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Lyme disease is commonly diagnosed by serologic response to Borrelia burgdorferi and related species, but the relationship between serologic targets and clinical features is unknown. We developed a multiantigen Luminex-based panel and evaluated IgG responses in 527 children 1 to 21 years of age assessed for Lyme disease across 4 Pedi Lyme Net emergency departments, including 127 Lyme cases defined by either an erythema migrans (EM) lesion or positive C6 enzyme immunoassay followed by immunoblotting and 400 patients considered clinical mimics. Of 42 antigens tested, 26 elicited specific reactivity in Lyme patients without marked age-dependent variation. Children with single EM lesions typically lacked Borrelia-specific IgG. By principal-component analysis, children with early disseminated and late Lyme disease clustered separately from clinical mimics and also from each other. Neurological disease and arthritis exhibited distinct serologic responses, with OspC variants overrepresented in neurological disease and p100, BmpA, p58, and p45 overrepresented in arthritis. Machine learning identified a 3-antigen panel (VlsE_Bb, p41_Bb, and OspC_Bafz) that distinguished Lyme disease from clinical mimics with a sensitivity of 86.6% (95% confidence interval [CI], 80.3 to 92.1) and a specificity of 95.5% (95% CI, 93.4 to 97.4). Sensitivity was much lower in early Lyme disease (38.5%; 95% CI, 15.4 to 69.2). Interestingly, 17 children classified as Lyme mimics had a positive 3-antigen panel, suggesting that more comprehensive serologic analysis could help refine Lyme diagnosis. In conclusion, multiplex antigen panels provide a novel approach to understanding the immune response in Lyme disease, potentially helping to facilitate accurate diagnosis and to understand differences between clinical stages.

Lyme disease is commonly diagnosed by serologic response to Borrelia burgdorferi and related species, but the relationship between serologic targets and clinical features is unknown. We developed a multiantigen Luminex-based panel and evaluated IgG responses in 527 children 1 to 21 years of age assessed for Lyme disease across 4 Pedi Lyme Net emergency departments, including 127 Lyme cases defined by either an erythema migrans (EM) lesion or positive C6 enzyme immunoassay followed by immunoblotting and 400 patients considered clinical mimics. Of 42 antigens tested, 26 elicited specific reactivity in Lyme patients without marked age-dependent variation. Children with single EM lesions typically lacked Borrelia-specific IgG. By principal-component analysis, children with early disseminated and late Lyme disease clustered separately from clinical mimics and also from each other. Neurological disease and arthritis exhibited distinct serologic responses, with OspC variants overrepresented in neurological disease and p100, BmpA, p58, and p45 overrepresented in arthritis. Machine learning identified a 3-antigen panel (VlsE_Bb, p41_Bb, and OspC_Bafz) that distinguished Lyme disease from clinical mimics with a sensitivity of 86.6% (95% confidence interval [CI], 80.3 to 92.1) and a specificity of 95.5% (95% CI, 93.4 to 97.4). Sensitivity was much lower in early Lyme disease (38.5%; 95% CI, 15.4 to 69.2). Interestingly, 17 children classified as Lyme mimics had a positive 3-antigen panel, suggesting that more comprehensive serologic analysis could help refine Lyme diagnosis. In conclusion, multiplex antigen panels provide a novel approach to understanding the immune response in Lyme disease, potentially helping to facilitate accurate diagnosis and to understand differences between clinical stages.

The first ever messenger RNA (mRNA) vaccines received emergency approvals in December 2020 and are highly protective against SARS-CoV-21–3. However, the contribution of each dose to the generation of antibodies against SARS-CoV-2 spike (S) protein and the degree of protection against novel variants, including delta, warrant further study. Here, we investigated the B cell response to the BNT162b2 vaccine by integrating repertoire analysis with single-cell transcriptomics of B cells from serial blood collections pre- and post-vaccination. The first vaccine dose elicits highly mutated IgA+ plasmablasts against the S protein subunit S2 at day 7, suggestive of recall of a memory B cell response generated by prior infections with heterologous coronaviruses. On day 21, we observed minimally-mutated IgG+ activated switched memory B cells targeting the receptor binding domain (RBD) of the S protein, likely representing a primary response derived from naïve B cells. The B cell response against RBD is specifically boosted by the second vaccine dose, and encodes antibodies that potently neutralize SARS-CoV-2 pseudovirus and partially neutralize novel variants, including delta. These results demonstrate that the first vaccine dose activates a non-neutralizing recall response predominantly targeting S2, while the second vaccine dose is vital to boosting neutralizing anti-S1 RBD B cell responses.

Managing patients with rheumatic disease during the COVID-19 pandemic has posed a unique challenge. Immunosuppressed patients are at an increased risk for developing severe COVID-19 and may not derive full protection from the vaccine (1-5). Thus, it is paramount we develop strategies whereby rheumatic disease patients can be protected from the pandemic virus and its variants.

Introduction: The protein-arginine deiminase (PAD) 4 enzyme plays an important role in the pathogenesis of rheumatoid arthritis (RA) and also represents an antigenic target. Anti-PAD4 antibodies can be present in RA and are associated with specific clinical features. Areas covered: This review aims to analyze the current knowledge and recent findings on anti-PAD4 antibodies in RA and their clinical and immunological significance. Expert opinion: Anti-PAD4 antibodies are not currently used in clinical practice for the management of RA. Nevertheless, there is growing evidence of their relevance in RA, and of their potential utility to improve diagnosis, patient stratification, and prognosis.

