ABSTRACT
The increasing prevalence of coal mine dust-related lung diseases in coal miners calls for urgent and meticulous scrutiny of airborne respirable coal mine dust (RCMD), specifically focusing on particles at the nano-level. This necessity is driven by expanding research, including the insights revealed in this paper, that establish the presence and significantly increased toxicity of nano-sized coal dust particles in contrast to their larger counterparts. This study presents an incontrovertible visual proof of these tiny particulates in samples collected from underground mines, utilizing advanced techniques such as scanning electron microscopy (SEM) and energy-dispersive spectroscopy (EDS). The intricate elemental composition of nano-sized coal dust identified through EDS analysis reveals the presence of elements such as silica and iron, which are known to contribute to lung pathologies when inhaled over prolonged periods. The outcomes of the statistical analyses reveal significant relationships between particle size and elemental composition, highlighting that smaller particles tend to have higher carbon content, while larger particles exhibit increased concentrations of elements like silica and aluminum. These analyses underscore the complex interactions within nano-sized coal dust, providing critical insights into their behavior, transport, and health impacts. The nano-sized coal dust could invade the alveoli, carrying these toxic elements from where they are impossible to exhale. The revelation of nano-sized coal dust's existence and the associated health hazards necessitate their incorporation into the regulatory framework governing the coal mining industry. This study lays the groundwork for heightened protective measures for miners, urging the invention of state-of-the-art sampling instruments, comprehensive physicochemical profiling of RCMD nanoparticles, and the pursuit of groundbreaking remedies to neutralize their toxic impact. These findings advocate for a paradigm shift in how the coal mining industry views and handles particulate matter, proposing a re-evaluation of occupational health standards and a call to action for protecting coal miners worldwide.
Subject(s)
Coal Mining , Coal , Dust , Microscopy, Electron, Scanning , Particle Size , Dust/analysis , Coal/analysis , Occupational Exposure/analysis , Spectrometry, X-Ray Emission , Appalachian Region , Nanoparticles/analysis , Nanoparticles/chemistry , Air Pollutants, Occupational/analysis , HumansABSTRACT
Objectives: Annual outbreaks of human respiratory syncytial virus (HRSV) are caused by newly introduced and locally persistent strains. During the COVID-19 pandemic, global and local circulation of HRSV significantly decreased. This study was conducted to characterize HRSV in 2018-2022 and to analyze the impact of COVID-19 on the evolution of HRSV. Design/methods: Combined oropharyngeal and nasopharyngeal swabs were collected from children hospitalized with severe acute respiratory infection at two hospitals in Zambia. The second hypervariable region of the attachment gene G was targeted for phylogenetic analysis. Results: Of 3113 specimens, 504 (16.2%) were positive for HRSV, of which 131 (26.0%) and 66 (13.1%) were identified as HRSVA and HRSVB, respectively. In early 2021, an increase in HRSV was detected, caused by multiple distinct clades of HRSVA and HRSVB. Some were newly introduced, whereas others resulted from local persistence. Conclusions: This study provides insights into the evolution of HRSV, driven by global and local circulation. The COVID-19 pandemic had a temporal impact on the evolution pattern of HRSV. Understanding the evolution of HRSV is vital for developing strategies for its control.
ABSTRACT
To ensure a robust immune response to pathogens without risking immunopathology, the kinetics and amplitude of inflammatory gene expression in macrophages need to be exquisitely well controlled. There is a growing appreciation for stress-responsive membraneless organelles (MLOs) regulating various steps of eukaryotic gene expression in response to extrinsic cues. Here, we implicate the nuclear paraspeckle, a highly ordered biomolecular condensate that nucleates on the Neat1 lncRNA, in tuning innate immune gene expression in murine macrophages. In response to a variety of innate agonists, macrophage paraspeckles rapidly aggregate (0.5 h poststimulation) and disaggregate (2 h poststimulation). Paraspeckle maintenance and aggregation require active transcription and MAPK signaling, whereas paraspeckle disaggregation requires degradation of Neat1 via the nuclear RNA exosome. In response to lipopolysaccharide treatment, Neat1 KO macrophages fail to properly express a large cohort of proinflammatory cytokines, chemokines, and antimicrobial mediators. Consequently, Neat1 KO macrophages cannot control replication of Salmonella enterica serovar Typhimurium or vesicular stomatitis virus. These findings highlight a prominent role for MLOs in orchestrating the macrophage response to pathogens and support a model whereby dynamic assembly and disassembly of paraspeckles reorganizes the nuclear landscape to enable inflammatory gene expression following innate stimuli.
