Mathematical models have long been used to describe complex biological interactions with the aim of predicting mechanistic interactions hard to distinguish from data. This dissertation uses modeling, mathematical analyses, and data fitting techniques to provide hypotheses on the mechanisms of immune response formation and function. The immune system, comprised of the innate and adaptive immune responses, is responsible for protecting the body against invading pathogens, with disease or vaccine induced immune memory leading to fast responses to subsequent infections. While there is some agreement about the underlying mechanisms of adaptive immune memory, innate immune memory is poorly understood. Stimulation with lipopolysaccharide induces differential phenotypes in innate immune cells depending on the strength of the stimulus, such that a secondary lipopolysaccharide encounter of a constant dose results in either strong or weak inflammatory cytokine expression. We model the biochemical kinetics of three molecules involved in macrophages responses to lipopolysaccharide and find that once a macrophage is programed to show a weak inflammatory response this cannot be reverted. Contrarily, a secondary lipopolysaccharide stimulus of a very high dose or applied prior to waning of the effects of the primary stimulus can induce a phenotype switch in macrophages initially programed to show strong inflammatory responses. Some pathogens, such as the hepatitis B virus, have developed strategies that hinder an efficient innate immune response. Hepatitis B virus infection is a worldwide pandemic with approximately 257 million chronically infected people. One beneficial event in disease progression is the seroclearance of hepatitis B e antigen often in combination with hepatitis B antibody formation. We propose mathematical models of within-host interactions and use them to predict that hepatitis B e antibody formation causes hepatitis B e antigen seroclearance and the subsequent reactivation of cytotoxic T cell immune responses. We use the model to quantify the time between antibody formation and antigen clearance and the average monthly hepatocyte turnover during that time. We further expand the study of hepatitis B infection, by investigating the kinetics of the virus under an experimental drug administered during a clinical trial. Available drugs usually fail to induce hepatitis B s antigen clearance, defined as the functional cure point of chronic hepatitis B infections. Drug therapy clinical trials that combined RNA interference drug ARC-520 with entecavir have shown promising results in reducing hepatitis B s antigen titers. We develop pharmacokinetic-pharmacodynamic models describing the mechanistic interactions of the drugs, hepatitis B virus DNA, and virus proteins. We fit the model to clinical trial data and predict that ARC-520 alone is responsible for the reduction of hepatitis B s and e antigens, while entecavir is the driving force behind viral reduction. This work was supported by Simons Foundation, Grant No. 427115, and National Science Foundation, Grant No. 1813011. / Doctor of Philosophy / Mathematical models have long been used to describe complex biological interactions with the aim of predicting interactions that explain observed data and informing new experiments. This dissertation uses modeling, mathematical analyses, and data fitting techniques to provide hypotheses on the mechanisms of immune response formation and function. The immune system, comprised of the innate and adaptive immune responses, is responsible for protecting the body against invading pathogens, such as viruses, bacteria, or fungi. If an immune response to a secondary pathogen encounter differs from the response when the body first encounters the specific pathogen, this is called immune memory. The mechanisms underlying the memory of immune responses are well understood in the context of adaptive immune responses, but less so for innate immune responses. Stimulation with lipopolysaccharide, a cell wall component of many bacteria, programs innate immune cells, such as macrophages, to be in one of two states, called phenotypes, depending on the strength of the stimulus. Based on their phenotype the macrophages show either a weak or strong inflammatory response upon a secondary lipopolysaccharide encounter of a constant dose. We model the biochemical kinetics of three molecules involved in macrophages responses to lipopolysaccharide. We find that once a macrophage is programed to show a weak inflammatory response this cannot be reverted. Contrarily, a secondary lipopolysaccharide stimulus that is either of a very high dose or applied before the effects of the primary stimulus have waned, can induce a phenotype switch in macrophages initially programed to show strong inflammatory responses. Some pathogens, such as the hepatitis B virus, have developed strategies that hinder an efficient innate immune response. Hepatitis B virus infection is a worldwide pandemic with approximately 257 million chronically infected people. Hepatitis B e antigen is a protein that infected liver cells release into blood and that impairs adaptive immune responses. It is considered a beneficial event in disease progression, and called hepatitis B e antigen clearance, when hepatitis B e antigen becomes indetectable in a patient's blood. We propose mathematical models of interactions between liver cells, the virus, hepatitis B e antigens and hepatitis B e antibodies, which neutralize the antigens. We predict that antibody formation causes antigen clearance and a reactivation of immune responses. We furthermore use the model to quantify the time between antibody formation and antigen clearance and the average number of liver cells killed during that time. We further expand the study of hepatitis B infection, by investigating the kinetics of the virus under an experimental drug administered during a clinical trial. Available drugs rarely induce hepatitis B s antigen clearance, but clinical trials that combined a novel drug, called ARC-520, with the commonly used drug entecavir have shown promising results in reducing hepatitis B s antigen titers in the blood of infected patients. Following the clearance of hepatitis B s antigen, a protein that is released by infected cells and impairs adaptive immunity, the body usually has the capability to control the infection without medication. We develop mathematical models describing the interactions of the drugs, hepatitis B virus, and virus proteins. We fit the model to clinical trial data and predict that ARC-520 alone is responsible for the reduction of hepatitis B s and e antigens, while entecavir is the driving force behind viral reduction.