There is intense clinical interest in the potential effects of platelet-rich plasma (PRP) for the treatment of osteoarthritis (OA). This study tested the hypotheses that (i) "lower" levels of the inflammatory mediators (IMs), interleukin-1β, and tumor necrosis factor α (TNF-α) and (ii) "higher" levels of the growth factors (GFs), insulin-like growth factor 1, and transforming growth factor β1 within leukocyte-poor PRP correlate with more favorable chondrocyte and macrophage responses in vitro. Samples were collected from 10 "healthy" young male (23-33 years old) human subjects (H-PRP) and nine older (62-85 years old) male patients with severe knee OA (OA-PRP). The samples were separated into groups of "high" or "low" levels of IM and GF based on multiplex cytokine and enzyme-linked immunosorbent assay data. Three-dimensional (3D) alginate bead chondrocyte cultures and monocyte-derived macrophage cultures were treated with 10% PRP from donors in different groups. Gene expression was analyzed by quantitative polymerase chain reaction. Contrary to our hypotheses, the effect of PRP on chondrocytes and macrophages was mainly influenced by the age and disease status of the PRP donor as opposed to the IM or GF groupings. While H-PRP showed similar effects on expression of chondrogenic markers (Col2a1 and Sox9) as the negative control group (p > 0.05), OA-PRP decreased chondrocyte expression of Col2a1 and Sox-9 messenger RNA by 40% and 30%, respectively (Col2a1, p = 0.015; Sox9, p = 0.037). OA-PRP also upregulated TNF-α and matrix metallopeptidase 9 (p < 0.001) gene expression in macrophages while H-PRP did not. This data suggests that PRP from older individuals with OA contain factors that may suppress chondrocyte matrix synthesis and promote macrophage inflammation in vitro. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:1760-1770, 2019.

Tendinopathy is a common and disabling condition that is difficult to treat. The pathomolecular events behind tendinopathy remain uncertain. Micro-RNAs (miRNAs, miRs) are short non-coding RNAs that regulate gene expression and may play a role in tendinopathy development. Tenocytes were obtained from human patellar tendons in patients undergoing anterior cruciate ligament (ACL) reconstruction. Micro-RNA mimics and antagomirs for miR-30d, 26a, and 29a were separately transfected into tenocyte culture. Gene expression for scleraxis, collagen 1 alpha 1 (COL1A1), collagen 3 alpha 1 (COL3A1), interleukin-1-beta (IL-1β), interleukin-6 (IL-6), bone morphogenic protein 2 (BMP2), bone morphogenic protein 12 (BMP12), and osteocalcin was determined for each miRNA mimic and antagomir transfection using real-time quantitative PCR (qPCR). The results showed that exogenous miR-29a downregulated BMP2 and BMP12, while miR-26a and miR-30d did not have a significant effect on tenocyte gene expression. These findings suggest miR-29a contributes to tendon homeostasis and can serve as a potential therapeutic target in treating tendinopathy.

B cells have important functions in the pathogenesis of autoimmune diseases, including autoimmune rheumatic diseases. In addition to producing autoantibodies, B cells contribute to autoimmunity by serving as professional antigen-presenting cells (APCs), producing cytokines, and through additional mechanisms. B cell activation and effector functions are regulated by immune checkpoints, including both activating and inhibitory checkpoint receptors that contribute to the regulation of B cell tolerance, activation, antigen presentation, T cell help, class switching, antibody production and cytokine production. The various activating checkpoint receptors include B cell activating receptors that engage with cognate receptors on T cells or other cells, as well as Toll-like receptors that can provide dual stimulation to B cells via co-engagement with the B cell receptor. Furthermore, various inhibitory checkpoint receptors, including B cell inhibitory receptors, have important functions in regulating B cell development, activation and effector functions. Therapeutically targeting B cell checkpoints represents a promising strategy for the treatment of a variety of autoimmune rheumatic diseases. B cells contribute to the pathogenesis of many rheumatic diseases. Targeting immune checkpoints that control the activation and effector function of B cells represents a promising therapeutic avenue.

Background Autoimmune disease prevention requires tools to assess an individual's risk of developing a specific disease. One tool is disease-associated autoantibodies, which accumulate in an asymptomatic preclinical period. However, patients sometimes exhibit autoantibodies associated with a different disease classification. When and how these alternative autoantibodies first appear remain unknown. This cross-sectional study characterizes alternative autoimmunity, and associated genetic and environmental factors, in unaffected first-degree relatives (FDRs) of patients, who exhibit increased future risk for the same disease. Methods Samples (n = 1321) from disease-specific autoantibody-positive (aAb+) systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and type 1 diabetes (T1D) patients; and unaffected aAb+ and autoantibody-negative (aAb–) SLE and RA FDRs were tested for SLE, RA, and T1D aAbs, as well as anti-tissue transglutaminase, anti-cardiolipin and anti-thyroperoxidase. FDR SLE and RA genetic risk scores (GRS) were calculated. Findings Alternative autoimmunity occurred in SLE patients (56%) and FDRs (57·4%), RA patients (32·6%) and FDRs (34·8%), and T1D patients (43%). Expanded autoimmunity, defined as autoantibodies spanning at least two other diseases, occurred in 18·5% of SLE patients, 16·4% of SLE FDRs, 7·8% of RA patients, 5·3% of RA FDRs, and 10·8% of T1D patients. SLE FDRs were more likely to have alternative (odds ratio [OR] 2·44) and expanded (OR 3·27) autoimmunity than RA FDRs. Alternative and expanded autoimmunity were associated with several environmental exposures. Alternative autoimmunity was associated with a higher RA GRS in RA FDRs (OR 1·41), and a higher SLE GRS in aAb+ RA FDRs (OR 1·87), but not in SLE FDRs. Interpretation Autoimmunity commonly crosses disease-specific boundaries in systemic (RA, SLE) and organ-specific (T1D) autoimmune diseases. Alternative autoimmunity is more common in SLE FDRs than RA FDRs, and is influenced by genetic and environmental factors. These findings have substantial implications for preclinical disease pathogenesis and autoimmune disease prevention studies. Fund NIH U01AI101981, R01AR051394, U19AI082714, P30AR053483, P30GM103510, U54GM104938, U01AI101934, R01AI024717, U01AI130830, I01BX001834, & U01HG008666.