Subject(s)
Paraspeckles , RNA, Long Noncoding , Humans , Animals , Mice , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Macrophages/metabolismABSTRACT
Rapid molecular testing for severe acute respiratory coronavirus 2 (SARS-CoV-2) variants may contribute to the development of public health measures, particularly in resource-limited areas. Reverse transcription recombinase polymerase amplification using a lateral flow assay (RT-RPA-LF) allows rapid RNA detection without thermal cyclers. In this study, we developed two assays to detect SARS-CoV-2 nucleocapsid (N) gene and Omicron BA.1 spike (S) gene-specific deletion-insertion mutations (del211/ins214). Both tests had a detection limit of 10 copies/µL in vitro and the detection time was approximately 35 min from incubation to detection. The sensitivities of SARS-CoV-2 (N) RT-RPA-LF by viral load categories were 100% for clinical samples with high (>9015.7 copies/µL, cycle quantification (Cq): < 25) and moderate (385.5-9015.7 copies/µL, Cq: 25-29.9) viral load, 83.3% for low (16.5-385.5 copies/µL, Cq: 30-34.9), and 14.3% for very low (<16.5 copies/µL, Cq: 35-40). The sensitivities of the Omicron BA.1 (S) RT-RPA-LF were 94.9%, 78%, 23.8%, and 0%, respectively, and the specificity against non-BA.1 SARS-CoV-2-positive samples was 96%. The assays seemed more sensitive than rapid antigen detection in moderate viral load samples. Although implementation in resource-limited settings requires additional improvements, deletion-insertion mutations were successfully detected by the RT-RPA-LF technique.
Subject(s)
COVID-19 , Reverse Transcription , Humans , Recombinases/genetics , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity , Mutagenesis, Insertional , COVID-19/diagnosis , COVID-19/genetics , Nucleic Acid Amplification Techniques/methods , Nucleotidyltransferases/geneticsABSTRACT
One major cyclical environmental parameter within the underground mine space is the fluctuation of relative humidity, which varies daily and seasonally. Therefore, moisture and dust particle interactions are inevitable and indirectly control dust transport and fate. After being released into the environment, the coal dust particles stay there for a long period depending upon several parameters such as particle size, specific gravity, ventilation etc. Due to their smaller size, nano-sized coal dust particles could remain in the mine environment indefinitely while interacting with it. Correspondingly the primary characteristic of nano-sized coal dust particles could get modified. The nano-sized coal dust samples were prepared in the lab and characterized using different techniques. The prepared samples were allowed to interact with moisture using the dynamic vapor sorption technique. It was found that the lignite coal dust particles could adsorb up to 10 times more water vapor than the bituminous coal dusts. Oxygen content is one of the primary factors in deciding the total effective moisture adsorption in the nano-sized coal dust, with moisture adsorption proportional to the oxygen content of the coal. This means that lignite coal dust is more hygroscopic when compared to bituminous coal dust. GAB and Freundlich's models perform well for water uptake modeling. Because of interaction with atmospheric moisture, particularly swelling, adsorption, moisture retention, and particle size changes, such interactions will significantly change the physical characteristics of nano-sized coal dust. This will affect the transport and deposition behavior of coal dust in the mine atmosphere.