<p>Hepatitis E virus (HEV) je uzročnik akutne hepatis E infekcije kod ljudi. HEV se prenosi putem zagaĎene vode i odgovoran je za nastanak mnogobrojnih epidemija velikih razmera u zemljama u razvoju Azije i Afrike. Hepatitis E je prvi put kod svinja izolovan 1997. godine, a kasnije je dokazan i kod ostalih ţivotinjskih vrsta, kao &scaron;to su: divlje svinje, jelen, zečevi, pacovi, ptice i ostalo.<br />Prva istraţivanja prisustva HEV infekcije kod domaćih i divljih svinja u Srbiji sprovedena su 2008. godine. HEV RNK je dokazana u 30% uzoraka fecesa i 45% uzoraka organa (Petrovic et al., 2008). Analizom uzoraka krvnih seruma svinja u individualnim gazdinstvima ustanovljena je seroprevalencija od 34,6% (Lupulovic et al, 2010). Cilj ovog istraţivanja je ispitivanje ra&scaron;irenosti HEV infekcije kod svinja na farmama na teritoriji Vojvodine, kao i ispitivanje HEV seroprevalencije kod ljudi u Vojvodini.<br />Od metoda za istraţivanje kori&scaron;ćene su: nekomercijalni ELISA test (in-house ELISA), komercijalni ELISA test, Western-blot metod, real-time RT -PCR i imunohistohemijska metoda za detekciju HEV antigena.<br />Materijal za ispitivanje su bili uzorci krvi svinja (300) sa 3 farme na teritoriji Juţne Bačke i Srema i uzorci krvi ljudi (294), kao i uzorci fecesa, ţuči, jetre i mesa sakupljeni u klanicama od 95 tovljenika i 50 prasadi.<br />Prisustvo specifičnih antitela IgG klase protiv hepatitis E virusa dokazano je kod svinja na sve tri ispitujuće farme. Primenom in house ELISA testa ustanovljena je seroprevalencija od 37% na farmi A, 31% na farmi B i 54% na farmi C, dok je primenom komercijalnog ELISA testa utvrĎeno 40% seropozitivnih svinja na farmi A, 41% na fami B i 65% na farmi C. Uporednom analizom rezultata dobijenih sa oba ELISA testa, ustanovljena je prosečna seroprevalencija od 40,66% in house ELISA testom, odnosno 48,66% komercijalnim ELISA testom.<br />Sprovedena su i istraţivanja prisustva specifičnih antitela IgG klase protiv HEV u krvnim serumima dobrovoljnih davalaca krvi i kod pacijenata. Primenom in house ELISA testa utvrĎena je<br />seroprevalencija od 15% kod dobrovoljnih davalaca krvi, dok su uzorci krvi pacijenata bili seronegativni. Testiranjem komercijalnim ELISA testom kod dobrovoljnih davalaca krvi pozitivan serolo&scaron;ki nalaz je ustanovljen kod 17,86% dobrovoljnih davalaca krvi (pregledani su serumi koji su u in house testu dali pozitivan ili sumnjiv nalaz, kao i odreĎen broj seronegativnih uzoraka), a kod pacijenata 2,12%.<br />Kao tzv. &bdquo;zlatni standard&ldquo; za definisanje rezultata sa sumnjivim serolo&scaron;kim nalazom čije su ekstinkcije bile blizu cut off vrednosti u in house ELISA testu, kori&scaron;ćen je Western blot metod. Pozitivan rezultat je potvrĎen kod 6 od ukupno pregledanih 11 uzoraka krvi svinja, odnosno od ukupno pregledanih 11 uzoraka seruma ljudi, pozitivan nalaz je ustanovljen kod 7 uzoraka.<br />Uzorci sa klanica pregledani su real-time RT- PCR metodom, a HEV RNK je dokazana u u fecesu (54%), ţuči (26%), jetri (16%) i mesu (10%) prasadi. Kod tovljenika prisustvo HEV RNK je potvrĎeno samo u fecesu (7,27%), dok su svi uzorci tkiva bili negativni.<br />Patahistolo&scaron;kim pregledom dokazane su mikroskopske lezije II stepena kod 3 uzorka (11,53%) jetri prasadi od ukupno pregledanih 26 uzoraka sa pozitivnim RT-PCR. Imunohistohemijskim pregledom uzoraka jetre prasadi nije dokazano prisustvo antigena hepatitis E virusa.<br />Definisani su protokoli laboratorijskog ispitivanja hepatitis E infekcije kod svinja i ljudi, kao i u uzorcima mesa i jetri svinja u klanicama</p> / <p>Hepatitis E virus (HEV) is the causative agent of acute hepatitis E infection in humans. HEV is transmitted through contaminated water and is responsible for the outbreaks of many large-scale epidemics in the developing countries of Asia and Africa. Swine HEV was first isolated in 1997, and was later detected in other animal species, such are: wild boar, deer, rabbits, rats, birds and more.