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1.  Identification of Novel Autoantigens by a Triangulation Approach 
Journal of immunological methods  2012;385(1-2):35-44.
High titer autoantibodies, which are often associated with specific clinical phenotypes, are useful diagnostically and prognostically in systemic autoimmune diseases. In several autoimmune rheumatic diseases (e.g. myositis and Sjogren’s syndrome), 20–40% of patients are autoantibody negative as assessed by conventional assays. The recent discovery of new specificities (e.g., anti-MDA5) in a subset of these autoantibody-negative subjects demonstrates that additional specificities await identification. In this manuscript, we describe a rapid multidimensional method to identify new autoantigens. A central foundation of this rapid approach is the use of an antigen source in which a pathogenic pathway active in the disease is recapitulated. Additionally, the method involves a modified serological proteome analysis strategy which allows confirmation that the correct gel plug has been removed prior to sending for sequencing. Lastly, the approach uses multiple sources of information to enable rapid triangulation and identification of protein candidates. Possible permutations and underlying principles of this triangulation strategy are elaborated to demonstrate the broad utility of this approach for antigen discovery.
PMCID: PMC3457001  PMID: 22910000
2.  Erosive rheumatoid arthritis is associated with antibodies that activate PAD4 by increasing calcium sensitivity 
Science translational medicine  2013;5(186):186ra65.
Peptidylarginine deiminases (PADs) play a critical role in generating autoantigens in rheumatoid arthritis (RA), but the mechanisms underlying their dysregulation in this disease remain unknown. Although PADs require supraphysiologic concentrations of calcium for activity in vitro, the enzymes are clearly active in vivo (e.g. in RA synovial fluid) where calcium concentrations are much lower. In this study, we have discovered a novel subset of anti-PAD4 autoantibodies (identified by their cross-reactivity with PAD3) which strikingly increase the catalytic efficiency of PAD4 by decreasing the enzyme’s requirement for calcium into the physiologic range. Patients with these novel PAD3/PAD4 cross-reactive autoantibodies had higher baseline radiographic damage scores and a higher likelihood of radiographic progression compared to individuals negative for these antibodies. The ability of autoantibodies to activate an enzyme that itself generates citrullinated autoantigens identifies an important feed-forward loop which may drive the erosive outcome observed in RA patients with these autoantibodies. PAD3 autoantibodies may therefore identify RA patients who would benefit from early aggressive treatment or addition of PAD-inhibitor therapy.
PMCID: PMC3740946  PMID: 23698378
3.  Isolated elevation of aldolase in the serum of myositis patients: a potential biomarker of damaged early regenerating muscle cells 
Elevated serum aldolase A levels occur in the absence of elevated creatine kinase M (CK) levels in a subset of myositis patients. This study was undertaken to investigate the cell biology of this unexplained clinical observation.
Cultured human myoblasts were differentiated in vitro. RNA and protein lysates were prepared and used to determine aldolase and CK gene and protein expression by QPCR and immunoblotting. Cardiotoxin was used to induce muscle injury and repair in an experimental mouse model, and aldolase A and CK were immunoblotted in the muscle lysates. Immunohistochemical staining was performed on myositis patient muscle paraffin sections to assess aldolase A and CK staining in vivo.
Aldolase A mRNA and protein expression is highest in differentiating myoblasts, and remains robust throughout differentiation. In contrast, CK mRNA and protein levels are low in undifferentiated myoblasts and become strikingly upregulated as differentiation progresses. Aldolase A protein expression is high in regenerating muscle in the mouse model of injury/repair, while CK expression was low. Immunohistochemical staining of human myositis biopsies showed that muscle cells with the highest levels of aldolase and no CK staining have features of regeneration.
In undifferentiated muscle cells, and those early in the differentiation process, aldolase A is expressed in the absence of CK. Thereafter, both are expressed. We propose that isolated serum aldolase A elevation in myositis patients (i) reflects preferential immune-mediated damage of early regenerative cells, and (ii) is a biomarker of damaged early regenerating muscle cells.
PMCID: PMC3786178  PMID: 22703875
myositis; aldolase; creatine kinase; muscle regeneration
4.  A Novel Dermato-Pulmonary Syndrome Associated With MDA-5 Antibodies 
Medicine  2012;91(4):220-228.
Melanoma differentiation-associated protein 5 (MDA-5) is a novel autoantibody frequently characterized by interstitial lung disease and a distinct cutaneous phenotype with palmar papules, ulceration, and rash. Virtually all patients have underlying dermatomyositis, but many lack the characteristic clinical myopathy associated with it. In the setting of amyopathic disease, the absence of clinically available biomarkers or clear pathologic diagnosis can complicate effective prognostic and therapeutic intervention. Until recently the presence of MDA-5 antibody associated dermato-pulmonary syndrome was described only in Asian populations. We present 2 cases of MDA-5-associated dermato-pulmonary syndrome and provide a comprehensive review of available literature.
PMCID: PMC3726263  PMID: 22732950
5.  Type I interferons: crucial participants in disease amplification in autoimmunity 
Nature reviews. Rheumatology  2010;6(1):40-49.
