Evaluation of TLR2, TLR4, and TOLLIP polymorphisms for their role in tuberculosis susceptibility

Autophagopathies: from autophagy gene polymorphisms to precision medicine for human diseases

At a time when complex diseases affect globally 280 million people and claim 14 million lives every year, there is an urgent need to rapidly increase our knowledge into their underlying etiologies. Though critical in identifying the people at risk, the causal environmental factors (microbiome and/or pollutants) and the affected pathophysiological mechanisms are not well understood. Herein, we consider the variations of autophagy-related (ATG) genes at the heart of mechanisms of increased susceptibility to environmental stress. A comprehensive autophagy genomic resource is presented with 263 single nucleotide polymorphisms (SNPs) for 69 autophagy-related genes associated with 117 autoimmune, inflammatory, infectious, cardiovascular, neurological, respiratory, and endocrine diseases. We thus propose the term 'autophagopathies' to group together a class of complex human diseases the etiology of which lies in a genetic defect of the autophagy machinery, whether directly related or not to an abnormal flux in autophagy, LC3-associated phagocytosis, or any associated trafficking. The future of precision medicine for common diseases will lie in our ability to exploit these ATG SNP x environment relationships to develop new polygenetic risk scores, new management guidelines, and optimal therapies for afflicted patients.Abbreviations: ATG, autophagy-related; ALS-FTD, amyotrophic lateral sclerosis-frontotemporal dementia; ccRCC, clear cell renal cell carcinoma; CD, Crohn disease; COPD, chronic obstructive pulmonary disease; eQTL, expression quantitative trait loci; HCC, hepatocellular carcinoma; HNSCC, head and neck squamous cell carcinoma; GTEx, genotype-tissue expression; GWAS, genome-wide association studies; LAP, LC3-associated phagocytosis; LC3-II, phosphatidylethanolamine conjugated form of LC3; LD, linkage disequilibrium; LUAD, lung adenocarcinoma; MAF, minor allele frequency; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NSCLC, non-small cell lung cancer; OS, overall survival; PtdIns3K CIII, class III phosphatidylinositol 3 kinase; PtdIns3P, phosphatidylinositol-3-phosphate; SLE, systemic lupus erythematosus; SNPs, single-nucleotide polymorphisms; mQTL, methylation quantitative trait loci; ULK, unc-51 like autophagy activating kinase; UTRs, untranslated regions; WHO, World Health Organization.

Association of Three SNPs Loci of Kelch-Like-ECH-Associated Protein 1 (Human) with Tuberculosis in Chinese Han Population

Purpose

Progression from latent tuberculosis infection (LTBI) to pulmonary TB (PTB) was associated with genetic polymorphisms, but there were limited genetic polymorphism data on LTBI and PTB. We aimed at examining the association of KEAP1 gene polymorphisms with PTB and LTBI.

Patients and Methods

PTB patients and close contacts of PTB patients were recruited from West China Hospital of Sichuan University. After obtaining the patient’s consent, we draw 2–5mL of blood from the patient’s peripheral vein. Tag-SNPs of KEAP1 were chosen according to previous studies. The genotyping was done by improved multiplex ligase detection reaction (iMLDR). We used logistic regression to assess the association of SNPs with LTBI/PTB, with sex and age as covariates.

Results

A total of 209 PTB patients, 201 LTBI, and 204 HCS were included in the present study. Three Tag-SNPs were included in this study. Significant association was found for KEAP1 rs1048290 between LTBI and HCS. Compared with the KEAP1 rs1048290 CC genotype, genotype GC had an 38% decreased risk for development LTBI (P = 0.043, OR = 0.62, 95% CI: 0.039–0.98). We also found that SNPs in KEAP1 were significantly related to PTB compared to LTBI. Compared with the rs11545829G allele, allele A had an 30% decreased risk for development PTB (P = 0.034, OR = 0.70, 95% CI: 0.51–0.97). We also found the rs11668429 polymorphism was related to PTB. Compared with TT, GT had a significantly increased risk of LTBI developing into PTB (P = 0.041, OR = 1.68, 95% CI: 1.02–2.77).