Subject(s)
Coal Mining , Steam , Coal , Dust/analysis , Minerals , OxygenABSTRACT
Coal dust is the major hazardous pollutant in the coal mining environment. Recently environmentally persistent free radicals (EPFRs) were identified as one of the key characteristics which could impart toxicity to the particulates released into the environment. The present study used Electron Paramagnetic Resonance (EPR) spectroscopy to analyze the characteristics of EPFRs present in different types of nano-size coal dust. Further, it analyzed the stability of the free radicals in the respirable nano-size coal dust and compared their characteristics in terms of EPR parameters (spin counts and g-values). It was found that free radicals in coal are remarkably stable (can remain intact for several months). Also, Most of the EPFRs in the coal dust particles are either oxygenated carbon centered or a mixture of carbon and oxygen-centered free radicals. EPFRs concentration in the coal dust was found to be proportional to the carbon content of coal. The characteristic g-values were found to be inversely related to the carbon content of coal dust. The spin concentrations in the lignite coal dust were between 3.819 and 7.089 µmol/g, whereas the g-values ranged from 2.00352 to 2.00363. The spin concentrations in the bituminous coal dust were between 11.614 and 25.562 µmol/g, whereas the g-values ranged from 2.00295 to 2.00319. The characteristics of EPFRs present in coal dust identified by this study are similar to the EPFRs, which were found in other environmental pollutants such as combustion-generated particulates, PM2.5, indoor dust, wildfires, biochar, haze etc., in some of the previous studies. Considering the toxicity analysis of environmental particulates containing EPFRs similar to those identified in the present study, it can be confidently hypothesized that the EPFRs in the coal dust might play a major role in modulating the coal dust toxicity. Hence, it is recommended that future studies should analyze the role of EPFR-loaded coal dust in mediating the inhalation toxicity of coal dust.
ABSTRACT
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has stressed the global health system to a significant level, which has not only resulted in high morbidity and mortality but also poses a threat for future pandemics. This situation warrants efforts to develop novel therapeutics to manage SARS-CoV-2 in specific and other emerging viruses in general. This study focuses on SARS-CoV2 RNA-dependent RNA polymerase (RdRp) mutations collected from Saudi Arabia and their impact on protein structure and function. The Saudi SARS-CoV-2 RdRp sequences were compared with the reference Wuhan, China RdRp using a variety of computational and biophysics-based approaches. The results revealed that three mutations-A97V, P323I and Y606C-may affect protein stability, and hence the relationship of protein structure to function. The apo wild RdRp is more dynamically stable with compact secondary structure elements compared to the mutants. Further, the wild type showed stable conformational dynamics and interaction network to remdesivir. The net binding energy of wild-type RdRp with remdesivir is -50.76 kcal/mol, which is more stable than the mutants. The findings of the current study might deliver useful information regarding therapeutic development against the mutant RdRp, which may further furnish our understanding of SARS-CoV-2 biology.
Subject(s)
COVID-19 Drug Treatment , COVID-19 , SARS-CoV-2 , Antiviral Agents/chemistry , COVID-19/genetics , Humans , Molecular Docking Simulation , Mutation , Pandemics , Protein Binding , RNA, Viral/metabolism , RNA-Dependent RNA Polymerase/genetics , SARS-CoV-2/genetics , Saudi ArabiaABSTRACT
Although mutations in mitochondrial-associated genes are linked to inflammation and susceptibility to infection, their mechanistic contributions to immune outcomes remain ill-defined. We discovered that the disease-associated gain-of-function allele Lrrk2G2019S (leucine-rich repeat kinase 2) perturbs mitochondrial homeostasis and reprograms cell death pathways in macrophages. When the inflammasome is activated in Lrrk2G2019S macrophages, elevated mitochondrial ROS (mtROS) directs association of the pore-forming protein gasdermin D (GSDMD) to mitochondrial membranes. Mitochondrial GSDMD pore formation then releases mtROS, promoting a switch to RIPK1/RIPK3/MLKL-dependent necroptosis. Consistent with enhanced necroptosis, infection of Lrrk2G2019S mice with Mycobacterium tuberculosis elicits hyperinflammation and severe immunopathology. Our findings suggest a pivotal role for GSDMD as an executer of multiple cell death pathways and demonstrate that mitochondrial dysfunction can direct immune outcomes via cell death modality switching. This work provides insights into how LRRK2 mutations manifest or exacerbate human diseases and identifies GSDMD-dependent necroptosis as a potential target to limit Lrrk2G2019S-mediated immunopathology.
