The characteristics of HIV-1 subtype B on phylogenetic dynamic and molecular transmission network in Fuyang City, China, 2011 to 2019.

Introduction: HIV-1 subtype B, as once one of the earliest strains introduced into mainland China rapidly spread in commercial plasma donors and heterosexuals in 1990s. Here, we aim to investigate the origin and evolutionary history of HIV-1 subtype B in Fuyang city, China. Methods: We collected sequences tested from Fuyang in the east of China where higher prevalence of HIV-1 among commercial plasma donors and heterosexuals to construct a phylogenetic tree using the Markov chain Monte Carlo (MCMC) algorithm, infer molecular transmission network using TN93 model and visualize it with Cytoscape software. Results and discussion: Our results showed that >99% of subtype B sequences belonged to Thai B. The sequences from Fuyang often cluster closer to those from other its adjacent cities, which clustered together and formed a monophyletic cluster. HIV-1 B circulating in Fuyang dates back to approximately 1990. Among the 1,437 sequences, 166 clustered at a genetic distance of ≤1.2%, resulting in 73 clusters. The degree of clustering with at least one other person was 11.55%. Among the transmission clusters, 50 (80.65%) comprised two individuals. Most clusters consisted of both heterosexual transmission routes and men who have sex with men. Phylogenetic and molecular network analyses revealed a common origin with neighboring regions in mainland China, local onwards transmission after its introduction, and a limited clustering degree. However, at least two co-existing transmission routes in most transmission clusters imply a greater challenge in controlling the spread of HIV-1. Our findings highlight the value on tailoring prevention interventions by combination of molecular surveillance and epidemiology.

Trace the History of HIV and Predict Its Future through Genetic Sequences.

Traditional methods of quantifying epidemic spread are based on surveillance data. The most widely used surveillance data are normally incidence data from case reports and hospital records, which are normally susceptible to human error, and sometimes, they even can be seriously error-prone and incomplete when collected during a destructive epidemic. In this manuscript, we introduce a new method to study the spread of infectious disease. We gave an example of how to use this method to predict the virus spreading using the HIV gene sequences data of China. First, we applied Bayesian inference to gene sequences of two main subtypes of the HIV virus to infer the effective reproduction number (GRe(t)) to trace the history of HIV transmission. Second, a dynamic model was established to forecast the spread of HIV medication resistance in the future and also obtain its effective reproduction number (MRe(t)). Through fitting the two effective reproduction numbers obtained from the two separate ways above, some crucial parameters for the dynamic model were obtained. Simply raising the treatment rate has no impact on lowering the infection rate, according to the dynamics model research, but would instead increase the rate of medication resistance. The negative relationship between the prevalence of HIV and the survivorship of infected individuals following treatment may be to blame for this. Reducing the MSM population's number of sexual partners is a more efficient strategy to reduce transmission per the sensitivity analysis.

miR-642 serves as a tumor suppressor in hepatocellular carcinoma by regulating SEMA4C and p38 MAPK signaling pathway.

Hepatocellular carcinoma (HCC) is a malignant tumor with high incidence and high risk. Study of the role and mechanism of miRNAs are a hot spot of research providing new treatment ideas in malignant tumors. The effect of miR-642a on HCC progression and the underlying molecular mechanism were investigated. Expression of miR-642a and SEMA4C was measured by western blot analysis and RT-PCR. miR-642a expression was elevated while SEMA4C expression was attenuated in HCC tissues and cells. Results of luciferase reporter and western blot analyses show that miR-642a modulated SEMA4C expression by binding to its 3'UTR. Moreover, miR-642a negatively regulated SEMA4C expression. HCC cell migration and invasion was tested by Transwell assays. The findings revealed that the number of migrated and invaded cells were reduced by miR-642a mimic and raised by miR-642a inhibitor, indicating that miR-642a showed a suppression effect on HCC cell migration and invasion. Additionally, the migration and invasion of HCC cells were inhibited by SEMA4C siRNA, and SEMA4C reversed miR-642a effect on HCC migration and invasion. Furthermore, p38 MAPK signaling pathway was proven to be inhibited by miR-642a mimic, whereas facilitated by miR-642a inhibitor and SEMA4C siRNA could overturn the promotion effect of miR-642a inhibitor. Briefly, miR-642a targeted SEMA4C to repress HCC cell migration and invasion through p38 MAPK signaling pathway providing a new strategy for treatment of HCC patients.