Conclusion

Our study suggested that KEAP1 polymorphisms were significantly related to susceptibility to PTB and LTBI subjects.

Toll-interacting protein polymorphisms in viral bronchiolitis outcomes

BACKGROUND

Toll-interacting protein is a key factor in regulating innate immunity responses via gatekeeping Toll-like receptors. Genetic variance in innate immunity has been linked with susceptibility to infections. Children with viral bronchiolitis in infancy are at increased risk of later asthma. The aim was to evaluate the role of toll-interacting protein gene point mutations in severity of bronchiolitis and subsequent risk of asthma.

METHODS

Infants less than 6 months old were recruited during hospitalization due to bronchiolitis. In all, 166 children were prospectively followed up to age of 1.5, 6, and 11 years. Clinical data on viral etiology and severity markers, and further post-bronchiolitis asthma and lung function outcomes were compared with genetic differences in two single-nucleotide point mutations rs116938768 and rs5743854 in the toll-interacting protein gene.

RESULTS

Toll-interacting protein rs116938768 or rs5743854 did not show significant associations with severity markers or viral etiology of bronchiolitis. Follow-up data on current asthma or lung function at 6 or 11 years of age after bronchiolitis were not associated with the investigated mutations.

CONCLUSION

Toll-interacting protein gene point mutations in rs116938768 or rs5743854 were not involved with the clinical course of viral bronchiolitis in early infancy, and did not predict post-bronchiolitis asthma or lung function reduction by the age of 11 years.

Toll-Interacting Protein in Pulmonary Diseases. Abiding by the Goldilocks Principle

TOLLIP (Toll-interacting protein) is an intracellular adaptor protein with diverse actions throughout the body. In a context- and cell type–specific manner, TOLLIP can function as an inhibitor of inflammation and endoplasmic-reticulum stress, an activator of autophagy, or a critical regulator of intracellular vacuole trafficking. The distinct functions of this protein have been linked to innate immune responses and lung epithelial-cell apoptosis. TOLLIP genetic variants have been associated with a variety of chronic lung diseases, including idiopathic pulmonary fibrosis, asthma, and primary graft dysfunction after lung transplantation, and with infections, such as tuberculosis, Legionella pneumonia, and respiratory viruses. TOLLIP exists in a delicate homeostatic balance, with both positive and negative effects on the trajectory of pulmonary diseases. This translational review summarizes the genetic and molecular associations that link TOLLIP to the development and progression of noninfectious and infectious pulmonary diseases. We highlight current limitations of in vitro and in vivo models in assessing the role of TOLLIP in these conditions, and we describe future approaches that will enable a more nuanced exploration of the role of TOLLIP in pulmonary conditions. There has been a surge in recent research evaluating the role of this protein in human diseases, but critical mechanistic pathways require further exploration. By understanding its biologic functions in disease-specific contexts, we will be able to determine whether TOLLIP can be therapeutically modulated to treat pulmonary diseases.

Genetic association of TOLLIP gene polymorphisms and HIV infection: a case-control study

Background

Previous studies have indicated that host genetic factors play an essential role in immunity to human immunodeficiency virus (HIV) infection. We aimed to investigate the association between the toll-interacting protein (TOLLIP) and mannose-binding lectin 2 (MBL2) genes and HIV infection susceptibility among Chinese Han patients.

Methods

This is a case-control study. A total of 435 HIV-infected patients and 1013 seronegative healthy individuals were recruited. DNA was extracted from whole blood. Two SNPs in the MBL2 gene (rs7096206 and rs1800450) and three SNPs in the TOLLIP gene (rs5743899, rs3750920, and rs5743867) were selected and genotyped using a SNPscan Kit (Cat#: G0104, Genesky Biotechnologies Inc., Shanghai, China). Odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated using unconditional binary logistic regression.

