and activity of thymidine kinase 1 and deoxycytidine kinase are modulated by hydrogen peroxide and nucleoside analogs.

Nucleosides Nucleotides Nucleic Acids 2020 19;39(10-12):1347-1358. Epub 2020 Mar 19.

Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Thymidine kinase 1 (TK1) and deoxycytidine kinase (dCK) are required for the activation of thymidine and deoxycytidine analogs used in antiviral and anticancer therapies. Many anticancer drugs cause oxidative stress, and the rise of GSSG and other reactive oxygen species may lead to alteration in gene expression, protein, nucleic acids and lipid modifications. Here, we investigated the effects of oxidative stress and nucleoside analog on the expression and activity of TK1 and dCK. Treatment with GSSG resulted in glutathionylation of dCK and dGK but not TK1 and Dm-dNK, and glutathionylation led to increased dCK activity but decreased dGK activity. Treatment with hydrogen peroxide resulted in induction of TK1, however, the TK1 activity did not correlate with TK1 protein levels, indicating that TK1 protein was inactive. The cellular expression of dCK, however, was reduced but dCK activity was not affected at concentration ≤ 4 mM. Treatment with TFT or 5FdU resulted in downregulation of both TK1 and dCK. However, araC and dFdC treatment led to increased dCK protein but decreased dCK activity. In contrast, both TK1 protein and activity were upregulated after araC and dFdC treatment. Doxorubicin treatment led to upregulation of the TK1 but downregulation of dCK. In conclusion TK1 and dCK expression and activity are apparently affected by oxidative stress and treatment by nucleoside analogs. These results demonstrate the pharmacokinetic importance of characterizing the expression and activity of TK1 and dCK during chemotherapy with thymidine and deoxycytidine analogs in order to optimize their efficacy.
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http://dx.doi.org/10.1080/15257770.2020.1720234DOI Listing
March 2020

Benchmarking of computational error-correction methods for next-generation sequencing data.

Genome Biol 2020 03 17;21(1):71. Epub 2020 Mar 17.

Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA.

Background: Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequencing technologies in clinical tools. Computational error correction promises to eliminate sequencing errors, but the relative accuracy of error correction algorithms remains unknown.

Results: In this paper, we evaluate the ability of error correction algorithms to fix errors across different types of datasets that contain various levels of heterogeneity. We highlight the advantages and limitations of computational error correction techniques across different domains of biology, including immunogenomics and virology. To demonstrate the efficacy of our technique, we apply the UMI-based high-fidelity sequencing protocol to eliminate sequencing errors from both simulated data and the raw reads. We then perform a realistic evaluation of error-correction methods.

Conclusions: In terms of accuracy, we find that method performance varies substantially across different types of datasets with no single method performing best on all types of examined data. Finally, we also identify the techniques that offer a good balance between precision and sensitivity.
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http://dx.doi.org/10.1186/s13059-020-01988-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079412PMC
March 2020

Zika Virus Mucosal Infection Provides Protective Immunity.

J Virol 2020 04 16;94(9). Epub 2020 Apr 16.

Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California, USA

Zika virus (ZIKV) is a major human pathogen. ZIKV can replicate in female and male reproductive organs, thus facilitating the human-human transmission cycle. Viral shedding in the semen can increase the risk of ZIKV transmission through sexual mode. Therefore, the vaginal and anorectal mucosa are relevant sites for ZIKV infection. However, the pathobiology of ZIKV transmission through the rectal route is not well understood. Here, we utilize a mouse model system to investigate the immunopathological consequences following ZIKV infection of the rectal mucosa compared to a subcutaneous route of infection. We show that ZIKV-rectal inoculation results in viremia with subclinical infection. ZIKV infects the mucosal epithelium and submucosal dendritic cells, inducing immune and inflammatory cell infiltration. Rectal transmission of ZIKV resulted in the generation of serum-neutralizing antibody responses. Mass cytometry analyses of splenocytes showed a significantly reduced level of inflammatory monocyte and neutrophil cellular responses in the rectal route group. Furthermore, immunological priming through the rectal mucosa with an attenuated ZIKV strain resulted in significant protection from lethal subcutaneous ZIKV challenge, further eliciting robust memory CD4-positive (CD4) and CD8 T-cell and ZIKV-specific serum-neutralizing antibody responses. Thus, our study provides deeper immunopathobiological insights on rectal transmission and highlights a rational strategy for mucosal immunization. This model system recapitulates clinical aspects of human ZIKV disease outcome, where most infections are well controlled and result in subclinical and asymptomatic outcomes. Zika virus is a clinically significant human pathogen that is primarily transmitted and spread by species mosquitoes but is also sexually transmissible. The recent pandemic in the Americas led to an unprecedented increase of newborn babies with developmental brain and eye abnormalities. To date, there is no licensed vaccine or therapeutic intervention available for the fight against ZIKV. Understanding the sexual transmission of ZIKV through vaginal and rectal routes is necessary to restrict virus transmission and spread. This study examines the early immunological and pathological consequences of rectal and subcutaneous routes of ZIKV infection using a mouse model. We characterized the primary target cells of ZIKV infection and the subsequent mucosal immune responses to infection, and we demonstrate the protective effect of mucosal rectal immunization using an attenuated ZIKV strain. This mucosal vaccination approach can be further developed to prevent future ZIKV outbreaks.
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http://dx.doi.org/10.1128/JVI.00067-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163142PMC
April 2020

Spleen tyrosine kinase expression is correlated with human papillomavirus in head and neck cancer.

Oral Oncol 2020 02 19;101:104529. Epub 2019 Dec 19.

Department of Otolaryngology, London Health Sciences Centre, London, Ontario, Canada; Department of Oncology, London Health Sciences Centre, London, Ontario, Canada. Electronic address:

Objectives: Spleen tyrosine kinase (SYK) is a promoter of cell survival in a variety of cell types, including normal and cancerous epithelial cells. We hypothesized that SYK would an important therapeutic target to inhibit for the treatment of HNSCC.

Materials And Methods: SYK protein abundance in patient tumours was evaluated. SYK protein and mRNA abundance was used to examine patient survival and human papillomavirus (HPV) status. Small-interfering RNAs and gene editing with CRISPR/Cas9 were used to evaluate SYK expression on proliferation in HNSCC cell lines. The potency of SYK inhibitor ER27319 maleate on cellular proliferation was tested using a panel of 28 HNSCC cell lines and in vivo in HNSCC patient-derived xenograft (PDX) models.

Results: Moderate to high protein expression of SYK was observed in 24% of patient tumors and high SYK expression was exclusively observed in HPV-positive samples (p < 0.001). SYK inhibition with RNA interference, gene editing or a SYK inhibitor (ER27319) decreased cell proliferation and migration. Treatment of PDXs with ER27319 maleate was observed to reduce tumour burden in vivo in two of three models.

Conclusions: HPV-positive HNSCC harbours high SYK protein levels. We demonstrate that proliferation, migration and overall burden of these tumours can be reduced by genetic or pharmacologic inhibition of SYK. Taken together, these data establish SYK as a therapeutic target for HNSCC.
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http://dx.doi.org/10.1016/j.oraloncology.2019.104529DOI Listing
February 2020

Are the Effects of Independent Biophysical Factors Linearly Additive? A 3D Tumor Migration Model.

Biophys J 2019 11 2;117(9):1702-1713. Epub 2019 Oct 2.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts; Howard Hughes Medical Institute, Boston University, Boston, Massachusetts. Electronic address:

Interstitial fluid flow plays a critical role in tumor cell invasion, yet this role has not been explored extensively in combination with other microenvironmental factors. Here, we establish a novel computational model of three-dimensional breast cancer cell migration to unveil the effect of interstitial fluid flow in the dependence of various extracellular matrix (ECM) physical properties. Our model integrates several principal factors: fluid dynamics, autologous chemotaxis, collagen fiber network structure, ECM stiffness, and cell-fiber and cell-flow interaction. First, independently with an aligned collagen fiber network and interstitial fluid flow, this model is validated by successfully reproducing the cell migration patterns. In the model, the interstitial fluid flow leads to directional symmetry breaking of chemotactic migration and synergizes with the ECM orientation to regulate cell migration. This synergy is universal in both the mesenchymal and the amoeboid migration modes, despite the fact that the cell-ECM interaction are different. Consequently, we construct a cell displacement function depending on these factors. Our cell migration model enables three-dimensional cancer migration prediction, mechanism exploration, and inhibition treatment design in a complex tumor microenvironment.
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http://dx.doi.org/10.1016/j.bpj.2019.09.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838959PMC
November 2019

Comparative toxicoproteogenomics of mouse and rat liver identifies TCDD-resistance genes.

