Deisy Contreras

Systematic Analysis of Enhancer and Critical cis-Acting RNA Elements in the Protein-Encoding Region of the Hepatitis C Virus Genome

ABSTRACT Hepatitis C virus (HCV) causes chronic hepatitis, cirrhosis, and liver cancer. cis-acting RNA elements of the HCV genome are critical for translation initiation and replication of the viral genome. We hypothesized that the coding regions of nonstructural proteins harbor enhancer and essential cis-acting replication elements (CRE). In order to experimentally identify new cis RNA elements, we utilized an unbiased approach to introduce synonymous substitutions. The HCV genome coding for nonstructural proteins (nucleotide positions 3872 to 9097) was divided into 17 contiguous segments. The wobble nucleotide positions of each codon were replaced, resulting in 33% to 41% nucleotide changes. The HCV genome containing one of each of 17 mutant segments (S1 to S17) was tested for genome replication and infectivity. We observed that silent mutations in segment 13 (S13) (nucleotides [nt] 7457 to 7786), S14 (nt 7787 to 8113), S15 (nt 8114 to 8440), S16 (nt 8441 to 8767), and S17 (nt 8768 to 9097) resulted in impaired genome replication, suggesting CRE structures are enriched in the NS5B region. Subsequent high-resolution mutational analysis of NS5B (nt 7787 to 9289) using approximately 51-nucleotide contiguous subsegment mutant viruses having synonymous mutations revealed that subsegments SS8195-8245, SS8654-8704, and SS9011-9061 were required for efficient viral growth, suggesting that these regions act as enhancer elements. Covariant nucleotide substitution analysis of a stem-loop, JFH-SL9098, revealed the formation of an extended stem structure, which we designated JFH-SL9074. We have identified new enhancer RNA elements and an extended stem-loop in the NS5B coding region. Genetic modification of enhancer RNA elements can be utilized for designing attenuated HCV vaccine candidates.

Zika Virus Infectious Cell Culture System and the In Vitro Prophylactic Effect of Interferons

Zika Virus (ZIKV) is an emerging pathogen that is linked to fetal developmental abnormalities such as microcephaly, eye defects, and impaired growth. ZIKV is an RNA virus of the Flaviviridae family. ZIKV is mainly transmitted by mosquitoes, but can also be spread by maternal to fetal vertical transmission as well as sexual contact. To date, there are no reliable treatment or vaccine options available to protect those infected by the virus. The development of a reproducible, effective Zika virus infectious cell culture system is critical for studying the molecular mechanisms of ZIKV replication as well as drug and vaccine development. In this regard, a protocol describing a mammalian cell-based in vitro Zika virus culture system for viral production and growth analysis is reported here. Details on the formation of plaques by Zika virus on a cell monolayer and plaque assay for measuring viral titer are presented. Viral genome replication kinetics and double-stranded RNA genome replicatory intermediates are determined. This culture platform was utilized to screen against a library of a small set of cytokines resulting in the identification of interferon-α (IFN-α), IFN-β and IFN-γ as potent inhibitors of Zika viral growth. In summary, an in vitro infectious Zika viral culture system and various virological assays are demonstrated in this study, which has the potential to greatly benefit the research community in elucidating further the mechanisms of viral pathogenesis and the evolution of viral virulence. Antiviral IFN-alpha can further be evaluated as a prophylactic, post-exposure prophylactic, and treatment option for Zika virus infections in high-risk populations, including infected pregnant women.

Characterization of type I interferon pathway during hepatic differentiation of human pluripotent stem cells and hepatitis C virus infection