Results

A significant association between the minor alleles rs5743899 (C allele) and rs5743867 (G allele) in the TOLLIP gene and susceptibility to HIV infection was found in this study after adjusting for age and sex (P^a = 0.011 and < 0.001, respectively). The rs5743867 in the TOLLIP gene was significantly associated with the risk of HIV infection in dominant, recessive, and additive models when adjusted for age and sex (P^a < 0.05). No significant association was found between MBL2 gene polymorphisms and HIV infection.

Conclusion

Our study found a statistically significant association between the two SNPs (rs5743867 and rs5743899) in the TOLLIP gene and susceptibility to HIV infection in a Chinese Han population.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06303-4.

Polymorphisms of TLR2, TLR4 and TOLLIP and tuberculosis in two independent studies

Genetic polymorphisms for tuberculosis (TB) susceptibility have been researched by some studies, but few have studied multiple innate immunity genes associated with TB. Evidence suggests that the toll-like receptor 2, 4 (TLR2, TLR4) and toll interacting protein (TOLLIP) may be associated with TB susceptibility. In this self-validated study, we explored the association between common single nucleotide polymorphisms (SNPs) of TLR2, TLR4 and TOLLIP in the Chinese Han and Tibetan populations. A SNPscan™ method was used to genotype SNPs in the three genes. Multiple logistic regression adjusted by sex and age was used to detect the association between SNPs and TB. In TLR2, rs1898830 was associated with decreased risk against TB in the Chinese Han population, which was validated in the Tibetan population. In TLR4, rs11536889 was a protective factor for TB in the Tibetan population, but not in the Han population. Additionally, in the Tibetan population, we also found that the frequency of genotypes of TOLLIP rs11536889 differs significantly between TB patients and controls. We found rs1898830 in TLR2 was associated with TB susceptibility in both Chinese Han and Tibetan populations while rs11536889 in TLR4 and rs3750920 in TOLLIP were protective factors against TB in the Tibetan population.

Biomarkers of treatment success in fully sensitive pulmonary tuberculosis patients: a multicenter longitudinal study

Aim: Novel biomarkers that are able to accurately monitor tuberculosis (TB) treatment effectiveness are needed to adjust therapy and identify a need for a regimen change. Materials & methods: In our study, conducted on a cohort comprising 100 pulmonary TB patients, we analyzed the role of plasma cytokines and Toll-like receptors expression as biomarkers of treatment response. Results: Changes in toll-interacting protein (TOLLIP) and lymphocyte antigen 96 (LY96) gene expression as well as nine cytokine levels over the first 2 months were significantly associated with successful treatment outcome. Successful treatment was associated with higher serum concentration of Toll-like receptor-2. Conclusion: Our results suggest that differential expression of specific effector molecules and dynamics of selected cytokines may help to identify those responding to TB treatment early.

Pathogenic Single Nucleotide Polymorphisms on Autophagy-Related Genes

In recent years, the study of single nucleotide polymorphisms (SNPs) has gained increasing importance in biomedical research, as they can either be at the molecular origin of a determined disorder or directly affect the efficiency of a given treatment. In this regard, sequence variations in genes involved in pro-survival cellular pathways are commonly associated with pathologies, as the alteration of these routes compromises cellular homeostasis. This is the case of autophagy, an evolutionarily conserved pathway that counteracts extracellular and intracellular stressors by mediating the turnover of cytosolic components through lysosomal degradation. Accordingly, autophagy dysregulation has been extensively described in a wide range of human pathologies, including cancer, neurodegeneration, or inflammatory alterations. Thus, it is not surprising that pathogenic gene variants in genes encoding crucial effectors of the autophagosome/lysosome axis are increasingly being identified. In this review, we present a comprehensive list of clinically relevant SNPs in autophagy-related genes, highlighting the scope and relevance of autophagy alterations in human disease.

