What laboratory tests and treatment options are recommended for a patient suspected of having an autoimmune disorder?

Laboratory Evaluation for Suspected Autoimmune Disorders

Begin with a core panel of inflammatory markers (ESR, CRP), complete blood count with differential, comprehensive metabolic panel, and first-line autoantibodies (ANA, RF, anti-CCP) to establish the presence of systemic inflammation and guide further disease-specific testing. 1

Initial Core Laboratory Panel

Inflammatory Markers and Complete Blood Count

• ESR and CRP are highly elevated in inflammatory/autoimmune conditions, while normal or mildly elevated levels suggest non-inflammatory causes 1
• These markers help distinguish autoimmune arthritis from non-inflammatory joint disease 1
• Obtain complete blood count with differential to detect cytopenias (anemia, leukopenia, thrombocytopenia) that may indicate systemic lupus erythematosus or other systemic autoimmune diseases 2, 1
• Confirm thrombocytopenia by direct peripheral blood smear examination, as pseudothrombocytopenia can occur due to platelet clumping with EDTA anticoagulant 1
• Lymphopenia may suggest underlying immunodeficiency disorders 1

Metabolic and Organ Function Assessment

• Comprehensive metabolic panel including serum creatinine, albumin, and liver function tests to assess organ involvement 2, 1
• Quantitative immunoglobulin levels (IgG, IgA, IgM) to identify immunodeficiency states 2, 1
• Electrolyte abnormalities may indicate adrenal insufficiency in autoimmune polyendocrine syndromes 1

First-Line Autoantibody Screening

• ANA (antinuclear antibody) by indirect immunofluorescence on HEp-2 cells at 1:160 dilution is the mandatory first test for systemic autoimmune diseases 3
• Both titer and pattern (nuclear, cytoplasmic, or mitotic) must be reported, as patterns provide critical diagnostic information 3
• RF (rheumatoid factor) and anti-CCP antibodies are essential for diagnosing rheumatoid arthritis 2, 1
• Autoantibody positivity alone does not make a diagnosis—nonspecific autoantibodies can be persistently or transiently present at mildly or moderately increased levels 1

Disease-Specific Autoantibody Testing Based on Clinical Presentation

Autoimmune Hepatitis

• Test for ANA, smooth muscle antibody (SMA), anti-LKM1, and anti-LC1 using indirect immunofluorescence as the primary screening method 2, 1
• ELISA alone is inappropriate as the sole screening test for autoimmune hepatitis-related autoantibodies 1
• Anti-LKM1 antibodies should be routinely investigated to avoid overlooking type 2 autoimmune hepatitis 2
• If conventional autoantibodies are negative but suspicion remains high, test for anti-SLA (soluble liver antigen) and atypical pANCA 2

Sjögren's Syndrome

• Order anti-SSA (anti-Ro) and anti-SSB (anti-La) antibodies when patients have clinically significant dry eye and dry mouth symptoms 1, 3
• RF and ANA should also be tested in this context 1

Autoimmune Encephalitis

• CSF analysis is the most important test and should include cell count with differential, protein, glucose, oligoclonal bands, and autoimmune encephalopathy panel 2
• Test for antibodies to surface antigens (NMDAR, AMPAR, LGI1, CASPR2, GABA-R) and intracellular antigens in both serum and CSF 2, 1
• Brain MRI with gadolinium contrast is essential to identify anatomical patterns and exclude alternative diagnoses 2
• Serum studies should include thyroid panel with TPO and thyroglobulin antibodies, morning cortisol and ACTH, paraneoplastic panel, and inflammatory markers 2
• Lumbar puncture should proceed even if MRI is normal when clinical suspicion is high 2

Inflammatory Arthritis

• Test for HLA-B27 if axial symptoms or entheseal involvement suggest spondyloarthropathy 2, 1
• Anti-CCP antibodies have high specificity for rheumatoid arthritis and may identify patients prone to severe disease 2, 1
• Consider ultrasound or MRI imaging of affected joints if persistent arthritis is unresponsive to treatment 2

Thyroid Autoimmunity

• Measure antithyroid peroxidase antibody and antithyroglobulin antibody in patients with features of thyroid dysfunction 1, 3
• These should be screened soon after diagnosis in patients with type 1 diabetes 3

