Reverse Transcriptase Research Articles

Association of hTERT expression, Her2Neu, estrogen receptors, progesterone receptors, with telomere length before and at the end of treatment in breast cancer patients.

Breast cancer shows significant clinical, morphologic, and molecular variation. Telomeres are nucleoprotein complexes composed of hexanucleotide repeat DNA sequence, TTAGGG, and numerous telomere-associated proteins. The maintenance of telomere length is carried out by a ribonucleoprotein called telomerase, which consists of two main components: a catalytic subunit called hTERT (human telomerase reverse transcriptase) and an RNA template called hTR (human telomerase RNA). The importance of evaluating hTERT expression lies in its potential therapeutic application, being an attractive target due to its almost non-existent expression in normal somatic cells. It is also expected that the anti-neoplastic effect would appear earlier in neoplastic cells with shorter telomeres. Additionally, a significant relationship has been observed between Her2-Neu overexpression and Her2-Neu positivity, which could suggest new combined therapies.The aim of this study was to detect the expression of hTERT, estrogen receptor (ER), progesterone receptor (PR), and HER2-Neu in neoplastic breast tissue embedded in paraffin before treatment and to investigate the relationship between them and with baseline and post-treatment telomere length, as well as with various clinicopathological parameters. A cross-sectional-correlational, 21 women diagnosed with breast cancer at the Oncology Service of the High Specialty Medical Unit No. 1 of Bajio of the Mexican Institute of Social Security. The study complies with the Helsinki Declaration and was approved by the Institutional Ethical Committee of the Mexican Institute of Social Security (R-2019-1001-127). A peripheral blood sample was obtained before oncological treatment and at the end of oncological treatment for the measurement of telomere length by extracting DNA from leukocytes, was performed by the quantitative polymerase chain reaction (PCR) method described by Cawthon. Tumor samples were collected from each patient at the oncology department for immunohistochemical determination of biomarker expression (ER, PR, Her2/neu) and hTERT. Of the 21 cases included in the study, the median age was 57.57 years. Eighteen cases were classified as invasive ductal carcinoma NOS (85.71%), 10 were histologic grade 2 (47.61%), 16 cases were hormone receptor positive (76.19%), 7 were Her2Neu positive (33.33%), and only 2 cases were triple negative (9.52%). Positive hTERT expression was detected in 11 cases (52.38%) and was negative in the remaining cases. A significant association was identified between hTERT-positive cases and Her2-Neu positive cases (p = 0.04). Baseline and post-treatment telomere lengths showed a significant difference using the non-parametric Wilcoxon t-test (p = 0.002). In hTERT-positive cases, there was significant telomere shortening at the end of oncological treatment (6.14 ± 1.54 vs. 4.75 ± 1.96 Kb, p = 0.007). Positive hTERT immunostaining cases were associated with poor prognostic factors, such as Her2-Neu overexpression and post-treatment telomere shortening. In the future, hTERT immunostaining could be used to select patients for therapies with antagonistic effects on hTERT, as well as in the selection of more appropriate chemotherapy regimens for patients who express it.

Nucleoside/nucleotide reverse transcriptase inhibitor-associated weight gain in people living with HIV: data from the Copenhagen Comorbidity in HIV Infection (COCOMO) study

ABSTRACT Weight gain effects of Nucleoside/Nucleotide Reverse Transcriptase Inhibitors in people with HIV (PWH) have been sparsely studied. Participants were enrolled in the Copenhagen Comorbidity in HIV Infection (COCOMO) study. PWH receiving a backbone of emtricitabine, or lamivudine combined with abacavir, tenofovir disoproxil, or tenofovir alafenamide were analysed. Weight gain according to ART backbone and to the third drug was analysed using a multiple linear regression model. Non-ART risk factors were also determined using multiple linear regression. A total of 591 participants were included in the analysis. The majority were middle-aged, virally suppressed males with a mean BMI just above the normal range. Both tenofovir disoproxil/emtricitabine or lamivudine and abacavir /emtricitabine or lamivudine, but not tenofovir alafenamide /emtricitabine or lamivudine were associated with weight gain over two years (0.6 kg, p = 0.025; 1.0 kg, p = 0.005). The third drugs associated with weight increase were non-nucleoside reverse transcriptase inhibitors (NNRTI) (p = 0.035), dolutegravir (p = 0.008) and atazanavir (p = 0.040). Non-ART risk factors for gaining weight were low or normal BMI, age <40 years, underweight, inactivity or highly active at baseline. Tenofovir disoproxil and abacavir-based ART regimens were associated with a small weight gain. Third drug NNRTI, dolutegravir and atazanavir were associated with an increase in weight.

Investigation of a Serine Protease Inhibitor Active in the Infectious Stage of the Human Liver Fluke Opisthorchis viverrini.