Subject(s)
Mitochondria , Necroptosis , Phosphate-Binding Proteins/metabolism , Pore Forming Cytotoxic Proteins/metabolism , Animals , Humans , Inflammasomes , Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 , Macrophages , Mice , Mitochondria/metabolism , Reactive Oxygen Species/metabolismABSTRACT
The TREX-TAP pathway is vital for mRNA export. For spliced mRNA, the TREX complex is recruited during splicing; however, for intronless mRNA, recruitment is sequence dependent. However, the export of cytoplasmic long noncoding RNA (lncRNA) is poorly characterized. We report the identification of a cytoplasmic accumulation region (CAR-N) in the intronless lncRNA, NKILA. CAR-N removal led to strong nuclear retention of NKILA, and CAR-N insertion promoted the export of cDNA transcripts. In vitro RNP purification via CAR-N, mass spectrometry, and siRNA screening revealed that SRSF1 and SRSF7 were vital to NKILA export, and identified a cluster of SRSF1/7 binding sites within a 55 nucleotide sequence in CAR-N. Significant nuclear enrichment of NKILA was observed for NKILA lacking CAR-N or the cluster of binding sites in knock-in models. Depletion of TREX-TAP pathway components resulted in strong nuclear retention of NKILA. RNA and protein immunoprecipitation verified that SRSF1/7 were bound to NKILA and interacted with UAP56 and ALYREF. Moreover, NKILA lacking CAR-N was unable to inhibit breast cancer cell migration. We concluded that the binding of SRSF1/7 to clustered motifs in CAR-N facilitated TREX recruitment, promoting the export of NKILA, and confirmed the importance of NKILA localization to its function.
Subject(s)
Cell Nucleus/metabolism , RNA, Long Noncoding/metabolism , Serine-Arginine Splicing Factors/metabolism , Active Transport, Cell Nucleus , Binding Sites , Cell Movement , Cytoplasm/genetics , DEAD-box RNA Helicases/metabolism , DNA, Complementary/metabolism , Humans , MCF-7 Cells , Nuclear Proteins/metabolism , Nucleocytoplasmic Transport Proteins/metabolism , Nucleotide Motifs , RNA, Long Noncoding/chemistry , RNA-Binding Proteins/metabolism , Transcription Factors/metabolismABSTRACT
XAB2 is a multi-functional protein participating processes including transcription, splicing, DNA repair and mRNA export. Here, we report POLR2A, the largest catalytic subunit of RNA polymerase II, as a major target gene down-regulated after XAB2 depletion. XAB2 depletion led to severe splicing defects of POLR2A with significant intron retention. Such defects resulted in substantial loss of POLR2A at RNA and protein levels, which further impaired global transcription. Treatment of splicing inhibitor madrasin induced similar reduction of POLR2A. Screen using TMT-based quantitative proteomics identified several proteins involved in mRNA surveillance including Dom34 with elevated expression. Inhibition of translation or depletion of Dom34 rescued the expression of POLR2A by stabilizing its mRNA. Immuno-precipitation further confirmed that XAB2 associated with spliceosome components important to POLR2A expression. Domain mapping revealed that TPR motifs 2-4 and 11 of XAB2 were critical for POLR2A expression by interacting with SNW1. Finally, we showed POLR2A mediated cell senescence caused by XAB2 deficiency. Depletion of XAB2 or POLR2A induced cell senescence by up-regulation of p53 and p21, re-expression of POLR2A after XAB2 depletion alleviated cellular senescence. These data together support that XAB2 serves as a guardian of POLR2A expression to ensure global gene expression and antagonize cell senescence.