Timing analysis and timing closure are critical steps in digital circuit design. To ensure an error-free design, timing constraints are usually set-based upon the longest path delay from static timing analysis. However, a circuit could have dramatically different internal activity because of the variation of input workload. The path with the longest delay may not be active for certain input workloads, which would enable timing speculation for increased performance. This paper describes an approach to identify the greatest contributors of timing errors and mitigate those errors by replacing certain standard cells in the design. We evaluated our mitigation for several benchmark designs and demonstrated an error-free performance gain up to 37%. The entire design flow uses Synopsys electronic design automation tools and customized scripts, which can be adapted for other designs.

OBJECTIVES: We aimed to assess whether serum cytokine/chemokine concentrations predict incident cancer in RA patients. METHODS: Data from cancer-free enrollees in the Veterans Affairs Rheumatoid Arthritis (VARA) Registry were linked to a national VA oncology database and the National Death Index (NDI) to identify incident cancers. Seventeen serum cytokines/chemokines were measured from enrollment serum and an overall weighted cytokine/chemokine score (CK score) was calculated. Associations of cytokines/chemokines with all-site, lung, and lymphoproliferative cancers were assessed in Cox regression models accounting for relevant covariates including age, sex, RA disease activity, and smoking. RESULTS: In 1,216 patients, 146 incident cancers (42 lung and 23 lymphoproliferative cancers) occurred over 10,072 patient-years of follow-up with a median time of 4.6 years from enrollment (cytokine/chemokine measurement) to cancer incidence. In fully adjusted models, CK score was associated with a higher risk of all-site (aHR 1.32, 95% CI 1.01-1.71, p

Although widely prevalent, Lyme disease is still under-diagnosed and misunderstood. Here we followed 73 acute Lyme disease patients and uninfected controls over a period of a year. At each visit, RNA-sequencing was applied to profile patients' peripheral blood mononuclear cells in addition to extensive clinical phenotyping. Based on the projection of the RNA-seq data into lower dimensions, we observe that the cases are separated from controls, and almost all cases never return to cluster with the controls over time. Enrichment analysis of the differentially expressed genes between clusters identifies up-regulation of immune response genes. This observation is also supported by deconvolution analysis to identify the changes in cell type composition due to Lyme disease infection. Importantly, we developed several machine learning classifiers that attempt to perform various Lyme disease classifications. We show that Lyme patients can be distinguished from the controls as well as from COVID-19 patients, but classification was not successful in distinguishing those patients with early Lyme disease cases that would advance to develop post-treatment persistent symptoms.

COVID-19 is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. Here we develop three protein arrays to measure IgG autoantibodies associated with connective tissue diseases, anti-cytokine antibodies, and anti-viral antibody responses in serum from 147 hospitalized COVID-19 patients. Autoantibodies are identified in approximately 50% of patients but in less than 15% of healthy controls. When present, autoantibodies largely target autoantigens associated with rare disorders such as myositis, systemic sclerosis and overlap syndromes. A subset of autoantibodies targeting traditional autoantigens or cytokines develop de novo following SARS-CoV-2 infection. Autoantibodies track with longitudinal development of IgG antibodies recognizing SARS-CoV-2 structural proteins and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins., Infection with SARS-CoV2 and the development of Coronavirus disease 2019 (COVID-19) has been linked to induction of autoimmunity and autoantibody production. Here the authors characterise the new-onset IgG autoantibody response in hospitalised patients with COVID-19 which they correlate to the magnitude of the SARS-CoV2 response.

Protecting computation systems against soft errors is expensive. Unoptimized soft error mitigation schemes can cause area, power, and performance overheads. Therefore, efficient fault-tolerant design should be guided by assessing the cost of developing reliable systems. We present a method to quantify and evaluate trade-offs to protect the system. Using gem5Panalyzer, the toolset we developed to estimate vulnerability factors of microprocessors, we conducted sweeps of Program Vulnerability Factor (PVF) masking to collect the PVF responses to instruction-level masking. We evaluated the confidence in PVF estimations made by gem5Panalyzer with multiple benchmarks from the MiBench suite. Then, we analyzed PVF-masking sweep results. The sensitivity of vulnerability improvement to mitigation techniques varies with the types of applications. When the instruction-level masking effect is 90%, time-averaged PVF reductions of selected benchmarks range from a high of 67% to a low of 10%. The differences in PVF reduction inform designers whether it is worth improving the masking level. As the masking factor is correlated with the efforts to implement mitigations, our method can help to optimize system design choices.

Rheumatoid arthritis (RA) is a systemic and incurable autoimmune disease characterized by chronic inflammation in synovial lining of joints. To identify the signaling pathways involved in RA, its disease activity, and treatment response, we adapted a systems immunology approach to simultaneously quantify 42 signaling nodes in 21 immune cell subsets (e.g., IFNα→p-STAT5 in B cells) in peripheral blood mononuclear cells (PBMC) from 194 patients with longstanding RA (including 98 patients before and after treatment), and 41 healthy controls (HC). We found multiple differences between patients with RA compared to HC, predominantly in cytokine-induced Jak/STAT signaling in many immune cell subsets, suggesting pathways that may be associated with susceptibility to RA. We also found that high RA disease activity, compared to low disease activity, was associated with decreased (e.g., IFNα→p-STAT5, IL-10→p-STAT1) or increased (e.g., IL-6→STAT3) response to stimuli in multiple cell subsets. Finally, we compared signaling in patients with established, refractory RA before and six months after initiation of methotrexate (MTX) or TNF inhibitors (TNFi). We noted significant changes from pre-treatment to post-treatment in IFNα→p-STAT5 signaling and IL-10→p-STAT1 signaling in multiple cell subsets; these changes brought the aberrant RA signaling profiles toward those of HC. This large, comprehensive functional signaling pathway study provides novel insights into the pathogenesis of RA and shows the potential of quantification of cytokine-induced signaling as a biomarker of disease activity or treatment response.

