Autoimmune diseases are mostly characterized by autoantibodies in the patients' serum or cerebrospinal fluid, representing diagnostic or prognostic biomarkers. For decades, research has focused on ...single autoantigens or panels of single autoantigens. In this article, we advocate to broaden the focus by addressing the entire autoantigen repertoire in a systemic “omics-like” way. This approach aims to capture the enormous biodiversity in the sets of targeted antigens and pave the way toward a more holistic understanding of the concerted character of antibody-related humoral immune responses. Ongoing technological progress permits high-throughput screenings of thousands of autoantigens in parallel, e.g., via protein microarrays, phage display, or immunoprecipitation with mass spectrometry. We argue that the time is right for combining omics and autoantibody screening approaches into “autoantigenomics” as a novel omics subcategory. In this article, we introduce the concept of autoantigenomics, describe its roots and application options, and demarcate the method from related holistic approaches such as systems serology or immune-related transcriptomics and proteomics. We suggest the following extendable method set to be applied to autoantigen repertoires: (1) principal component analysis, (2) hierarchical cluster analysis, (3) partial least-square discriminant analysis or orthogonal projections to latent structures discriminant analysis, (4) analysis of the repertoire sizes in disease groups and clinical subgroups, (5) overrepresentation analyses using databases like those of Gene Ontology, Reactome Pathway, or DisGeNET, (6) analysis of pathways that are significantly targeted by specific repertoires, and (7) machine learning approaches. In an unsupervised way, these methods can identify clusters of autoantigens sharing certain functional or spatial properties, or clusters of patients comprising clinical subgroups potentially useful for patient stratification. In a supervised way, these methods can lead to prediction models that may eventually assist diagnosis and prognosis. The untargeted autoantigenomics approach allows for the systematic survey of antibody-related humoral immune responses. This may enhance our understanding of autoimmune diseases in a more comprehensive way compared to current single or panel autoantibodies approaches.
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•Larger parts of entire autoantigen repertoires may play (patho)physiological roles.•High-throughput screenings permit parallel detection of thousands of autoantigens.•Autoantigenomics analyzes entire autoantigen repertoires in a systemic way.•We suggest an extendable method set to be applied to autoantigenomes.•Prediction models may eventually assist diagnosis, prognosis, or stratification.
BACKGROUND: Fatigue is the most prevalent symptom among people with multiple sclerosis (PwMS). Although exercise effectively reduces fatigue, the relationship between daily physical activity and ...fatigue has only recently been demonstrated. OBJECTIVE: The aim of this study was to evaluate the prevalence of fatigue and to understand the relationship with several variables in French PwMS. METHODS: Data were collected from 191 PwMS using Modified Fatigue Impact Scale (MFIS) and Fatigue Severity Scale (FSS) for fatigue, and the Godin Leisure-Time Exercise Questionnaire (GLTEQ) for physical activity. RESULTS: 110 PwMS (57%), 35 PwMS (18%) and 46 PwMS (24%) were considered as fatigued, non-fatigued and in the grey zone, respectively. Greater physical activity was observed in non-fatigued PwMS (20.2±19.8) compared to fatigued PwMS (12.5±14.1). FSS and MFIS scores were associated with physical activity (r = –0.28 and r = –0.25, respectively, p < 0.05). Using multivariate analysis, disability, physical activity and being unemployed explained 21% of the variance of the MFIS. CONCLUSIONS: The present study confirms that physical activity and fatigue are associated. Disability and unemployment status should also to be consider when assessing fatigue. Activity-oriented health policies should be redesigned to improve fatigue among PwMS.
Patients with TARDBP mutations have so far been classified as ALS, sometimes with frontal lobe dysfunction. A 66-year-old patient progressively developed a severe sensory disorder, followed by a ...motor disorder, which evolved over nine years. Symptoms started in the left hand and slowly involved the four limbs. Investigations were consistent with a mixed sensory and motor neuronopathy. A heterozygous change from an alanine to a proline at amino acid 382 was identified in exon 6 of the TARDPB gene (p.A382P). This case expands the phenotypic spectrum associated with mutations in the TARDBP gene and shows that sensory neurons can be severely damaged early in the course of the disease, following a propagating process, with an orderly progression from a focal starting point. A combination of severe sensory and motor neuronopathy is rarely encountered in clinical practice. The possibility of an A382P TDP-43 mutation should be considered in patients with such an association.