<br />The first investigations of HEV infection in domestic and wild pigs in Serbia were carried out in 2008. HEV RNA was detected in 30% of faecal samples and 45% of the tissue samples (Petrovic et al., 2008). Analysing the blood samples of beckyard pigs, the seroprevalence of 34,6% was determined (Lupulovic et al, 2010). The aim of this study was to investigate the prevalence of HEV infection in pigs on farms in Vojvodina, as well as testing the HEV seroprevalence in humans.<br />The methods used for this study were: non-commercial ELISA (in house ELISA), the commercial ELISA, Western blot method, real-time RT-PCR and immunohistochemical method for the detection of HEV antigen.<br />Material for the study were: blood samples of pigs (300) from 3 farms on the territory of South Backa and Srem and blood samples of people (294), as well as faeces, bile, liver and meat collected in slaughterhouses from 95 fatteners and 50 piglets.<br />The presence of specific IgG antibodies against the hepatitis E virus in pigs has been detected on all three examinated farms. Upon the application of in house ELISA, the seroprevalence of 37% was establised on farm A, 31% in farm B and 54% on farm C, while using a commercial ELISA , 40% of seropositive pigs were detected on farm A, 41% of fami B and 65% Farm C. The comparative analysis of the results obtained with both ELISA, determined the average seroprevalence of 40,66% by in house ELISA and 48,66% by commercial ELISA.<br />The research of the presence of specific IgG antibodies against HEV in the serum of blood donors and patients were also conducted. Upon the application of in house ELISA, the seroprevalence of 15% were recorded in blood donors, while blood samples of patients were seronegative. Testing by commercial ELISA, positiv serological findings were diagnosed in 17,86% of blood donors (serums with positive or suspicious results in in house ELISA and a number of seronegative samples were tested), and in patients 2, 12%.<br />As so-called &quot;gold standard&quot; for defining the serological results with suspiciousserological findings, which extinctions were close to cut off values in in house ELISA, we used the Western</p>

Hepatitis C virus (HCV) is remarkably efficient at evading host immunity to establish chronic infection. During chronic HCV infection, interleukin-12 (IL-12) produced by monocytes/macrophages (M/Mφ) is significantly suppressed. Programmed death-1 (PD-1), an inhibitory receptor on immune cells, plays a pivotal role in suppressing T-cell responses during chronic viral infection. To determine whether PD-1 regulates IL-12 production by M/Mφ during chronic HCV infection, we examined the expressions of PD-1, its ligand PDL-1, and their relationship with IL-12 production in M/Mφ from HCV-infected, HCV-resolved, and healthy subjects by flow cytometry. Toll-like receptor (TLR) -mediated IL-12 production by M/Mφ was selectively suppressed, while PD-1/PDL-1 expressions were up-regulated, in HCV-infected subjects compared with HCV-resolved or healthy subjects. Up-regulation of PD-1 was inversely associated with the degree of IL-12 inhibition in HCV infection. Interestingly, the reduced response of M/Mφ from HCV-infected individuals to TLR ligands appeared not to be the result of a lack of the ability to sense pathogen, but to an impaired activation of intracellular janus kinase/signal transducer and activator of transfection (STAT) pathway as represented by inhibited STAT-1 phosphorylation in M/Mφ from HCV-infected individuals compared with HCV-negative subjects. Successful HCV treatment with pegylated interferon/ribavirin or blocking PD-1/PDL-1 engagement ex vivo led to reduced PD-1 expression and improved IL-12 production as well as STAT-1 activation in M/Mφ from HCV-infected individuals. These results suggest that the PD-1 inhibitory pathway may negatively regulate IL-12 expression by limiting STAT-1 phosphorylation in M/Mφ during chronic HCV infection. No claim to original US government works.