Serine protease inhibitors (serpins) participate in the regulation of inflammation, blood coagulation, and complement activation in humans. This research aimed to identify and characterize such inhibitors of the human liver fluke Opisthorchis viverrini. Parasite proteins that might contribute to the modulation of host physiology are of particular interest, especially as chronic opisthorchiasis increases the risk of developing biliary cancer. BLAST was used to find hypothetical serpins predicted from the parasite genome data. RNA extraction and reverse transcriptase PCR were used to isolate a serpin cDNA and to determine developmental transcript abundance. The evolutionary relation to other trematode serpins was revealed by phylogenetic analysis. Recombinant serpin was expressed in Escherichia coli and used to test the immunoreactivity of human opisthorchiasis sera and the inhibition of human serine proteases. A substantial serpin family with high sequence divergence among the members was found in the genus Opisthorchis. A serpin, different from previously analyzed trematode serpins, was cloned. The transcript was only detected in metacercariae and newly excysted juveniles. Human opisthorchiasis sera showed statistically significant reactivity to recombinant serpin. The serpin caused moderate inhibition of thrombin and low inhibition of kallikrein and chymotrypsin. This parasite serpin could be further evaluated as a diagnostic tool for early infection. Kallikrein and thrombin are involved in fibrinolysis; therefore, further research should explore the effects of the parasite serpin on this process.

Molecular GBM versus Histopathological GBM: Radiology-Pathology-Genetic Correlation and the New WHO 2021 Definition of Glioblastoma.

Given the recent advances in molecular pathogenesis of tumors, with better correlation with tumor behavior and prognosis, major changes were made to the new 2021 World Health Organization (WHO) classification of CNS tumors, including updated criteria for diagnosis of glioblastoma (GBM). Diagnosis of GBM now requires absence of isocitrate dehydrogenase and histone 3 mutations (IDH-wild-type and H3-wild-type) as the basic cornerstone, with elimination of the IDH-mutant category. The requirements for diagnosis were conventionally histopathological, based on the presence of pathognomonic features such as microvascular proliferation and necrosis. However, even if these histologic features are absent, many lower-grade (WHO grade 2/3) diffuse astrocytic gliomas behave clinically similar to GBM (grade 4). The 2021 WHO classification introduced new molecular criteria that can be used to upgrade the diagnosis of such histologically lower-grade, IDH-wild-type, astrocytomas to GBM. The 3 molecular criteria include: concurrent gain of whole chromosome 7 and loss of whole chromosome 10 (+7/-10); telomerase reverse transcriptase promoter mutation; and epidermal growth factor receptor amplification. Given these changes, it is now strongly recommended to have molecular analysis of WHO grade 2/3 diffuse astrocytic, IDH-wild-type, gliomas in adult patients, as identification of any of the above mutations allows for upgrading the tumor to WHO grade 4 ("molecular GBM") with important prognostic implications. Despite an early stage, there is active ongoing research on the unique MR imaging features of molecular GBM. This paper highlights the differences between "molecular" and "histopathological" GBM, with the aim of providing a basic understanding about these changes.

Genome-wide search and gene expression studies reveal candidate effectors with a role in pathogenicity and virulence in Fusarium graminearum

ABSTRACT Fusarium graminearum causes Fusarium head blight (FHB) disease in wheat worldwide. Although F. graminearum is reported to secrete several effectors, their role in virulence and pathogenicity is unknown. The study aimed at identifying candidate genes with a role in pathogenicity and virulence using two different host systems, Arabidopsis thaliana and wheat, challenged with F. graminearum TN01. Detached leaf assay and histological studies revealed the virulent nature of TN01. A genome-wide in silico search revealed several candidate genes, of which 23 genes were selected based on reproducibility. Gene expression studies by reverse transcriptase–polymerase chain reaction (RT-PCR) in leaf tissues of Arabidopsis and the two wheat genotypes, the susceptible (Sonalika) and the resistant (Nobeoka Bozu/Nobeoka), compared with mock-treated controls in a time-course study using fungal- and plant-specific genes as internal controls revealed that these genes were differentially regulated. Further, expression of these candidates in F. graminearum–inoculated Sonalika and Nobeoka spikes compared with mock-treated controls revealed their role in pathogenicity and virulence. Gene ontology studies revealed that some of these secretory proteins possessed a role in apoptosis and ceratoplatanin and KP4 killer toxin syntheses. A three-dimensional protein configuration was performed by homology modeling using trRosetta. Further, real-time quantitative PCR (RT-qPCR) studies in F. graminearum–inoculated Arabidopsis and wheat at early time points of inoculation revealed an increased expression of the majority of these genes in Sonalika, suggesting their possible role in pathogenicity, whereas low mRNA abundance was observed for 11 of these genes in the resistant genotype, Nobeoka, compared with Sonalika, indicating their role in virulence of F. graminearum.

First Report of Impatiens Necrotic Spot Virus (INSV) Infecting Tomatoes in North Carolina.

