An HLA-DR3 association with membranous nephropathy (MN) was described in 1979 and additional evidence for a genetic component to MN was suggested in 1984 in reports of familial MN. In 2009, a ...pathogenic autoantibody was identified against the phospholipase A2 receptor 1 (PLA2R1). Here we discuss the genetic studies that have proven the association of human leucocyte antigen class II and PLA2R1 variants and disease in MN. The common variants in PLA2R1 form a haplotype that is associated with disease incidence. The combination of the variants in both genes significantly increases the risk of disease by 78.5-fold. There are important genetic ethnic differences in MN. Disease outcome is difficult to predict and attempts to correlate the genetic association to outcome have so far not been helpful in a reproducible manner. The role of genetic variants may not only extend beyond the risk of disease development, but can also help us understand the underlying molecular biology of the PLA2R1 and its resultant pathogenicity. The genetic variants identified thus far have an association with disease and could therefore become useful biomarkers to stratify disease risk, as well as possibly identifying novel drug targets in the near future.
Class 2 HLA and PLA2R1 alleles are exceptionally strong genetic risk factors for membranous nephropathy (MN), leading, through an unknown mechanism, to a targeted autoimmune response. Introgressed ...archaic haplotypes (introduced from an archaic human genome into the modern human genome) might influence phenotypes through gene dysregulation. Here, we investigated the genomic region surrounding the PLA2R1 gene. We reconstructed the phylogeny of Neanderthal and modern haplotypes in this region and calculated the probability of the observed clustering being the result of introgression or common descent. We imputed variants for the participants in our previous genome-wide association study and we compared the distribution of Neanderthal variants between MN cases and controls. The region associated with the lead MN risk locus in the PLA2R1 gene was confirmed and showed that, within a 507 kb region enriched in introgressed sequence, a stringently defined 105 kb haplotype, intersecting the coding regions for PLA2R1 and ITGB6, is inherited from Neanderthals. Thus, introgressed Neanderthal haplotypes overlapping PLA2R1 are differentially represented in MN cases and controls, with enrichment In controls suggesting a protective effect.
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Background: Epithelial-mesenchymal transition (EMT) is a complex process, in which epithelial cells acquire the characteristics of invasive mesenchymal cells. EMT has been implicated in cancer ...progression and metastasis as well as the formation of many tissues and organs during development.
Aim: The aim of the study was to ascertain the role of hypoxia-mediated signaling pathways influencing EMT and angiogenesis in progression of oral submucous fibrosis (OSMF).
Materials and Methods: Evaluation of the immunoexpression of alpha-smooth muscle actin (α-SMA), E-cadherin, vimentin, and factor VIII receptor antigen in OSMF and oral squamous cell carcinoma (OSCC) arising from OSMF was done. Differences between the different variables were analyzed using ANOVA test and Pearson's Chi-square test, and Mann-Whitney test was also calculated.
Results: The mean α-SMA positive myofibroblasts increased from Group 1 (OSMF) to Group 2 (OSCC), especially those in the deeper connective tissue stroma. The mean labeling index of vimentin and mean vessel density immunoexpression was more in Group 2 (OSCC) as compared to Group 1 (OSMF). Mean α-SMA correlated negatively with E-cadherin expression and positively with vimentin and factor VIII immunoexpression. E-cadherin expression correlated negatively with factor VIII and positively with Vimentin expression.
Conclusions: The molecular mechanisms responsible for the development of OSCC in patients with OSMF require unification of multiple progressive pathogenetic mechanisms involved in the progression of the disease.
Cells use complex signaling systems to constantly detect environmental changes, relay extracellular information from the cell membrane to the nucleus, and drive cell responses, such as transcription. ...The ability of each single cell to dynamically respond to changes in its environment is the basis for healthy, functioning, multicellular beings. Diseases often arise from dysregulated signaling, and our ability to manipulate cell responses, that stems from our growing understanding of signaling processes, is often the basis for disease treatments. Computational approaches can complement experimental studies of cellular systems, allowing us to formalize our growing body of knowledge of cellular biochemistry. Mechanistic modeling provides a natural framework to describe and simulate complex systems with many system components and causal interactions that often lead to non-intuitive emergent behavior, lending itself well to the analysis of signaling systems. Statistical approaches can complement mechanistic modeling by enabling an analysis of complex input-output relationships in the data, providing insight into how cells translate input environmental cues into output responses, even when the underlying mechanisms are only partially understood. In this thesis, we explore both mechanistic and statistical approaches and address several challenges in modeling signaling processes within a cell, and signaling heterogeneity between cells, using the NF-kB pathway as a model system. First, we evaluate methods to efficiently determine numerical values of model parameters, enabling model simulations that are comparable to experimental data. Second, we develop methods to identify reduced submodels that are sufficient for the data, highlighting simple mechanisms that drive emergent behavior. Third, switching gears to study signaling heterogeneity, we use information-theoretic analyses to evaluate the capabilities of the NF-kB pathway to effectively transduce cytokine dosage information in the presence of biochemical noise. Finally, we develop a framework to calibrate mechanistic models to heterogeneous signaling data, enabling simulation-based analyses of single-cell signaling capabilities.