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2014-10-06T15:17:41Z No. of bitstreams: 2 Dissertação - Helen de Oliveira Soares - 2013.pdf: 801287 bytes, checksum: 7d8d0899bf1a66a37c47e1cc61097a1e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2014-10-06T15:55:38Z (GMT) No. of bitstreams: 2 Dissertação - Helen de Oliveira Soares - 2013.pdf: 801287 bytes, checksum: 7d8d0899bf1a66a37c47e1cc61097a1e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-10-06T15:55:38Z (GMT). No. of bitstreams: 2 Dissertação - Helen de Oliveira Soares - 2013.pdf: 801287 bytes, checksum: 7d8d0899bf1a66a37c47e1cc61097a1e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2013-04-29 / Hepatitis A virus (HAV) is mainly transmitted by the oral-fecal route. HAV infection prevalence is associated with socio-economic and hygienic conditions. In Brazil, hepatitis A is considered an endemic infection and some studies have shown a shift from high to intermediate endemicity pattern. Almost recyclable waste collectors have a lifestyle that is characterized by precarious social, cultural and environmental factors. The epidemiological status of HAV infections of these workers remains unknown. So, this study aimed to investigate the hepatitis A virus infection profile in recyclable waste collectors in Goiânia, Goiás. A cross-sectional survey was carried out with 431 individuals who were recruited in all 15 recycling cooperatives in Goiânia, Goiás. All individuals were interviewed and their serum samples were tested for anti-HAV total marker by enzyme-linked immunosorbent assay (ELISA). Total anti-HAV positive samples were tested for IgM anti-HAV marker by ELISA. Almost all population (429/431) was positive for total anti-HAV antibodies. By contrast, none were IgM anti-HAV positive. The seroprevalence of HAV infection among recyclable waste collectors in Goiânia-Goiás was 99,5% (IC 95%: 98,1-99,9). Unfavorable socio-economic, sanitary and house conditions (low education and family income, high number of people at home and lack of treated/filtered water), as well as risk practices (contact with contaminated waste, irregular use of gloves and eating from the garbage) were reported by a considerable percentage of participants. These findings highlight the need of actions of health promotion and diseases prevention to the population of recyclable waste collectors in Goiânia, Goiás. / O vírus da hepatite A (HAV) é transmitido principalmente pela via oral-fecal. A prevalência da infecção pelo HAV está associada às condições socioeconômicas e de higiene. No Brasil, a hepatite A é considerada uma infecção endêmica e alguns estudos têm revelado uma mudança no perfil de endemicidade de alto para intermediário. A maioria dos catadores de materiais recicláveis vive em condições sociais, culturais e ambientais precárias. A situação epidemiológica da infecção pelo HAV desses trabalhadores permanece desconhecida. Assim, este estudo teve como objetivo investigar o perfil da infecção pelo vírus da hepatite A em catadores de materiais recicláveis em Goiânia, Goiás. Constitui-se em estudo transversal realizado com 431 indivíduos recrutados nas 15 cooperativas de reciclagem em Goiânia, Goiás. Todos os participantes foram entrevistados e suas amostras de soros testadas para o marcador anti-HAV total pelo ensaio imunoenzimático (ELISA). As amostras positivas foram testadas para o marcador anti-HAV IgM também por ELISA. A quase totalidade da população (429/431) apresentou positividade para o marcador anti-HAV total, porém nenhum indivíduo foi positivo para anti-HAV IgM. A soroprevalência da infecção pelo HAV em catadores de materiais recicláveis em Goiânia-Goiás foi de 99,5% (IC 95%: 98,1-99,9). Características socioeconômicas, sanitárias e de moradia desfavoráveis (baixa escolaridade e renda familiar, número elevado de pessoas no domicílio e falta de água tratada/filtrada), bem como práticas de risco (contato com resíduos contaminados, uso irregular de luvas e ingestão de alimentos encontrados no lixo) foram relatadas por percentuais consideráveis dos participantes. Esses achados evidenciam a necessidade de ações de promoção da saúde e prevenção de doenças para a população de catadores de materiais recicláveis em Goiânia, Goiás.

No description available.

