Padmalatha S. Reddy

High bone mass in mice expressing a mutant LRP5 gene

A unique mutation in LRP5 is associated with high bone mass in man. Transgenic mice expressing this LRP5 mutation have a similar phenotype with high bone mass and enhanced strength. These results underscore the importance of LRP5 in skeletal regulation and suggest targets for therapies for bone disease.

Pathways Activated during Human Asthma Exacerbation as Revealed by Gene Expression Patterns in Blood

Background Asthma exacerbations remain a major unmet clinical need. The difficulty in obtaining airway tissue and bronchoalveolar lavage samples during exacerbations has greatly hampered study of naturally occurring exacerbations. This study was conducted to determine if mRNA profiling of peripheral blood mononuclear cells (PBMCs) could provide information on the systemic molecular pathways involved during asthma exacerbations. Methodology/Principal Findings Over the course of one year, gene expression levels during stable asthma, exacerbation, and two weeks after an exacerbation were compared using oligonucleotide arrays. For each of 118 subjects who experienced at least one asthma exacerbation, the gene expression patterns in a sample of peripheral blood mononuclear cells collected during an exacerbation episode were compared to patterns observed in multiple samples from the same subject collected during quiescent asthma. Analysis of covariance identified genes whose levels of expression changed during exacerbations and returned to quiescent levels by two weeks. Heterogeneity among visits in expression profiles was examined using K-means clustering. Three distinct exacerbation-associated gene expression signatures were identified. One signature indicated that, even among patients without symptoms of respiratory infection, genes of innate immunity were activated. Antigen-independent T cell activation mediated by IL15 was also indicated by this signature. A second signature revealed strong evidence of lymphocyte activation through antigen receptors and subsequent downstream events of adaptive immunity. The number of genes identified in the third signature was too few to draw conclusions on the mechanisms driving those exacerbations. Conclusions/Significance This study has shown that analysis of PBMCs reveals systemic changes accompanying asthma exacerbation and has laid the foundation for future comparative studies using PBMCs.

Dynamic Changes in the MicroRNA Expression Profile Reveal Multiple Regulatory Mechanisms in the Spinal Nerve Ligation Model of Neuropathic Pain

Neuropathic pain resulting from nerve lesions or dysfunction represents one of the most challenging neurological diseases to treat. A better understanding of the molecular mechanisms responsible for causing these maladaptive responses can help develop novel therapeutic strategies and biomarkers for neuropathic pain. We performed a miRNA expression profiling study of dorsal root ganglion (DRG) tissue from rats four weeks post spinal nerve ligation (SNL), a model of neuropathic pain. TaqMan low density arrays identified 63 miRNAs whose level of expression was significantly altered following SNL surgery. Of these, 59 were downregulated and the ipsilateral L4 DRG, not the injured L5 DRG, showed the most significant downregulation suggesting that miRNA changes in the uninjured afferents may underlie the development and maintenance of neuropathic pain. TargetScan was used to predict mRNA targets for these miRNAs and it was found that the transcripts with multiple predicted target sites belong to neurologically important pathways. By employing different bioinformatic approaches we identified neurite remodeling as a significantly regulated biological pathway, and some of these predictions were confirmed by siRNA knockdown for genes that regulate neurite growth in differentiated Neuro2A cells. In vitro validation for predicted target sites in the 3′-UTR of voltage-gated sodium channel Scn11a, alpha 2/delta1 subunit of voltage-dependent Ca-channel, and purinergic receptor P2rx ligand-gated ion channel 4 using luciferase reporter assays showed that identified miRNAs modulated gene expression significantly. Our results suggest the potential for miRNAs to play a direct role in neuropathic pain.