Arch Toxicol 2019 10 11;93(10):2961-2978. Epub 2019 Sep 11.

Computational Biology, Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada.

The aryl hydrocarbon receptor (AHR) mediates many toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, the AHR alone does not explain the widely different outcomes among organisms. To identify the other factors involved, we evaluated three transgenic mouse lines, each expressing a different rat AHR isoform (rWT, DEL, and INS) providing widely different resistance to TCDD toxicity, as well as C57BL/6 and DBA/2 mice which exhibit a ~ tenfold divergence in TCDD sensitivity (exposures of 5-1000 μg/kg TCDD). We supplement these with whole-genome sequencing, together with transcriptomic and proteomic analyses of the corresponding rat models, Long-Evans (L-E) and Han/Wistar (H/W) rats (having a ~ 1000-fold difference in their TCDD sensitivities; 100 μg/kg TCDD), to identify genes associated with TCDD-response phenotypes. Overall, we identified up to 50% of genes with altered mRNA abundance following TCDD exposure are associated with a single AHR isoform (33.8%, 11.7%, 5.2% and 0.3% of 3076 genes altered unique to rWT, DEL, C57BL/6 and INS respectively following 1000 μg/kg TCDD). Hepatic Pxdc1 was significantly repressed in all three TCDD-sensitive animal models (C57BL/6 and rWT mice, and L-E rat) after TCDD exposure. Three genes, including Cxxc5, Sugp1 and Hgfac, demonstrated different AHRE-1 (full) motif occurrences within their promoter regions between rat strains, as well as different patterns of mRNA abundance. Several hepatic proteins showed parallel up- or downward alterations with their RNAs, with three genes (SNRK, IGTP and IMPA2) showing consistent, strain-dependent changes. These data show the value of integrating genomic, transcriptomic and proteomic evidence across multi-species models in toxicologic studies.
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http://dx.doi.org/10.1007/s00204-019-02560-0DOI Listing
October 2019

Negative Cooperative Binding of Thymidine, Ordered Substrate Binding, and Product Release of Human Mitochondrial Thymidine Kinase 2 Explain Its Complex Kinetic Properties and Physiological Functions.

ACS Omega 2018 Aug 13;3(8):8971-8979. Epub 2018 Aug 13.

Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, SE-750 07 Uppsala, Sweden.

Mitochondrial thymidine kinase 2 (TK2) catalyzes the phosphorylation of thymidine (dT) and deoxycytidine (dC) and is essential for mitochondrial function in post-mitotic tissues. The phosphorylation of dT shows negative cooperativity, but the phosphorylation of dC follows classical Michaelis-Menten kinetics. The enzyme is feedback-inhibited by its end products deoxythymidine triphosphate (dTTP) and deoxycytidine triphosphate (dCTP). In order to better understand the reaction mechanism and the negative cooperative behavior, we conducted isothermal titration calorimetry (ITC) and intrinsic tryptophan fluorescence (ITF) quenching studies with purified recombinant human TK2. Cooperative binding was observed with dT but not dC by the ITC analysis in accordance with earlier enzyme kinetic studies. The phosphate donor adenosine triphosphate (ATP) did not bind to either dTTP-bound or dTTP-free enzymes but bound tightly to the dT- or dC-TK2 complexes with large differences in enthalpy and entropy changes, strongly suggesting an ordered binding of the substrates and different conformational states of the ATP and dT- and dC-TK2 ternary complexes. dTTP binding was endothermic; however, dCTP could not be shown to interact with the enzyme. ITF quenching studies also revealed tight binding of dT, dC, deoxythymidine monophosphate, deoxycytidine monophosphate, and dTTP but not adenosine 5'-diphosphate or ATP. These results strongly indicate an ordered sequential binding of the substrates and ordered release of the products as well as different conformational states of the active site of TK2. These results help to explain the different kinetics observed with dT and dC as substrates, which have important implications for TK2 regulation in vivo.
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http://dx.doi.org/10.1021/acsomega.8b01376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6644362PMC
August 2018

DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV.