Impatiens necrotic spot virus (INSV) (Orthotospovirus impatiensnecromaculae) is a virus in the Order Bunyavirales and Family Tospoviridae. The virus is vectored by several species of thrips and is a serious pathogen of ornamentals and lettuce in the United States (Hasegawa & Del Pozo-Valdivia 2023; Daughtrey, M. L., et al. 1997; Webster, C. G., et al. 2015). In January 2023, tomato plants (Solanum lycopersicum,'Big Dena') with viral symptoms of reduced vigor, wilting, necrotic spots on leaves, and sunken lesions on the stem were observed in one greenhouse in Guilford County, North Carolina (NC) (Figure 1A-C). Disease incidence was low (2%), with only three symptomatic plants in the single greenhouse. Affected plants also had signs of thrips feeding (dead thrips, frass, and feeding scars) present across the whole plant (Figure 1D). Samples were submitted to the NC State Plant Disease and Insect Clinic and tested positive for INSV, but negative for TSWV, using Agdia ImmunoStrips®. RNA was extracted from symptomatic leaf tissue using the IBI Total RNA Mini kit (Plant), and complementary DNA (cDNA) was generated using the ThermoFisher Verso cDNA synthesis kit. A reverse transcriptase (RT)-PCR with INSV nucleocapsid (N) primers (F:5'-ATGAACAAAGCAAAGATTACC-3' and R:5'- TTAAATAGAATCATTTTTCCC-3') was used to confirm INSV presence (Hassani-Mehraban et al. 2016). Full length N cDNA amplicon sequencing [GenBank No. PP658213] revealed 99.62% nucleotide identity to NCBI GenBank accessions KF926828 (orchid in California), MH453554.1 (hosta from NY), and MH453552.1 (foxglove from NY), all of which are INSV N sequences. The infected leaf samples were used to mechanically inoculate Emilia sonchifolia and tomato (cv.'Moneymaker') using standard virological methods. We successfully infected E. sonchifolia with INSV (confirmed with visual mosaic symptoms and positive INSV ImmunoStrip). However, mechanical inoculation of the tomato plants proved unsuccessful. Using the INSV infected E. sonchifolia leaves as an inoculum source, we generated a viruliferous Frankliniella occidentalis (Western flower thrips) cohort and challenged three week old tomatoes using thrips mediated inoculation (adapted from Aramburu et al. 2009 and Rotenberg et al., 2009). Twenty days post-inoculation, tomatoes with thrips feeding scars were symptomatic for INSV infection with chlorotic and necrotic spots, stunting, and reduced vigor. INSV infection of these tomato plants was verified with a positive INSV ImmunoStrip® result, two-step RT-PCR amplification of N, and Sanger sequencing of N. Samples from thrips-inoculated tomato plants did not test positive for TSWV. Sequence alignment showed that the recovered virus sequence was 99.85% identical to the original INSV sequence from the diagnostic sample (a single nucleotide difference). To the best of our knowledge, this is the first instance of INSV infecting tomato in NC production systems. Although TSWV is more common in vegetable production in NC (253 cases of TSWV compared to 1 case of INSV in vegetable crops based on NC State Plant Disease and Insect Clinic records since 2008), INSV incursion into tomato producing areas is concerning and should be closely monitored, especially at the transplant stage. This report also underscores the importance of using thrips vectors to transmit virus in screening for susceptibility to orthotospoviruses.

Transmitted Antiretroviral Drug Resistance to Integrase Strand Transfer Inhibitors Class in São Paulo Metropolitan Area, Brazil.

A newer integrase strand transfer inhibitor (INSTI) cabotegravir was recently approved for both therapy and prophylaxis and can play an essential role in the fight against AIDS. It shares similar resistance profile to dolutegravir, the cornerstone of Brazilian antiretroviral (ARV) treatment, with about 600 thousand people living with HIV in Brazil currently on regimens that contain this INSTI. Health services in the São Paulo metropolitan area are responsible for a large proportion of ARV dispensation in the country. Estimating transmitted drug resistance mutation (TDRM) in the area before cabotegravir introduction may provide a useful baseline information. Partial HIV-1 pol gene was sequenced (Sanger) from 192 newly diagnosed individuals from São Paulo and nearby cities (2020 to March 2023) at integrase, with 85 also at protease/reverse transcriptase regions. Retrotranscribed plasma RNA, amplified with nested PCR, was edited (Recall or Sequencher) and analyzed at Rega and Stanford db. Surveillance drug resistance mutations (SDRM) to INSTI class was detected in three cases (1.6%; 95% CI: 0.5%-5%), two E138K and one R263K, with 7.8% (95% CI: 5%-13%) with resistance mutations (major or accessory). SDRM for nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, and PI classes were identified in 7 (8.2% CI: 95% 4%-16%) cases. Subtype B predominated (69%), followed by subtype C (16%), now the second most prevalent infection in this area. Among 131 patients treated for over 6 months, 92% were virally suppressed below 200 copies/mL, with low TCD4 counts independently associated to failure. SDRM to INSTI class is rare in the area. Intermediate rates of transmitted resistance to other ARV classes are comparable to previous estimates. Viral suppression rates may depend on TCD4 counts, another negative impact of late diagnosis in care that deserves more attention.