Near Full-Length Genomic Characterization of a Novel Unique Recombinant (CRF01_AE/CRF07_BC) in Fuyang City of China.

Recombinant forms contribute substantially to the genetic diversity of HIV-1. Recent studies have also revealed that three major viral strains (CRF07_BC, CRF01_AE, and subtype B) have been cocirculating among men who have sex with men (MSM) in Anhui, suggesting a high probability of generating new recombinants. In this study, we reported a novel CRF01_AE and CRF07_BC HIV-1 recombinant form in MSM in Fuyang city of China. Two near full-length genome (NFLG) named FY184 and FY208 were successfully obtained. The genomic composition analysis of the NFLG reveals that it was divided into four segments by three breakpoints, with two regions of CRF07_BC inserted into a CRF01_AE backbone's gag and pol regions. The CRF01_AE regions were originated from a subcluster lineage of CRF01_AE, which is mainly circulating among MSM in China. The emergence of a novel recombinant of CRF01_AE/CRF07_BC is indicative of the increasing genetic diversity of the HIV epidemic in MSM in Anhui.

Genetic characterization of HIV-1 epidemic in Anhui Province, China.

BACKGROUND: Anhui Province in China is facing a severe HIV epidemic with an increasing number of newly diagnosed cases. METHODS: In this study, HIV genetic characteristics in the province were investigated. Newly reported HIV-positive individuals from 15 districts of Anhui Province were enrolled and interviewed. Total viral RNA was extracted from plasma isolated from blood samples. We amplified and sequenced an HIV pol fragment of the 1062 bp. The sequences were used for determination of HIV subtypes and the presence of drug resistance mutations. Transmission networks were constructed to explore possible relationships. And all of assembled partial pol genes were submitted to the Stanford HIV Drug Resistance Database website to find the transmitted drug resistance. RESULTS: Partial pol gene sequences were obtained from 486 cases. The results showed that MSM was the most dominant transmission route (253, 52.06%), followed by heterosexual transmission (210, 43.21%) and blood-borne transmission (1, 0.21%). Many subtypes were identified, including CRF01_AE (226, 46.50%), CRF07_BC (151, 31.07%), subtype B (28, 5.76%), CRF08_BC (20, 4.12%), CRF55_01B (15, 3.09%), CRF68_01B (7, 1.44%), CRF67_01B (3, 0.62%), CRF57_BC (2, 0.41%), CRF59_01B (2, 0.41%), CRF79_0107 (2, 0.41%), subtype C (2, 0.41%), CRF64_BC (1, 0.21%), and circulating recombinant forms (URFs) (27, 5.55%). Four transmission subnetworks containing high transmission risk individuals (with degree ≥4) were identified based on CRF01_AE and CRF07_BC sequences, including two CRF01_AE transmission subnetworks constituted by elderly people with average ages of 67.9 and 61.5 years. Infection occurred most likely through heterosexual transmission, while the other two CRF07_BC transmission subnetworks consist mainly of MSMs with average ages of 31.73 and 34.15. The level of HIV-transmitted drug resistance is 3.09%. CONCLUSIONS: The simultaneous spread of multiple HIV subtypes in Anhui province underscores that close surveillance of the local HIV epidemic is necessary. Furthermore, the elderly people were frequently involved, arguing for behaviour intervention in this specific population besides the MSM risk group.

The inference of HIV-1 transmission direction between HIV-1 positive couples based on the sequences of HIV-1 quasi-species.