Most of what we know about adaptive immunity has come from inbred mouse studies, using methods that are often difficult or impossible to confirm in humans. In addition, vaccine responses in mice are often poorly predictive of responses to those same vaccines in humans. Here we use human tonsils, readily available lymphoid organs, to develop a functional organotypic system that recapitulates key germinal center features in vitro, including the production of antigen-specific antibodies, somatic hypermutation and affinity maturation, plasmablast differentiation and class-switch recombination. We use this system to define the essential cellular components necessary to produce an influenza vaccine response. We also show that it can be used to evaluate humoral immune responses to two priming antigens, rabies vaccine and an adenovirus-based severe acute respiratory syndrome coronavirus 2 vaccine, and to assess the effects of different adjuvants. This system should prove useful for studying critical mechanisms underlying adaptive immunity in much greater depth than previously possible and to rapidly test vaccine candidates and adjuvants in an entirely human system.

The importance of citrullination in rheumatoid arthritis (RA) has been reported, but the degree to which individual citrullinated proteins affect the onset and progression of RA is still unclear. We aimed to identify citrullinated proteins that may play an important role in the onset and progression of RA using an individualised anti-citrullinated protein antibody (ACPA) evaluation system with citrullinated peptides as probes.Serum samples from 50 normal donors and 51 RA patients were evaluated using a custom MagPlexTM bead array with 13 types of citrullinated peptide. The presence/absence of ACPAs that react to each citrullinated peptide in each subject was determined using the Z-score, which was calculated based on the fluorescence intensity distribution of a sample from a normal donor. Whether the fluorescence intensity was inhibited when free citrullinated peptides were added to a system was also evaluated.Median fluorescence intensities obtained from beads coupled with the 13 types of citrullinated peptide were all significantly higher in RA patients versus normal donors. With a Z-score ≥2 as the cut-off value for the presence of ACPAs, ACPAs that recognised five types of citrullinated peptides derived from fibrinogen A, fillagrin, clusterin, and vimentin were widely detected in RA patients. In addition, inhibition experiments showed that citrullinated vimentin, clusterin, and enolase 1A peptides inhibited coupling of ACPAs to other citrullinated peptides.ACPAs to many citrullinated proteins exhibited cross-reactivity to citrullinated clusterin and vimentin, suggesting the importance of citrullinated clusterin and vimentin in the early stages of RA pathogenesis.

In this research, we explore the viability of using a biologically-inspired design to develop a host-based next generation firewall. Many of the firewall designs in use today are still signature-based (with very few exceptions just released in 2020), which tend to struggle to protect against zero-day attacks and against encrypted traffic. By applying cellular membrane concepts such as endocytosis and ligand-receptor interactions along with machine learning, we created a feasible next generation firewall prototype capable of defending against zero-day threats even within encrypted traffic. Specifically, we built both supervised and unsupervised machine learning models, optimized their results, then we exported the models, and tested the exported models on zero-day malicious network traffic. Finally, we modified the open source Linux IP Tables firewall software to use our exported model as the packet filtering mechanism. The end result was a working host-based, supervised machine learning driven, next generation firewall prototype that demonstrated very promising results, nearly 100% of normal connections were passed and 77% of zero-day malicious connections were blocked.

Lyme disease, caused by the bacteria Borrelia burgdorferi, is the most common and rapidly growing vector-borne infectious disease in the United States and Europe. High variability in disease burden among Lyme patients suggests that individual immune responses may be key drivers of clinical presentation and patient outcomes. Use of high resolution flow-based immunosorbent profiling revealed that a subset of Lyme patients with persistent symptoms were producing high concentrations of IgE specific to B. burgdorferi. Comparing C57B/6 mice, which are tolerant to B. burgdorferi, and C3H/HeJ mice, which are susceptible to disease, we find high levels of IgE specific for B. burgdorferi in C3H/HeJ but not C57B/6 mice. Furthermore, IgE was found to target Borrelia peptidoglycan in both acute and chronic infection models. Histologic analysis of mouse Lyme arthritic ankle tissue showed mast cells, which release highly immunogenic effectors upon activation by bound IgE, degranulating at significantly higher rates compared to uninfected controls. Forced mast cell degranulation exacerbated Lyme arthritis in infected mice. This data suggests that a subset of Lyme patients with persistent symptoms may have developed an allergic response to conserved bacterial antigens from a B. burgdorferi infection, as opposed to an autoimmune type response. Inclusion of IgE reactivity in diagnostic testing and examination of pathological immune responses to bacterial antigens could assist clinicians in patient care and effective treatments. Research reported in this publication was supported by the Fairbairn family foundation; Bay Area Lyme Foundation; the Younger family foundation; the Robert J. Kleberg, Jr., and Helen C. Kleberg Foundation; the Virginia and D. K. Ludwig Fund for Cancer Research; M.C.T. was supported by Stanford Immunology training grant 5T32AI007290, and the NIH NRSA 1 F32 AI124558-01 award. L.B.T.D. was supported by a Stanford Diversifying Academia Recruiting Excellence fellowship. S.D.G was supported by the California Institute for Regenerative Medicine Bridges 2.0 Training Program grant EDUC2-08397. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Citrullination is recognized as a key pathogenic process in rheumatoid arthritis (RA), as evidenced by the formation of anti-citrullinated protein antibodies (APCAs) in the majority of patients; however, the mechanisms that result in citrullinated autoantigen generation are not fully understood. Although the citrullinating enzyme peptidylarginine deiminase IV (PAD4) is predominantly expressed by neutrophils and monocytes, the contribution of monocytes to the citrullinated autoantigen pool has been underexplored. In this study, we utilized multiple complementary methods including flow cytometry, immunofluorescence, and transmission electron microscopy, which revealed a predominantly extranuclear localization of PAD4 in monocytes with a fraction present on the cell surface. Surface PAD4 was enzymatically active and citrullinated both extracellular fibrinogen and endogenous surface proteins in a calcium dose–dependent manner. In addition, human monoclonal ACPAs cloned from patients with RA recognized fibrinogen citrullinated by monocyte-surface PAD4. Mass spectrometry analysis of citrullinated proteins from the cell surface fraction revealed CD11b to be a novel PAD4 substrate. Citrullinated CD11b was recognized by autoantibodies in 60% of ACPA+ RA patients compared to 6% of healthy controls (p=0.0021) and 0% of ACPA− RA patients (p≤0.001). Taken together, our study demonstrates that PAD4 is expressed on the surface of monocytes in an enzymatically active state that renders the monocyte surface a novel site of citrullinated autoantigen generation in RA. Supported by funds received from Bristol-Myers Squibb.