Subject(s)
Cellular Senescence/genetics , DNA-Directed RNA Polymerases/genetics , Introns/genetics , Transcription Factors/genetics , Transcription, Genetic , Cell Line , Cell Line, Tumor , DNA-Directed RNA Polymerases/metabolism , HEK293 Cells , HeLa Cells , Humans , RNA Interference , RNA Splicing , RNA Splicing Factors , RNA, Messenger/genetics , RNA, Messenger/metabolism , Transcription Factors/metabolism , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolismABSTRACT
In contrast to cytoplasmic localization of spliced mRNAs, many spliced lncRNAs are localized in the nucleus. To investigate the mechanism, we used lncRNA MEG3 as a reporter and mapped a potent nuclear retention element (NRE), deletion of this element led to striking export of MEG3 from the nucleus to the cytoplasm. Insertion of the NRE resulted in nuclear retention of spliced lncRNA as well as spliced mRNA. We further purified RNP assembled on the NRE in vitro and identified the proteins by mass spectrometry. Screen using siRNA revealed depletion of U1 snRNP components SNRPA, SNRNP70 or SNRPD2 caused significant cytoplasmic localization of MEG3 reporter transcripts. Co-knockdown these factors in HFF1 cells resulted in an increased cytoplasmic distribution of endogenous lncRNAs. Together, these data support a model that U1 snRNP components restrain spliced lncRNAs in the nucleus via the interaction with nuclear retention element.
Subject(s)
Ribonucleoprotein, U1 Small Nuclear/genetics , snRNP Core Proteins/genetics , Cell Nucleus/genetics , Cytoplasm/genetics , Cytosol/metabolism , HeLa Cells , Humans , RNA Splicing/genetics , RNA, Long Noncoding/genetics , Ribonucleoprotein, U1 Small Nuclear/chemistry , Spliceosomes/geneticsABSTRACT
Xeroderma pigmentosum group A (XPA)-binding protein 2 (XAB2) is a multi-functional protein that plays critical role in processes including transcription, transcription-coupled DNA repair, pre-mRNA splicing, homologous recombination and mRNA export. Microarray analysis on gene expression in XAB2 knockdown cells reveals that many genes with significant change in expression function in mitotic cell cycle regulation. Fluorescence-activated cell scanner analysis confirmed XAB2 depletion led to cell arrest in G2/M phase, mostly at prophase or prometaphase. Live cell imaging further disclosed that XAB2 knockdown induced severe mitotic defects including chromosome misalignment and defects in segregation, leading to mitotic arrest, mitotic catastrophe and subsequent cell death. Among top genes down-regulated by XAB2 depletion is mitotic motor protein centrosome-associated protein E (CENPE). Knockdown CENPE showed similar phenotypes to loss of XAB2, but CENPE knockdown followed by XAB2 depletion did not further enhance cell cycle arrest. Luciferase assay on CENPE promoter showed that overexpression of XAB2 increased luciferase activity, whereas XAB2 depletion resulted in striking reduction of luciferase activity. Further mapping revealed a region in CENPE promoter that is required for the transcriptional regulation by XAB2. Moreover, ChIP assay showed that XAB2 interacted with CENPE promoter. Together, these results support a novel function of XAB2 in mitotic cell cycle regulation, which is partially mediated by transcription regulation on CENPE.