BACKGROUND: To infer transmission direction of a HIV transmission chain is helpful not only in legal jurisdiction but also in precise intervention to prevent HIV spread. Recently, the direction of transmission is inferred by whether paraphyletic-monophyletic (PM) or a combination of paraphyletic and polyphyletic (PP) topologies is observed or not between the sequences of source and recipient in the phylogenetic tree. However, paraphyly between them often declines over time and may disappear between spouses due to bidirectional transmission after primary infection. In this study, our aim is to test the reliability of inferring HIV transmission direction between epidemiologically linked HIV-1 positive couples using whether or not paraphyly is observed in phylogenetic tree. METHODS: HIV quasi-species were sequenced using PCR product clones, and then Bayesian analysis of molecular sequences with MCMC was employed to construct phylogenetic relationship of env, gag, pol gene fragments of HIV-1 positive couples using BEAST software. RESULTS: Our results showed that all sequences of seven couples except pol sequences of couple 12 and 13 form their own monophyletic cluster in phylogenetic tree including the closest control sequences from GenBank or other studies on local samples, which are supported by significant Bayesian posterior probabilities more than 0.9932. Of seven couples, paraphyly is only observed in phylogenetic tree constructed with env and pol gene sequences of three couples and gag gene sequences of four couples. Paraphyly is not observed in half of HIV positive couples. Pol sequences of couple 13 is separated by Blast selected controls; pol sequences of couple 12 in phylogenetic tree is supported by a lower Bayesian posterior value. CONCLUSION: Paraphyly relationship between sequences of donator and recipient is only observed among partial HIV-1 positive couples with epidemiological link. Phylogenetic relationship is not always the same when various gene regions of HIV are used to conduct phylogenetic analysis. The combination of phylogenetic analysis based on various gene regions of HIV and enough epidemiology investigation is essential when inferring transmission direction of HIV in a transmission chain or in one couple. However, while observed paraphyly can be used to infer transmission direction in HIV-1 positive couple, no observed paraphyly cannot deny it.

Phylogenetic analysis highlights the role of older people in the transmission of HIV-1 in Fuyang, Anhui Province, China.

BACKGROUND: The proportion of older HIV-1 infected people in China has increased rapidly in recent years. Elucidation of the transmission characteristics of this high-risk population subgroup is helpful for the development of tailored interventions. METHODS: A phylogenetic analysis was performed that uses available HIV-1 pol sequences amplified with nested RT-PCR from plasma samples of all newly diagnosed participants spanning from October 2017 to September 2018 in Fuyang, Anhui Province. Transmission clusters were identified as two or more sequences that shared a corresponding node with an aLRT-SH value ≥90 in the maximum-likelihood phylogenetic tree and had an overall mean genetic distance of ≤1.5%. A local transmission cluster was defined as a cluster that had more than 80% of its sequences from Fuyang. The role of older people in local HIV-1 transmission was determined using an integration of molecular and demographic data. RESULTS: Of 362 available sequences, 14 subtypes, and 28 local transmission clusters were identified. It was found that the proportion of older people in the local transmission cluster (69/77, 89.61%) was much higher than that of younger people (46/114, 40.35%) (χ2 test, P < 0.001). In the pretreatment drug resistance analysis, the proportion of sequences with PDRMs in the local transmission cluster was not significantly different between the older people group (57.14%, 4/7) and non-old-aged group (11.11%, 1/9) (Fisher's exact test, P > 0.05). CONCLUSION: By combining phylogenetic analyses with demographic data, more detailed information was provided about the local transmission structure in Fuyang. These findings suggested that older people play an important role in local transmission, and more tailored interventions for this population subgroup are urgently needed.

The Epidemic History of HIV-1 CRF07_BC in Hetian Prefecture and the Role of It on HIV Spreading in China.

CRF07_BC is one of the most prevalent HIV-1 strains in China, and Xinjiang Uygur Autonomous Region has ever been considered to be a second epidemic center after Yunnan Province in previous studies. Here we use HIV-1 pol gene sequences identified from Hetian Prefecture located in Xinjiang Autonomous Region to reconstruct the epidemic history of HIV CRF07_BC strain circulating in this region. We found that CRF07_BC is the predominant HIV-1 form in Hetian Prefecture, and the estimated tMRCA analysis shows that there is no enough evidence supporting Xinjiang Autonomous Region as a second epidemic center of spreading HIV-1. It may imply that every city may be only a point among the HIV spreading network because of the frequent migration of population in the whole country nowadays.

The predominant cluster of CRF01_AE circulating among newly diagnosed HIV-1-positive people in Anhui Province, China.