Previous reports show a small subset of CD8+ T cells expressing Ly49 proteins in mice can suppress autoimmunity in a model of demyelinating disease. Here we find a markedly increased frequency of CD8+ T cells expressing inhibitory Killer cell Immunoglobulin like Receptors (KIR), the human equivalent of the Ly49 family, in the blood and inflamed tissues of various human autoimmune diseases. Increased KIR+ CD8+ T cells in the gut also correlate with disease activity in Celiac disease (CeD) patients. Moreover, KIR+ CD8+ T cells can efficiently eliminate pathogenic gliadin-specific CD4+ T cells from CeD patients’ leukocytes in vitro. Together with gene expression data, this shows that these cells are the likely equivalent of the mouse Ly49+ CD8+ T cells. Furthermore, we observe elevated levels of KIR+ CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 and influenza-infected patients, and this correlates with disease severity and vasculitis in COVID-19. Single-cell RNA and parallelized TCR sequencing reveals that expanded KIR+ CD8+ T cells from these different diseases and healthy subjects display shared phenotypes and similar T cell receptor sequences. Selective ablation of the murine counterpart in virus-infected mice leads to exacerbated autoimmunity developed after infection. These results characterize a regulatory CD8+ T cell subset in humans which we hypothesize functions to control pathogenic cells in autoimmune and infectious diseases, with important implications for the cellular dynamics and possible therapeutic approaches to suppress unwanted autoimmunity. Supported by National Institutes of Health U19-AI057229 Howard Hughes Medical Institute Stanford Diabetes Research Center (P30DK116074)

Background IgG4-related disease (IgG4-RD) is a fibroinflammatory condition involving loss of B-cell tolerance and production of autoantibodies. However, the relevant targets and role of these aberrant humoral immune responses are not defined. Objective Our aim was to identify novel autoantibodies and autoantigen targets that promote pathogenic responses in IgG4-RD. Methods We sequenced plasmablast antibody repertoires in patients with IgG4-RD. Representative mAbs were expressed and their specificities characterized by using cytokine microarrays. The role of anti–IL-1 receptor antagonist (IL-1RA) autoantibodies was investigated by using in vitro assays. Results We identified strong reactivity against human IL-1RA by using a clonally expanded plasmablast-derived mAb from a patient with IgG4-RD. Plasma from patients with IgG4-RD exhibited elevated levels of reactivity against IL-1RA compared with plasma from the controls and neutralized IL-1RA activity, resulting in inflammatory and fibrotic mediator production in vitro. IL-1RA was detected in lesional tissues from patients with IgG4-RD. Patients with anti–IL-1RA autoantibodies of the IgG4 subclass had greater numbers of organs affected than did those without anti–IL-1RA autoantibodies. Peptide analyses identified IL-1RA epitopes targeted by anti–IL-1RA antibodies at sites near the IL-1RA/IL-1R interface. Serum from patients with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) also had elevated levels of anti–IL-1RA autoantibodies compared with those of the controls. Conclusion A subset of patients with IgG4-RD have anti–IL-1RA autoantibodies, which promote proinflammatory and profibrotic meditator production via IL-1RA neutralization. These findings support a novel immunologic mechanism underlying the pathogenesis of IgG4-RD. Anti–IL-1RA autoantibodies are also present in a subset of patients with SLE and RA, suggesting a potential common pathway in multiple autoimmune diseases.

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by B cell dysregulation and breaks in tolerance that lead to the production of pathogenic autoantibodies. We performed single-cell RNA sequencing of B cells from healthy donors and individuals with SLE which revealed upregulated CD52 expression in SLE patients. We further demonstrate that SLE patients exhibit significantly increased levels of B cell surface CD52 expression and plasma soluble CD52, and levels of soluble CD52 positively correlate with measures of lupus disease activity. Using CD52-deficient JeKo-1 cells, we show that cells lacking surface CD52 expression are hyperresponsive to B cell receptor (BCR) signaling, suggesting an inhibitory role for the surface-bound protein. In healthy donor B cells, antigen-specific BCR-activation initiated CD52 cleavage in a phospholipase C dependent manner, significantly reducing cell surface levels. Experiments with recombinant CD52-Fc showed that soluble CD52 inhibits BCR signaling in a manner partially-dependent on Siglec-10. Moreover, incubation of unstimulated B cells with CD52-Fc resulted in the reduction of surface immunoglobulin and CXCR5. Prolonged incubation of B cells with CD52 resulted in the expansion of IgD+IgMlo anergic B cells. In summary, our findings suggest that CD52 functions as a homeostatic protein on B cells, by inhibiting responses to BCR signaling. Further, our data demonstrate that CD52 is cleaved from the B cell surface upon antigen engagement, and can suppress B cell function in an autocrine and paracrine manner. We propose that increased expression of CD52 by B cells in SLE represents a homeostatic mechanism to suppress B cell hyperactivity.