Hepatitis C virus (HCV) infection globally affects 130-150 million people. It causes both acute and chronic infections. Due to the severe side effects and low success rates of interferon based treatments, which formed the standard treatment for HCV, the treatment paradigm shifted to direct acting antivirals (DAAs). DAAs have revolutionized the treatment of hepatitis C virus infection. Clinical trials with combinations of DAAs have recorded >90% response with shorter treatment durations and fewer side effects than earlier treatments involving IFN. Outside the controlled setting of a clinical trial, however, response rates with DAA combinations are much lower (<70%). DAAs can fail if HCV accumulates mutations that confer drug resistance. Interestingly, the pre-existence of mutant frequency in the virus appears not to influence treatment outcome. A better predictor for DAA treatment outcome is yet to be unravelled. Surprisingly, individuals who respond poorly to IFN appear to be more likely to fail DAA treatment. IFN is a generic antiviral that improves immune responses and is expected not to have any bearing on DAA treatment outcomes. Why individuals with poor IFN sensitivity fail DAA treatment remains a mystery. In a recent study of the IFN signalling network, HCV has been shown to compromise IFN activity. It induces bistability in the network leading to distinct phenotypic responses of cells to IFN exposure. In particular, individuals who respond poorly to IFN tend to have a higher percentage of cells that are refractory to IFN; these cells allow viral persistence despite IFN exposure. We hypothesized here that in such individuals, greater ongoing replication would allow increased development of resistance and thus lead to the failure of DAAs. We constructed a model of viral dynamics that accounts for the distinct phenotypic responses of cells to IFN, viral replication and mutation, and the development of resistance to DAAs. Our model predicted that although the relative prevalence of pre- existing mutants is unaffected by IFN sensitivity, in agreement with observations, the growth of drug resistant mutants is accelerated in individuals with poor IFN sensitivity. Based on a distribution of IFN sensitivity across individuals, our model accurately described clinical observations of the response rates to different current treatment protocols. With this model, we predict that the common strategy of increasing the genetic barrier by adding more drugs to the combination was not necessary to avert the development of drug resistance. Instead, an optimised increase in DAA dosage alone or DAA+PR or PR dosage depending on the patient’s IFN sensitivity could help achieve success.

Hepatitis C virus (HCV), a blood-borne pathogen, is a small enveloped RNA virus belonging to the Hepacivirus genus of the Flaviviridae family. HCV infection represents one of the major health concerns affecting approximately 170 million people globally. Patients with chronic HCV infection are at risk of developing hepatic fibrosis, cirrhosis and hepatocellular carcinoma. No protective anti-HCV vaccine is available yet. Until recently, standard therapy based on pegylated interferon plus ribavirin, was inadequate in treating all the patients as it results in a sustained virological response in only 40 to 50 percent of patients infected with the most common genotype (gt 1). Advances in understanding host-HCV interactions have helped developing newer anti-HCV agents such as telaprevir and boceprevir. However, treatment success is still limited due to different factors including genotype specificity, high cost, potential drug-drug interactions, substantial side effects etc. The positive-sense single-stranded RNA genome of HCV is approximately 9.6kb long which is flanked by highly structured and conserved 5’ and 3’ untranslated regions (UTRs) at both ends. Unlike cap-dependent translation of host cell mRNAs, HCV translation is mediated by an internal ribosomal entry site (IRES) present majorly within the 5’UTR. Several reports have demonstrated the interaction of different cellular proteins with HCV-5’UTR and/or 3’UTR, which include human La protein, polypyrimidine tract binding protein (PTB), poly (rC)-binding protein 2 (PCBP2) etc. These interactions of trans-acting factors with the UTRs may be important for HCV translation and/or replication. Earlier study from our laboratory revealed the importance of interaction of human La protein, by its central RNA recognition motif (RRM), with the HCV IRES around a tetranucleotide sequence GCAC near initiator AUG in influencing HCV translation. However, the role of this interaction, if any, in HCV RNA replication was not known. In the first part of the thesis, we characterized the interaction between human La protein and the GCAC to understand its role in HCV replication. We incorporated mutation, which altered the binding of La, in the GCAC motif in HCV monocistronic replicon and checked HCV RNA replication by reverse transcriptase polymerase chain reaction (RT-PCR). The mutation drastically inhibited HCV replication. Interestingly, overexpression of La could reverse the effect of this mutation and significantly enhanced HCV RNA levels. Using a bicistronic replicon, we observed that decrease in replication was independent of translation inhibition. Furthermore, mutation at the GCAC motif reduced the association between La and