Toll-interacting protein impacts on inflammation, autophagy, and vacuole trafficking in human disease

Toll-interacting protein (TOLLIP) is a ubiquitous intracellular adaptor protein involved in multiple intracellular signaling pathways. It plays a key role in mediating inflammatory intracellular responses, promoting autophagy, and enabling vacuole transport within the cell. TOLLIP is being increasingly recognized for its role in disease pathophysiology through involvement in these three primary pathways. Recent research also indicates that TOLLIP is involved in nuclear-cytoplasmic transfer, although this area requires further exploration. TOLLIP is involved in the pathophysiologic pathways associated with neurodegenerative diseases, pulmonary diseases, cardiovascular disease, inflammatory bowel disease, and malignancy. We postulate that TOLLIP plays an integral role in the disease pathophysiology of other conditions involved in vacuole trafficking and autophagy. We suggest that future research in this field should investigate the role of TOLLIP in the pathogenesis of these multiple conditions. This research has the potential to inform disease mechanisms and identify novel opportunities for therapeutic advances in multiple disease processes.

Genetic Polymorphisms of IFNG and IFNGR1 with Latent Tuberculosis Infection

Previous studies indicated that single-nucleotide polymorphisms (SNPs) of interferon gamma (IFNG) and IFNG receptor 1 (IFNGR1) may be involved in the pathogenesis of pulmonary tuberculosis (PTB) in different populations. In order to further explore the results in a Chinese Han population, this study was designed to investigate potential associations between the polymorphisms in IFNG and IFNGR1 and susceptibility to latent tuberculosis infection (LTBI) and/or PTB in a Chinese Han population. A total of 209 PTB, 173 LTBI, and 183 healthy control subjects (HCS) were enrolled in our study. Genotyping was conducted using an improved multiplex ligase detection reaction (iMLDR). We performed a logistic regression including sex and age as covariates to test the effect of alleles/genotypes on LTBI and/or TB. All six markers studied in IFNG and IFNGR1 conformed to the Hardy-Weinberg equilibrium (HWE). The IFNG rs1861494 was significantly associated with LTBI in recessive model, and the CC+CT genotype decreased risk of LTBI by 50% (P = 0.046, OR = 0.50, 95%CI: 0.25-0.99). The IFNGR1 rs2234711 was significantly associated with LTBI, and allele A increased the risk of LTBI by 55% (P = 0.047, OR = 1.55, 95%CI: 1.00-2.40). In the present study, we found that IFNG and IFNGR1 polymorphisms were associated with LTBI.

Genetic predisposition for medication-related osteonecrosis of the jaws: a systematic review

The purpose of this study was to assess whether genetic variation is a predictor for the development of medication-related osteonecrosis of the jaws (MRONJ) in patients receiving bisphosphonate therapy for various conditions. A systematic review based on the PRISMA guidelines was performed. A search strategy was developed. Comprehensive searches of major databases were conducted for studies published January 2003 through July 2018. The PICOS strategy was used to develop the inclusion criteria. The analysis in each study was performed primarily using single nucleotide polymorphism (SNP) frequency mean values and odds ratios between cases and controls. A total of 3301 patients were enrolled in the 15 included studies (two genome-wide association studies, n = 1877; 10 candidate gene studies, n = 1195; three whole genome/whole exome studies, n = 229). Multiple myeloma was the most prevalent primary disease (54.8%). Zoledronate was prescribed in 68.8% of patients. No one SNP was definitively identified as a risk factor for the development of MRONJ. To date, studies have failed to show a single gene as a risk factor for MRONJ. Heterogeneity of case and control populations may be contributory. Next generation sequencing studies may help elucidate the role and interplay of genetic events in the development of MRONJ.

Toll-like receptor-4 299Gly allele is associated with Guillain-Barré syndrome in Bangladesh

Objective

TLR4 plays an important role in the pathogenesis of Guillain‐Barré syndrome (GBS). The relationships between TLR4 polymorphisms and susceptibility to GBS are poorly understood. We investigated the frequency and assessed the association of two single nucleotide polymorphisms (SNPs) in the extracellular domain of TLR4 (Asp299Gly and Thr399Ile) with disease susceptibility and the clinical features of GBS in a Bangladeshi cohort.

