Correlation between antibodies against the pathogenic pHERV-W envelope protein and the inflammatory phase of multiple sclerosis.

The role of retroviral envelope proteins belonging to the Human Endogenous Retroviral family 'W' (HERV-W), specifically syncytin-1 and pathogenic HERV-W (pHERV-W), as potential risk factors in multiple sclerosis (MS) has been established. This study aimed to investigate the humoral response to syncytin-1 and pHERV-W-derived peptides in a group of relapsing remitting MS patients categorized as having acute or stable disease. Furthermore, an inhibition assay was conducted to assess the extent of cross-reactivity between the two epitopes. The findings revealed that MS patients in the acute phase exhibited a higher specific antibody response to the pHERV-W env epitope compared to syncytin-1. This suggests a potential pathogenic role for pHERV-W env during the inflammatory stages of central nervous system involvement, and these antibody responses could serve as useful biomarkers for monitoring the progression of the disease.

A Multigene-Panel Study Identifies Single Nucleotide Polymorphisms Associated with Prostate Cancer Risk.

The immune system plays a critical role in modulating cancer development and progression. Polymorphisms in key genes involved in immune responses are known to affect susceptibility to cancer. Here, we analyzed 35 genes to evaluate the association between variants of genes involved in immune responses and prostate cancer risk. Thirty-five genes were analyzed in 47 patients with prostate cancer and 43 healthy controls using next-generation sequencing. Allelic and genotype frequencies were calculated in both cohorts, and a generalized linear mixed model was applied to test the relationship between prostate cancer risk and nucleotide substitution. Odds ratios were calculated to describe the association between each single nucleotide polymorphism (SNP) and prostate cancer risk. Significant changes in allelic and genotypic distributions were observed for IL4R, IL12RB1, IL12RB2, IL6, TMPRSS2, and ACE2. Furthermore, a generalized linear mixed model identified statistically significant associations between prostate cancer risk and SNPs in IL12RB2, IL13, IL17A, IL4R, MAPT, and TFNRS1B. Finally, a statistically significant association was observed between IL2RA and TNFRSF1B and Gleason scores, and between SLC11A1, TNFRSF1B and PSA values. We identified SNPs in inflammation and two prostate cancer-associated genes. Our results provide new insights into the immunogenetic landscape of prostate cancer and the impact that SNPs on immune genes may have on affecting the susceptibility to prostate cancer.

Latent Potential of Multifunctional Selenium Nanoparticles in Neurological Diseases and Altered Gut Microbiota.

Neurological diseases remain a major concern due to the high world mortality rate and the absence of appropriate therapies to cross the blood-brain barrier (BBB). Therefore, the major focus is on the development of such strategies that not only enhance the efficacy of drugs but also increase their permeability in the BBB. Currently, nano-scale materials seem to be an appropriate approach to treating neurological diseases based on their drug-loading capacity, reduced toxicity, targeted delivery, and enhanced therapeutic effect. Selenium (Se) is an essential micronutrient and has been of remarkable interest owing to its essential role in the physiological activity of the nervous system, i.e., signal transmission, memory, coordination, and locomotor activity. A deficiency of Se leads to various neurological diseases such as Parkinson's disease, epilepsy, and Alzheimer's disease. Therefore, owing to the neuroprotective role of Se (selenium) nanoparticles (SeNPs) are of particular interest to treat neurological diseases. To date, many studies investigate the role of altered microbiota with neurological diseases; thus, the current review focused not only on the recent advancement in the field of nanotechnology, considering SeNPs to cure neurological diseases, but also on investigating the potential role of SeNPs in altered microbiota.

Antibodies against HSV-1 and Curli Show the Highest Correlation in Parkinson's Disease Patients in Comparison to Healthy Controls.