viral polymerase, NS5B as seen in co-immunoprecipitation assays. Moreover, this mutation affected translation to replication switch regulated by the interplay between HCV-NS3 protease and human La protein. Our analyses of point mutations, based on RT-PCR and luciferase assays, revealed distinct roles of each nucleotide of the GCAC motif in HCV replication and translation. Finally, 5’-3’ crosslink assays revealed that specific interaction of the GCAC motif with human La protein is important for linking 5’ and 3’ends of HCV genome. Results clearly demonstrate the mechanism of regulation of HCV replication by interaction of cis-acting element GCAC within the HCV IRES with human La protein. HCV is highly species-specific. Under natural conditions, HCV infects only humans and chimpanzees. This restricted host-tropism has prevented the development of a small animal model to study HCV infection in vivo. Although several human-specific entry factors have been identified to be responsible for this species selectivity, full multiplication of the HCV in animals (other than humans and chimpanzees) is still not possible. In the second part of the thesis, we showed that a post-entry host factor –‘La protein’ may also contribute in determining HCV host tropism. We aligned La protein sequences from different species and interestingly we found that HCV RNA interacting beta-turn sequence (KYKETDL) in central RRM (residues 112-184) is conserved only in human and chimpanzee. Earlier, it was shown from our laboratory that a heptameric peptide comprising of this sequence (derived from human La) could inhibit HCV translation by competing with La interaction with the IRES element. However, in the current study, another peptide corresponding to the mouse La sequence (KYKDTNL) was unable to inhibit HCV RNA translation. Similarly, wild-type mouse La (mLa) failed to stimulate HCV IRES function, but addition of chimeric mouse La protein bearing human beta-turn sequence (mLahN7) significantly increased HCV IRES mediated translation in vitro. Also, exogenous supplementation of mLahN7 enhanced HCV translation in cell culture system. Moreover, quantitative as well as tagged RT-PCR analyses showed an enhanced HCV replication upon overexpression of mLahN7. The findings obtained in this part raise a possibility of creating HCV mouse model using human specific cellular entry factors and a humanized form of La protein. Hepatitis C has emerged as a major challenge to the medical community. Developing more potent and safe anti-HCV regimens is need of the hour. As described above, a linear hepatapeptide (KYKETDL) was synthesized and shown to reduce HCV translation. However, this linear peptide was stable only for a shorter time scale. Therefore, in the third part of the thesis, effect of a more stable cyclic form of this peptide has been described. NMR spectroscopy suggested that the beta turn conformation is preserved in cyclic peptide as well. Also, using in vitro bicistronic reporter assay, we demonstrated that cyclic peptide inhibits HCV translation in a dose dependent manner. In fact, due to its higher stability, cyclic peptide reduced HCV translation and replication more efficiently than the corresponding linear peptide at longer post-treatment time point. Additionally, we observed that cyclic peptide is non-toxic in cell culture system. Our results suggest that cyclic peptide might emerge as a promising lead compound against hepatitis C. Due to availability of only partially effective liver protective drugs in modem medicine, complementary and alternative medicine approach, based on plant derived compounds, is also being utilised against HCV. Plant derived compounds have advantages of having high chemical diversity, drug-likeliness properties and ability of being metabolized by the body with little or no toxicity than synthetic ones. Different studies have shown that phytochemicals may exert anti-HCV activities by acting as direct-acting antivirals and play a potential therapeutic role in treating HCV infection. Also, from our laboratory, it was shown that methanolic extract of Phyllanthus amarus (P. amarus) plant inhibited HCV replication. The fourth part of the thesis describes the study on the anti-HCV properties of several bioactive components from P. amarus extract. Using a fluorimetric assay, we demonstrated that two principal components of this extract, phyllanthin and corilagin reduced the HCV NS3 protease activity significantly in vitro. We also observed a sharp reduction in HCV negative sense RNA levels in cell culture system. Structural knowledge-based molecular docking studies showed interactions of phyllanthin and corilagin with the amino acid residues of the catalytic triad of NS3 protease. Further, these compounds were found to be non-toxic in cell culture. Also, phyllanthin and corilagin displayed antioxidant properties by blocking HCV induced oxidative stress generated by reactive oxygen species suggesting their hepatoprotective nature. More importantly, our in vivo toxicity analyses and pharmacokinetics studies proved their safety, tolerability, metabolic stability, and systemic oral bioavailability and support their potential as novel anti-HCV therapeutic candidates. Altogether, the study deciphers mechanistic details of translation and replication of HCV RNA and demonstrates novel antiviral agents targeting these important viral processes.