Predictors of Resolution of Meningitis Symptoms in Tuberculous Meningitis: A Clinical, Magnetic Resonance Imaging, and Biomarker Study.

In tuberculous meningitis (TBM), the meningeal symptoms and their resolution after treatment may be dependent on clinical-radiological severity, cerebrospinal fluid (CSF), and proinflammatory cytokines, and these findings may be associated with outcome. There is a paucity of studies on the resolution of meningitis symptoms in TBM. We report on associations of clinical, magnetic resonance imaging (MRI), laboratory, and proinflammatory cytokines [tumor necrosis factor (TNF)-α and interleukin 6 (IL-6)] findings with the resolution of meningitis symptoms (RMS), and the impact of RMS duration on the outcome in TBM. Seventy-one patients with TBM were included, and their clinical, laboratory, and MRI findings at baseline were recorded. mRNA profiling of TNF-α and IL-6 was done by reverse transcriptase polymerase chain reaction. The day of RMS (fever, headache, and vomiting) after treatment was noted. Predictors of long duration of RMS (>3 weeks) were evaluated by univariate followed by multivariate analysis. The impact of RMS on 6-month mortality and outcome was analyzed. Patients' median age was 25 years, and 45 (63.4%) were males. After antitubercular treatment, meningeal symptoms resolved in 35 (50.70%) by 21 days and in 90% of patients by 49 days. Longer time of RMS was associated with TBM stage, pretreatment duration, seizure, and hydrocephalus but not with TNF-α and IL-6. Seven (9.8%) patients died at 6 months, and duration of RMS predicted death (hazard ratio = 25.55, 95% CI: 1.108-589.40; P = 0.04).

Circular RNA ACVR2A promotes the progression of hepatocellular carcinoma through mir-511-5p targeting PI3K-Akt signaling pathway

Circular RNA (circRNA) is thought to mediate the occurrence and development of human cancer and usually acts as a tiny RNA (miRNA) sponge to regulate downstream gene expression. However, it is not clear whether and how circACVR2A (hsa_circ_0001073) is involved in the progression of HCC. The purpose of this study is to clarify the potential role and molecular mechanism of circACVR2A in regulating the progression of hepatocellular carcinoma cells (HCC). The abundance of related proteins in circACVR2A, microRNA (miR511-5p) and PI3K-Akt signaling pathway was determined by quantitative reverse transcriptase polymerase chain reaction (RT-PCR) or Western blotting. Cell viability, invasion and apoptosis were analyzed by CCK-8, Transwell analysis and Tunel staining, respectively. The interaction between circACVR2A and microRNA was evaluated by double luciferase reporter gene assay. The results showed that circACVR2A was highly expressed in hepatocellular carcinoma cell lines. Our in vivo and in vitro data showed that circACVR2A promoted the proliferation, migration and invasion of HCC. In terms of mechanism, we found that circACVR2A can directly interact with miR511-5p and act as a miRNA sponge to regulate the expression of related proteins in PI3K-Akt signaling pathway.In HCC, circACVR2A can mediate miR-511-5p/mRNA network to activate PI3K signal pathway. This shows that the molecular regulatory network with circACVR2A as the core is a new potential target for diagnosis and treatment of hepatocellular carcinoma.

Analysis of virus gene subtypes and drug resistance monitoring results of newly reported HIV/AIDS population in Anhui Province from 2020 to 2023

Objective: To investigate the genetic subtypes and drug resistance monitoring of newly reported human immunodeficiency virus (HIV) infection/AIDS virus in Anhui Province from 2020 to 2023. Methods: An observational design study was used to collect blood samples from patients diagnosed with HIV/AIDS in the AIDS Prevention and Control Department of Anhui Provincial Center for Disease Control and Prevention from January 2020 to December 2023.The HIV-1 pol gene was amplified by reverse transcription-nested PCR, and the genetic subtypes were identified by phylogenetic tree analysis using MEGA 7.0 software. The mutation sites of drug resistance were analyzed by the online software tool of Stanford University's HIV Drug resistance database. The influencing factors of drug resistance before treatment were analyzed by multivariate logistic analysis. Results: A total of 335 plasma samples were collected, and 332 HIV-1 pol gene sequences were obtained successfully. The main gene subtypes were CRF01-AE, accounting for 35.55% (118/332), followed by CRF07-BC, B and B+C types [29.22% (97/332), 11.74% (39/332), 9.93% (33/332)]. The total drug resistance rate before treatment was 30.12%(32/100), and the drug resistance rate of protease inhibitor (PIs) in HIV-1 was 6.33% (21/332). The drug resistance rate of nucleoside reverse transcriptase inhibitors (NRTI) before treatment was 6.33% (21/332). The drug resistance rate of non-nucleoside reverse transcriptase inhibitors (NNRTI) before treatment was 17.47% (58/332).The comparison of drug resistance rate of different drug types showed statistical significance (χ2=30.435, P<0.05).Among the 100 cases of drug resistance, the main mutation point of HIV-1 protease inhibitor was Q58E (21.00%), and the main mutation point of nucleoside reverse transcriptase inhibitor was M184V/I (6.00%). Non-nucleoside reverse transcriptase inhibitor resistance mutation points mainly K103N (22.00%).There were statistically significant differences in the starting time of antiviral therapy, the number of CD4+T cells at baseline and the drug resistance rate of gene subtypes (the chi-square values are respectively 24.152, 32.516, 11.652, P<0.05).Multivariate logistic analysis showed that the baseline CD4+T cell count was <200/μl, subtype B, subtype B+C, CRF01-AE subtype, CRF55-01B subtype and 01-BC subtype was the influential factor of drug resistance before treatment (the chi-square values are respectively 4.577, 8.202, 4.416, 5.206, 7.603 and 4.804, P<0.05). Conclusion: The newly reported HIV/AIDS population in Anhui Province from 2020 to 2023 has a variety of viral gene subtypes, and NNRTIs are the main types of drug resistance gene mutations before treatment. Attention should be paid to the number of baseline CD4+T cells, the duration of antiviral treatment, and the distribution of gene subtypes to reduce the drug resistance of HIV/AIDS patients before treatment.