CRF01_AE, which has led a new epidemic in many provinces in China and has displayed complex characteristics, has now evolved into multiple clusters in China. Some clusters often circulate in specific regions or among specific risk populations in China. To better determine the characteristics of CRF01_AE circulating in Anhui Province, we analyzed CRF01_AE based on gag and pol sequences. Our results showed that CRF01_AE circulating in Anhui Province was clearly divided into three clusters. Cluster 1 covered 90% of the sequences in all CRF01_AE. Among Cluster 1, the sequences from men who have sex with men (MSM) and heterosexuals were interwoven. It is suggested that MSM may play a bridge role in transmitting HIV-1 among the different risk groups.

The prevalence of transmitted HIV drug resistance among MSM in Anhui province, China.

BACKGROUND: To optimize treatment regimens, we assessed human immunodeficiency virus (HIV) diversity and the prevalence of transmitted drug resistance (TDR) among men who have sex with men (MSM) in Anhui province, China. METHODS: A total of 139 MSM who were newly diagnosed and antiretroviral treatment-naive were enrolled in Anhui in 2011. A partial pol fragment was amplified and sequenced, and HIV subtypes were determined by phylogenetic analyses. Surveillance/transmitted drug resistance mutations (SDRMs) were identified according to the 2009 World Health Organization (WHO) list. RESULTS: A total of 133 (95.7%) samples were successfully amplified and sequenced. Based on phylogenetic analyses of the pol fragment, CRF01_AE accounted for 55.6% (74/133) of the infections, followed by CRF07_BC with 32.3% (43/133), B with 5.3% (7/133), and unique recombinant forms with 6.8% (9/133). A total of 3.0% (4/133) of the subjects were found to harbor HIV variants with SDRMs, including 1.5% with NRTI-related mutations and 1.5% with NNRTI-related mutations. PI-related mutations were absent. The SDRMs included L210W (1.5%), Y181C (0.8%), and G190A (0.8%). CONCLUSIONS: In Anhui, CRF01_AE strains contributed to most of the HIV infections among MSM, and the prevalence of TDR was relatively low in this population. Further studies should be performed to evaluate the trend of TDR among MSM in Anhui and to inform first-line antiretroviral treatment.

[Construction of cell line of small hairpin RNA-mediated inhibition of HER2/neu gene expression].

OBJECTIVE: To establish the stable inhibition of HER2/neu expression by vector-mediated small hairpin RNA in malignant transformed human bronchial epithelial cell line induced by anti-benzo(a)pyrene-trans-7, 8-dihydrodiol-9, 10-epoxide (anti-BPDE). METHODS: The pSIREN-RetroQ-neu recombinant vector targeting HER2/neu was constructed and confirmed by restriction and sequencing analysis, then it was transfected into anti-BPDE malignant transformed 16HBE cells (16HBE-T) through lipofectamine 2000. The control groups included the 16HBE-T cells transfected with negative control vector (negative control) and 16HBE-T. The cells transfected with vectors were screened by puromycin. The HER2/neu mRNA and protein expressions in the vector-transfected 16HBE-T cells were detected by RT-PCR and Western blot method respectively. RESULTS: The pSIREN-RetroQ-neu recombinant vector which inhibited HER2/neu mRNA and protein expressions in the 16HBE-T was constructed. The level of HER2/neu mRNA in the 16HBE-T cells transfected with pSIREN-RetroQ-neu was significantly reduced as compared to the negative control and blank control cells (0.114 +/- 0.003 vs.blank control 0.186 +/- 0.001, t = 39.154, P < 0.05; and negative control 0.182 +/- 0.015, t = 7.564, P < 0.05), while its level did not differ significantly between negative control cells and blank control of 16HBE-T (t = -0.409, P > 0.05). HER2/neu protein level in pSIREN-RetroQ-neu transfected cells was inhibited by 40% and 39% respectively. CONCLUSION: Plasmid-based shRNA expression systems targeted against HER2/neu gene were generated successfully, which resulted in down-regulation of HER2/neu gene expression in the 16HBE-T efficiently.

MicroRNA expression profiles and miR-10a target in anti-benzo[a] pyrene-7, 8-diol-9, 10-epoxide-transformed human 16HBE cells.