Background: IFN-gamma and natural killer (NK) cells have been considered the most effective cells in the combat of cancer, contributing to better prognosis and longer survival. The aim of the study ...was to analyze and correlate the CD 57 immunopositive NK cell-mediated Interferon-γ pathway in regulating immune mechanisms in Oral Squamous Cell Carcinoma.
Materials and Methodology: The study sample was composed of a total of 40 cases of histopathologically confirmed cases of Oral Squamous cell carcinoma (OSCC). Clinical data such as age, gender, habit history, signs and symptoms, and TNM staging were obtained for each case. The biopsy specimens of the cases obtained were fixed with 10% neutral buffered formalin and processed and embedded in paraffin wax. 3-4 μ thick sections were taken for hematoxylin and eosin staining and immunohistochemistry procedure. A saliva sample was collected from each patient and stored at 20 degree Celsius for estimation of salivary interferon-gamma levels using the sandwich ELISA technique.
Results: CD 57 NK cells quantitative assessment was significantly associated with tumor budding, cell nest size, the pattern of invasion, lymphocytic host response, NK cell morphology, Depth of invasion, and Tumor thickness. The ratio of CD 57 immunopositive NK cells to salivary IFN-γ levels showed a significant association with histopathological grades, tumor size, and lymph node status.
Conclusion: Adoptive cellular transfer therapy with NK cells has been advocated in both experimental models and clinical trials in treating hematopoietic malignancies. The strategy is based on reviving the patient innate immune surveillance and control of tumor invasion by the infusion of activated NK cells. The IFN-gamma and NK cell infiltration in oral squamous cell carcinoma might show a distinctive tumor microenvironment with a favorable local cytotoxic immune response against neoplastic cells.
Abstract
Background
As part of its End TB strategy, the WHO has identified the need for non-sputum-based diagnostics that meet target product profiles (TPP) of 90% sensitivity and 70% specificity for ...diagnosis of Active TB (ATB) and 75% sensitivity and specificity for predicting progression from Latent TB (LTB) to ATB. The successful translation of a 3-gene blood-based signature, identified using diverse datasets, into a prototype point-of-care diagnostic, that meets the WHO TPPs, has demonstrated the power of integrating large amounts of heterogeneous data to identify generalizable disease signatures. We hypothesized that integration of more diverse datasets, comprising patients with ATB or other inflammatory lung diseases, would identify novel, robust signatures, for diagnosing ATB and predicting progression from LTB to ATB, that meet the WHO TPPs.
Methods
Using multi-cohort analyses, we integrated and analyzed data from 3,615 peripheral blood samples, in 49 publicly available transcriptomic datasets (discovery cohorts), from healthy controls and patients with LTB, ATB, and other diseases (COPD, viral infections, sarcoidosis, etc.). We used data from (1) 3,836 blood samples in 28 retrospective datasets and (2) 360 prospectively collected blood samples, from a household contact study in Moldova, as validation cohorts.
Results
Using the discovery cohorts we identified a 9-gene signature for diagnosing ATB patients from healthy controls, or individuals with LTB or other diseases. The signature achieved 90% sensitivity and 82% specificity in retrospective validation (Figure 1A) and 90% sensitivity and 69% specificity in the prospective cohort from Moldova (Figure 1B). In a longitudinal cohort of adolescents, the 9-gene signature predicted progression from LTB to ATB up to 1 year prior to sputum conversion with 76% sensitivity and 83% specificity (Figure 1C). Finally, the signature predicted prolonged lung inflammation post-treatment in the Catalysis Treatment Response Cohort (Figure 1D).
9-gene TB signature validates in independent retrospective and prospective cohorts.
(A) ROC curves for comparing ATB vs. all other samples (All), or individually comparing ATB vs. Healthy, LTBI or Other Disease (OD) samples in independent retrospective validation and (B) a prospective Moldova cohort. (C) ROC curves comparing progressor and non-progressor samples collected at different time points in the Adolescent Cohort Study (ACS), for the 9-gene signature in solid lines and a previous 3-gene signature in dashed lines, (D) Distribution of the 9-gene score at different time points post-treatment in the Catalysis Treatment Response Cohort Study, for individuals with persistent lung inflammation at 24 weeks compared with those who had clear lungs at 24 weeks.
Conclusion
Overall, the 9-gene signature meets the WHO TPPs required for the End TB strategy.
Disclosures
Purvesh Khatri, PhD, Cepheid, Inc.: Advisor/Consultant|Inflammatix, Inc.: Advisor/Consultant|Inflammatix, Inc.: Inflammatix is in negotiations to license the 9-gene signature discussed here.|Inflammatix, Inc.: Stocks/Bonds.