A significant body of data implicates the type I interferon (IFN) pathway in the pathogenesis of autoimmune rheumatic diseases. In these disorders, a reinforcing cycle of IFN production can contribute to immunopathology through multiple mechanisms. The type I IFN cytokines are pleiotropic in their effects, mediating anti-viral and anti-tumor activities, and possessing numerous immunomodulatory functions for both the innate and adaptive immune responses. A key principle of the type I IFN system is rapid induction and amplification of the signaling pathway, which generates a feed-forward loop of IFN production, ensuring that a vigorous anti-viral immune response is mounted. While such feed-forward pathways are highly adaptive when it comes to rapid and effective virus eradication, this amplification can be maladaptive in immune responses directed against host tissues. Such feed-forward loops, however, create special opportunities for therapy.
PMCID: PMC3622245  PMID: 20046205
6.  Peptidylarginine deiminase 2, 3 and 4 have distinct specificities against cellular substrates: Novel insights into autoantigen selection in rheumatoid arthritis 
To define the relationship between autoantigen citrullination and different peptidylarginine deiminase (PAD) enzymes in rheumatoid arthritis (RA).
Citrullinated autoantigens were identified by immunoblotting control and ionomycin-activated human primary neutrophil lysate with RA sera. Autoantigen identity and citrullination sites were defined by mass spectrometry. PAD isoenzyme expression in human neutrophils was determined by immunoblotting. PAD substrate specificity was addressed in HL-60 cell lysates co-incubated with human recombinant PAD2, PAD3 and PAD4.
Although prominent protein citrullination is observed in ionomycin activated neutrophils, RA sera only recognized a limited number of these citrullinated molecules. Among these, we identified that beta and gamma actins are citrullinated on at least ten arginine residues, generating a novel 47kDa species that is frequently recognized by RA autoantibodies. Interestingly, we showed that the PAD enzymes expressed in human neutrophils (i.e. PAD2, PAD3 and PAD4) have unique substrate specificities, independent of their subcellular distribution. Thus, only PAD2 was able to citrullinate native beta/gamma-actin, while histone H3 was only citrullinated by PAD4.
These studies identified beta and gamma actins as novel citrullinated autoantigens in RA, allowing enzyme specificity against intracellular substrates to be addressed. The studies provide evidence that PAD enzymes have the intrinsic capacity to select unique protein targets. We propose that unique PAD specificity may play a role in autoantigen selection in RA.
PMCID: PMC3302156  PMID: 21859690
Citrullination; rheumatoid arthritis; anti-CCP; actin; peptidylarginine deiminase
7.  Antibodies recognizing sulfated carbohydrates are prevalent in systemic sclerosis and associated with pulmonary vascular disease 
Annals of the rheumatic diseases  2011;70(12):2218-2224.
Glycosylation represents an important modification that regulates biological processes in tissues relevant for disease pathogenesis in systemic sclerosis (SSc), including the endothelium and extracellular matrix. Whether patients with systemic sclerosis (SSc) develop antibodies to carbohydrates is not known.
To determine the prevalence and clinical phenotype associated with serum IgG antibodies recognizing distinct glycans in patients with systemic sclerosis (SSc).
Pooled sera from patients with SSc and controls were screened for the presence of specific anti-carbohydrate antibodies using a novel array containing over 300 glycans. Antibody titers to 4-sulfated N-Acetyl-lactosamine (4S-LacNAc, [4OSO3]Galβ1-4GlcNAc) were determined in 181 individual sera from SSc patients by ELISA and associated with disease phenotype.
4S-LacNAc was identified as a target in pooled SSc serum. Anti-4SLAcNAc antibodies were detected in 27/181 (14.9%) of SSc patients compared to 1/40 (2.5%) of healthy controls. Sulfation at position C-4 of galactose (4S-LacNAc) was found to be critical for immunogenicity. Anti-4SLacNAc antibody positive SSc patients had a higher prevalence of pulmonary hypertension by echocardiography (15/27; 55.7% versus anti-4S LacNac negative patients 49/154; 31.8% p=0.02) with an odds ratio of 2.6 (CI 1.1, 6.3). Anti-4S-LacNAc positive patients accounted for 23.4% of all patients with pulmonary hypertension.
Sera from SSc patients contain IgG antibodies targeting distinct sulfated carbohydrates. The presence of anti-4S-LacNAc antibodies is associated with a high prevalence of pulmonary hypertension. These results suggest that specific posttranslational carbohydrate modifications may act as important immunogens in SSc and may contribute to disease pathogenesis.
PMCID: PMC3409247  PMID: 21873333
Scleroderma; carbohydrates; antibodies; pulmonary hypertension
8.  Increased Generation of TRAP Expressing Multinucleated Giant Cells in Patients with Granulomatosis with Polyangiitis 
PLoS ONE  2012;7(8):e42659.
Tissue-infiltrating multinucleated giant cells (MNGs) within geographic necrosis are pathologic hallmarks of granulomatosis with polyangiitis (GPA). However, the origin, phenotype, and function of these cells in GPA remain undefined.