Intracellular islatravir-triphosphate half-life supports extended dosing intervals.

Antiretroviral therapy has substantially reduced morbidity, mortality, and disease transmission in people living with HIV. Islatravir is a nucleoside reverse transcriptase translocation inhibitor that inhibits HIV-1 replication by multiple mechanisms of action, and it is in development for the treatment of HIV-1 infection. In preclinical and clinical studies, islatravir had a long half-life (t½) of 3.0 and 8.7 days (72 and 209 hours, respectively); therefore, islatravir is being investigated as a long-acting oral antiretroviral agent. A study was conducted to definitively elucidate the terminal t½ of islatravir and its active form islatravir-triphosphate (islatravir-TP). A single-site, open-label, non-randomized, single-dose phase 1 study was performed to evaluate the pharmacokinetics and safety of islatravir in plasma and the pharmacokinetics of islatravir-TP in peripheral blood mononuclear cells after administration of a single oral dose of islatravir 30 mg. Eligible participants were healthy adult males without HIV infection between the ages of 18 and 65 years. Fourteen participants were enrolled. The median time to maximum plasma islatravir concentration was 1 hour. Plasma islatravir concentrations decreased in a biphasic manner, with a t½ of 73 hours. The t½ (percentage geometric coefficient of variation) of islatravir-TP in peripheral blood mononuclear cells through 6 weeks (~1008 hours) after dosing was 8.1 days or 195 hours (25.6%). Islatravir was generally well tolerated with no drug-related adverse events observed. Islatravir-TP has a long intracellular t½, supporting further clinical investigation of islatravir administered at an extended dosing interval.

Prospects for breast cancer immunotherapy using microRNAs and transposable elements as objects.

One of the directions in treatment of chemoresistant breast cancer (BC) may include new methods of activating the immune response against tumor cells. Clinically used checkpoint inhibition using antibodies to PD-1 and PD-L1 works in some patients, but the lack of biomarkers means number of respondents is low. The possibility of combining this method with chemotherapy is limited by an increased risk of toxic liver damage, development of immune-related pneumonitis, and thyroid dysfunction. This article includes introduction into the clinic of new methods of immunotherapy for BC, among which epigenetic activation of retroelements, double-stranded transcripts of which stimulate the interferon response against the tumor, is promising. For this purpose, inhibitors of DNA methyltransferase*, histone deacetylase* and histone methyltransferase* are used (* subtitles in the main text). Their antitumor effect is also mediated by removal of repressive epigenetic marks from tumor suppressor genes. However, numerous studies have proven the role of retroelements in the carcinogenesis of various malignant neoplasms, including BC. Moreover, endogenous retroviruses HERV-K and LINE1 retrotransposons are planned to be used as diagnostic biomarkers for BC. Therefore, a rational approach to using viral mimicry in antitumor therapy of BC may be the simultaneous suppression of specific retrotransposons (drivers for carcinogenesis) using reverse transcriptase inhibitors and silencing of specific transposons involved in carcinogenesis using complementary microRNAs. To determine possible pathways of influence in this direction, 35 specific transposon-derived microRNAs* changes in BC were identified, which can become guides for targeted therapy of BC.