Parkinson's disease (PD) is a neurodegenerative disorder involving the accumulation of alpha-synuclein (α-syn)/Lewy bodies in the brain and -enteric nervous system. The etiology of the disease is not well understood, but bacterial and viral infections may contribute to the pathogenesis of PD. It has been suggested that the gastrointestinal (GI) complications observed in PD patients may arise from bacterial dysbiosis, leading to curli/α-syn deposits in the enteric nervous system. Enteric bacteria secrete curli, a functional amyloid peptide involved in adhesion to surfaces, cell invasion, and biofilm formation. However, these bacterial amyloids can initiate additional α-syn deposits through immune system activation and cross-seeding. In this study, we investigate the humoral response against α-syn, curli peptides, and various bacterial and viral immunogen peptides in PD patients, and compare them with those in healthy controls (HCs). Polyclonal IgG antibodies (Abs) were detected against peptides derived from α-syn (α-syn100−114), curli (Curli133−141), Porphyromonas gingivalis Pg (RgpA800−812, Kpg328−339), Aggregatibacter actinomycetemcomitans (LtxA1429−445, LtxA264−80), Mycobacterium avium subsp. paratuberculosis (MAP3865c125−133, MAP1,4-a-gbp157−173 and MAP_402718−32), Epstein−Barr virus (EBNA1400−413, BOLF1305−320), and Herpes Simplex virus 1 (UI4222−36), as investigated by indirect ELISA of 51 serum samples from PD and 58 sex and age-matched HCs. Significant differences in OD (optical density) values and Abs positivity between PD patients and HCs were observed for Kpg (82.3% vs. 10.3%), followed by RgpA (60.7% vs. 24.1%), curli (51% vs. 22.4%), and UI42 (43.1% vs. 25.8%) in PD, compared to HCs sera (p < 0.001). No significant difference was found in the ODs obtained from other tested peptides in PD patients, compared to HCs. Significant positive correlations between OD values obtained by ELISA were observed for UI42 and curli (r = 0.811, p < 0.0001), Kpg and RgpA (r = 0.659, p < 0.0001), followed by LtxA1 and LtxA2 (r = 0.653, p < 0.0001). The correlation between the HY scale (Hoehn and Yahr Scale) and LtxA1 (r = 0.306, p < 0.028) and HY and Kpg (r = 0.290, p < 0.038) were significantly positive. This study reports a significantly increased humoral response against curli, Pg, and HSV-1 in PD patients, implying that they could be important factors in the pathogenesis of the disease. In addition, the high positive correlation between UI42 and curli may suggest the involvement of HSV-1 in GI dysbiosis. Therefore, the role of each individual pathogen and curli in PD needs to be further investigated.

HERV-K Envelope Protein Induces Long-Lasting Production of Autoantibodies in T1DM Patients at Onset in Comparison to ZNT8 Autoantibodies.

Human endogenous retroviruses (HERVs) have been thought of as silent passengers within our genomes, but their reactivation has been linked with several autoimmune diseases, including type 1 diabetes (T1DM). In order to evaluate the potential role of HERVs, in addition to the recognized role of HERV-W, we focused on the debated role of the HERV-K family in T1DM. Therefore, we performed a serological evaluation of IgG antibodies against HERV-K Env epitope (HERV-K Env19−37) in comparison to an important ß-cellular autoimmunity biomarker, ZnT8, from plasma samples of Sardinian children at the onset of T1DM, different T1DM groups (1−5 and 6−12 years since diagnosis), and healthy controls (HCs), by an indirect enzyme-linked immunosorbent assay (ELISA). A significant antibody response was observed against HERV-K Env19−37 (p < 0.0001) in T1DM patients compared to HCs, and significantly higher IgG responses were detected in the group at the onset compared to the other T1DM groups and HCs. Unlike the trend of the ß-cellular autoimmunity autoantibodies, for HERV-K Env antibodies we observed positive values that persist over time up to 5 years since the onset of T1DM. Our results add new evidence about the presence of antibodies against HERV-K in T1DM, but further investigations are necessary to relate these results with the established role of HERVs, considering the contrasting results for HERV-K.

Bisphenols induce human genomic damage and modulate HERVs/env expression.