Methodology/Principal Findings
MNG phenotype in GPA lung tissue was examined by immunohistochemistry using antibody directed against cathepsin K and calcitonin-receptor. Tartrate-resistant-acid-phosphatase (TRAP) expression was assessed using enzymatic color reaction. Peripheral blood mononuclear cells (PBMCs) from 13 GPA patients (5 with localized and 8 with systemic disease) and 11 healthy controls were cultured in the presence of RANKL and M-CSF for 9 days, and TRAP+ MNGs containing 3 or more nuclei were identified. GPA lung granulomata contained numerous MNGs that expressed osteoclastic TRAP and cathepsin K but not calcitonin receptors. In the presence of RANKL and M-CSF, PBMCs of GPA patients formed significantly more MNGs than healthy controls (114±29 MNG/well vs. 22±9 MNG/well, P = 0.02). In a subgroup analysis, patients with systemic disease generated significantly more MNGs than patients with localized disease (161±35 MNG/well vs. 39±27 MNG/well, P<0.01) or healthy controls (P<0.01). MNG production did not differ between localized GPA and control subjects (P = 0.96).
MNGs in granulomata in the GPA lung express osteoclastic enzymes TRAP and cathepsin K. GPA patients have a higher propensity to form TRAP+ MNGs from peripheral blood than healthy controls. These data suggest that (i) the tendency to form MNGs is a component of the GPA phenotype itself, and (ii) that lesional MNGs might participate in the destructive process through their proteolytic enzymes.
PMCID: PMC3414441  PMID: 22905158
9.  The mucocutaneous and systemic phenotype of dermatomyositis patients with antibodies to MDA5 (CADM-140): A retrospective study 
Dermatomyositis (DM) is a multisystem autoimmune disease, in which serologic evidence of immune responses to disease-specific antigenic targets is found in approximately 50% to 70% of patients. Recently, melanoma differentiation-associated gene 5 (MDA5) has been identified as a DM-specific autoantigen that appears to be targeted in patients with DM and mild or absent muscle inflammation and with an increased risk of interstitial lung disease.
We wished to understand the role of MDA5 in DM skin inflammation by testing it to determine if a specific cutaneous phenotype is associated with MDA5 reactivity.
We retrospectively screened plasma from 77 patients with DM in the outpatient clinics at the Stanford University Department of Dermatology in California.
We found that 10 (13%) patients had circulating anti-MDA5 antibodies, and had a characteristic cutaneous phenotype consisting of skin ulceration, tender palmar papules, or both. Typical areas of skin ulceration included the lateral nailfolds, Gottron papules, and elbows. Biopsy specimens of the palmar papules showed a vasculopathy characterized by vascular fibrin deposition with variable perivascular inflammation. Patients with anti-MDA5 antibodies also had an increased risk of oral pain and/or ulceration, hand swelling, arthritis/arthralgia, and diffuse hair loss. Consistent with previous reports, these patients had little or no myositis and had increased risk of interstitial lung disease.
This study was conducted at a tertiary referral center. Multiple associations with MDA5 antibodies were tested retrospectively on a relatively small cohort of 10 anti-MDA5-positive patients.
We suggest that MDA5 reactivity in DM characterizes a patient population with severe vasculopathy.
PMCID: PMC3167687  PMID: 21531040
autoantibodies; clinically amyopathic dermatomyositis antibody; 140 kd (CADM-140) peptide; dermatomyositis; human; interferon-induced helicase 1 protein; interstitial; lung diseases; phenotype; ulcer
10.  Cancer and systemic sclerosis: novel insights into pathogenesis and clinical implications 
Current Opinion in Rheumatology  2011;23(6):530-535.
Purpose of review
Most epidemiologic studies have demonstrated an increased risk of cancer in scleroderma patients. Reasons for this risk increase have been poorly understood and often attributed to cytotoxic therapies or damage from scleroderma. Recognition that some patients have a close temporal relationship between cancer diagnosis and scleroderma clinical onset has focused attention on the possibility that scleroderma may be a paraneoplastic syndrome in a subset of patients. This review will discuss the latest epidemiologic data linking cancer and scleroderma and explore a model for the development of paraneoplastic scleroderma.
Recent findings
New investigations have demonstrated an association between RNA polymerase III autoantibodies and a close temporal relationship between cancer diagnosis and the development of clinical scleroderma. A unique nucleolar RNA polymerase III expression pattern has been identified in malignant tissue from these scleroderma patients suggesting that autoantigen expression in the cancer and the autoantibody response are associated. Similar data in inflammatory myositis have illustrated that disease-specific autoantigens may be expressed in cancers and damaged target tissues (muscle) undergoing regeneration.
These data suggest a model of paraneoplastic autoimmunity in which cross-reactive immune responses may target autoantigens that are expressed in both cancers and diseased autoimmune target tissues.
PMCID: PMC3373179  PMID: 21825998
autoantibodies; cancer; paraneoplastic; systemic sclerosis
11.  Autoantibodies against 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase (HMGCR) in Patients with Statin-Associated Autoimmune Myopathy 
Arthritis and Rheumatism  2011;63(3):713-721.
In addition to inducing a self-limited myopathy, statin use is associated with an immune-mediated necrotizing (IMNM) myopathy with autoantibodies recognizing ~ 200 and ~100 kDa autoantigens. Identifying these molecules will clarify disease mechanism and facilitate diagnosis.