Cell 2019 09 22;178(6):1329-1343.e12. Epub 2019 Aug 22.

Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute (CNSI), University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes (CATCs) and facilitates translocation of an ∼150-kb dsDNA genome, followed by acquisition of a pleomorphic tegument and envelope. Because of deviation from icosahedral symmetry, KSHV portal and tegument structures have largely been obscured in previous studies. Using symmetry-relaxed cryo-EM, we determined the in situ structure of the KSHV portal and its interactions with surrounding capsid proteins, CATCs, and the terminal end of KSHV's dsDNA genome. Our atomic models of the portal and capsid/CATC, together with visualization of CATCs' variable occupancy and alternate orientation of CATC-interacting vertex triplexes, suggest a mechanism whereby the portal orchestrates procapsid formation and asymmetric long-range determination of CATC attachment during DNA packaging prior to pleomorphic tegumentation/envelopment. Structure-based mutageneses confirm that a triplex deep binding groove for CATCs is a hotspot that holds promise for antiviral development.
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http://dx.doi.org/10.1016/j.cell.2019.07.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753055PMC
September 2019

Fascia iliaca compartment block reduces pain and opioid consumption after total hip arthroplasty: A systematic review and meta-analysis.

Int J Surg 2019 May 25;65:70-79. Epub 2019 Mar 25.

Department of Anesthesia, The First People's Hospital of Zhangjiagang, Soochow University, 215600, China. Electronic address:

Background: Optimal pain management after total hip arthroplasty (THA) remains controversial. We perform a meta-analysis from randomized controlled trials (RCTs) to evaluate the efficacy and safety of fascia iliaca compartment block (FICB) in THA.

Methods: In this meta-analysis, we conducted electronic searches of Pubmed, Medline, Cochrane library, and Web of Science before February 2019. We collected RCTs to compare FICB and placebo for pain control after THA. The outcome measurements consisted of pain score, opioid consumption, length of hospitalization and postoperative complications. All data analyses were conducted using STATA 13.0. Cochrane Collaboration's tool was adopted to assess the risk of bias.

Results: Seven RCTs met our inclusion criteria with 165 patients in the FICB groups, and 160 patients in the placebo groups. The present meta-analysis indicated that there were significant differences between the groups in terms of pain score at postoperative 12 h (WMD = -0.285, 95% CI [-0.460, -0.109], P = 0.002) and 24 h (WMD = -0.391, 95% CI [-0.723, -0.059], P = 0.021). FICB was associated with significant superior in opioid consumption at postoperative 12 h (WMD = -5.394, 95% CI [-8.772, -2.016], P = 0.002) and 24 h (WMD = -6.376, 95% CI [-10.737, -2.016], P = 0.004) compared with placebo. No significant difference was identified regarding length of hospitalization (WMD = 0.112, 95% CI [-0.125, 0.350], P = 0.354).

Conclusion: Fascia iliaca compartment block was effective for pain relief during the early post-operative period after total hip arthroplasty. Meanwhile, it reduced the cumulative morphine consumption and the risk of opioid-related adverse effects.
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http://dx.doi.org/10.1016/j.ijsu.2019.03.014DOI Listing
May 2019

Increased risk for T cell autoreactivity to ß-cell antigens in the mice expressing the A obesity-associated gene.

Sci Rep 2019 03 12;9(1):4269. Epub 2019 Mar 12.

Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095-1735, United States.