18 Unraveling the Impact of Tumor Microenvironment on Immunotherapy Response/Resistance in Human Sarcomatoid Clear Cell Renal Cell Carcinoma: Insights from a Novel Mouse Model

Abstract Background Renal cell carcinoma (RCC) with histological sarcomatoid de-differentiation (sRCC) has a historically poor prognosis across all RCC subtypes. Recently, immunotherapy with anti-PD1 + anti-CTLA4 combo has significantly improved disease-specific survival, and complete response are seen in upwards of 20% of patients. However, half of sRCC patients still have no response to this immunotherapy, and the mechanism of response remains unclear. Methods Our preliminary bulk RNA sequencing data reveal a distinct tumor microenvironment (TME) in human sRCC tumors, characterized by heightened immune cell infiltration, particularly enriched for regulatory T cells (Tregs). Subsequently, we delineated the spatial gene expression topography within sRCC and clear cell renal cell carcinoma (ccRCC) regions, culminating in the development of the sRCC signature. Concurrently, we established an innovative immunocompetent murine model of sRCC. Leveraging CRISPR technology, we replicated the human sRCC genotype by knocking out Vhl, Bap1, and Cdkn2a/2b genes in a mouse telomerase reverse transcriptase (mTERT) overexpressing renal proximal tubule epithelial cell line. This effort yielded a successfully engineered mouse implantable sRCC cell line bearing VhlMutBap1DelCdkn2aDelCdkn2bDel (HJRCC68N). Results The syngeneic mouse sRCC model we developed faithfully replicates human sRCC histology and tumor microenvironment and recapitulates the sRCC signature identified in human sRCC regions. Importantly, like in humans, mouse sRCC tumors exhibit a heterogeneous response to anti-PD1 + anti-CTLA4 combination, and anti-CTLA4 monotherapy, reflecting the clinical variability observed in human patients. Furthermore, transcriptomic analysis from our mouse model reveals the involvement of type 1 immunity in responder, providing insights into overcoming immunotherapy resistance. Conclusions In conclusion, our study unveiled distinct changes in the TME at the transcriptomic and spatial gene expression levels in human sRCC. Leveraging our novel murine model, which faithfully replicates human sRCC histology, TME characteristics, and mixed response to immunotherapy, we elucidated the involvement of type 1 immunity in treatment response. These insights offer valuable pathways for overcoming immunotherapy resistance and pave the way for the development of tailored treatment strategies aimed at improving outcomes for sRCC patients.

Predicting telomerase reverse transcriptase promoter mutation in glioma: A systematic review and diagnostic meta-analysis on machine learning algorithms.

Glioma is one of the most common primary brain tumors. The presence of the telomerase reverse transcriptase promoter (pTERT) mutation is associated with a better prognosis. This study aims to investigate the TERT mutation in patients with glioma using machine learning (ML) algorithms on radiographic imaging. This study was prepared according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The electronic databases of PubMed, Embase, Scopus, and Web of Science were searched from inception to August 1, 2023. The statistical analysis was performed using the MIDAS package of STATA v.17. A total of 22 studies involving 5371 patients were included for data extraction, with data synthesis based on 11 reports. The analysis revealed a pooled sensitivity of 0.86 (95% CI: 0.78-0.92) and a specificity of 0.80 (95% CI 0.72-0.86). The positive and negative likelihood ratios were 4.23 (95% CI: 2.99-5.99) and 0.18 (95% CI: 0.11-0.29), respectively. The pooled diagnostic score was 3.18 (95% CI: 2.45-3.91), with a diagnostic odds ratio 24.08 (95% CI: 11.63-49.87). The Summary Receiver Operating Characteristic (SROC) curve had an area under the curve (AUC) of 0.89 (95% CI: 0.86-0.91). The study suggests that ML can predict TERT mutation status in glioma patients. ML models showed high sensitivity (0.86) and moderate specificity (0.80), aiding disease prognosis and treatment planning. However, further development and improvement of ML models are necessary for better performance metrics and increased reliability in clinical practice.

Aerobic phenol degradation using native bacterial consortium via ortho-and meta-cleavage pathways.

Effective bioremediation of a phenol-polluted environment harnesses microorganisms' ability to utilize hazardous compounds as beneficial degraders. In the present study, a consortium consisting of 15 bacterial strains was utilized. The current study aims to monitor the phenol biodegradation pathway. The tested consortium showed effective potential in the bioremediation of phenol-contaminated industrial wastewater. The enzymatic studies conducted brought to light that the bacterial consortium under test was proficient in degrading phenol under aerobic conditions while exhibiting the simultaneous expression of both ortho- and meta-cleavage pathways. It was observed that pheA, pheB, and C12O genes were maximally expressed, and the enzymes responsible for phenol degradation, namely, phenol hydroxylase, catechol 1,2-dioxygenase, and catechol 2,3-dioxygenase, reached maximum activity after 48 h of incubation with a 20-ppm phenol concentration. To gain a deeper understanding of the activation of both ortho- and meta-cleavage pathways involved in phenol degradation, a technique known as differential display reverse transcriptase polymerase chain reaction (DDRT-PCR) was applied. This method allowed for the specific amplification and detection of genes responsible for phenol degradation. The expression levels of these genes determined the extent to which both ortho- and meta-cleavage pathways were activated in response to the presence of phenol.

Trends and correlates in HIV viral load monitoring and viral suppression among adolescents and young adults in Dar es Salaam, Tanzania.