The effect of statin treatment on autoantigen expression was addressed by immunoprecipitation using patient sera. The identity of the ~100 kDa autoantigen was confirmed by immunoprecipitating in vitro-translated HMGCR protein. HMGCR expression in muscle was analyzed by immunofluorescence. A cohort of myopathy patients was screened for anti-HMGCR autoantibodies by ELISA and genotyped for the rs4149056 C allele, a predictor of self-limited statin myopathy.
Statin exposure induced expression of the ~200/~100 kDa autoantigens in cultured cells. HMGCR was identified as the ~100 kDa autoantigen. Competition experiments demonstrated no distinct autoantibodies recognizing the ~200 kDa protein. In muscle biopsies from anti-HMGCR positive patients, HMGCR expression was up-regulated in cells expressing NCAM, a marker of muscle regeneration. Anti-HMGCR autoantibodies were found in 45 of 750 patients presenting to the Johns Hopkins Myositis Center (6%). Among patients age 50 or older, 92% were exposed to statins. The prevalence of the rs4149056 C allele was not increased in anti-HMGCR subjects.
Statins up-regulate expression of HMGCR, the major target of autoantibodies in statin-associated IMNM. Regenerating muscle cells express high levels of HMGCR, which may sustain the immune response even after statins are discontinued. These studies demonstrate a mechanistic link between an environmental trigger and the development of sustained autoimmunity. Detection of anti-HMGCR autoantibodies may facilitate diagnosis and direct therapy.
PMCID: PMC3335400  PMID: 21360500
12.  Myocardial citrullination in rheumatoid arthritis: a correlative histopathologic study 
The aim of this study was to explore the presence and localization of myocardial citrullination in samples from rheumatoid arthritis (RA) patients compared to rheumatic and non-rheumatic disease control groups.
Archived myocardial samples obtained during autopsy from 1995 to 2009 were assembled into four groups: RA; scleroderma; fatal myocarditis; and non-rheumatic disease controls. Samples were examined by immunohistochemistry (IHC) for the presence and localization of citrullination and peptidyl arginine deiminase enzymes (PADs) by a single cardiovascular pathologist blinded to disease group and clinical characteristics.
Myocardial samples from seventeen RA patients were compared with those from fourteen controls, five fatal myocarditis patients, and ten scleroderma patients. Strong citrullination staining was detected exclusively in the myocardial interstitium in each of the groups. However, average and peak anti-citrulline staining was 59% and 44% higher, respectively, for the RA group compared to the combined non-RA groups (P < 0.05 for both comparisons). Myocardial fibrosis did not differ between the groups. In contrast to citrullination, PADs 1 to 3 and 6 were detected in cardiomyocytes (primarily PADs 1 and 3), resident inflammatory cells (primarily PADs 2 and 4), and, to a smaller extent, in endothelial cells and vascular smooth muscle cells. PAD staining did not co-localize with anti-citrulline staining in the interstitium and did not vary by disease state.
Staining for citrullination was higher in the myocardial interstitium of RA compared to other disease states, a finding that could link autoimmunity to the known increase in myocardial dysfunction and heart failure in RA.
PMCID: PMC3392839  PMID: 22364592
13.  A Novel Conserved Isoform of the Ubiquitin Ligase UFD2a/UBE4B Is Expressed Exclusively in Mature Striated Muscle Cells 
PLoS ONE  2011;6(12):e28861.
Yeast Ufd2p was the first identified E4 multiubiquitin chain assembly factor. Its vertebrate homologues later referred to as UFD2a, UBE4B or E4B were also shown to have E3 ubiquitin ligase activity. UFD2a function in the brain has been well established in vivo, and in vitro studies have shown that its activity is essential for proper condensation and segregation of chromosomes during mitosis. Here we show that 2 alternative splice forms of UFD2a, UFD2a-7 and -7/7a, are expressed sequentially during myoblast differentiation of C2C12 cell cultures and during cardiotoxin-induced regeneration of skeletal muscle in mice. UFD2a-7 contains an alternate exon 7, and UFD2a-7/7a, the larger of the 2 isoforms, contains an additional novel exon 7a. Analysis of protein or mRNA expression in mice and zebrafish revealed that a similar pattern of isoform switching occurs during developmental myogenesis of cardiac and skeletal muscle. In vertebrates (humans, rodents, zebrafish), UFD2a-7/7a is expressed only in mature striated muscle. This unique tissue specificity is further validated by the conserved presence of 2 muscle-specific splicing regulatory motifs located in the 3′ introns of exons 7 and 7a. UFD2a interacts with VCP/p97, an AAA-type ATPase implicated in processes whose functions appear to be regulated, in part, through their interaction with one or more of 15 previously identified cofactors. UFD2a-7/7a did not interact with VCP/p97 in yeast 2-hybrid experiments, which may allow the ATPase to bind cofactors that facilitate its muscle-specific functions. We conclude that the regulated expression of these UFD2a isoforms most likely imparts divergent functions that are important for myogenisis.
PMCID: PMC3235170  PMID: 22174917
14.  Autoimmunity to Peptidyl Arginine Deiminase Type 4 Precedes Clinical Onset of Rheumatoid Arthritis 
Arthritis and rheumatism  2010;62(9):2633-2639.