Bisphenol A (BPA), a recognized endocrine-disrupting chemical, is used in the production of epoxy and polycarbonate resins. Since human exposure to BPA has been associated with increased cancer susceptibility, the market has shifted to products often labeled as "BPA free" containing BPA analogs such as bisphenol F (BPF) and bisphenol S (BPS). However, the European legislation on BPF and BPS is still unclear. This study analyzed the effects of BPA, BPF, and BPS exposure on human peripheral blood mononuclear cells by using in vitro micronucleus assay. Furthermore, it investigated the impact of bisphenols exposure on human endogenous retroviruses (HERVs) expression, which is implicated with the pathogenesis of several human diseases. The micronucleus assay revealed a significant genotoxic effect in peripheral blood cells after exposure to BPA and BPF at concentrations of 0.1, 0.05, and 0.025 µg/ml, and to BPS at 0.1 and 0.05 µg/ml. In addition, BPA exposure seems to upregulate the expression of HERVs, while a downregulation was observed after BPF and BPS treatments. Overall, our data showed the toxic effect of BPA and its analogs on circulating cells in the blood and demonstrated that they could modulate the HERVs expression.

Increased Presence of Antibodies against Type I Interferons and Human Endogenous Retrovirus W in Intensive Care Unit COVID-19 Patients.

In this work, we observed an increased presence of antibodies (Abs) against type I interferon (IFN-I) in coronavirus disease 2019 (COVID-19) patients admitted to the intensive care unit (ICU) compared to non-ICU COVID-19 patients and healthy control (HC) subjects. Human endogenous retrovirus W (HERV-W) can reactivate after viral infection; therefore, we also investigated the presence of antibodies against HERV-W envelope (HERV-W-env)-derived epitopes. A total of 113 subjects (41 female and 72 male subjects) were analyzed. A significant difference in autoantibodies against IFN-α, IFN-ω, and HERV-W was observed between HCs and ICU patients; indeed, the latter have higher levels of autoantibodies against IFN-α, IFN-ω, and HERV-W than subjects with mild COVID-19 and HCs. Neutralizing anti-IFN-I autoantibodies may affect the ability of IFN-I to bind to the type I interferon receptor (IFNAR), blocking the activation of the antiviral response. IMPORTANCE In this work, we report the increased presence of IFN autoantibodies in correlation with HERV-W-env autoantibodies in ICU COVID-19 patients. The novelty of the results is in the association of these IFN autoantibodies with autoantibodies against HERV-W-env, a protein recently discovered to be overexpressed in lymphocytes of COVID-19 patients and correlated with severe disease and pneumonia. Type I IFNs are part of a complex cross-regulatory network; however, in a small percentage of cases, the increase in autoantibodies against these proteins may lead to damage to the host instead of protection against infectious diseases.

Antihuman Endogenous Retrovirus Immune Response and Adaptive Dysfunction in Autism.

ASD is a neurodevelopmental disorder of unknown aetiology but with a known contribution of pathogenic immune-mediated mechanisms. HERVs are associated with several neuropsychiatric diseases, including ASD. We studied anti-HERV-W, -K and -H-env immune profiles in ASD children to analyse differences between their respective mothers and child/mother control pairs and possible correlations to ASD severity and loss of adaptive abilities. Of the 84 studied individuals, 42 children (23 ASD and 19 neurotypical) and their paired mothers underwent clinical and neuropsychological evaluations. ASD severity was analysed with standardised tests. Adaptive functioning was studied with ABAS-II and GAC index. Plasma anti-env responses of HERV-K, -H and -W were tested with indirect ELISA. ASD and neurotypical children did not differ in age, gender, comorbidities and anti-HERV responses. In children with ASD, anti-HERV levels were not correlated to ASD severity, while a significant inverse correlation was found between anti-HERV-W-248-262 levels and adaptive/social abilities. Upregulation of anti-HERV-W response correlates to dysfunctional social and adaptive competences in ASD but not in controls, suggesting anti-HERV response plays a role in the appearance of peculiar ASD symptoms.

HERV-K and HERV-H Env Proteins Induce a Humoral Response in Prostate Cancer Patients.