Mapping similarities in mTOR pathway perturbations in mouse lupus nephritis models and human lupus nephritis

IntroductionTreatment with sirolimus, a mammalian target of rapamycin (mTOR) inhibitor, has been shown to be efficacious in the MRL/lpr and NZB × NZW F1 mouse models of lupus nephritis, indicating a critical role for the mTOR pathway in both models. This type of demonstration of efficacy in animal models is usually a pre-requisite for advancement into clinical development. However, efficacy in an animal model often has not translated to the desired activity in the clinic. Therefore, a more profound understanding of the mechanistic similarities and differences between various animal models and human diseases is highly desirable.MethodsTranscriptional profiling was performed on kidneys from mice with lupus nephritis; from mice who had efficacious drug treatment; and from mice before they developed nephritis. Analysis of variance with false discovery rate adjusted to p < 0.05 and an average fold change of two or more was used to identify transcripts significantly associated with disease and response to therapy. Pathway analyses (using various bioinformatics tools) were carried out to understand the basis for drug efficacy in the mouse model. The relevance in human lupus of the pathways identified in the mouse model was explored using information from several databases derived from the published literature.ResultsWe identified a set of nephritis-associated genes in mouse kidney. Expression of the majority of these returned to asymptomatic levels on sirolimus treatment, confirming the correlation between expression levels and symptoms of nephritis. Network analysis showed that many of these nephritis genes are known to interact with the mTOR pathway. This led us to ask what human diseases are linked to the mTOR pathway. We constructed the mTOR pathway interactome consisting of proteins that interact with members of the mTOR pathway and identified a strong association between mTOR pathway genes and genes reported in the literature as being involved in human lupus.ConclusionsOur findings implicate the mTOR pathway as a critical contributor to human lupus. This broad pathway-based approach to understanding the similarities in, and differences between, animal models and human diseases may have broader utility.

Tofacitinib attenuates pathologic immune pathways in patients with psoriasis: A randomized phase 2 study

BACKGROUND Tofacitinib is an oral Janus kinase inhibitor being investigated for psoriasis. OBJECTIVE We sought to elucidate the molecular mechanisms underlying the clinical efficacy of tofacitinib in patients with psoriasis. METHODS Twelve patients with plaque psoriasis were randomized (3:1) to receive 10 mg of tofacitinib or placebo twice daily for 12 weeks. Biopsy specimens were taken from nonlesional (baseline) and lesional (baseline, days 1 and 3, and weeks 1, 2, 4, and 12) skin. Biopsy specimens were examined for psoriatic epidermal features (thickness, Ki67(+) keratinocytes and keratin 16 [KRT16] mRNA expression, and phosphorylated signal transducer and activator of transcription [pSTAT](+) nuclei) and T-cell and dendritic cell (DC) subsets by using immunohistochemistry, and mRNA transcripts were quantified by using a microarray. RESULTS In lesional skin keratinocyte pSTAT1 and pSTAT3 staining was increased at baseline but reduced after 1 day of tofacitinib (baseline, median of 1290 pSTAT1(+) cells/μm(2); day 1, median of 332 pSTAT1(+) cells/μm(2); and nonlesional, median of 155 pSTAT1(+) cells/μm(2)). Epidermal thickness and KRT16 mRNA expression were significantly and progressively reduced after days 1 and 3 of tofacitinib administration, respectively (eg, KRT16 decreased 2.74-fold, day 3 vs baseline, P = .016). Decreases in DC and T-cell numbers were observed after weeks 1 and 2, respectively. At week 4, significant decreases in IL-23/TH17 pathways were observed that persisted through week 12. Improvements in clinical and histologic features were strongly associated with changes in expression of psoriasis-related genes and reduction in IL-17 gene expression. CONCLUSIONS Tofacitinib has a multitiered response in patients with psoriasis: (1) rapid attenuation of keratinocyte Janus kinase/STAT signaling; (2) removal of keratinocyte-induced cytokine signaling, leading to reductions in pathologic DC and T-cell numbers to nonlesional levels; and (3) inhibition of the IL-23/TH17 pathway.