Adolescents and young adults (AYA) living with HIV have been shown to have lower rates of viral load testing and viral suppression as compared to older adults. We examined trends over time and predictors of HIV viral load monitoring and viral suppression among AYA in a large HIV treatment programme in Dar es Salaam, Tanzania. We analysed longitudinal data of AYA aged 10-24 years initiated on antiretroviral therapy between January 2017 and October 2022. Trend models were used to assess changes in HIV viral load testing and viral suppression by calendar year. Generalised estimating equations were used to examine the relationship of sociodemographic and clinical factors with HIV viral load testing and viral suppression. Out of 15,759 AYA, the percentage of those who received a 6-month HIV viral load testing increased from 40.6% in 2017 to 64.7% in 2022 and, a notable annual increase of 5.6% (p < 0.001). A higher HIV viral load testing uptake was observed among 20- to 24-year-olds (87.7%) compared to 10- to 19-year-olds (80.2%) (p < 0.001). The likelihood of not receiving an HIV viral load test within 12 months of antiretroviral therapy initiation was higher among 10- to 19-year-olds (adjusted odds ratio [aOR] = 1.7; 95% confidence interval [CI] = 1.4-2.0), advanced HIV disease (aOR = 1.3; 95% CI = 1.12-1.53), normal nutrition status at enrolment aOR 2.6 (95% CI = 1.59-4.26) and initiation of non-nucleoside reverse transcriptase inhibitors regimen aOR 1.2 (95% CI = 1.08-1.34). The proportion of AYA with viral suppression increased from 83.0% in 2017 to 94.6% in 2022. Notably, the overall trend in viral suppression increased significantly at 2.4% annually. The risk of not achieving viral suppression was greater among 10- to 14-year-olds (aOR = 2; 95% CI = 1.75-2.43) and 15- to 19-year-olds (aOR = 1.4; 95% CI = 1.24-1.58) as compared to 20-24 years; being male (aOR = 1.16; 95% CI = 1.02-1.32); undernourished (aOR = 1.53; 95% CI = 1.17-1.99); in WHO Stage II (aOR = 1.16; 95% CI = 1.02-1.33) and III (aOR = 1.21; 95% CI = 1.03-1.42) and being on an non-nucleoside reverse transcriptase inhibitors regimen (aOR = 1.32; 95% CI = 1.18-1.48). HIV viral load testing uptake at 6 months of antiretroviral therapy initiation and viral suppression increased from 2017 to 2022; however, overall HIV viral load testing was suboptimal. Demographic and clinical characteristics can be used to identify AYA at greater risk for not having HIV viral load test and not achieving viral suppression.

TERT upstream promoter methylation regulates TERT expression and acts as a therapeutic target in TERT promoter mutation-negative thyroid cancer

BackgroundDNA hypermethylation and hotspot mutations were frequently observed in the upstream and core promoter of telomerase reverse transcriptase (TERT), respectively, and they were associated with increased TERT expression and adverse clinical outcomes in thyroid cancer. In TERT promoter mutant cancer cells, the hypomethylated TERT mutant allele was active and the hypermethylated TERT wild-type allele was silenced. However, whether and how the upstream promoter methylation regulates TERT expression in TERT mutation-negative cells were largely unknown.MethodsDNA demethylating agents 5-azacytidine and decitabine and a genomic locus-specific demethylation system based on dCas9-TET1 were used to assess the effects of TERT upstream promoter methylation on TERT expression, cell growth and apoptosis of thyroid cancer cells. Regulatory proteins binding to TERT promoter were identified by CRISPR affinity purification in situ of regulatory elements (CAPTURE) combined with mass spectrometry. The enrichments of selected regulatory proteins and histone modifications were evaluated by chromatin immunoprecipitation.ResultsThe level of DNA methylation at TERT upstream promoter and expression of TERT were significantly decreased after treatment with 5-azacytidine or decitabine in TERT promoter wild-type thyroid cancer cells. Genomic locus-specific demethylation of TERT upstream promoter induced TERT downregulation, along with cell apoptosis and growth inhibition. Consistently, demethylating agents sharply inhibited the growth of thyroid cancer cells harboring hypermethylated TERT but had little effect on cells with TERT hypomethylation. Moreover, we identified that the chromatin remodeling protein CHD4 binds to methylated TERT upstream promoter and promotes its transcription by suppressing the enrichment of H3K9me3 and H3K27me3 at TERT promoter.ConclusionsThis study uncovered the mechanism of promoter methylation mediated TERT activation in TERT promoter mutation-negative thyroid cancer cells and indicated TERT upstream promoter methylation as a therapeutic target for thyroid cancer.