Steroid-sensitive nephrotic syndrome (SSNS), the most common form of nephrotic syndrome in childhood, is considered an autoimmune disease with an established classic HLA association. However, the ...precise etiology of the disease is unclear. In other autoimmune diseases, the identification of loci outside the classic HLA region by genome-wide association studies (GWAS) has provided critical insights into disease pathogenesis. Previously conducted GWAS of SSNS have not identified non-HLA loci achieving genome-wide significance.
In an attempt to identify additional loci associated with SSNS, we conducted a GWAS of a large cohort of European ancestry comprising 422 ethnically homogeneous pediatric patients and 5642 ethnically matched controls.
The GWAS found three loci that achieved genome-wide significance, which explain approximately 14% of the genetic risk for SSNS. It confirmed the previously reported association with the HLA-DR/DQ region (lead single-nucleotide polymorphism SNP rs9273542,
=1.59×10
; odds ratio OR, 3.39; 95% confidence interval 95% CI, 2.86 to 4.03) and identified two additional loci outside the HLA region on chromosomes 4q13.3 and 6q22.1. The latter contains the calcium homeostasis modulator family member 6 gene
(previously called
).
is implicated in immune response modulation; the lead SNP (rs2637678,
=1.27×10
; OR, 0.51; 95% CI, 0.44 to 0.60) exhibits strong expression quantitative trait loci effects, the risk allele being associated with lower lymphocytic expression of
.
Because
is implicated in regulating the immune response to infection, this may provide an explanation for the typical triggering of SSNS onset by infections. Our results suggest that a genetically conferred risk of immune dysregulation may be a key component in the pathogenesis of SSNS.
Background
Idiop athic nephrotic syndrome (INS) is classified in children according to response to initial corticosteroid therapy into steroid-sensitive (SSNS) and steroid-resistant nephrotic ...syndrome (SRNS), and in adults according to histology into minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS). However, there is well-recognised phenotypic overlap between these entities. Genome-wide association studies (GWAS) have shown a strong association between SSNS and variation at HLA, suggesting an underlying immunological basis. We sought to determine whether a risk score generated from genetic variants associated with SSNS could be used to gain insight into the pathophysiology of INS presenting in other ways.
Methods
We developed an SSNS genetic risk score (SSNS-GRS) from the five variants independently associated with childhood SSNS in a previous European GWAS. We quantified SSNS-GRS in independent cohorts of European individuals with childhood SSNS, non-monogenic SRNS, MCD, and FSGS, and contrasted them with SSNS-GRS quantified in individuals with monogenic SRNS, membranous nephropathy (a different immune-mediated disease-causing nephrotic syndrome), and healthy controls.
Results
The SSNS-GRS was significantly elevated in cohorts with SSNS, non-monogenic SRNS, MCD, and FSGS compared to healthy participants and those with membranous nephropathy. The SSNS-GRS in all cohorts with non-monogenic INS were also significantly elevated compared to those with monogenic SRNS.
Conclusions
The shared genetic risk factors among patients with different presentations of INS strongly suggests a shared autoimmune pathogenesis when monogenic causes are excluded. Use of the SSNS-GRS, in addition to testing for monogenic causes, may help to classify patients presenting with INS.
Graphical abstract
A higher resolution version of the Graphical abstract is available as
Supplementary information
Although cytokine-dependent dynamics of nuclear factor κB (NF-κB) are known to encode information that regulates cell fate decisions, it is unclear whether single-cell responses are switch-like or ...encode more information about cytokine dose. Here, we measure the dynamic subcellular localization of NF-κB in response to a range of tumor necrosis factor (TNF) stimulation conditions to determine the prevailing mechanism of single-cell dose discrimination. Using an information theory formalism that accounts for signaling dynamics and non-responsive cell subpopulations, we find that the information transmission capacity of single cells exceeds that predicted from a switch-like response. Instead, we observe that NF-κB dynamics within single cells contain sufficient information to encode multiple, TNF-dependent cellular states, and have an activation threshold that varies across the population. By comparing single-cell responses to an internal, experimentally observed reference, we demonstrate that cells can grade responses to TNF across several orders of magnitude in concentration. This suggests that cells contain additional control points to fine-tune their cytokine responses beyond the decision to activate.
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•Graded dose discrimination provides more control points to fine-tune cell responses•Mechanisms of dose discrimination cannot be determined from population data•Information transmission capacity varies between subpopulations of isogenic cells•Single cells are capable of graded responses with respect to cytokine strength
Using an information theory framework and single-cell data, Zhang et al. set out to distinguish between different mechanisms for activation of intracellular signals. They show that heterogeneity between cellular states can lead to underestimates in the capabilities of single cells. In contrast with a switch-like model for pathway activation, they find that single cells can encode multiple levels of response that increase with stimulation strength.
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