Subject(s)
Chromosomal Proteins, Non-Histone/genetics , Gene Expression Regulation , Mitosis/genetics , Transcription Factors/metabolism , Transcription, Genetic , Cell Cycle Checkpoints/genetics , Cell Death/genetics , Cell Nucleus/metabolism , Chromosomal Proteins, Non-Histone/metabolism , Chromosome Segregation/genetics , DNA Breaks , Gene Deletion , Gene Knockdown Techniques , HEK293 Cells , HeLa Cells , Humans , Microtubules/metabolism , Oligonucleotide Array Sequence Analysis , RNA Splicing Factors , Spindle Apparatus/metabolism , Transcription Factors/deficiency , Transcription Factors/geneticsABSTRACT
WT1 + KTS and -KTS isoforms only differ in 3 amino acids in protein sequence but show significant functional difference. The +/-KTS isoforms were generated by alternative usage of 2 adjacent 5' splice sites at RNA level, however, how these 2 isoforms are regulated is still elusive. Here we report the identification of an intronic pyrimidine-rich sequence that is critical for the ratio of +/-KTS isoforms, deletion or partial replacement of the sequence led to full/significant shift to -KTS isoform. To identify trans-factors that can regulate +/-KTS isoforms via the binding to the element, we performed RNP assembly using in vitro transcribed RNA with or without the pyrimidine-rich sequence. Mass spectrometry analysis of purified RNPs showed that the element associated with many splicing factors. Co-transfection of these factors with WT1 reporter revealed that HuR promoted the production of -KTS isoform at the reporter level. RNA immuno-precipitation experiment indicated that HuR interacted with the pyrimidine-rich element in WT1 intron 9. We further presented evidence that transient or stable over-expression of HuR led to enhanced expression of endogenous -KTS isoform. Moreover, knockdown of HuR resulted in decreased expression of endogenous -KTS isoform in 293T, SW620, SNU-387 and AGS cell lines. Together, these data indicate that HuR binds to the pyrimidine-rich sequence and antagonize its effect in regulating WT1 +/-KTS isoforms.
Subject(s)
Amino Acids/metabolism , ELAV-Like Protein 1/metabolism , Introns/genetics , Pyrimidines/metabolism , WT1 Proteins/chemistry , WT1 Proteins/metabolism , Base Sequence , Gene Knockdown Techniques , Genes, Reporter , HeLa Cells , Humans , Molecular Sequence Data , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/metabolism , RNA Precursors/genetics , Ribonucleoproteins/metabolism , WT1 Proteins/geneticsABSTRACT
Unfortunately Pakistan carries one of the world's highest burdens of chronic hepatitis along with mortality due to liver failure and hepatocellular carcinoma. Scientists after extensive research have come up with this outcome that host genetics play a vital role in dictating the type of treatment response produced by the patients. In 2009, a genome wide association study (GWAS) revealed that genetic variants in close proximity to the IL28B (IFNL3) gene predicted greater likelihood of achieving sustained virological response (SVR) following treatment with pegylated IFN-alpha (peg INF-α) and ribavirin. IL28B (rs12979860 and rs8099917) single nucleotide polymorphisms (SNPs) have been recently found among the Pakistani population associated with response to chronic HCV infection INF-α + ribavirin therapy. Therefore, this study was aimed to investigate the IL-28B protein levels in the HCV infected patients. The findings showed that the serum IL28B protein level was higher in HCV infected patients as compared to healthy controls (7.743 ± 1.519 pg/mL versus 1.600 ± 0.06054 [mean ± SEM], p < 0.05). When the chronic hepatitis C (CHC) patients were further categorized into SVR and NR (non-responders) on the basis of treatment outcomes, the mean IL28B protein level was higher in NRs (15.54 ± 3.609) than SVRs (4.259 ± 0.3405). Thus, there was a significant correlation between IL28B protein level in varied treatment response (p < 0.05). However, the findings can lead us to propose that IL28B could be used as a prognostic marker. It can help the clinicians to take better pre-informed decisions whether to take combinational therapy of peg IFN ± ribavirin or not. This will in turn prove beneficial for the patient by saving patients' health, treatment cost and undesirable treatment side effects.