Pluripotent stem cells are being actively studied as a cell source for regenerating damaged liver. For long-term survival of engrafting cells in the body, not only do the cells have to execute liver-specific function but also withstand the physical strains and invading pathogens. The cellular innate immune system orchestrated by the interferon (IFN) pathway provides the first line of defense against pathogens. The objective of this study is to assess the innate immune function as well as to systematically profile the IFN-induced genes during hepatic differentiation of pluripotent stem cells. To address this objective, we derived endodermal cells (day 5 post-differentiation), hepatoblast (day 15) and hepatocyte-like cells (day 21) from human embryonic stem cells (hESCs). Day 5, 15 and 21 cells were stimulated with IFN-α and subjected to IFN pathway analysis. Transcriptome analysis was carried out by RNA sequencing. The results showed that the IFN-α treatment activated STAT-JAK pathway in differentiating cells. Transcriptome analysis indicated stage specific expression of classical and non-classical IFN-stimulated genes (ISGs). Subsequent validation confirmed the expression of novel ISGs including RASGRP3, CLMP and TRANK1 by differentiated hepatic cells upon IFN treatment. Hepatitis C virus replication in hESC-derived hepatic cells induced the expression of ISGs--LAMP3, ETV7, RASGRP3, and TRANK1. The hESC-derived hepatic cells contain intact innate system and can recognize invading pathogens. Besides assessing the tissue-specific functions for cell therapy applications, it may also be important to test the innate immune function of engrafting cells to ensure adequate defense against infections and improve graft survival.

Comparative analysis of protein evolution in the genome of pre-epidemic and epidemic Zika virus

Zika virus (ZIKV) causes microcephaly in congenital infection, neurological disorders, and poor pregnancy outcome and no vaccine is available for use in humans or approved. Although ZIKV was first discovered in 1947, the exact mechanism of virus replication and pathogenesis remains unknown. Recent outbreaks of Zika virus in the Americas clearly suggest a human-mosquito cycle or urban cycle of transmission. Understanding the conserved and adaptive features in the evolution of ZIKV genome will provide a hint on the mechanism of ZIKV adaptation to a new cycle of transmission. Here, we show comprehensive analysis of protein evolution of ZIKV strains including the current 2015-16 outbreak. To identify the constraints on ZIKV evolution, selection pressure at individual codons, immune epitopes and co-evolving sites were analyzed. Phylogenetic trees show that the ZIKV strains of the Asian genotype form distinct cluster and share a common ancestor with African genotype. The TMRCA (Time to the Most Recent Common Ancestor) for the Asian lineage and the subsequently evolved Asian human strains was calculated at 88 and 34years ago, respectively. The proteome of current 2015/16 epidemic ZIKV strains of Asian genotype was found to be genetically conserved due to genome-wide negative selection, with limited positive selection. We identified a total of 16 amino acid substitutions in the epidemic and pre-epidemic strains from human, mosquito, and monkey hosts. Negatively selected amino acid sites of Envelope protein (E-protein) (positions 69, 166, and 174) and NS5 (292, 345, and 587) were located in central dimerization domains and C-terminal RNA-directed RNA polymerase regions, respectively. The predicted 137 (92 CD4 TCEs; 45 CD8 TCEs) immunogenic peptide chains comprising negatively selected amino acid sites can be considered as suitable target for sub-unit vaccine development, as these sites are less likely to generate immune-escape variants due to strong functional constrains operating on them. The targeted changes at the amino acid level may contribute to better adaptation of ZIKV strains to human-mosquito cycle or urban cycle of transmission.

Bioartificial Liver Device Based on Induced Pluripotent Stem Cell-Derived Hepatocytes

Decompensated liver disorders require liver transplantation. However, the donor organ shortage is a limiting factor. Harnessing the power of human induced pluripotent stem cell (iPSC) technology in combination with hollow fiber-based bioartificial liver (BAL) device can be beneficial to patients with liver failure. Our goal is to develop a BAL module comprised of iPSC-derived hepatocytes (iHeps) arrayed on the extracapillary space (ECS) of hollow fiber membranous capillaries that allow the flow of blood through the intracapillary space (ICS), thus mimicking the tissue microarchitecture. For the proof-of-concept in vitro study, a cartridge having semipermeable polysulfone membrane fibers was used as an artificial liver device. As a source for human liver cells, we derived metabolically active hepatocytes from iPSCs. The iHeps on microcarrier beads were loaded into the ECS of a hollow fiber bioreactor cartridge and cultured using a closed-circuit continuous flow system. The iHeps secreted human albumin, prothrombin, and apolipoprotein B into the hollow fiber ICS media, and the continuous flow system also improved maturation of iHeps. In conclusion, the iPSC-hepatocytes in the bioartificial liver device maintained the secretory function and exhibited cell maturation. The iPSC-hepatocyte BAL has the potential to be further developed as a liver support device for the treatment of decompensated liver diseases.