A higher expression of human endogenous retroviruses (HERVs) has been associated with several malignancies, including prostate cancer, implying a possible use as a diagnostic or prognostic cancer biomarker. For this reason, we examined the humoral response against different epitopes obtained from the envelope protein of HERV-K (HERV-K env-su19-37, HERV-K env-su109-126), HERV-H (HERV-H env-su229-241, HERV-H env387-399) and HERV-W (HERV-W env-su93-108, HERV-W env-su248-262) in the plasma of patients affected by prostate cancer (PCa), and compared to that of benign prostate hyperplasia (BPH) and a borderline group of patients with atypical small acinar proliferation (ASAP) and prostate intraepithelial neoplasia (PIN) and healthy controls. A significant antibody response was observed against HERV-K env-su109-126 (p = 0.004) and HERV-H env-su229-241 (p < 0.0001) in PCa patients compared to HCs, BPH and borderline cohorts, whilst no significance difference was found in the antibodies against HERV-W env-su93-108 and HERV-W env-su248-262 in patients with PCa. Our results provided further proof of the association between HERV-K and PCa and added new evidence about the possible involvement of HERV-H in PCa pathogenesis, highlighting their possibility of being used as biomarkers of the disease.

Efficacy of BCG vaccine in animal models of neurological disorders.

The Bacillus Calmette-Guerin (BCG) vaccine can modulate the immune response via antigen-specific immune response, but also it can confer nonspecific protection and therapeutic benefits in several neurological conditions through different heterologous effects of vaccination. However, the precise mechanism of action of BCG remains unclear. In this review, different mechanisms underlying BCG-mediated immunity will be explained in animal models that reflects characteristic feature of neuroinflammatory and neurodegenerative disorders such as multiple sclerosis, Alzheimer's and Parkinson's diseases. Furthermore, evidence for a beneficial effect of the BCG on neuropsychiatric disorders, will be also discussed.

GSTT1, GSTP1 and XPC genes are associated with longevity in an Italian cohort.

Longevity is a complex process controlled by environmental and genetic factors. We evaluated the association of seven drug metabolising and DNA-repair gene polymorphisms with longevity in an Italian cohort. A sample of 756 subjects aged 18-98 was genotyped for CYP1A1 (rs1048943, A>G), GSTM1 (rs 1183423000, presence/absence), GSTT1 (rs1601993659, presence/absence), GSTP1 (rs1695, A>G), XRCC1 (rs1799782, C>T), XRCC1 (rs25489, A>G) and XPC (rs2228001, A>C) gene polymorphisms. The association between the studied gene polymorphisms and longevity was evaluated by dividing the sample into three age groups: 18-50, 51-85, and 86-98. We observed a significant decrease in the frequency of the GSTT1 null, GSTP1 G and XPC C alleles in the oldest group with respect to the youngest one. We also obtained the same results when dividing the sample into 18-85 and 86-98 age groups. The general linear model analyses confirmed a significant decreasing trend with age of the above mentioned alleles. We hypothesised that these minor alleles, being important in the sensitivity against the development of different types of cancer, may reflect a reduced life-expectancy in carrier subjects and may explain their significantly lower frequency observed among subjects belonging to the oldest age group.

Association of TGFß1 codon 10 (T>C) and IL-10 (G>C) cytokine gene polymorphisms with longevity in a cohort of Italian population.