Subject(s)
Biomarkers/metabolism , Hepatitis C, Chronic/diagnosis , Hepatitis C, Chronic/drug therapy , Interferon-alpha/therapeutic use , Interleukins/metabolism , Adolescent , Adult , Case-Control Studies , Drug Therapy, Combination/methods , Female , Genotype , Hepatitis C, Chronic/genetics , Hepatitis C, Chronic/metabolism , Humans , Interferons , Interleukins/genetics , Male , Pakistan , Polymorphism, Single Nucleotide/genetics , Prognosis , Ribavirin/therapeutic use , Treatment Outcome , Young AdultABSTRACT
Hepatitis C virus (HCV) pathogenesis and treatment outcomes are multifactorial phenomena involving both viral and host factors. This study was designed to determine the role of tumor necrosis factor-related apoptosis-inducing ligand receptor 1(TRAIL-R1) and interferon gamma (IFN-γ) genetic mutations in susceptibility and response to interferon-based therapy of hepatitis C virus (HCV) infection. The detection of TRAIL-R1 rs4242392 and IFN-γ rs2069707 single nucleotide polymorphisms was completed in 118 chronic HCV patients and 96 healthy controls by allele-specific polymerase chain reaction and restriction fragment length polymorphisms polymerase chain reaction. Patients were further categorized into sustained virological responder (SVR) and nonresponder (NR) groups on the basis of their response to interferon-based therapy for HCV infection. Real-time PCR was used for HCV quantification. HCV genotyping was performed by Ohno's method. The results demonstrated that the distribution of the TRAIL-R1 rs4242392TT genotype was significantly higher in the SVR group (78%) compared to the NR group (36%). It showed that chronic HCV patients possessing the TRAIL-R1 rs4242392TT genotype are better responders to interferon-based therapy (p<0.05). The prevalence of the TRAIL-R1 rs4242392TT genotype in healthy controls and chronic HCV patients was 56% and 65% respectively. It indicated that there is the TRAIL-R1 rs4242392 genetic variation plays no role in the spontaneous clearance of HCV infection (p>0.05). The distribution of IFN-γ rs2069707 was the opposite to TRAIL-R1 rs4242392 prevalence, that is, there was high distribution of the IFN-γ rs2069707GG genotype in patients and healthy controls (p<0.05), while the prevalence of IFN-γ rs2069707GG in SVR and NR groups was comparable (p>0.05). In conclusion, genetic variation of TRAIL-R1 rs4242392 is linked with response to interferon-based therapy for HCV infection, and genetic variation IFN-γ rs2069707 is associated with natural clearance of HCV infection.
Subject(s)
Antiviral Agents/therapeutic use , Hepatitis C, Chronic/drug therapy , Hepatitis C, Chronic/immunology , Interferon-gamma/genetics , Interferons/therapeutic use , Polymorphism, Single Nucleotide , Receptors, TNF-Related Apoptosis-Inducing Ligand/genetics , Adult , Female , Genotyping Techniques , Humans , Male , Middle Aged , Polymorphism, Restriction Fragment Length , Real-Time Polymerase Chain Reaction , Treatment Outcome , Viral LoadABSTRACT
Hepatitis C virus (HCV) genotypes and genetic variants of interleukin 28B (IL28B) are significantly associated with interferon plus ribavirin treatment of HCV infection. We investigated the distribution of HCV genotypes and single-nucleotide polymorphisms (SNPs) of IL28B (rs12979860 and rs8099917) in Pakistani population. IL28B genotyping was performed by allele-specific PCR and restriction fragment length polymorphism PCR in 140 chronic hepatitis C patients (CHC) and 120 healthy controls. HCV genotype 3 (HCVG3) was the most prevalent genotype, 71.4% (n = 100/140) and with the highest treatment response of 90% (n = 90/100). The overall treatment response of all the HCV genotypes was 82% (n = 115/140). The distribution of IL28B rs12979860CC genotype in treatment responder and non-responder groups was 40.8% (n = 47/115) and 16% (n = 4/25) respectively. IL28B rs12979860CC genotype demonstrated a significant correlation (p = 0.019) with interferon-based therapy of HCV infection. However, there was no observed association of IL28B rs8099917 polymorphism with treatment response in CHC patients (p = 0.264). In conclusion, HCV genotypes and IL28B rs12979860 are predictive markers for the efficiency of interferon plus ribavirin combinational therapy of HCV infection. We recommend the inclusion of testing for these markers in the clinical criteria for decision making for HCV therapy in Pakistani population.