Background We have previously demonstrated adaptive antibody responses targeting public tumor antigens in cancer patients. ATRC-101, a clinical stage, engineered version of an antibody identified in such a patient, displays robust single-agent activity in syngeneic tumor models requiring Fc receptors (FcRs) expressed by innate immune cells and the presence of CD8+ T cells. The novel target of ATRC-101 was found to be a tumor-restricted ribonucleoprotein (RNP) complex, and because RNP complexes drive T cell responses in infectious and autoimmune disease via innate immune cells, we further characterized the mechanism-of-action of ATRC-101. Here we describe changes in immune cell populations in a tumor model proximal to treatment initiation with ATRC-101. Methods Mice bearing EMT6 tumors received ATRC-101 beginning on day 7 post-tumor inoculation. Tissues were harvested between days 7 and 14 and analyzed by flow cytometry and immunohistochemistry. Transcriptome analysis was performed using RNA sequencing on whole tumors taken on days 7, 9, and 12. Results The earliest significant changes induced by ATRC-101, relative to vehicle, were noted just 24 hours after dosing: increased numbers of cDC1 cells in blood, and decreased numbers of cDC2 cells in blood and M-MDSCs in tumor. A significant increase of CD8+ T cells was observed in blood 48 hours after dosing and in tumor 96 hours after dosing. Increased numbers of NK cells were also observed in blood and tumor at this later time. Multiplex analysis of circulating cytokines demonstrated a very early increase in myeloid chemo-attractants, such as MCP1 and MIP1a.Whole exome sequencing of tumor samples showed that ATRC-101 dosing drives a significant increase, relative to vehicle, in the expression of interferon-stimulated genes. Co-culturing experiments demonstrated that induced, bone marrow-derived dendritic cells are activated by ATRC-101 and its target in a dose-dependent fashion. Conclusions Dosing with ATRC-101 in the EMT6 syngeneic tumor model, in which ATRC-101 displays notable single-agent activity, leads to changes in immune cell composition in the blood and tumor, with the earliest changes observed in myeloid or myeloid-derived cell populations, and to the early appearance of myeloid chemo-attractants. We believe these data indicate that ATRC-101 acts proximally on the myeloid cell populations in the tumor, leading to a remodeling of the tumor environment and an adaptive immune response that includes CD8+ T cells driving tumor regression. Our data demonstrate that ATRC-101, bound to its target which is an RNP complex, can activate myeloid cells and are consistent with this activation occurring via FcR and Toll-like receptor (TLR) pathways.

Background We have previously described ATRC-101, a fully human, engineered IgG1 antibody binding a tumor-restricted ribonucleoprotein (RNP) complex as its target. ATRC-101 is currently under evaluation in the clinic as a monotherapy for solid tumors. Following target engagement, ATRC-101 functions in an Fc-mediated fashion to deliver the target to the innate immune system, which modifies the tumor microenvironment and generates an adaptive immune response involving CD8+ T cells leading to anti-tumor activity in syngeneic mouse models. Binding of ATRC-101 appears restricted to malignant tissues in both mouse models and human, across a range of cancer histologic phenotypes, including carcinomas that are known candidates for anti-PD-1 treatment. In the EMT6 mouse model, representing a T cell-excluded phenotype in which anti-PD-1 agents display limited activity, ATRC-101 monotherapy was uniformly vigorous with persistent anti-tumor memory. When co-administered at a lower dose with anti-PD-1, the combination of therapy demonstrated a robust and heightened anti-tumor response relative to either agent dosed as monotherapy at similar concentrations. Methods To gain insight into the mechanisms that contribute to the anti-tumor effect with combination therapy, in vivo experiments in the EMT6 syngeneic mouse model were performed to determine temporal and spatial patterns of infiltrates and assessed tumors by using whole exome sequencing following administration of ATRC-101 vs. vehicle control. Within naive human tumor samples, coincident immunoreactivities of ATRC-101 and PD-L1 were also characterized. Results In mice treated with ATRC-101, analysis by immunofluorescence revealed a significant increase in the percentage of PD-1 reactive T cells within the tumor microenvironment. Elevated transcripts for PD-L1 also were detected in tumors from mice administered ATRC-101 vs baseline levels or vehicle control. When human tumor tissues were characterized for coincident expression of these targets, a high prevalence of ATRC-101 immunoreactivity was noted in both PD-L1 reactive and non-reactive tumor cores. Across multiple indications, ATRC-101 immunoreactivity was apparent in > 50% of PD-L1+ cores. Conclusions In situ studies suggest the target of ATRC-101 may co-locate with PD-L1, and in vivo studies indicate that ATRC-101 administration increases PD-L1 transcripts and PD-1-positive infiltrates in mouse tumor. Altogether, our data support studies to combine ATRC-101 with agents targeting PD-1 in the clinical treatment of solid tissue malignancies. Acknowledgements We acknowledge the significant effort and contributions of our colleagues from the clinical, in vivo pharmacology, translational sciences, in vitro pharmacology, and cell biology groups. This includes Mark Armanini, Erin Brosey, Chantia Carroll, Sean M. Carroll, Nicole Haaser, Benjamin Haugen, Dongkyoon Kim, Beatriz Millare, Yann Chong Tan, Danhui Zhang, and Patricia Zuno. Trial Registration NCT04244552 Ethics Approval The study was approved by WIRB (Western Institutional Review Board) on Jun 11, 2013. The WIRB study number is 20130121. Reference DeFalco J, Harbell M, Manning-Bog A, et al. Non-progressing cancer patients have persistent B cell responses expressing shared antibody paratopes that target public tumor antigens. Clinical Immunology 2018; 187:37–45.

Autonomous capabilities have emerged as a ubiquitous technology in cars, robots, drones and many other useful devices that are destined to transform our society. Many of the more advanced autonomous devices use computer vision to track and recognize objects, while others may use LIDAR or SONAR or other forms of radar. Since many of these devices are positioned to be disruptive technologies in our society, the fidelity of their abilities is paramount. In this paper, we introduce our black box approach, which can accurately infer, characterize, and break native device autonomy. We demonstrate this approach by using the tightly guarded autonomy code in the immensely popular computer vision driven autonomous DJI drones (i.e., ActiveTrack Mode) as the target native autonomy. We illustrate that this method allows us to quickly infer detailed information about the computer vision tracking algorithm, characterize the autonomous capability, and identify targets that defy these algorithms. We posit that this approach can be extended to other computer vision driven autonomous systems and is a necessary step in developing nondestructive privacy preserving mechanisms that foil the presumed tracking process.