There has been considerable debate as to whether obesity can act as an accelerator of type 1 diabetes (T1D). We assessed this possibility using transgenic mice (MIP-TF mice) whose ß-cells express enhanced green fluorescent protein (EGFP). Infecting these mice with EGFP-expressing murine herpes virus-68 (MHV68-EGFP) caused occasional transient elevation in their blood glucose, peri-insulitis, and Th1 responses to EGFP which did not spread to other ß-cell antigens. We hypothesized that obesity-related systemic inflammation and ß-cell stress could exacerbate the MHV68-EGFP-induced ß-cell autoreactivity. We crossed MIP-TF mice with A mice which develop obesity and provide models of metabolic disease alongside early stage T2D. Unlike their MIP-TF littermates, MHV68-EGFP-infected A/MIP-TF mice developed moderate intra-insulitis and transient hyperglycemia. MHV68-EGFP infection induced a more pronounced intra-insulitis in older, more obese, A/MIP-TF mice. Moreover, in MHV68-EGFP-infected A/MIP-TF mice, Th1 reactivity spread from EGFP to other ß-cell antigens. Thus, the spreading of autoreactivity among ß-cell antigens corresponded with the transition from peri-insulitis to intra-insulitis and occurred in obese A/MIP-TF mice but not lean MIP-TF mice. These observations are consistent with the notion that obesity-associated systemic inflammation and ß-cell stress lowers the threshold necessary for T cell autoreactivity to spread from EGFP to other ß-cell autoantigens.
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http://dx.doi.org/10.1038/s41598-019-38905-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6414670PMC
March 2019

Differential Metabolic Reprogramming by Zika Virus Promotes Cell Death in Human versus Mosquito Cells.

Cell Metab 2019 05 28;29(5):1206-1216.e4. Epub 2019 Feb 28.

Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

Zika virus is a pathogen that poses serious consequences, including congenital microcephaly. Although many viruses reprogram host cell metabolism, whether Zika virus alters cellular metabolism and the functional consequences of Zika-induced metabolic changes remain unknown. Here, we show that Zika virus infection differentially reprograms glucose metabolism in human versus C6/36 mosquito cells by increasing glucose use in the tricarboxylic acid cycle in human cells versus increasing glucose use in the pentose phosphate pathway in mosquito cells. Infection of human cells selectively depletes nucleotide triphosphate levels, leading to elevated AMP/ATP ratios, AMP-activated protein kinase (AMPK) phosphorylation, and caspase-mediated cell death. AMPK is also phosphorylated in Zika virus-infected mouse brain. Inhibiting AMPK in human cells decreases Zika virus-mediated cell death, whereas activating AMPK in mosquito cells promotes Zika virus-mediated cell death. These findings suggest that the differential metabolic reprogramming during Zika virus infection of human versus mosquito cells determines whether cell death occurs.
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http://dx.doi.org/10.1016/j.cmet.2019.01.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6818653PMC
May 2019

BPG: Seamless, automated and interactive visualization of scientific data.

BMC Bioinformatics 2019 Jan 21;20(1):42. Epub 2019 Jan 21.

Ontario Institute for Cancer Research, Toronto, Canada.

Background: We introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment.

Results: This open-source package includes multiple methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it suitable for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for integration with computational pipelines.

Conclusion: BPG provides a new approach for linking interactive and scripted data visualization and is available at http://labs.oicr.on.ca/boutros-lab/software/bpg or via CRAN at https://cran.r-project.org/web/packages/BoutrosLab.plotting.general.
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http://dx.doi.org/10.1186/s12859-019-2610-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341661PMC
January 2019

The Ca sensor STIM1 regulates the type I interferon response by retaining the signaling adaptor STING at the endoplasmic reticulum.

Nat Immunol 2019 02 14;20(2):152-162. Epub 2019 Jan 14.

Department of Physiology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.