Evolutionary and biochemical differences between human and monkey acidic mammalian chitinases

Acidic mammalian chitinase (AMCase), an enzyme implicated in the pathology of asthma, is capable of chitin cleavage at a low pH optimum. The corresponding gene (CHIA) can be found in genome databases of a variety of mammals, but the enzyme properties of only the human and mouse proteins were extensively studied. We wanted to compare enzymes of closely related species, such as humans and macaques. In our attempt to study macaque AMCase, we searched for CHIA-like genes in human and macaque genomes. We found that both genomes contain several additional CHIA-like sequences. In humans, CHIA-L1 (hCHIA-L1) is an apparent pseudogene and has the highest homology to CHIA. To determine which of the two genes is functional in monkeys, we assessed their tissue expression levels. In our experiments, CHIA-L1 expression was not detected in human stomach tissue, while CHIA was expressed at high levels. However, in the cynomolgus macaque stomach tissue, the expression pattern of these two genes was reversed: CHIA-L1 was expressed at high levels and CHIA was undetectable. We hypothesized that in macaques CHIA-L1 (mCHIA-L1), and not CHIA, is a gene encoding an acidic chitinase, and cloned it, using the sequence of human CHIA-L1 as a guide for the primer design. We named the new enzyme MACase (Macaca Acidic Chitinase) to emphasize its differences from AMCase. MACase shares a similar tissue expression pattern and pH optimum with human AMCase, but is 50 times more active in our enzymatic activity assay. DNA sequence of the mCHIA-L1 has higher percentage identity to the human pseudogene hCHIA-L1 (91.7%) than to hCHIA (84%). Our results suggest alternate evolutionary paths for human and monkey acidic chitinases.

The balance of expression of PTPN22 splice forms is significantly different in rheumatoid arthritis patients compared with controls

BackgroundThe R620W variant in protein tyrosine phosphatase non-receptor 22 (PTPN22) is associated with rheumatoid arthritis (RA). The PTPN22 gene has alternatively spliced transcripts and at least two of the splice forms have been confirmed to encode different PTPN22 (LYP) proteins, but detailed information regarding expression of these is lacking, especially with regard to autoimmune diseases.MethodsWe have investigated the mRNA expression of known PTPN22 splice forms with TaqMan real-time PCR in relation to ZNF592 as an endogenous reference in peripheral blood cells from three independent cohorts with RA patients (n = 139) and controls (n = 111) of Caucasian origin. Polymorphisms in the PTPN22 locus (25 SNPs) and phenotypic data (gender, disease activity, ACPA and RF status) were used for analysis. Additionally, we addressed possible effects of methotrexate treatment on PTPN22 expression.ResultsWe found consistent differences in the expression of the PTPN22 splice forms in unstimulated peripheral blood mononuclear cells between RA patients and normal controls. This difference was more pronounced when comparing the ratio of splice forms and was not affected by methotrexate treatment.ConclusionsOur data show that RA patients and healthy controls have a shift in balance of expression of splice forms derived from the PTPN22 gene. This balance seems not to be caused by treatment and may be of importance during immune response due to great structural differences in the encoded PTPN22 proteins.

The Biomarkers of Lupus Disease Study: A Bold Approach May Mitigate Interference of Background Immunosuppressants in Clinical Trials

Molecular medicine raised expectations for strategically targeted biologic agents in systemic lupus erythematosus (SLE), but clinical trial results have been disappointing and difficult to interpret. Most studies add investigational agents to various, often effective, standard therapy immunosuppressants used at baseline, with unknown treatment interactions. Eliminating polypharmacy in trials of active lupus remains controversial. We undertook the Biomarkers of Lupus Disease study to test withdrawal of immunosuppressants as a novel approach to rendering SLE trials interpretable.