Profile of Inflammation-associated genes during Hepatic Differentiation of Human Pluripotent Stem Cells.

Expression of genes associated with inflammation was analyzed during differentiation of human pluripotent stem cells (PSCs) to hepatic cells. Messenger RNA transcript profiles of differentiated endoderm (day 5), hepatoblast (day 15) and hepatocyte-like cells (day 21) were obtained by RNA sequencing analysis. When compared to endoderm cells an immature cell type, the hepatic cells (days 15 and 21) had significantly higher expression of acute phase protein genes including complement factors, coagulation factors, serum amyloid A and serpins. Furthermore, hepatic phase of cells expressed proinflammatory cytokines IL18 and IL32 as well as cytokine receptors IL18R1, IL1R1, IL1RAP, IL2RG, IL6R, IL6ST and IL10RB. These cells also produced CCL14, CCL15, and CXCL- 1, 2, 3, 16 and 17 chemokines. Endoderm cells had higher levels of chemokine receptors, CXCR4 and CXCR7, than that of hepatic cells. Sirtuin family of genes involved in aging, inflammation and metabolism were differentially regulated in endoderm and hepatic phase cells. Ligands and receptors of the tumor necrosis factor (TNF) family as well as downstream signaling factors TRAF2, TRAF4, FADD, NFKB1 and NFKBIB were differentially expressed during hepatic differentiation.

Pathogenesis of Zika Virus Infection via Rectal Route

Zika virus (ZIKV) is a mosquito borne flavivirus originally confined to Africa and Asia that has spread to islands located in Southeast Asia, and most recently to the Americas and the Caribbean. Approximately 80% of infected individuals are asymptomatic, while the remaining infected population exhibit mild febrile syndrome such as rash, conjunctivitis, and arthralgia. In some adults, ZIKV causes neurotropic Guillain Barre syndrome (1). Vertical transmission of ZIKV in infected mothers causes fetal growth restriction, microcephaly, and congenital eye disease (2-5). Cases of ZIKV sexual transmission from male to female (6-8), male to male (9), and a suspected case of female to male transmission (10) have been reported. ZIKV has been detected in the semen of infected males (11-15), even after months of symptom onset (16-19). Viral persistence in the testes and semen can increase the risk of ZIKV transmission through rectal route in men having sex with men (MSM) and between heterosexual partners. The anorectal mucosa is a major entry site for HIV-1 transmission among MSM (20), and for the acquisition and transmission of other sexually transmitted diseases, such as syphilis, chlamydia, and gonorrhea. Although the risk of ZIKV acquisition through the rectal route is high, no pathobiological information is available. Here, we describe the establishment of a rectal route of ZIKV infection system using immunocompromised (ifnar1 -/-) male mice to determine their susceptibility to ZIKV and to assess viral dissemination to male reproductive organs. We found that rectal inoculation of ZIKV results in viremia with non-lethal infection. The rectal mucosa is susceptible to ZIKV entry and replication. Following rectal inoculation, ZIKV establishes active testicular infection that persists at least 21 days. During the acute phase of infection, the highest viral load was observed in the spleen, with inflammatory and immune cellular infiltration. Macrophages in the splenic red pulp are the target cells for ZIKV infection.

Dysregulation of Long Non-coding RNA (lncRNA) Genes and Predicted lncRNA-protein Interactions during Zika Virus Infection