Longevity is a complex process controlled by both environmental and genetic factors. We evaluated the association of four cytokine gene polymorphisms with longevity in an Italian cohort. A sample of 1019 subjects aged 10 to 100 and belonging to the North-Italian population was genotyped for IL-6 (G>C, rs1800796), IL-10-1082 (G>A, rs1800896), TNF-α-308 (G>A, rs1800629), and TGFß1 codon 10 (T>C, rs1800471) gene polymorphisms. The association between cytokine gene polymorphisms and longevity was evaluated by dividing the sample into four age groups: 10 to 24, 25 to 49, 50 to 85, and 86 to 100. We observed a significant decrease in the frequency of IL-10 A allele in the 25 to 49 (P = 1.1 × 10-3 ), 50 to 85 (P < 1 × 10-4 ), and 86 to 100 (P = 2 × 10-3 ) age groups compared to that in the youngest age group. Similarly, we found a significant decrease (P < 1 × 10-4 ) in the frequency of TGFß1 C allele in the 50 to 85 and 86 to 100 age groups compared to that in the 10 to 24 and 25 to 49 age groups. Previously, high levels of TGFß1 were detected in elderly subjects, suggesting that this cytokine could counterbalance the harmful effects of inflammation. Similarly, IL-10 has strong anti-inflammatory properties and can inhibit the production of proinflammatory cytokines. In the literature, the lowest levels of functional cytokines were found to be associated with TGFß1 (T>C) and IL-10 (G>A) gene polymorphisms, with consequent increase in the duration of inflammation and cancer risk. For these reasons, it is plausible to observe low rates of these mutations in elderly subjects, as found in our study.

Embedding covariate adjustments in tree-based automated machine learning for biomedical big data analyses.

BACKGROUND: A typical task in bioinformatics consists of identifying which features are associated with a target outcome of interest and building a predictive model. Automated machine learning (AutoML) systems such as the Tree-based Pipeline Optimization Tool (TPOT) constitute an appealing approach to this end. However, in biomedical data, there are often baseline characteristics of the subjects in a study or batch effects that need to be adjusted for in order to better isolate the effects of the features of interest on the target. Thus, the ability to perform covariate adjustments becomes particularly important for applications of AutoML to biomedical big data analysis. RESULTS: We developed an approach to adjust for covariates affecting features and/or target in TPOT. Our approach is based on regressing out the covariates in a manner that avoids 'leakage' during the cross-validation training procedure. We describe applications of this approach to toxicogenomics and schizophrenia gene expression data sets. The TPOT extensions discussed in this work are available at https://github.com/EpistasisLab/tpot/tree/v0.11.1-resAdj . CONCLUSIONS: In this work, we address an important need in the context of AutoML, which is particularly crucial for applications to bioinformatics and medical informatics, namely covariate adjustments. To this end we present a substantial extension of TPOT, a genetic programming based AutoML approach. We show the utility of this extension by applications to large toxicogenomics and differential gene expression data. The method is generally applicable in many other scenarios from the biomedical field.

Evaluation of the possible association of body mass index and four metabolic gene polymorphisms with longevity in an Italian cohort: a role for APOE, eNOS and FTO gene polymorphisms.

Background: Longevity is considered the result of interactions between environmental and genetic factors.Aim: To investigate the possible association of body mass index and the frequencies of APOE, ACE, eNOS and FTO gene polymorphisms with longevity.Subjects and methods: In total, 1100 healthy volunteers aged 10-100 were recruited. Subjects were genotyped for APOE, ACE, eNOS and FTO gene polymorphisms. Data about height and weight were also collected. The sample was split into four age groups: 1-24, 25-49, 50-85 and 86-100 years.Results: Significant differences were found in BMI values between age groups. A significant decrease of the APOE4, eNOS 393 and FTO A and allele frequencies was observed in the 86-100 age group compared to the younger groups. For ACE gene, no significant differences were found in the allele frequencies between groups. A similar trend was also observed when the sample was subdivided into two main age groups: 1-85 and 86-100 years.Conclusion: This study provides evidence for a role of APOE, eNOS and FTO gene polymorphisms in longevity. It has been estimated that the number of centenarians worldwide will double each decade until 2100, making population data about gene polymorphisms relevant for further studies about longevity.

Induction of chromosomal aberrations and micronuclei by 2-hydroxy-4-methoxybenzophenone (oxybenzone) in human lymphocytes.