In bring-your-own-device (BYOD) and guest wireless networks, the use of mobile devices within industry, government, and academic enterprise networks represents a difficult security challenge for system administrators. Devices not owned by the enterprise can pose additional risk. Our prior research demonstrated a dynamic anomaly detection method that used side-channel analysis of ping responses to infer whether devices were compromised. Initial results showed promise for a limited dataset. Our extension of this prior work now uses deep learning, twice as many features, and analyzes ten times more malware. Additional experiments demonstrate that our deep learning model generalizes to the detection of unseen threats across multiple families of malware.

Background: Immediately following a lateral ligament reconstruction of the ankle, the strength of the repair is far less than that of the native anterior talofibular ligament (ATFL). Additionally, early functional rehabilitation has been shown to increase laxity of the repair. We hypothesized that a Broström procedure augmented with a suture-tape construct would allow early functional rehabilitation while maintaining patient reported outcomes within a military population. Methods: This study is a retrospective study of 93 consecutive patients with chronic lateral ankle instability that were treated with a Broström procedure augmented with a suture-tape construct. Subjects were evaluated at 2, 6, and 12 weeks postoperatively, with yearly satisfaction reviews. Demographics and functional outcomes including Foot and Ankle Disability Index (FADI), visual analog scale (VAS), satisfaction score, and clinical measures including single-leg hop and single-leg heel raise were recorded. Our patients included 75 males and 18 females with a mean age of 30 ± 7 (range, 19-51) years; our mean follow-up was 19 (range, 3-48) months. Results: The mean FADI score improved from 67 preoperatively to 87 and 90 at 6 and 12 weeks ( P < .001), with 60 patients (65%) obtaining a score greater than 90. The mean VAS scores improved from 4.8 preoperatively to 1.4 and 1.3 at 6 and 12 weeks ( P < .001). Eighty-two (96%) of the patients asked were able to complete a single-leg hop and single-leg heel raise at 6 weeks. The 12-, 24-, 36-, and 48-month satisfaction scores were 8.5, 9.8, 9.2, and 8.9, respectively. Demographics collected did not impact results. Conclusion: This study suggests that a Broström procedure augmented with suture tape enabled early safe functional rehabilitation without subsequent failure. Our data also demonstrated a sustained high level of patient satisfaction while preventing reoccurrence within a high-demand military population. Level of Evidence: Level IV, retrospective case series.

Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS), with characteristic inflammatory lesions and demyelination. The clinical benefit of cell-depleting therapies targeting CD20 has emphasized the role of B cells and autoantibodies in MS pathogenesis. We previously introduced an enzyme-linked immunospot spot (ELISpot)-based assay to measure CNS antigen-specific B cells in the blood of MS patients and demonstrated its usefulness as a predictive biomarker for disease activity in measuring the successful outcome of disease-modifying therapies (DMTs). Here we used a planar protein array to investigate CNS-reactive antibodies in the serum of MS patients as well as in B cell culture supernatants after polyclonal stimulation. Anti-CNS antibody reactivity was evident in the sera of the MS cohort, and the antibodies bound a heterogeneous set of molecules, including myelin, axonal cytoskeleton, and ion channel antigens, in individual patients. Immunoglobulin reactivity in supernatants of stimulated B cells was directed against a broad range of CNS antigens. A group of MS patients with a highly active B cell component was identified by the ELISpot assay. Those antibody reactivities remained stable over time. These assays with protein arrays identify MS patients with a highly active B cell population with antibodies directed against a swathe of CNS proteins.

Aggressive technology scaling boosts the embedded processor performance but deteriorates the system resilience to soft errors. To balance trade-offs between reliability and design overheads, we developed Gem5Panalyzer: a novel light-weight reliability evaluation tool built on top of the gem5 simulator. It computes vulnerability factors (VFs) of the programs running on ARMv7-like CPUs and constructs a dataset for machine learning studies. Gem5Panalyzer features satisfactory compatibility and extensibility. Another highlight of our tool is the integration of reliability and machine learning. We validated Gem5Panalyzer by evaluating the behavior of selected MiBench programs’ VFs. Additionally, a study using Neural Network and Gem5Panalyer to predict VFs shows that for the qsort application, the predictor performance has become saturated when the training set size reaches 43%. This finding attests the idea that predicting future VFs of large applications is possible based on a limited prior knowledge of vulnerability.

Technology scaling impacts the probability of masking a propagating transient pulse. This paper presents a technique to improve the electrical masking of logic gates when considering the variation in the process, voltage, and temperature (PVT) for a 45-nm technology. The worst cases were exhibited in high temperature and low voltage, which enhanced the transient pulse to traverse to the primary outputs (POs). The vulnerable paths were used to select vulnerable gates for the mitigation approach. Due to worst cases of low voltage and high temperature, the gates at the POs were also selected for mitigation. The approach improved the electrical masking of the circuit by reducing the amplitudes of the transient pulses by 93% and 90% for low voltage and high temperature respectively with 57% area overhead.

Lyme disease is a tick-borne infection caused by the bacteria Borrelia burgdorferi. Current diagnosis of early Lyme disease relies heavily on clinical criteria, including the presence of an erythema migrans rash. The sensitivity of current gold-standard diagnostic tests relies upon antibody formation, which is typically delayed and thus of limited utility in early infection. We conducted a study of blood and skin biopsy specimens from 57 patients with a clinical diagnosis of erythema migrans. Samples collected at the time of diagnosis were analyzed using an ultrasensitive, PCR-based assay employing an isothermal amplification step and multiple primers. In 75.4% of patients, we directly detected one or more B. burgdorferi genotypes in the skin. Two-tier testing showed that 20 (46.5%) of those found to be PCR positive remained serologically negative at both acute and convalescent time points. Multiple genotypes were found in three (8%) of those where a specific genotype could be identified. The 13 participants who lacked PCR and serologic evidence for exposure to B. burgdorferi could be differentiated as a group from PCR-positive participants by their levels of several immune markers as well as by clinical descriptors such as the number of acute symptoms and the pattern of their erythema migrans rash. These results suggest that within a Mid-Atlantic cohort, patient subgroups can be identified using PCR-based direct detection approaches. This may be particularly useful in future research such as vaccine trials and public health surveillance of tick-borne disease patterns.