FRI0003 Determination of interferon (IFN) signatures for sle patients may be critical for optimal treatment selection but depends on the genes chosen: report from the bold (biomarkers of lupus disease) study

Background Elevated expression of IFN pathway genes, known as the IFN signature (IS) is found in roughly half of SLE patients1. Various studies have used different IFN genes to define the IS, and different methods to assign patients to “IFN high” or “low” expression groups. Importantly a recent report from the Genentech ROSE study found higher responsiveness to an interferon antagonist in patients with lower IFN expression using a 7 gene set (G-7), suggesting that IS might inform optimal selection of treatments in the future2. Objectives As a step toward understanding the clinical relevance and molecular drivers of the IS, we used data from the BOLD study to test the difference between IS-derived patient groupings derived from different sets of IFN genes. Methods The BOLD study enrolled SLE patients with active disease (minimum SLEDAI of 6 or two BILAG B scores). 41 patients had background immune suppressives withdrawn, were given brief steroids until improvement, then followed with serial samples until disease flare. 62 additional active SLE patients were evaluated only once. RNA expression levels for 329 genes were assayed using TaqMan® Low Density Arrays. 238 SLE patient-visits were partitioned into two groups by unsupervised hierarchical clustering of the expression levels of IFN-related genes. Results Clustering was done separately for 5 gene sets, denoted B-30, P-11, M-20, G-7, and O-3. Two of the gene sets (M-20 and G-7) were 95% and 100% matched to sets used in clinical trials of IFN-inhibiting treatments. Consistent with previous reports, all of the gene sets assigned about 40-50% of visits (96 to 118 patient-visits) to an “IFN high” group characterized by IFN pathway expression that was higher than healthy volunteers. In a cross-sectional analysis using the P-11 gene set, membership in the IFN high group was associated with higher SLEDAI score than IFN low assignment (9.73 vs. 7.70, p<0.0001) and higher TNFSF13B (BLYS/BAFF) gene expression (2.4 fold increase, p=0.0005). Most of the patients followed longitudinally remained in the same group over the course of the study, despite changes of gene expression with disease improvement and flare. IFN group assignments were similar for the B-30 and P-11 gene sets, and also similar among the M-20, G-7, and O-3 gene sets, but differed more across these groups. For instance, 21 patient-visits (9%) were assigned to the IFN high group by the G-7 gene set, but placed in the IFN low group by the P-11 gene set. Conclusions The comparison of IFN group assignments for the same samples, derived using different IFN gene sets, highlights the need for more investigation of the molecular and cellular drivers of IFN gene expression in SLE blood. An optimal IFN gene set, once determined, might improve how patients are selected for targeted therapies in the future. References Baechler et al., PNAS 100(5) 2610-2615 (2003); Kalunian et al., ACR 2012 Washington D.C, Abstract 2622. Disclosure of Interest None Declared

The expression of splice forms for the rheumatoid arthritis risk associated gene PTPN22 is significantly different for patients compared to controls

Background Several genetic risk factors have been revealed for rheumatoid arthritis (RA) whereof HLA-DRB1 shared epitope alleles and PTPN22 remains the two most undisputed for the disease. Hypotheses for how these associations confer their risk exist but the etiology is still not completely explained. The PTPN22 risk allele is associated with a gain of function of the protein product. However, the PTPN22 gene has alternatively spliced transcripts where at least two of the splice forms have confirmed different PTPN22 (LYP) proteins, which may influence the proteins pathways. Objectives Our hypothesis was that PTPN22 splice forms may have a different expression pattern in patients compared to controls. Such an effect could enhance other effects from the associated risk alleles. Material and methods The authors have investigated the expression of PTPN22 splice forms in peripheral blood cells and used genotypic and phenotypic data for analysis of RA patients and controls of Caucasian origin. Results PTPN22 was found to be different in individuals with RA compared to controls. On average, the shorter splice form was reduced (0.8-fold, p=0.08) and the longer was increased (1.2-fold, p=0.006) for patients. This effect was further enhanced if the ratio of the transcripts for each individual was compared (1.4-fold, p=6 × 10−9). This finding was replicated in two independent cohorts of the total size of 165 individuals. Conclusions The authors found important differences in expression of PTPN22 splice forms between healthy individuals and RA patients, which may increase a gain of function that influence development of the disease. The balance between splice forms may also be of importance during immune response due to great structural differences in the encoded PTPN22 proteins.