Methods

A total of 290 subjects were included in this study: 141 patients with GBS and 149 unrelated healthy controls. The TLR4 polymorphisms Asp299Gly and Thr399Ile were genotyped using polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) assay.

Results

The minor 299Gly allele was significantly associated with GBS susceptibility (P = 0.0137, OR = 1.97, 95% CI = 1.17–3.31), and was present at a significantly higher frequency in patients with the acute motor axonal neuropathy (AMAN) subtype of GBS (P = 0.0120, OR = 2.37, 95% CI = 1.26–4.47) than acute inflammatory demyelinating polyneuropathy (AIDP) subtype (P = 0.961, OR = 1.15, 95% CI = 0.38–3.48); when compared to healthy controls. The genotype frequency of the Asp299Gly polymorphism was not significantly different between patients with GBS and healthy controls. The Asp299‐Thr399 haplotype was associated with a significantly lower risk of developing GBS (P = 0.0451, OR = 0.63, 95% CI = 0.40–0.99). No association was observed between the Thr399Ile polymorphism and GBS disease susceptibility.

Interpretation

The TLR4 minor 299Gly allele was associated with increased susceptibility to GBS and the axonal GBS subtype in the Bangladeshi population. However, no associations were observed between the genotypes of the Asp299Gly and Thr399Ile SNPs and antecedent C. jejuni infection or disease severity in Bangladeshi patients with GBS.

Polymorphisms of cytokine genes and tuberculosis in two independent studies

Cytokine gene single nucleotide polymorphisms (SNPs) can influence cytokine levels, which may be associated with tuberculosis (TB) susceptibility. There is evidence that interleukin 1B (IL1B), tumor necrosis factor-alpha (TNF-alpha), and IL6 may be involved in the progression of TB. Using a self-validating case-control design, we selected eleven functional SNPs in IL1B, TNF and IL6 to detect their association with TB in Chinese Han and Tibetan populations. The associations between SNPs and TB were estimated by computing the odds ratios (ORs) and 95% confidence intervals (95% CI) using logistic regression analyses. We found that the IL1B rs16944 polymorphism was associated with decreased risk of TB in the two studies. The G allele at rs2069837 of IL6 was significantly more common in controls than in TB patients in the Han population. Moreover, TNF rs1799964 and rs1800630 were risk factors for susceptibility to TB, which were validated in the Chinese Tibetan population. In addition, TNF rs1799724 and rs1800629 were associated with TB, but only in the Tibetan population. In conclusion, SNPs of the IL1B and TNF gene were associated with TB susceptibility in Chinese Han and Tibetan populations. IL6 polymorphism may be considered as a protective factor for TB in the Chinese Han population, but not the Tibetan population.

Polymorphisms in the STAT4 gene and tuberculosis susceptibility in a Chinese Han population

The signal transducer and activator of transcription 4 (STAT4) gene encodes a transcription factor that transmits signals induced by several cytokines which play critical roles in the development of autoimmune and chronic inflammatory diseases. We performed an association study between STAT4 single nucleotide polymorphisms (SNPs) and tuberculosis (TB). 624 TB cases and 598 healthy controls were studied to compare allele/genotype frequencies of 4 SNPs in STAT4. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using logistic regression. Genotyping was performed with the Sequenom MassARRAY SNP genotyping platform. Out of 4 SNPs tested in the study, rs4853542 allele A showed a 25% decreased risk of TB compared with allele G (P = 0.013, OR = 0.75, 95%CI: 0.60-0.94). However, it did not show significant differences under any genetic model after Bonferroni correction. No association was found for the other 3 SNPs with TB. In subgroup analyses, the protective effects of rs485342 allele A were stronger among younger subjects <25 years (P = 0.002, OR = 0.49, 95%CI: 0.31-0.76). Allele A of the rs4853542 polymorphism in STAT4 is not associated with TB susceptibility, but we demonstrated that rs4853542A allele decreased risk of TB in younger adults after Bonferroni correction.