The current treatment for hepatitis C virus (HCV) infection – combination therapy with pegylated interferon and ribavirin – elicits sustained responses in only ~50% of the patients treated. Greater cumulative exposure to ribavirin increases response to interferon-ribavirin combination therapy. A key limitation, however, is the toxic sideeffect of ribavirin, hemolytic anemia, which often necessitates a reduction of ribavirin dosage and compromises treatment response. Maximizing treatment response thus requires striking a balance between the antiviral and hemolytic activities of ribavirin. Current models of viral kinetics describe the enhancement of treatment response due to ribavirin. Ribavirin-induced anemia, however, remains poorly understood and precludes rational optimization of combination therapy. Here, we develop a new mathematical model of the population dynamics of erythrocytes that quantitatively describes ribavirin-induced anemia in HCV patients. Based on the assumption that ribavirin accumulation decreases erythrocyte lifespan in a dose-dependent manner, model predictions capture several independent experimental observations of the accumulation of ribavirin in erythrocytes and the resulting decline of hemoglobin in HCV patients undergoing combination therapy, estimate the reduced erythrocyte lifespan in patients and describe inter-patient variations in the severity of ribavirin-induced anemia. Further, model predictions estimate the threshold ribavirin exposure beyond which anemia becomes intolerable and suggest guidelines for the usage of growth hormones. A small fraction of the population (~30%) with polymorphisms in the ITPA gene shows protection from ribavirin-induced anemia. The optimum dosage of ribavirin that can be tolerated is then dependent on the ITPA polymorphisms. Coupled with a previous population pharmacokinetic study, our model yields a facile formula for estimating the optimum dosage given a patient’s weight, creatinine clearance, pretreatment hemoglobin levels, and ITPA polymorphism. The reduced lifespan we predict is in agreement with independent measurements from breath tests as well as estimates derived from in vitro studies of ATP depletion. The latter estimates also agree with the extent of ATP depletion due to ribavirin that we predict from a detailed analysis of the nucleoside metabolism in erythrocytes. Our model thus facilitates in conjunction with models of viral kinetics the rational identification of treatment protocols. Our formula for optimum dose presents an avenue for personalizing ribavirin dosage. By keeping anemia tolerable, the predicted optimal dosage may improve adherence, reduce the need for drug monitoring, and increase response rates.

Hepatitis C virus (HCV) represents a global health threat. HCV is a blood-borne positive-strand RNA virus belonging to the Flaviviridae family that infects ~160 million people worldwide. About 70% of infected individuals fail to clear the virus and subsequently develop chronic hepatitis, frequently leading to liver cirrhosis and in some cases hepatocellular carcinoma. Therapeutic options for HCV infection are still limited and a protective vaccine is not yet available. Currently available therapies include administration of pegylated alpha interferon in combination with ribavirin. The recently approved protease inhibitors Boceprevir and Telaprevir are also included in the treatment regimen. However, limitations to the treatment with direct-acting antivirals (DAAs) are associated with severe side effects and low sustained virological response (SVR) rates that vary depending on the virus and host genotype. The replication step of the viral life cycle is mostly targeted by majority of DAAs. Recent findings have suggested that a combination of entry inhibitors together with DAAs exhibit a synergistic effect in the treatment of HCV. Therefore, identification of efficient HCV entry inhibitors is of high priority In vitro studies have shown that HCV attachment and subsequent entry into the host cells is mediated by E1 and E2 viral envelope proteins. HCV entry requires interaction with a number of receptors which include CD81, scavenger receptor B1 (SR-B1) and the tight junction proteins, claudin 1 (CLDN1) and occludin (OCLN). Since the E2 glycoprotein is reported to interact directly with cellular receptors, it is an attractive target for neutralisation. The present study focuses on the establishment and characterisation of entry inhibitors as antivirals for HCV. The thesis is presented in three chapters: Chapter 1- ‘Introduction’, provides a brief overview on HCV genotypes, genome organisation, life cycle including details on the entry process and therapies used for the treatment of HCV. Chapter 2 describes the generation of monoclonal antibodies (mAbs) against HCV envelope proteins as potent anti-viral agents for the prevention of HCV infection. Data on the identification and characterization of the neutralizing epitopes of HCV envelope proteins have been presented. Chapter 3 includes isolation of entry inhibitors of HCV from natural sources and identification and characterization of the active components exhibiting antiviral property. A number of studies have reported the role of neutralizing antibodies in the course of HCV infection and emerging data suggest protective effect of antibodies against HCV infection. Most of the ongoing studies are based on HCV genotype 1a which is prevalent globally. However in India, the prevalent genotype is 3a. Therefore, we established a panel of mAbs against HCV-LPs comprising of core-E1-E2 derived from genotype 3a as described in chapter 2. HCV-LP based system has been used in this study since it mimics the biophysical conformation, morphology and antigenic properties of the native virion and represents a model system for studies on viral binding and entry. MAbs were characterised and analyzed for their ability to prevent viral binding and entry into host cells. Three mAbs namely E3D8, H6D3 and A10F2 were identified to recognize the E2 viral glycoprotein which