Antibodies against FGFR3 define a subgroup of sensory neuropathy (SN). The aim of this study was to identify the epitope(s) of anti-FGFR3 autoantibodies and potential epitope-dependent clinical ...subtypes. Using SPOT methodology, five specific candidate epitopes, three in the juxtamembrane domain (JMD) and two in the tyrosine kinase domain (TKD), were screened with 68 anti-FGFR3-positive patients and 35 healthy controls. The identified epitopes cover 6/15 functionally relevant sites of the protein. Four patients reacted with the JMD and 11 with the TKD, partly even in a phosphorylation-state dependent manner. The epitope could not be identified in the others. Patients with antibodies recognizing TKD exhibited a more severe clinical and electrophysiological impairment than others.
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•Anti-FGFR3 antibodies are associated with sensory neurons disorders.•In 22% of patients the epitope is located in the FGFR3 juxta-membrane and tyrosine kinase domains (TKD).•Several epitopes are recognized depending on their phosphorylation state.•The identified epitopes cover functionally relevant sites of FGFR3.•Patients reacting with the FGFR3 TKD have more severe sensory neuropathy than others.
A 67-year-old woman with a history of smoking and cardiovascular risk factors was admitted to the emergency room for uncontrolled diabetes, loss of appetite, nausea, significant weight loss and ...asthenia. The initial investigation, including cerebral and gastrointestinal explorations, were normal. One month later, she started presenting severe asymmetric proprioceptive ataxia of the lower extremities. She also reported paresthesia and neuropathic pain in both feet and ankles. A positron emission tomography (PET)-scanner showed a hypermetabolic nodule in the right lung. The neurological symptoms were attributed to paraneoplastic sensory and dysautonomic neuropathy, even though the bronchoscopic biopsies came back negative at first. Anti-Hu, anti-CV2/CRMP5 and anti-SOX1 antibodies were documented. Due to the severity and rapid progression of symptoms (from the lower to the upper limbs), corticosteroids, intravenous immunoglobulins and immunosuppressants were introduced prior to biopsies revealing a small-cell lung cancer. Despite these treatments and antineoplastic chemotherapy, her status deteriorated rapidly.
BRAF/MEK inhibitors and immunotherapy agents were recently approved for the treatment of metastatic BRAF-mutated melanoma, which represents approximately 50% of cutaneous melanoma. Devic et. al ...reported the case of a sub-acute inflammatory demyelinating sensorimotor polyradiculoneuropathy (sub-AIDP) that occurred during treatment with BRAF/MEK inhibitors.
•There are no standards for defining sets of antibody-targeted autoantigens (autoantigen-omes).•Common methods can unevenly affect the size of the autoantigen-omes.•A balanced choice of statistical ...reference groups reduces risks of bias.•Our findings contribute to a standardization of defining autoantigen-omes.
Autoimmune diseases are frequently associated with autoantibodies. Recently, large sets of autoantibody-targeted antigens (“autoantigen-omes”) of patient and control sera have been revealed, enabling autoantigen-omic approaches. However, statistical standards for defining such autoantigen-omes are lacking. The z-score indicates how many standard deviations an antigen reactivity of a given sample is from the mean reactivity of the corresponding antigen in a reference group. Hence, it is a common measure to define significantly positive reactivity in autoantigen profiling approaches. Here, we address the risk of biased analyses resulting from unbalanced selection of the reference group. Three study groups were selected. Patients-of-interest were chronic inflammatory demyelinating polyneuropathy (CIDP); controls were other neuropathies (ONP); and healthy controls (HC). Each serum was screened for significant autoantigen reactivity using HuProt™ protein arrays. We compared three possible selections of reference groups for statistical z-score calculations: method#1, the control groups (ONP + HC); method #2, all groups together; method #3, the respective other groups (e.g., CIDP + HC for the ONP autoantigen-ome). The method selection seriously affected the size of the autoantigen-omes. Method #1 introduced a bias favoring significantly more antigens per patient in the CIDP group (for z >4: 19 ± 3 antigens) than in the control groups (ONP: 2 ± 1; HC: 0 ± 0). The more balanced methods #2 and #3 did not result in significant differences. This contribution may help to avoid interpretation biases and to develop guidelines for population studies revealing autoantigen-omes via high throughput studies such as protein microarrays, immunoprecipitation with mass spectrometry, or phage display assays.
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