To determine if antibodies against peptidyl arginine deiminase Type 4 (PAD-4) are present in the pre-clinical phase of rheumatoid arthritis (RA), and to compare their appearance to other pre-clinical autoantibodies.
Prediagnosis serum samples from 83 subjects with RA were evaluated for presence of anti-PAD-4 antibody, anti-cyclic citrullinated peptide (anti-CCP) antibody, and rheumatoid factor (RF). In addition, a control cohort (N = 83) matched on age, gender, race, number of samples, and duration of serum storage were tested for antibody against PAD-4 to determine its sensitivity and specificity for future RA.
Fifteen of 83 (18.1%) subjects with RA had at least one prediagnosis sample positive for anti-PAD-4. One of 83 (1.2%) control subjects had at least one sample positive, resulting in a sensitivity and specificity of anti-PAD-4 for the future development of RA of 18.1% and 98.8%, respectively. The mean time of first positivity for anti-PAD-4 was ~4.6 years prior to diagnosis. Anti-PAD-4 positivity was associated with anti-CCP positivity (OR 5.13, 95%CI 1.07–24.5, p = 0.04). In subjects with prediagnosis samples positive for both antibodies, anti-CCP positivity predated anti-PAD-4 in 9 of 13 (69%) cases.
Autoantibodies to PAD-4 are present in the pre-clinical phase of RA in a subset of patients and are associated with anti-CCP positivity. Further exploration is needed regarding the timing of appearance and disease-related effects of PAD-4 autoimmunity.
PMCID: PMC2946499  PMID: 20496417
Rheumatoid arthritis; pre-clinical; peptidyl arginine deiminase type 4; anti-citrullinated peptide antibodies
15.  Close Temporal Relationship Between Onset of Cancer and Scleroderma in Patients with RNA Polymerase I/III Antibodies 
Arthritis and rheumatism  2010;62(9):2787-2795.
We examined the temporal relationship between scleroderma development and malignancy, and evaluated whether this differed by autoantibody status among affected patients.
Participants had a diagnosis of scleroderma, cancer, an available serum sample, and a cancer pathology specimen. Sera were tested for autoantibodies against topoisomerase I, centromere, and RNA polymerase I/III by immunoprecipitation and/or ELISA. Clinical and demographic characteristics were compared across autoantibody categories. Expression of RNA polymerases I and III was evaluated by immunohistochemistry using cancerous tissue from patients with anti-RNA polymerase antibodies.
Twenty three subjects were enrolled. Six subjects tested positive for anti-RNA polymerase I/III (Pol), 5 for anti-topoisomerase I (Topo), 8 for anti-centromere (CENP), and 4 recognized none of these antigens (Negative). The median duration of scleroderma at cancer diagnosis differed significantly between groups: −1.2 years (Pol), +13.4 years (Topo), +11.1 years (CENP), and +2.3 years (Negative) (p=0.027). RNA polymerase III demonstrated a robust nucleolar staining pattern in 4 of 5 available tumors from patients with antibodies to RNA polymerase I/III. In contrast, nucleolar RNA polymerase III staining was not detected in any of 4 examined tumors in the RNA polymerase antibody-negative group (p=0.048).
There is a close temporal relationship between onset of cancer and scleroderma in patients with antibodies to RNA polymerase I/III, which is distinct from scleroderma patients with other autoantibody specificities. In this study, autoantibody response and tumor antigen expression are associated. We propose that malignancy may initiate the scleroderma-specific immune response and drive disease in a subset of scleroderma patients.
PMCID: PMC2946521  PMID: 20506513
16.  Granzyme B cleavage of autoantigens in autoimmunity 
Cell death and differentiation  2010;17(4):624-632.
The systemic autoimmune diseases are a complex group of disorders characterized by elaboration of high titer autoantibodies and immune-mediated damage of tissues. Two striking features of autoimmune rheumatic diseases are their self-sustaining nature and capacity for auto-amplification, exemplified by disease flares. These features suggest the presence of a feed-forward cycle in disease propagation, in which immune effector pathways drive the generation/release of autoantigens, which in turn fuel the immune response. There is a growing awareness that structural modification during cytotoxic granule-induced cell death is a frequent and striking feature of autoantigens, and may be an important principle driving disease. This review focuses on granzyme B (GrB)-mediated cleavage of autoantigens including (i) features of GrB cleavage sites within autoantigens, (ii) co-location of cleavage sites with autoimmune epitopes, and (iii) GrB-sensitivity of autoantigens in disease-relevant target tissue. The mechanisms whereby GrB-induced changes in autoantigen structure may contribute to the initiation and propagation of autoimmunity are reviewed and reveal that GrB has the potential to create or destroy autoimmune epitopes. As there remains no direct evidence demonstrating a causal role for GrB-cleavage of antigens in the generation of autoimmunity, this review highlights important outstanding questions about the role of GrB in autoantigen selection.