OBJECTIVE: To screen miRNA profiles of malignantly transformed human bronchial epithelial cells, 16HBE-T, induced by anti-benzo[a]pyrene-trans-7,8-diol-9,10-epoxide (anti-BPDE), and to analyze putative miR-10a targets in 16HBE-T. METHODS: A novel microarray platform was employed to screen miRNA profiles of 16HBE-T cells transformed by anti-BPDE. Microarray data for miR-10a and miR-320 were validated using quantitative real time polymerase chain reaction (QRT-PCR). The expression of a putative target for miR-10a, HOXA1, was analyzed by reverse transcription polymerase chain reaction (RT-PCR) and QRT-PCR. RESULTS: In comparison with the vehicle-treated cells (16HBE-N), 16HBE-T exhibited differential expression of 54 miRNAs, in which, 45 were over-expressed and 9 were down-regulated. The five most highly expressed miRNAs were miR-494, miR-320, miR-498, miR-129, and miR-106a. The lowest expressed miRNAs were miR-10a, miR-493-5p, and miR-363*. Three members of miR-17-92 cluster, miR-17-5p, miR-20a, and miR-92, showed significantly higher abundance in 16BHE-T as miR-21, miR-141, miR-27a, miR-27b, miR-16 and miRNAs of the let-7 family. The putative target for miR-10a, HOXA1 mRNA was up-regulated 3-9-fold in 16HBE-T, as compared with 16HBE-N. CONCLUSION: The findings of the study provide information on differentially expressed miRNA in malignant 16HBE-T, and also suggest a potential role of these miRNAs in cell transformation induced by anti-BPDE. HOXA1 is similarly up-regulated, suggesting that miR-10a is associated with the process of HOXA 1-mediated transformation.

Effects of silencing of HER2/neu gene in anti-BPDE-transformed cells.

Anti-benzo[a]pyrene-7,8-diol-9,10-epoxide (anti-BPDE) is a metabolite of benzo[a]pyrene (B[a]P) and acts as a potent mutagen in mammalian systems. However, the molecular mechanisms related to anti-BPDE-induced carcinogenesis are poorly understood. We have used malignant human bronchial epithelial cells (16HBE-T) transformed by exposure to anti-BPDE to help characterize these possible molecular mechanisms. We have previously observed overexpression of HER2/neu in 16HBE-T. To further investigate the effects of HER2/neu on 16HBE-T cell biologic phenotype, we inhibited HER2/neu expression using RNA interference. Silencing of HER2/neu in 16HBE-T cells was performed in vitro using retrovirus-delivered short hairpin RNA (shRNA). Silencing of HER2/neu in 16HBE-T cells resulted in significant increases and decreases in the proportions of cells in G0/G1 phase (67.1+/-2.1%) and in S phase (17.3+/-4.1%), respectively, and significantly reduced cell viability and colony formation rate. These results may help to explain epithelial cell transformation following exposure to anti-BPDE, and suggest an oncogenic role for HER2/neu in anti-BPDE-induced carcinogenesis.

[Study on expression of Ras family gene in transformed cells induced by BPDE].

OBJECTIVE: To explore the expression of Ras family gene in the malignantly transformed human bronchial epithelial cell line induced by anti-benzo(a)pyrene-trans-7,8- dihydrodiol-9,10-epoxide(BPDE). METHODS: The levels of H-Ras, K-Ras and N-Ras mRNA expression in BPDE transformed 16HBE cells (16HBE-T) and untransformed control 16HBE cells (16HBE-N) were examined using RT-PCR. Expression levels of those three proteins in both kinds of cells were analyzed by western blot and immunocytochemical method. RESULTS: Compared with 16HBE-N, the levels of H-Ras, K-Ras and N-Ras mRNA expression were significantly increased to 2.237, 1.254 and 3.616 times in 16HBE-T, and the protein levels of those genes were increased to 1.273, 1.547 and 1.600 times, respectively. Immunocytochemical method showed expression levels of those proteins in 16HBE-T were significantly higher than those in 16HBE-N. CONCLUSION: H-Ras, K-Ras and N-Ras are overexpressed in 16HBE-T. The activation of oncogenic Ras may participate in malignant transformation of 16HBE induced by BPDE.