OBJECTIVE Osteoarthritis (OA) is a common cause of joint pain and disability, and effective treatments are lacking. Extracellular adenosine has antiinflammatory effects and can prevent and treat OA in animal models. Ticagrelor and clopidogrel are both used in patients with coronary artery disease, but only ticagrelor increases extracellular adenosine levels. This study was undertaken to determine whether treatment with ticagrelor was associated with a lower risk of OA. METHODS We conducted a 1:2 propensity score-matching analysis using data from 2011-2017 in the Optum Clinformatics Data Mart. Patients who had received either ticagrelor or clopidogrel for ≥90 days were included in our study, and patients with a prior diagnosis of OA or inflammatory arthritis were excluded. OA was identified using International Classification of Diseases codes. The primary outcome was the time to diagnosis of OA after treatment with ticagrelor versus clopidogrel. RESULTS Our propensity score-matched cohort consisted of 7,007 ticagrelor-treated patients and 14,014 clopidogrel-treated patients, with a median number of days receiving treatment of 287 and 284, respectively. For both groups, the mean age was 64 years, and 73% of the patients were male. Multivariate Cox regression analysis estimated a hazard ratio for developing OA of 0.71 (95% confidence interval 0.64-0.79) (P < 0.001) after treatment with ticagrelor compared to clopidogrel. CONCLUSION Treatment with ticagrelor was associated with a 29% lower risk of developing OA compared to treatment with clopidogrel over 5 years of follow-up. We hypothesize that the reduction in OA seen in patients who received ticagrelor may in part be due to increased extracellular adenosine levels.

Open Source Intelligence (OSINT) is the process of using tools and information to passively learn enough information about an organization to begin the cyber attack cycle. OSINT gathering is often the first step in a malicious cyber campaign. Social Media and the Internet (e.g., search engines, open source tools, blogs) are quickly becoming invaluable sources of information for malicious cyber actors. These two very popular forms of technology are notorious for inherently accumulating and archiving personal information about people, organizations, and networks. These technologies also give information perpetual life, which can be summoned at any time by those in possession of the right knowledge (i.e., Data Science) and tools to extract this information. We posit that the extent of these privacy violations have increased to the point where OSINT identified vulnerabilities may be as useful to attackers as zero-day vulnerabilities, since organizations are likely just as unaware of their presence. We refer to the tools and techniques used to identify these types of vulnerabilities as privacy violating OSINT (PV-OSINT). In this paper, we bring to light the very serious damage that can be done to critical infrastructure (CI), by the use of PV-OSINT. We tested our methodology with a real CI, we then shared our findings with the CI owner to verify the efficacy of our approach. Then we developed a framework that could be used by CI owners to constantly assess the security of their networks using PV-OSINT.

Background: Human epidermal growth factor receptor 2 (HER2) positivity in breast cancer portends an aggressive tumor behavior and poor prognosis and is associated with a positive response to trastuzumab treatment. Prior immunohistochemistry and RNA sequencing of breast tumor tissues suggest that trastuzumab may recruit and activate anti-tumor T cells. Tumor infiltrating lymphocytes have been associated with improved response in patients with HER2+ early breast cancer treated with neoadjuvant trastuzumab plus chemotherapy. However, these cells have not previously been characterized at the single cell level in tumor tissue or in the periphery. Assessing the T cell component in the peripheral blood via single-cell sequencing enables high sensitivity detection of rare cells, may identify T cell antigen receptors (TCR) involved in the anti-tumor response, and could lead to a non-invasive means of monitoring trastuzumab-mediated immune activity. Here we perform single cell sequencing of the blood T cell repertoire in breast cancer patients pre- and post-trastuzumab treatment. Methods: To characterize T cell response in trastuzumab plus chemotherapy treated patients, we profiled peripheral CD3+ T cells using 10x Genomics VDJ single-cell sequencing in paired samples from five patients with HER2+ breast cancer. Patients had stage IIA (n=2), stage IIIC (n=2) or stage IV (n=1) breast cancer and were treated with preoperative docetaxel, carboplatin, trastuzumab, pertuzumab (TCHP). Two patients had a pathological complete response (pCR), and three patients had partial clinical response with residual disease at surgery. Peripheral blood mononuclear cells (PMBCs) were collected at a C1D1 pre-treatment and day 1 of cycles 3, 4, or 5. Results: Eleven T cell subpopulations, including naïve and memory CD4+ and CD8+ T cells, activated CD4+ and CD8+ T effector cells, activated CD4+ T regulatory cells, were characterized in the five patients’ peripheral blood based on their transcriptional profiles. T cell subpopulation distribution and clonal expansion profiles were similar in pre- and post- treatment samples in all five donors. Large T cell clonal expansions were detected in the peripheral blood of the two patients who had a pCR, but were not detected in the three patients who had residual disease at surgery. The patients who had a pCR exhibited large expansions in activated CD8+ terminal effector memory/effector memory (TEM/EM) cells followed by expansions in activated CD4+ TEM/EM cells. A minor increasing trend in activated CD4+ Treg cells was observed across all patients upon treatment with TCHP. Conclusions: Single-cell sequencing enables high-resolution characterization of immune cell subsets and represents a promising approach to assess the immune response to trastuzumab and other cancer therapeutics. In this study, single-cell sequencing of peripheral CD3+ T cells identified clonal expansions in activated CD8+ and CD4+ T cells in HER2+ breast cancer patients who had a pCR with preoperative TCHP treatment. These data are consistent with the model that T cells play a key role in trastuzumab-mediated tumor control, and warrant further investigation in a larger sample population. Citation Format: John Vivian, Kimberly Walter, Elliott Drabek, Nicole Haaser, Maren K. Levin, Esther San Roman Rodriguez, Kendra Peck, Ngan Nguyen, Carl Millward, Jonathan Benjamin, William H. Robinson, Joyce A. O'Shaughnessy. Single-cell sequencing of the blood T cell repertoire before and after trastuzumab treatment in early stage HER2+ breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-01-11.