significantly inhibited HCV-LP binding to Huh7 cells in vitro. The neutralizing epitopes corresponding to the mAbs were identified using overlapping truncated fragments and synthetic peptides of the E2 protein. Our experiments suggest that the epitopes recognised by the inhibitory mAbs are unique and different from those reported till now. The synergistic effect of a combination of mAbs on virus neutralization has shown promising results for treatment of viral infections. Since in the present study the epitopes recognised by the mAbs are non-overlapping, we went ahead to determine whether a combination of these mAbs would enhance the ability to block HCV-LP binding. Indeed, flow cytometry and fluorescence microscopy studies revealed that a combination of the antibodies efficiently blocked the binding of HCV-LP to human hepatoma cells. More importantly and of relevance is the observation that the mAbs in combination inhibited viral infection (JFH1 strain) and replication in permissive human hepatocytes as determined by real time RT-PCR. Phytochemicals present in plants have been considered as conducive for prevention of several viral infections and are found to be promising antiviral agents. Natural products which are biologically active disclose drug-like properties since they are small molecules and can be easily metabolised and absorbed by the body. In our study as described in chapter 3, we evaluated extracts from Indian medicinal plants and fruits which are known to have hepato-protective effect, for natural potent attachment and entry inhibitors for HCV. Flow cytometric analysis suggested that the root extract of the herb Boerhavia diffusa and fruit extract of Prunus domestica exhibited high antiviral activity by inhibiting the binding of Hepatitis C virus like particles (HCV-LPs) to the human hepatoma cells. We went on to isolate, identify and confirm the active principles to be Boeravinone H, a dehydrorotenoid, (from Boerhavia diffusa) and Rutin, a flavonoid, (from Prunus domestica) by LC-ESI-MS, NMR, UV and IR spectral analysis. Our study revealed that the compounds block the attachment as well as entry step probably by targeting the viral particle. We also assessed the efficiency of these small molecules (Boeravinone H and Rutin) to inhibit HCV negative strand synthesis post entry by real time RT-PCR. Results suggest significant inhibition of viral entry and infection in the HCV cell culture (ex vivo). To our knowledge it is the first report on Boeravinone H and Rutin as entry inhibitor for HCV. In conclusion, our findings support the potential of employing a cocktail of neutralizing mAbs and antiviral agents from natural source in the management of HCV infection.

Le virus de l’hépatite C (HCV) est un problème majeur de santé publique. Le développement de nouveaux traitements pour lutter contre le HCV a été ralenti par l’absence de modèles d’études in vitro et in vivo convenables. Le but de mon travail de thèse a été, dans un premier temps, de caractériser les facteurs déterminant le tropisme hépatique du HCV. En exprimant des facteurs clés dans une lignée cellulaire humaine non-hépatocytaire, nous avons reconstitué in fine l’ensemble du cycle viral dans ces cellules. L’entrée du virus dans la cellule hôte fait intervenir différents récepteurs d’entrée dont CD81, occludin (OCLN), claudin-1 (CLDN1) et scavenger receptor class B type I (SR-BI). L’expression de ces quatre récepteurs sur cette lignée la rend hautement permissive à l’entrée du virus, mais ne permet pas de rétablir la réplication du virus. L’expression du micro-ARN 122, un micro-RNA important pour l’infection du HCV, dans les cellules exprimant les quatre récepteurs, restaure une forte réplication de l’ARN viral mais ne permet pas de détecter une production de particules infectieuses. L’expression de l’apolipoprotein E (apoE), jouant un rôle primordial dans l’assemblage et la sécrétion, rétablis cette dernière étape du cycle viral du HCV dans la lignée cellulaire humaine non-hépatocytaire. Dans un second temps, j’ai utilisé la stratégie, précédemment établie, pour étudier la spécificité d’espèce de l’infection du HCV dans plusieurs lignées hépatocytaires murines. Nous avons pu rendre ces cellules permissives à l’entrée du HCV et pu détecter une très faible réplication. L’ensemble de mes travaux apportent de nouvelles informations sur la compréhension des facteurs clés nécessaire au cycle viral du HCV dans des cellules murines et humaines. / Hepatitis C virus (HCV) is a global health burden. The development of new therapeutics to treat HCV infection has been hampered by the lack of convenient in vitro and in vivo model systems. The goal of my PhD work was, in a first time, to characterize the factors determining the hepatotropism of HCV. By expressing key factors within a non-hepatic cell line, we reconstituted in fine the full HCV life cycle in those cells. Virus entry into the host cell requires different entry factors which are CD81, occludin (OCLN), claudin-1 (CLDN1) and the scavenger receptor class B type I (SR-BI). The expression of these four factors in this cell line renders it highly permissive to viral entry, but does not allow restoring replication of the virus. The expression of miR-122, a micro-RNA important for HCV infection, into the cell lines expressing the four HCV entry factors restore a strong replication of the HCV RNA but does not allow detecting infectious viral particle production. Further expression of the apolipoprotein E (apoE), which plays a critical role in the assembly and release process, restore the last step of the HCV life cycle in a non-hepatic cell line. In a second part of my PhD, I have used the previously developed strategy to study the species specificity of HCV infection using different mouse hepatoma cell lines. We have been able to render these cell lines permissive to HCV entry and have been able to detect a slight replication. Altogether, my results bring new information on the understanding of key factors important for HCV life cycle in mouse and human cells.