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Navigating Lupus Diagnosis

Historical foundations to novel biomarkers

BY Brittany Partain, PhD, and Tyler Alexander, PhD  

Since its earliest descriptions, the diagnostic landscape has expanded significantly. The term “lupus” is a Latin word meaning “wolf,” which was first used to describe the erosive facial lesion associated with the disease resembling a wolf bite. Initial reports have been somewhat variable, but the Italian surgeon Rogerius Frugardi  is most often credited as the first to report the condition in the thirteenth century. Early on, lupus was considered a skin condition and not a systemic disease with both cutaneous and subcutaneous manifestations. Since then, many additional clinical features have been introduced to support lupus diagnosis, including serologic biomarkers. Early biomarkers included lupus erythematosus (LE) cells first reported by Malcolm McCallum Hargraves and colleagues in 1948. His team discovered LE cells in the bone marrow of patients with lupus resulting from phagocytosis of free nuclear material indicative of autoimmune reactivity. Biomarkers now central to lupus evaluation include antinuclear antibodies (ANA), anti-double-stranded DNA (anti-dsDNA), anti-Smith, complement C3 and C4 (C3/C4), antiphospholipid antibodies (aPL), anti-cardiolipin and anti-β2GPI antibodies. These autoantibodies are directed to discrete antigens associated with lupus pathology and are more commonly found in patients with lupus than in healthy individuals or those with other autoimmune diseases. 

It takes an average of nearly six years from the onset of symptoms to receive a lupus diagnosis.

Treatment Overview 

Once patients receive a diagnosis, it is imperative that appropriate treatment is implemented to reduce the risk of flares, organ damage or death. Quinine was first discovered as useful for the treatment of lupus by John B. Payne and colleagues, who documented successful management of discoid lupus erythematosus skin lesions in 1894. Chloroquine was introduced in 1953, followed by hydroxychloroquine (HCQ) in 1955. HCQ has demonstrated excellent efficacy and patient tolerability in SLE and is still considered a cornerstone in SLE treatment regimens to this day. Another hallmark of lupus therapy, corticosteroids, were discovered in 1948 by Philip Hench as a potent anti-inflammatory medication, which was initially used to treat rheumatoid arthritis but also showed favorable outcomes in patients with lupus. Shortly after, glucocorticoids were introduced for treatment of SLE and other autoimmune diseases. More recently, immunosuppressants and biologic disease modifying antirheumatic drugs (DMARDs) have become increasingly popular to treat SLE as they directly target overactive immune cells thus limiting side effects. 

Immunosuppressants, such as cyclophosphamide, mycophenolate mofetil (MMF) and azathioprine, reduce hyperactivity of B and T lymphocytes to induce disease remission. The introduction of biologic agents such as belimumab (introduced in 2011) and anifrolumab (introduced in 2021) has expanded treatment options by targeting distinct immune pathways, with belimumab inhibiting B-lymphocyte stimulator (BLyS) to reduce B-cell survival and autoantibody production, and anifrolumab blocking type I interferon receptor signaling to suppress interferon-mediated inflammation. 

Genetic & Environmental Factors 

The causes of lupus development are multifactorial including both genetic and environmental determinants. Genetic factors include defects in self-antigen clearance, innate immunity pathways, complement pathway proteins and autoreactive lymphocyte development and maintenance genes.  

The first animal model (F1 hybrid New Zealand Black/New Zealand White mouse) provided insights into autoantibody formation, immune tolerance and glomerulonephritis. 

The human leukocyte antigen (HLA) region genes, specifically HLA Class II genes, have shown the strongest genetic link to lupus development. Not all lupus cases, however, are directly related to genetic predisposition.  

Environmental factors such as Epstein-Barr virus infection; microbiome composition; smoking; and exposure to pollutants, silic and UV light have been linked to lupus development. No single factor has been independently associated with lupus development, but a combination of genetic predisposition and environmental exposures are most likely to cause disease. 

The Diagnostic Gap 

Timely diagnosis and prompt treatment initiation are important to reduce the risk of flares and organ damage, but these goals are not consistently achieved. According to a study conducted in partnership with the Lupus Foundation of America (LFA), it takes an average of nearly six years from the onset of symptoms to receive a lupus diagnosis, and many patients see multiple physicians before getting a definitive diagnosis. Patients typically undergo nearly 15 office visits and 58 lab procedures before receiving a diagnosis, and up to 70% experience misdiagnosis along the way.  