Identification of new banana endogenous virus sequences highlights the hallmark gene encoded by retroviruses integrated in banana genomes

Endogenous pararetrovirus sequences (EPRVs) originated from DNA viruses of the family Caulimoviridae are widely present in plant genomes. Banana streak viruses (BSVs) are a group of circular double-stranded DNA viruses in the genus Badnavirus of the family Caulimoviridae. Banana endogenous virus sequences (BEVs) derived from the ancestral genes of badnaviruses and fixed in the genomes of various bananas. However, the genomic characteristics of BEVs remain unknown. In this study, we identified 2 new variants of BEVs GZ5 and GZ13 by sequences analyses, Southern blot, and fluorescent in situ hybridization (FISH). BEV GZ5 had one copy of integration in the BB genome of bananas, while BEV GZ13 was only present in the genome of the variety Dajiao. Importantly, BEV GZ5 contained a complete gene of reverse transcriptase (RT) and ribonuclease H (RNase H) (RT/RNase H). In addition, a 340-bp inverted repeat sequence partially overlapping with RNase H was found upstream and downstream of BEV GZ5. However, the amino acid sequences of BEV GZ5 had deletions and mutations compared with BSVs. The bioinformatics analyses showed that BEV GZ5 protein composed of 412 amino acids with a molecular weight of 47.37 kDa and an isoelectric point of 9.40. Leucine, isoleucine, and lysine (Lys) were the main amino acids of BEV GZ5 protein. The analyses revealed that BEV GZ5 protein contained 35 potential phosphorylation sites. Additionally, it was a hydrophilic protein without a signal peptide and transmembrane region. The secondary structure of BEV GZ5 protein consisted of 37.26% α-helix, followed by 36.25% random coil. To our knowledge, this is the first report that novel BEVs with the complete gene of RT/RNase H has been characterized, which provide a basis for further exploration the function and integration mechanism of BEVs in bananas.

Establishment and application of PDCoV antigen-specific DAS-ELISA detection method

BackgroundPorcine deltacoronavirus (PDCoV) is a swine enteropathogenic coronavirus that affects young pigs, causing vomiting, acute diarrhea, dehydration, and even death. There is growing evidence that PDCoV can undergo cross-species as well as zoonotic transmissions. Due to the frequent outbreaks of this deadly virus, early detection is essential for effective prevention and control. Therefore, developing a more convenient and reliable method for PDCoV detection is the need of the hour.ResultsThis study utilized a high-affinity monoclonal antibody as the capture antibody and a horseradish peroxidase labeled polyclonal antibody as the detection antibody to develop an enzyme-linked immunosorbent assay (DAS-ELSA) for PDCoV detection.Both antibodies target the PDCoV nucleocapsid (N) protein. The findings of this study revealed that DAS-ELISA was highly specific to PDCoV and did not cross-react with other viruses to cause swine diarrhea. The limit of detection of the virus titer using this method was 103 TCID50/mL of PDCoV particles. The results of a parallel analysis of 239 known pig samples revealed a coincidence rate of 97.07% (κ = 0.922) using DAS-ELISA and reverse transcriptase PCR (RT-PCR). The DAS-ELISA was used to measure the one-step growth curve of PDCoV in LLC-PK cells and the tissue distribution of PDCoV in infected piglets. The study found that the DAS-ELISA was comparable in accuracy to the TCID50 method while measuring the one-step growth curve. Furthermore, the tissue distribution measured by DAS-ELISA was also consistent with the qRT-PCR method.ConclusionThe developed DAS-ELISA method can be conveniently used for the early clinical detection of PDCoV infection in pigs, and it may also serve as an alternative method for laboratory testing of PDCoV.

Endoplasmic Reticulum Stress Promotes Telomerase Reverse Transcriptase Expression Contributes to Development of Allergic Rhinitis.

The Th2 cell polarization is a crucial factor in the pathogenesis of allergic diseases. The underlying mechanism requires further investigation. Telomerase has an immune-regulating ability. The aim of this study is to elucidate the association between telomerase and Th2 cell polarization in patients with allergic rhinitis (AR). CD4+ T cells were isolated from blood samples collected from AR patients and healthy control subjects. RNA sequencing was employed to analyze RNA samples extracted from CD4+ T cells. An AR mouse model was established using the ovalbumin-alum protocol. High telomerase gene activity and high endoplasmic reticulum (ER) stress status were observed in CD4+ T-cells in patients with AR. Positive correlation between the telomerase reverse transcriptase (TERT) gene expression in CD4+ T cells and AR response in patients with AR. TERT facilitated the degradation of Foxp3 proteins in CD4+ T cells, resulting in the polarization of Th2 cells. Sensitization with the ovalbumin-alum protocol enhanced the Tert expression in CD4+ T cells by exacerbating ER stress. Conditional inhibition of the Tert or eukaryotic translation initiation factor 2-α (Eif2a) expression in CD4+ T cells effectively attenuated experimental AR in mice. Elevated amounts of telomerase in CD4+ T cells were found in CD4+ T cells of subjects with AR. Telomerase promoted Th2 cell polarization by inducing Foxp3 protein degradation and promotes GATA3 activation. Inhibition of TERT or eIF2a alleviated experimental AR.