PMCID: PMC3136751  PMID: 20075942
granzyme; autoimmunity; autoantibody; autoantigen; antigen processing; proteolysis
17.  Cleavage of Transaldolase by Granzyme B Causes the Loss of Enzymatic Activity with Retention of Antigenicity for Multiple Sclerosis Patients 
Multiple sclerosis (MS) is an autoimmune demyelinating disease of the CNS resulting from a progressive loss of oligodendrocytes. Transaldolase (TAL) is expressed at selectively high levels in oligodendrocytes of the brain, and postmortem sections show concurrent loss of myelin basic protein and TAL from sites of demyelination. Infiltrating CD8+ CTLs are thought to play a key role in oligodendrocyte cell death. Cleavage by granzyme B (GrB) is predictive for autoantigenicity of self-proteins, thereby further implicating CTL-induced death in the initiation and propagation of autoimmunity. The precursor frequency and CTL activity of HLA-A2–restricted TAL 168–176–specific CD8+ T cells is increased in MS patients. In this paper, we show that TAL, but not myelin basic protein, is specifically cleaved by human GrB. The recognition site of GrB that resulted in the cleavage of a dominant TAL fragment was mapped to a VVAD motif at aa residue 27 by N-terminal sequencing and confirmed by site-directed mutagenesis. The major C-terminal GrB cleavage product, residues 28–337, had no enzymatic activity but retained the antigenicity of full-length TAL, effectively stimulating the proliferation and CTL activity of PBMCs and of CD8+ T cell lines from patients with MS. Sera of MS patients exhibited similar binding affinity to wild-type and GrB-cleaved TAL. Because GrB mediates the killing of target cells and cleavage by GrB is predictive of autoantigen status of self proteins, GrB-cleaved TAL-specific T cell-mediated cytotoxicity may contribute to the progressive destruction of oligodendrocytes in patients with MS.
PMCID: PMC3117466  PMID: 20194725
18.  Autocitrullination of human peptidyl arginine deiminase type 4 regulates protein citrullination during cell activation 
Arthritis and rheumatism  2010;62(6):1630-1640.
To address mechanisms that control the activity of human peptidyl arginine deiminase type 4 (PAD-4).
PAD-4 autocitrullination was determined by anti–modified citrulline immunoblotting, using purified recombinant and endogenous PAD-4 from activated human primary neutrophils and cell lines expressing PAD-4. The citrullination sites in PAD-4 were determined by mass spectrometry. Mechanisms of autocitrullination-induced inactivation and the functional consequences of autocitrullination in PAD-4 polymorphic variants were addressed using purified components and cell lines expressing PAD-4 wild-type, PAD-4 mutant, and PAD-4 polymorphic variants relevant to rheumatoid arthritis (RA).
PAD-4 is autocitrullinated in vitro and during activation of primary cells and cell lines expressing PAD-4. Interestingly, this modification inactivated the function of the enzyme. The efficiency of inactivation differed among genetically defined PAD-4 variants relevant to RA. PAD-4 was citrullinated at 10 sites, which are clustered into 3 distinct regions, including a cluster of arginines around the active site cleft where Arg-372 and -374 were identified as the potential autocitrullination targets that inactivate the enzyme. Autocitrullination also modified the structure of PAD-4, abrogating its recognition by multiple rabbit antibodies, but augmenting its recognition by human anti–PAD-4 autoantibodies.
Our findings suggest that autocitrullination regulates the production of citrullinated proteins during cell activation, and that this is affected by structural polymorphisms in PAD-4. Autocitrullination also influences PAD-4 structure and immune response.
PMCID: PMC2951335  PMID: 20201080
19.  Abnormal Production of Pro- and Anti-Inflammatory Cytokines by Lupus Monocytes in Response to Apoptotic Cells 
PLoS ONE  2011;6(3):e17495.
Monocytes are a key component of the innate immune system involved in the regulation of the adaptive immune response. Previous studies have focused on apoptotic cell clearance abnormalities in systemic lupus erythematosus (SLE) monocytes. However, whether SLE monocytes might express unique patterns of cytokine secretion in response to apoptotic cells is still unknown. Here, we used monocytes from healthy controls and SLE patients to evaluate the production of TNF-α and TGF-β in response to apoptotic cells. Upon recognition of apoptotic material, monocytes from healthy controls showed prominent TGF-β secretion (mean ± SD: 824.6±144.3 pg/ml) and minimal TNF-α production (mean ± SD: 32.6±2.1 pg/ml). In contrast, monocytes from SLE patients had prominent TNF-α production (mean ± SD: 302.2±337.5 pg/ml) and diminished TGF-β secretion (mean ± SD: 685.9±615.9 pg/ml), a difference that was statistically significant compared to normal monocytes (p≤10−6 for TNF-α secretion, and p = 0.0031 for TGF-β, respectively). Interestingly, the unique cytokine response by SLE monocytes was independent of their phagocytic clearance efficiency, opsonizing autoantibodies and disease activity. We further showed that nucleic acids from apoptotic cells play important role in the induction of TNF-α by lupus monocytes. Together, these observations suggest that, in addition to potential clearance defects, monocytes from SLE patients have an abnormal balance in the secretion of anti- and pro-inflammatory cytokines in response to apoptotic cells. Since the abnormal cytokine response to apoptotic material in SLE is not related to disease activity and opsonizing autoantibodies, it is possible that this response might be an intrinsic property of lupus monocytes. The studies focus attention on toll-like receptors (TLRs) and their downstream pathways as mediators of this response.
PMCID: PMC3056659  PMID: 21423726
20.  Expression of the dermatomyositis autoantigen Mi-2 in regenerating muscle 
Arthritis and rheumatism  2009;60(12):3784-3793.