Lupus flares range considerably in severity, from mild episodes of fatigue, joint pain, and rash to life-threatening complications including nephritis, cardiovascular disease and neurological involvement. Critically, the period between symptom onset and diagnosis is not clinically silent. Ongoing immune dysregulation during this interval can cause cumulative, and sometimes irreversible, organ damage that timely treatment could have prevented or substantially reduced. The six-year average diagnostic delay is therefore not merely an inconvenience, but represents a window during which disease progression may go unchecked. 

Recent studies evaluating outcomes in a cohort of patients whose SLE was diagnosed early (within six months of symptom onset) and late (greater than six months from symptom onset) provide strong evidence that earlier diagnosis is associated with fewer hospitalizations and overall cost savings. When SLE was diagnosed within six months of symptom onset, patients experienced meaningful reductions across multiple categories. Specifically, earlier diagnosis was associated with a 20% reduction in SLE-related hospitalizations. This study reinforces that earlier diagnosis is associated with fewer flares across all severity levels (minor flares, moderate flares, severe flares). Beyond acute care, the early diagnosis group had a 16% lower rate of outpatient visits during follow-up, reflecting a more stable disease course and less need for ongoing evaluation. These patients also experienced 13% fewer severe flares, likely related to earlier initiation of appropriate treatment. 

Laboratory Testing & Novel Biomarkers 

To enhance the likelihood of timely diagnosis, new diagnostic tests have recently been introduced, and additional biomarker assessments are currently under development. Laboratory testing is an important part of the lupus evaluation. Physicians often start with tests that assess autoantibody levels. One of the most common screening tests is the ANA test, or antinuclear antibody test. This test is very sensitive for lupus, and nearly every patient with SLE will have a positive ANA.  

The challenge is that ANA is not specific and up to one-third of healthy individuals can also have a low positive ANA. While it is a useful starting point, it does not provide a definitive answer on its own. Antibodies that are highly specific for lupus including anti-Smith and anti-dsDNA are tested as well, but they are seen in only a subset of patients with SLE. Anti-Smith is detected in only 14% of patients, and anti-dsDNA in approximately one-third. 

AVISE® Lupus was designed specifically to address these limitations. Developed by Exagen Inc., a San Diego-based diagnostics company specializing in autoimmune disease testing, it is a multianalyte diagnostic test that combines novel cell-bound complement activation products (CB-CAPs) with standard serologic testing in a validated two-tiered algorithm. This approach generates a lupus risk score that reflects the likelihood of disease across a gradient rather than a binary positive/negative result. 

CB-CAPs were first described in 2004 and incorporated in AVISE Lupus testing in 2014. CB-CAPs include erythrocyte-bound C4d (EC4d) and B lymphocyte-bound C4d (BC4d), which represent complement activation fragments deposited on the surface of red blood cells and B lymphocytes, respectively. CB-CAPs have the added benefit of detecting complement products on the cell surface, such that they remain detectable for longer periods of time than traditional complement measures. CB-CAPs remain detectable for the duration of the cell’s life cycle, which enhances their ability to detect ongoing inflammation rather than a single signal at the time of evaluation. This elongated detectability allows for enhanced sensitivity (66%) and specificity of CB-CAPs over standard complement, anti-Smith, and anti-dsDNA. To further enhance diagnostic accuracy, AVISE Lupus combines these novel CB-CAPs with standard serology components (ANA, anti-Smith, and anti-dsDNA) in a two-tiered method to provide a serology-based gradient of likelihood for SLE. 

Earlier diagnosis is associated with fewer hospitalizations and overall cost savings.

Combining standard serology markers with CB-CAPs provides improved sensitivity (80%) and specificity against other autoimmune rheumatic diseases (86%) and healthy individuals (98%). In addition, AVISE Lupus uses a proprietary algorithm to assign a lupus risk score with the ability to classify the likelihood of lupus even in early disease stages. 

Multianalyte testing approaches, including AVISE Lupus, represent one category of emerging diagnostic tools designed to address the sensitivity and specificity limitations of standard serology alone. Building on these advances, additional markers have become available to improve the sensitivity for SLE. In 2025, T lymphocyte-associated markers including T cell-bound C4d (TC4d) and T cell-bound autoantibodies (TIgG and TIgM) were introduced for clinical use. These markers capture complementary aspects of the immune response not fully reflected by B cell-focused or traditional serologic markers.  