Zika Virus (ZIKV) is a causative agent for poor pregnancy outcome and fetal developmental abnormalities, including microcephaly and eye defects. As a result, ZIKV is now a confirmed teratogen. Understanding host-pathogen interactions, specifically cellular perturbations caused by ZIKV, can provide novel therapeutic targets. In order to complete viral replication, viral pathogens control the host cellular machineries and regulate various factors, including long noncoding RNA (lncRNA) genes, at transcriptional levels. The role of lncRNA genes in the pathogenesis of ZIKV-mediated microcephaly and eye defects is currently unknown. To gain additional insights, we focused on profiling the differentially expressed lncRNA genes during ZIKV infection in mammalian cells. For this study, we employed a contemporary clinical Zika viral isolate, PRVABC59, of Asian genotype. We utilized an unbiased RNA sequencing approach to profile the lncRNA transcriptome in ZIKV infected Vero cells. We identified a total of 121 lncRNA genes that are differentially regulated at 48 hours post-infection. The majority of these genes are independently validated by reverse-transcription qPCR. A notable observation was that the lncRNAs, MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and NEAT1 (Nuclear Paraspeckle Assembly Transcript 1), are down-regulated upon Zika viral infection. MALAT1 and NEAT1 are known as nuclear localized RNAs that regulate gene expression and cell proliferation. Protein-lncRNA interaction maps revealed that MALAT1 and NEAT1 share common interacting partners and form a larger network comprising of 71 cellular factors. ZIKV-mediated dysregulation of these two regulatory lncRNAs can alter the expression of respective target genes and associated biological functions, an important one being cell division. In conclusion, this investigation is the first to provide insight into the biological connection of lncRNAs and ZIKV which can be further explored for developing antiviral therapy and understanding fetal developmental processes.

A Protocol for Analyzing Hepatitis C Virus Replication

Hepatitis C Virus (HCV) affects 3% of the worlds population and causes serious liver ailments including chronic hepatitis, cirrhosis, and hepatocellular carcinoma. HCV is an enveloped RNA virus belonging to the family Flaviviridae. Current treatment is not fully effective and causes adverse side effects. There is no HCV vaccine available. Thus, continued effort is required for developing a vaccine and better therapy. An HCV cell culture system is critical for studying various stages of HCV growth including viral entry, genome replication, packaging, and egress. In the current procedure presented, we used a wild-type intragenotype 2a chimeric virus, FNX-HCV, and a recombinant FNX-Rluc virus carrying a Renilla luciferase reporter gene to study the virus replication. A human hepatoma cell line (Huh-7 based) was used for transfection of in vitro transcribed HCV genomic RNAs. Cell-free culture supernatants, protein lysates and total RNA were harvested at various time points post-transfection to assess HCV growth. HCV genome replication status was evaluated by quantitative RT-PCR and visualizing the presence of HCV double-stranded RNA. The HCV protein expression was verified by Western blot and immunofluorescence assays using antibodies specific for HCV NS3 and NS5A proteins. HCV RNA transfected cells released infectious particles into culture supernatant and the viral titer was measured. Luciferase assays were utilized to assess the replication level and infectivity of reporter HCV. In conclusion, we present various virological assays for characterizing different stages of the HCV replication cycle.

Modeling Liver Diseases Using Induced Pluripotent Stem Cell (Ipsc)-Derived Hepatocytes

The induced pluripotent stem cells (iPSCs) are reprogrammed somatic cells in a stem state. The iPSCs can give rise to cells of all three germ layers and provide an unlimited supply of tissue-specific differentiated cell types for disease modeling and cell therapy. The generation of patient-specific iPSC lines and studying disease phenotype in a dish using differentiated hepatocytes open up new avenue towards personalized medicine. There has been active investigation on generating homogenous functional human hepatocytes from iPSCs. Liver carries out secretory and metabolic functions. Recent studies showed that iPSC derived-human hepatocytes are useful for in vitro investigation of genetic liver disorders, drug screening and metabolism, hepatitis C viral infection and assessing efficacy of cell therapy. Inherited metabolic disorders, including α1-antitrypsin deficiency (A1AD), familial hypercholesterolemia, glycogen storage disease type 1a and Wilson’s disease have been modeled using disease-specific iPSC lines. The iPSC hepatocytes derived from patients with A1AD were used for drug screening. Advancement made in precise genetic engineering technology using designer nucleases provides a new tool for gene correction, and reverse genetic engineering of disease causing genotype in pluripotent stem cells. Moreover, iPSC-hepatocytes from various genetic backgrounds are valuable resource for evaluating drug interactions and drug metabolism. In this review, we summarize the recent developments on the various applications of iPSC-derived human hepatocytes for disease modeling.