Autoantibodies against the chromatin remodeler Mi-2 are found in a distinct subset of patients with dermatomyositis (DM). Previous quantitative immunoblotting experiments demonstrated that Mi-2 protein is up-regulated in DM muscle. We undertook this study to define the population of cells expressing high levels of Mi-2 in DM muscle and to explore the regulation and functional role of Mi-2 during muscle regeneration.
We analyzed the expression of Mi-2 in human muscle biopsy specimens using immunofluorescence. Then, we used cardiotoxin (CTX) to induce muscle injury and repair in the mouse; Mi-2 expression during muscle regeneration was studied in this model by immunofluorescence and immunoblotting analysis. Finally, we utilized a cell culture system of muscle differentiation to artificially modulate Mi-2 levels during myoblast proliferation and differentiation.
In DM muscle, increased Mi-2 expression is preferentially found in myofibers within fascicles affected by perifascicular atrophy, particularly in the centralized nuclei of small perifascicular muscle fibers expressing markers of regeneration. In the mouse, Mi-2 is dramatically and persistently up-regulated during muscle regeneration in vivo. Premature silencing of Mi-2 with RNAi in vitro resulted in accelerated myoblast differentiation.
Mi-2 expression is markedly up-regulated during muscle regeneration in the mouse model. It is also up-regulated in DM myofibers expressing markers of regeneration. In vitro studies suggest that this protein may play a role in modulating the kinetics of myoblast differentiation. We propose that high levels of Mi-2 expression in DM muscle biopsies reflect the presence of incompletely differentiated muscle cells.
PMCID: PMC2828900  PMID: 19950298
21.  Anti-β2 glycoprotein I antibodies are independently associated with macrovascular disease and mortality in scleroderma patients 
Arthritis and rheumatism  2009;60(8):2480-2489.
Scleroderma (SSc) is characterized by a unique widespread vascular disease that can lead to severe digital ischemia, pulmonary arterial hypertension (PAH) or other organ dysfunction. Microthrombotic events and pro-coagulable factors such as anti-beta 2 glycoprotein 1 (B2GPI) or anti-cardiolipin (aCL) antibodies may be implicated in the development of these manifestations. This study investigated whether anti-B2GPI and aCL antibodies are correlated with macrovascular disease including ischemic digital loss and PAH in SSc patients.
75 SSc patients with history of ischemic digital loss and 75 matched SSc controls were evaluated. Anti-centromere (ACA), anti-B2GPI and aCL antibodies were tested and clinical associations measured using conditional and simple logistic regression models.
Anti-B2GPI, but not aCL, were significantly more frequent (p=0.01) in digital loss patients, with IgA isotype showing the strongest association (OR 4.0). After adjusting for demographics, disease type, smoking and ACA, anti-B2GPI were significantly associated with active digital ischemia (OR 9.4), echocardiographic evidence for PAH (OR 4.8), and mortality (OR 2.9). ACA positivity was associated with history of digital loss (OR 3.8), but not with PAH or mortality. History of digital loss was strongly associated with increased mortality (OR 12.5).
Anti-B2GPI antibodies are significantly associated with macrovascular disease in SSc and independently predict mortality. It is unclear whether they play a pathogenic role or simply reveal the presence of underlying endothelial injury. The use of anti-B2GPI antibodies as a biomarker of vascular disease in SSc should be further explored.
PMCID: PMC2746063  PMID: 19644882
22.  GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data 
Microarray technology has become highly valuable for identifying complex global changes in gene expression patterns. The assignment of functional information to these complex patterns remains a challenging task in effectively interpreting data and correlating results from across experiments, projects and laboratories. Methods which allow the rapid and robust evaluation of multiple functional hypotheses increase the power of individual researchers to data mine gene expression data more efficiently.
We have developed (gene set matrix analysis) GSMA as a useful method for the rapid testing of group-wise up- or down-regulation of gene expression simultaneously for multiple lists of genes (gene sets) against entire distributions of gene expression changes (datasets) for single or multiple experiments. The utility of GSMA lies in its flexibility to rapidly poll gene sets related by known biological function or as designated solely by the end-user against large numbers of datasets simultaneously.
GSMA provides a simple and straightforward method for hypothesis testing in which genes are tested by groups across multiple datasets for patterns of expression enrichment.
PMCID: PMC2789691  PMID: 20066124
23.  Association of Autoimmunity to Peptidyl Arginine Deiminase Type 4 With Genotype and Disease Severity in Rheumatoid Arthritis 
Arthritis and rheumatism  2008;58(7):1958-1967.
Protein citrullination is an important posttranslational modification recognized by rheumatoid arthritis (RA)–specific autoantibodies. One of the citrullinating enzymes, peptidyl arginine deiminase type 4 (PAD-4), is genetically associated with development of RA in some populations, although the mechanism(s) mediating this effect are not yet clear. There have been descriptions of anti–PAD-4 autoantibodies in different rheumatic diseases. This study was undertaken to investigate whether anti–PAD-4 antibodies are specific to RA, are associated with disease phenotype or severity, and whether PAD-4 polymorphisms influence the anti–PAD-4 autoantibody response.