Primary Adrenal Insufficiency

• Measure 21-hydroxylase antibodies (21OH-Ab) as the primary etiologic test for autoimmune primary adrenal insufficiency 1

Reflex Testing Based on Positive ANA

When ANA is Positive

• If ANA is positive and SLE is clinically suspected, test anti-dsDNA antibodies using Crithidia luciliae immunofluorescence or Farr assay for high specificity 3
• Order specific antibodies panel including anti-Ro/SSA, anti-La/SSB, anti-RNP, anti-Sm based on clinical presentation and ANA pattern 3
• Measure complement levels (C3, C4) for SLE evaluation and monitoring 3
• Test anti-phospholipid antibodies (lupus anticoagulant, anticardiolipin, anti-β2-glycoprotein I) if thrombosis, recurrent pregnancy loss, or thrombocytopenia are present 3

When ANA is Negative but Suspicion Remains High

• If automated methods (ELISA, multiplex) are negative but clinical suspicion remains high, indirect immunofluorescence must be performed due to superior sensitivity for SLE and systemic sclerosis 3
• Consider testing for anti-SLA and atypical pANCA in patients with suspected autoimmune hepatitis who are negative for conventional autoantibodies 2, 1

Screening for Infectious Etiologies and Pre-Treatment Assessment

Exclude Infectious Causes

• Serologies for HIV and hepatitis B and C are suggested to exclude these as associated diagnoses 2
• CSF viral PCR including HSV1/2 and VZV, bacterial/fungal cultures when appropriate 2
• Consider empiric antiviral (IV acyclovir) and antibacterial therapy until CSF results are available in suspected autoimmune encephalitis 2

Before Initiating Immunosuppressive Therapy

• Screen for viral hepatitis B, C, and latent/active tuberculosis before initiating DMARD treatment if severe disease requires immunosuppression 2, 1
• Repeated screening labs annually in patients who require biologic treatment for 1 year until treatment is completed 2

Screening for Associated Autoimmune Conditions

Common Co-Existing Autoimmune Diseases

• Screen for diabetes mellitus with plasma glucose and HbA1c 1
• Monitor for B12 deficiency due to autoimmune gastritis 1
• Test for celiac disease (tissue transglutaminase 2 autoantibodies and total IgA) in patients with frequent or episodic diarrhea 1, 3
• Testing for antinuclear antibodies and rheumatoid factor is suggested to screen for associated systemic lupus erythematosus or idiopathic juvenile arthritis 2

Special Populations

• In young females, check anti-Ro and anti-La antibodies before pregnancy due to risk of congenital heart block 3
• For type 1 diabetes patients, screen thyroid autoantibodies and celiac disease soon after diagnosis 3

Critical Diagnostic Pitfalls to Avoid

Interpretation Caveats

• Clinical context is paramount when interpreting autoantibody results—do not diagnose based on serology alone 1
• Exclude infectious, malignant, and other causes before diagnosing autoimmune or autoinflammatory syndromes 1
• Consider drug-induced causes (quinidine, heparin, sulfonamides, aspirin) which may cause or exacerbate symptoms 1
• Recognize that some autoantibodies have low clinical relevance (e.g., VGKC, VGCC) and should not drive diagnosis alone 1

Timing and Repeat Testing

• Autoantibody titers may vary during disease course, and repeated testing may allow detection in initially seronegative individuals 1
• Routine CSF studies may be normal in some autoimmune encephalitis patients—this does not exclude the diagnosis when other parameters are consistent 2
• Blood samples should be collected prior to treatment with intravenous immunoglobulins or plasmapheresis to avoid false positive or false negative results 2

When to Refer to Specialists

Rheumatology Referral

• Refer early to rheumatology if joint swelling (synovitis) is present, symptoms persist despite initial management, or moderate to severe disease is present 2, 1
• Diagnostic uncertainty, particularly with complex presentations involving rash and migratory arthritis, warrants specialist referral 1

Other Specialist Referrals

• Refer to immunology when sterile recurrent paronychia occurs with systemic features (fever, arthritis, other skin manifestations) 1
• Neurology consultation for suspected autoimmune encephalitis or other neurologic autoimmune syndromes 2
• Consider referral to specialized center when multiple islet autoantibodies are identified in type 1 diabetes for further evaluation and potential clinical trial enrollment 2