Stimulator of interferon genes (STING) is an endoplasmic reticulum (ER) signaling adaptor that is essential for the type I interferon response to DNA pathogens. Aberrant activation of STING is linked to the pathology of autoimmune and autoinflammatory diseases. The rate-limiting step for the activation of STING is its translocation from the ER to the ER-Golgi intermediate compartment. Here, we found that deficiency in the Ca sensor stromal interaction molecule 1 (STIM1) caused spontaneous activation of STING and enhanced expression of type I interferons under resting conditions in mice and a patient with combined immunodeficiency. Mechanistically, STIM1 associated with STING to retain it in the ER membrane, and coexpression of full-length STIM1 or a STING-interacting fragment of STIM1 suppressed the function of dominant STING mutants that cause autoinflammatory diseases. Furthermore, deficiency in STIM1 strongly enhanced the expression of type I interferons after viral infection and prevented the lethality of infection with a DNA virus in vivo. This work delineates a STIM1-STING circuit that maintains the resting state of the STING pathway.
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http://dx.doi.org/10.1038/s41590-018-0287-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6340781PMC
February 2019

Proteomics of Bronchoalveolar Lavage Fluid Reveals a Lung Oxidative Stress Response in Murine Herpesvirus-68 Infection.

Viruses 2018 11 27;10(12). Epub 2018 Nov 27.

Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.

Murine herpesvirus-68 (MHV-68) productively infects mouse lungs, exhibiting a complex pathology characteristic of both acute viral infections and chronic respiratory diseases. We sought to discover proteins differentially expressed in bronchoalveolar lavage (BAL) from mice infected with MHV-68. Mice were infected intranasally with MHV-68. After nine days, as the lytic phase of infection resolved, differential BAL proteins were identified by two-dimensional (2D) electrophoresis and mass spectrometry. Of 23 unique proteins, acute phase proteins, vitamin A transport, and oxidative stress response factors Pdx6 and EC-SOD (Sod3) were enriched. Correspondingly, iNOS2 was induced in lung tissue by seven days post-infection. Oxidative stress was partly a direct result of MHV-68 infection, as reactive oxygen species (ROS) were induced in cultured murine NIH3T3 fibroblasts and human lung A549 cells infected with MHV-68. Finally, mice infected with a recombinant MHV-68 co-expressing inflammatory cytokine murine interleukin 6 (IL6) showed exacerbated oxidative stress and soluble type I collagen characteristic of tissue recovery. Thus, oxidative stress appears to be a salient feature of MHV-68 pathogenesis, in part caused by lytic replication of the virus and IL6. Proteins and small molecules in lung oxidative stress networks therefore may provide new therapeutic targets to ameliorate respiratory virus infections.
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http://dx.doi.org/10.3390/v10120670DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316452PMC
November 2018

A controlled trial of HNSCC patient-derived xenografts reveals broad efficacy of PI3Kα inhibition in controlling tumor growth.

Int J Cancer 2019 10 18;145(8):2100-2106. Epub 2018 Dec 18.

Department of Otolaryngology - Head and Neck Surgery, Western University, London, Canada.

Head and neck squamous cell carcinomas (HNSCCs) frequently harbor alterations in the PI3K/AKT/mTOR signaling axis, particularly in the PIK3CA gene. PI3K-targeted agents have therefore gained considerable preclinical and clinical interest as emerging therapies for HNSCC. Identification of predictive biomarkers of response would advance the clinical application of PI3K-targeted drugs for patients, in order to achieve maximal benefit. To date, studies of drug biomarkers have largely focused on screening cell lines, with much more limited in vivo testing, usually only as validation. This approach has rarely enabled accurate predictions of clinical efficacy. Recently, clinical trials of PDX models (PDX clinical trials) have been introduced as a preclinical approach to interrogate interpatient response heterogeneity. Already, PDX clinical trial responses have been demonstrated to correlate closely with patient outcomes. Here, using both an HNSCC specific, 28-cell line panel and a PDX clinical trial of 80 xenografts derived from 20 unique HNSCC tumors, we systematically examine patterns of response to PI3K inhibition in HNSCC. We find EGFR, AKT1 and CSMD1 copy number aberrations, but not PIK3CA mutations, to be associated with responsiveness to PI3K-targeted drugs. Further, we reveal PI3Kα inhibition to be almost globally tumoristatic in HNSCC xenografts regardless of PIK3CA mutational status, emphasizing its potential as a stabilizing neoadjuvant therapy for HNSCC patients.
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http://dx.doi.org/10.1002/ijc.32009DOI Listing
October 2019