Subject(s)
Hepacivirus/genetics , Hepatitis C, Chronic/drug therapy , Interleukins/genetics , Adult , Antiviral Agents/therapeutic use , Drug Therapy, Combination , Female , Genetic Markers , Humans , Interferon-alpha/therapeutic use , Interferons , Male , Pakistan , Polyethylene Glycols/therapeutic use , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length , Polymorphism, Single Nucleotide , Recombinant Proteins/therapeutic use , Ribavirin/therapeutic use , Treatment OutcomeABSTRACT
Hepatitis C virus (HCV) infection is the most important problem across the world. It causes acute and chronic liver infection. Different approaches are in use to inhibit HCV infection, including small organic compounds, siRNA, shRNA and peptide inhibitors. This review article summarizes the current and future therapies for HCV infection. PubMed and Google Scholar were searched for articles published in English to give an insight into the current inhibitors against this life-threatening virus. HCV NS3/4A protease inhibitors and nucleoside/nucleotide inhibitors of NS5B polymerase are presently in the most progressive stage of clinical development, but they are linked with the development of resistance and viral breakthrough. Boceprevir and telaprevir are the two most important protease inhibitors that have been approved recently for the treatment of HCV infection. These two drugs are now the part of standard-of-care treatment (SOC). There are also many other drugs in phase III of clinical development. When exploring the various host-cell-targeting compounds, the most hopeful results have been demonstrated by cyclophilin inhibitors. The current SOC treatment of HCV infection is Peg-interferon, ribavirin and protease inhibitors (boceprevir or telaprevir). The future treatment of this life-threatening disease must involve combinations of therapies hitting multiple targets of HCV and host factors. It is strongly expected that the near future, treatment of HCV infection will be a combination of direct-acting agents (DAA) without the involvement of interferon to eliminate its side effects.
Subject(s)
Antiviral Agents/therapeutic use , Hepacivirus , Hepatitis C/drug therapy , Hepatitis C/virology , Gene Expression Regulation, Viral/drug effects , Gene Silencing , HumansABSTRACT
The current standard of care (SOC) for hepatitis C virus (HCV) infection is the combination of pegylated interferon (PEG-IFN), Ribavirin and protease inhibitor for HCV genotype 1. Nevertheless, this treatment is successful only in 70-80% of the patients. In addition, the treatment is not economical and is of immense physical burden for the subject. It has been established now, that virus-host interactions play a significant role in determining treatment outcomes. Therefore identifying biological markers that may predict the treatment response and hence treatment outcome would be useful. Both IFN and Ribavirin mainly act by modulating the immune system of the patient. Therefore, the treatment response is influenced by genetic variations of the human as well as the HCV genome. The goal of this review article is to summarize the impact of recent scientific advances in this area regarding the understanding of human and HCV genetic variations and their effect on treatment outcomes. Google scholar and PubMed have been used for literature research. Among the host factors, the most prominent associations are polymorphisms within the region of the interleukin 28B (IL28B) gene, but variations in other cytokine genes have also been linked with the treatment outcome. Among the viral factors, HCV genotypes are noteworthy. Moreover, for sustained virological responses (SVR), variations in core, p7, non-structural 2 (NS2), NS3 and NS5A genes are also important. However, all considered single nucleotide polymorphisms (SNPs) of IL28B and viral genotypes are the most important predictors for interferon based therapy of HCV infection.