Oxybenzone or benzophenone-3 (2-hydroxy-4-methoxybenzophenone; BP-3) is a filter used in a variety of personal care products for protection of human skin and hair from damage by ultraviolet radiation. BP-3 is suspected to exhibit endocrine disruptive properties. Indeed, it was found to be able to interact with the endocrine system causing alteration of its homeostasis, with consequent adverse health effects. Moreover, it is ubiquitously present in the environment, mostly in aquatic ecosystems, with consequent risks to the health of aquatic organisms and humans. In the present study, we analyzed the cytogenetic effects of BP-3 on human lymphocytes using in vitro chromosomal aberrations and micronuclei assays. Blood samples were obtained from five healthy Italian subjects. Lymphocyte cultures were exposed to five concentrations of BP-3 (0.20, 0.10, 0.05, 0.025, and 0.0125 µg/mL) for 24 and 48 h (for chromosomal aberrations and micronuclei tests, respectively). The concentration of 0.10 µg/mL represents the acceptable/tolerable daily intake reference dose established by European Union, whereas 0.20, 0.05, 0.025, and 0.0125 µg/mL represent multiple and sub-multiple of this concentration value. Our results reported cytogenetic effects of BP-3 on cultured human lymphocytes in terms of increased micronuclei and chromosomal aberrations' frequencies at all tested concentrations, including concentrations lower than those established by European Union. Vice versa, after 48-h exposure, a significant reduction of the cytokinesis-block proliferation index value in cultures treated with BP-3 was not observed, indicating that BP-3 does not seem to produce effects on the proliferation/mitotic index when its concentration is equal to or less than 0.20 µg/mL.

In vitro evaluation of genomic damage induced by glyphosate on human lymphocytes.

Glyphosate is an important broad-spectrum herbicide used in agriculture and residential areas for weed and vegetation control, respectively. In our study, we analyzed the in vitro clastogenic and/or aneugenic effects of glyphosate by chromosomal aberrations and micronuclei assays. Human lymphocytes were exposed to five glyphosate concentrations: 0.500, 0.100, 0.050, 0.025, and 0.0125 µg/mL, where 0.500 µg/mL represents the established acceptable daily intake value, and the other concentrations were tested in order to establish the genotoxicity threshold for this compound. We observed that chromosomal aberration (CA) and micronuclei (MNi) frequencies significantly increased at all tested concentrations, with exception of 0.0125 µg/mL. Vice versa, no effect has been observed on the frequencies of nuclear buds and nucleoplasmic bridges, with the only exception of 0.500 µg/mL of glyphosate that was found to increase in a significant manner the frequency of nucleoplasmic bridges. Finally, the cytokinesis-block proliferation index and the mitotic index were not significantly reduced, indicating that glyphosate does not produce effects on the proliferation/mitotic index at the tested concentrations.

Genomic damage induced by the widely used fungicide chlorothalonil in peripheral human lymphocytes.

Chlorothalonil is an important broad spectrum fungicide widely used in agriculture, silviculture, and urban settings. As a result of its massive use, chlorothalonil was found in all environmental matrices, with consequent risks to the health of terrestrial and aquatic organisms, as well as for humans. We analyzed the effects of chlorothalonil on human lymphocytes using in vitro chromosomal aberrations (CAs) and micronuclei (MNi) assays. Lymphocytes were exposed to five concentrations of chlorothalonil: 0.600 µg/mL, 0.060 µg/mL, 0.030 µg/mL, 0.020 µg/mL, and 0.015 µg/mL, where 0.020 and 0.600 µg/mL represent the ADI and the ARfD concentration values, respectively, established by FAO/WHO for this compound; 0.030 and 0.060 µg/mL represent intermediate values of these concentrations and 0.015 µg/mL represents the ADI value established by the Canadian health and welfare agency. We observed cytogenetic effects of chlorothalonil on cultured human lymphocytes in terms of increased CAs and MNi frequencies at all tested concentrations, including the FAO/WHO ADI and ARfD values of 0.020 and 0.600 µg/mL, respectively, but with exception of the Canadian ADI value of 0.015 µg/mL. Finally, no sexes differences were found in the levels of CAs and MNi induced by different chlorothalonil concentrations. Similarly, the mitotic index and the cytokinesis-block proliferation index did not show any significant effect on the proliferative capacity of the cells, although at the chlorothalonil concentration of 0.600 µg/mL the P-values of both indices were borderline.