Published data specifically characterizing the sensitivity and specificity of TC4d, TIgG, and TIgM in SLE populations are emerging and further validation studies are ongoing as clinical use expands. Notably, CB-CAPs and T cell biomarkers are present in patients who test negative for standard serology, marking an important step forward in improving the ability to diagnose lupus. 

Disease Activity Monitoring 

Beyond diagnosis, CB-CAPs can evaluate lupus disease activity. In a recent investigation, erythrocyte-bound complement C4d (EC4d) levels were independently associated with SLE disease activity, as measured by clinical SELENA-SLEDAI scores, enabling improved monitoring capabilities beyond the current standard of care. For instance, treatment efficacy could be evaluated by monitoring the presence of CB-CAPs in the context of serum complement levels.  

A patient with normal complement measures without the presence of complement activation products could indicate adequate disease control. Further, EC4d remained associated with disease activity regardless of fluctuations in C3/C4 status, suggesting evidence of a more reliable indicator for disease activity over time. 

Barriers to Diagnosis & Access 

While the validity and utility of novel diagnostic approaches have been established, barriers to clinical implementation can limit patient access to these diagnostic technologies. In a report from the Addressing Lupus Pillars for Health Advancement (ALPHA) project (an independent multistakeholder initiative) representatives from academia, industry, regulatory agencies, clinicians, researchers, patient advocacy organizations and patients were queried about the most significant barriers to lupus diagnosis. Survey respondents indicated the lack of understanding by government payer/insurers about lupus, access to clinicians familiar with lupus and development of diagnostic and prognostic biomarkers as significant barriers to lupus diagnosis. 

In a separate collaborative study of patient perspectives from Exagen and the LFA, patients reported long wait times to see providers, high out-of-pocket costs for testing and insurance not covering costs of needed services as factors contributing to diagnostic delays. 

Broader engagement with rheumatology providers and payers on newer diagnostic approaches, including multianalyte assays like AVISE Lupus, can improve uptake and ensure providers have the tools needed to strengthen diagnostic capabilities. 

Regulatory & Guideline Context 

Currently, laboratory developed tests (LDTs) like AVISE Lupus are not subject to FDA medical device-level approval requirements (21 CFR 809). LDTs are instead regulated under the Clinical Laboratory Improvement Amendments (CLIA) program, administered by the Centers for Medicare and Medicaid Services (CMS), which sets standards for laboratory quality and accuracy. Insurance coverage for LDT-based diagnostics like AVISE Lupus varies by payer and plan. While some commercial insurers and Medicare Advantage plans provide coverage, others do not. This remains a prominent barrier patients and providers frequently encounter, as reflected in the access challenges described above. 

In the context of diagnostic guidelines, the American College of Rheumatology (ACR) and the European Alliance for Associations of Rheumatology (EULAR) endorse classification criteria for lupus centering around a combination of serology and other clinical features to standardize clinical trial eligibility and uniformity among comparison groups. These classification criteria are, however, often used clinically to diagnose lupus in patients. This contributes to diagnostic uncertainty as patients with lupus often present with diverse clusters of symptoms and serology that may not always align with established classification criteria.  

In academic medical centers, classification criteria may perform reasonably as these patients are likely to exhibit more severe or advanced disease stages. Community centers that may see patients with early-stage disease or uncommon symptomatology, however, may struggle to meet existing criteria. Therefore, it is imperative that the complete clinical picture is considered when evaluating a patient with suspected lupus. Diagnostic approaches that include additional biomarkers beyond standard serology help to widen the landscape to support a diagnosis, especially in ambiguous cases.  

Conclusion 

Timely lupus diagnosis enables earlier intervention with targeted therapy to reduce the risk of disease flares and associated morbidity. Current diagnostic standards rely on clinical features, including serologic biomarkers. Low sensitivity and/or specificity of conventional serology (including anti-dsDNA, anti-Smith, and complement) can delay diagnosis and treatment initiation, increasing the risk of lupus-related organ damage. Novel testing approaches, including CB-CAPs, T cell autoantibodies, and the AVISE Lupus multianalyte test, can enhance the clinical picture to substantiate diagnosis, thereby reducing the diagnostic journey for patients and opening the door for appropriate management strategies.  

Incorporating expanded biomarker panels in evaluating patients with clinical features suggestive of lupus, particularly those who do not fully meet ACR/EULAR classification criteria, represents a practical and evidence-supported step toward earlier, more confident diagnosis.

Brittany Partain, PhD, is the associate director of clinical affairs and physician education at Exagen Inc.

Tyler Alexander, PhD, is the medical affairs writer at Exagen Inc.