Silencing of N-Ras gene expression using shRNA decreases transformation efficiency and tumor growth in transformed cells induced by anti-BPDE.

Anti-benzo[a]pyrene-trans-7,8-diol-9,10-epoxide (anti-BPDE) is the most important metabolite of benzo[a]pyrene which is a ubiquitous environmental pollutant, and may cause human cancer, especially of the lung. Ras genes (H, K, and N) are activated in 40% of human tumors and may contribute to carcinogenesis. Here, we used malignant human bronchial epithelial cells transformed by anti-BPDE (16HBE-T) to help characterize possible molecular mechanisms of carcinogenesis. We compared H-, K-, and N-Ras mRNA and protein expression levels in 16HBE-T cells and untransformed control 16HBE cells (16HBE-N), using reverse transcription-PCR (RT-PCR) and Western blotting. We further used short hairpin RNA to silence N-Ras gene expression in 16HBE-T cells to determine the effects of silencing on the cell cycle, transformation efficiency and tumor growth. We observed overexpression of H-, K-, and N-Ras genes at both mRNA and protein levels in 16HBE-T cells, compared with 16HBE-N cells. Silencing of N-Ras in 16HBE-T cells using stable RNA interference increased the proportion of cells in G(0)/G(1) phase, decreased the proportion in S-phase, decreased transformation efficiency, and inhibited tumor growth. Our findings suggest that overexpression of N-Ras gene plays an important role in malignant transformation of 16HBE cells by anti-BPDE. N-Ras gene may be a useful target for gene therapy.

[MicroRNA profiles of malignantly transformed cells induced by anti-benzo-a-pyrene-trans-7, 8-dihydrodiol-9, 10-epoxide].

OBJECTIVE: To screen microRNA (miRNA) profiles of malignantly transformed cells induced by anti-benzo-a-pyrene-trans-7, 8-dihydrodiol-9, 10-epoxide (BPDE) and to look for miRNAs which is expressed differently between malignantly transformed cells and normal human bronchial epithelial cells 16HBE. METHODS: Experimental group was the malignantly transformed 16HBE which was induced by cultured with final concentration 2.0 micromol/L of BPDE which was dissolved in dimethyl sulphoxide. The control group was 16HBE that was cultured with minimal essential medium including dimethyl sulphoxide. 327 miR-NAs were tested be-tween those two groups with miRNA microarray analysis. MiR-10a that was down expressed and miR-320 that was overexpressed were selected to be validated by miRNA specific quantitative real-time reverse transcriptase chain reaction (miR qRT-PCR). RESULTS: 327 human miRNAs were tested with miRNA microarray analysis. 55 miRNAs were found expressing differently between those two groups and of which 46 were overexpressed and 9 were down expressed. Some data were validated by quantitative RT-PCR. CONCLUSION: miRNAs expressed significantly between malignantly transformed 16HBE and normal cells and this helps us look for unique miRNAs of malignantly transformed cells induced by BPDE, but there should have more sufficient evidences to prove their functions in malignant cells.

[Effect of anti-BPDE on expression of HER2/neu gene in the human bronchial epithelial cell line].

OBJECTIVE: To explore the effects of anti-benzo(a)pyrene-trans-7,8-dihydrodiol-9,10-epoxide (anti-BPDE) on expression of HER2/neu gene in the human bronchial epithelial cells. METHODS: The levels of HER2/neu mRNA and protein expressions, and its protein localization were examined in the malignant transformed 16HBE (16HBE-T) induced by 2.0 micromol/L anti-BPDE and untransformed control 16HBE (16HBE-N) using semi-quantitative RT-PCR, SYBR Green I Real time quantitative RT-PCR (QRT-PCR), western blot and immunocytochemical method respectively. RESULTS: The expressions of mRNA and protein of HER2/neu appeared to be a significant increase in 16HBE-T in comparison with those of 16HBE-N detected by several assays. HER2/neu protein showed membrane localization. CONCLUSION: HER2/neu could be overexpressed on treatment of human bronchial epithelial cells with anti-BPDE. The activity of HER2/neu oncogene might play an important role in the malignant transformed 16HBE induced by anti-BPDE.