Sera from patients with established RA, patients with other rheumatic diseases, and healthy adults were assayed for anti–PAD-4 autoantibodies by immunoprecipitation of in vitro–translated PAD-4. The epitope(s) recognized by PAD-4 autoantibodies were mapped using various PAD-4 truncations. PAD-4 genotyping was performed on RA patients with the TaqMan assay. Joint erosions were scored from hand and foot radiographs using the Sharp/van der Heijde method.
PAD-4 autoantibodies were found in 36–42% of RA patients, and were very infrequent in controls. Recognition by anti–PAD-4 autoantibodies required the 119 N-terminal amino acids, which encompass the 3 nonsynonymous polymorphisms associated with disease susceptibility. Strikingly, the anti–PAD-4 immune response was associated with the RA susceptibility haplotype of PADI4. Anti–PAD-4 antibodies were associated with more severe joint destruction in RA.
Our findings indicate that anti–PAD-4 antibodies are specific markers of RA, independently associated with more severe disease, suggesting that an anti–PAD-4 immune response may be involved in pathways of joint damage in this disease. Polymorphisms in the PADI4 gene influence the immune response to the PAD-4 protein, potentially contributing to disease propagation.
PMCID: PMC2692635  PMID: 18576335
24.  T Cell Polarization Identifies Distinct Clinical Phenotypes in Scleroderma Lung Disease 
Arthritis and rheumatism  2008;58(4):1165-1174.
Lung involvement is the leading cause of morbidity and mortality in systemic sclerosis (SSc; scleroderma), and interstitial lung disease (ILD) is the most common pulmonary manifestation. An abnormal profibrotic Th2/Tc2-polarized T cell response is postulated to mediate tissue damage and fibrosis. The aim of this study was to investigate whether a polarized T cell phenotype in SSc is associated with lung disease or other clinical manifestations of SSc.
Circulating T cells were characterized by flow cytometry in 62 patients with SSc and 36 healthy control subjects, using antibodies against CD3, CD4, CD8, chemokine receptor CCR5 (Th1/Tc1-specific), and prostaglandin D2 receptor CRTH2 (Th2/Tc2-specific). The ratio between CCR5 and CRTH2 T cell frequencies was used to quantify type 1 (high-ratio) or type 2 (low-ratio) immune polarization.
Patients with SSc exhibited lower CCR5/CRTH2 T cell ratios than those exhibited by control subjects (P < 0.0001), indicating a Th2/Tc2-polarized phenotype. Markedly reduced CCR5/CRTH2 T cell ratios were observed in SSc patients with ILD compared with SSc patients without ILD (P < 0.0001), particularly in patients with active ILD (P < 0.0001) compared with those with stable lung function. Lower CCR5/CRTH2 ratios were strongly associated with a lower value for the percent predicted forced vital capacity (P < 0.0001). In patients with an estimated right ventricular systolic pressure >35 mm Hg, suggestive of pulmonary vascular disease, a lower value for the percent predicted diffusing capacity (DLCO) was associated with higher CCR5/CRTH2 T cell ratios (Th1/Tc1) (P = 0.009), while in those with right ventricular systolic pressure <35 mm Hg, a lower value for the percent predicted DLCO correlated with lower ratios (Th2/Tc2) (P < 0.0001), as observed for ILD.
T cell polarization in SSc is strongly associated with specific manifestations of lung disease. Measurement of T cell polarization may represent a valuable tool to monitor disease activity and predict clinical outcomes in SSc patients with lung disease.
PMCID: PMC2662772  PMID: 18383361
25.  Regulatory subunits of PKA define an axis of cellular proliferation/differentiation in ovarian cancer cells 
BMC Medical Genomics  2008;1:43.
The regulatory subunit of cAMP-dependent protein kinase (PKA) exists in two isoforms, RI and RII, which distinguish the PKA isozymes, type I (PKA-I) and type II (PKA-II). Evidence obtained from a variety of different experimental approaches has shown that the relative levels of type I and type II PKA in cells can play a major role in determining the balance between cell growth and differentiation. In order to characterize the effect of PKA type I and type II regulatory subunits on gene transcription at a global level, the PKA regulatory subunit genes for RIα and RIIβ were stably transfected into cells of the ovarian cancer cell line (OVCAR8).
RIα transfected cells exhibit hyper-proliferative growth and RIIβ transfected cells revert to a relatively quiescent state. Profiling by microarray revealed equally profound changes in gene expression between RIα, RIIβ, and parental OVCAR cells. Genes specifically up-regulated in RIα cells were highly enriched for pathways involved in cell growth while genes up-regulated in RIIβ cells were enriched for pathways involved in differentiation. A large group of genes (~3600) was regulated along an axis of proliferation/differentiation between RIα, parental, and RIIβ cells. RIα/wt and RIIβ/wt gene regulation was shown by two separate and distinct gene set analytical methods to be strongly cross-correlated with a generic model of cellular differentiation.
Overexpression of PKA regulatory subunits in an ovarian cancer cell line dramatically influences the cell phenotype. The proliferation phenotype is strongly correlated with recently identified clinical biomarkers predictive of poor prognosis in ovarian cancer suggesting a possible pivotal role for PKA regulation in disease progression.
PMCID: PMC2577111  PMID: 18822129

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