Inflammatory and Autoimmune Lab Test Interpretation: ANA, RF, and More

Rheumatology Labs

May 16

Autoimmune conditions present extremely variably - some patients will present “textbook,” while others come in with vague complaints. We also have to contend with the fact that several autoimmune conditions overlap in terms of signs, symptoms, and lab test results. That’s why autoimmune and inflammatory labs can feel confusing to order and interpret. Let’s get into some pearls you can apply straight away to your practice.

The Case

You’re following up on a 30-year-old female patient who visited the emergency department a week ago with pleuritic chest pain. Review of her emergency investigations shows:

D-dimer: negative
Troponins: negative
eGRF, K and Na: within normal limits
ECG: tachycardia (HR 105), NSR
CBC: Hgb 110 g/L (low), WBC 3.0 (low), platelets 300 (normal)
Urinalysis: 2+ blood, 2+ protein, glucose negative, nitrites negative, leukocytes negative
Chest X-ray: clear

ED recommendation: follow-up with primary care.

Follow-Up Assessment

On follow-up, you discover:

Intermittent joint pain/swelling over 2-3 months (fingers, wrists, ankles), coinciding with chest pain episodes
No fever, weight loss, hair loss, oral ulcers, dry eyes/mouth, diarrhea, bloody stools, tenesmus, back pain, or new rashes
History: acne rosacea worsened by sun exposure, otherwise healthy, no family history of autoimmune disease, no recent travel or illness

Physical Exam:

BP: 145/95 (taken 3 times)
Mild swelling of both wrists, ankles, and 3 distal interphalangeal joints on left hand
No rash; normal cardio-respiratory exam

Summary: A young female with 2–3 months of polyarticular joint pain, pleuritic chest pain flares, hypertension, hematuria, proteinuria, anemia, and leukopenia. Primary concern: autoimmune/inflammatory process.

What illness script(s) does this trigger for you?

Differential Diagnoses to Consider

Autoimmune conditions present extremely variably - some patients will present “textbook,” while others come in with vague complaints. We also have to contend with the fact that several autoimmune conditions overlap in terms of signs, symptoms, and lab test results.

In this case, some top considerations could include:

Systemic lupus erythematosus (SLE) – multi-organ involvement
Rheumatoid arthritis (RA) – overlapping features with SLE
Mixed connective tissue disease (MCTD)
Systemic vasculitis – kidney involvement
Sjögren syndrome – can cause pneumonitis even without dry eyes/mouth

We know this patient requires further work up, including labs, so let’s do a deep-dive into lab investigations for suspected autoimmune/inflammatory conditions.

Lab Investigations for Autoimmune Disease: What to Know Before You Order

When the pre-test probability of autoimmune disease is moderate-to-high, it’s critical to understand test characteristics for accurate interpretation. Let’s dive into some common labs to understand in primary care:

  
    
  
      Test
      Description
      Test Characteristics
      Result Interpretation Tips
    

  
      Anti-nuclear antibody (ANA)
      Detects autoantibodies; primary screening for autoimmune disease
      High sensitivity; low specificity
      High titer = higher probability of autoimmune disease; positive alone ≠ SLE
    

      Extractable nuclear antigen (ENA)
      Sub-panel of ANAs that is sometimes ordered reflexively with a positive ANA: dsDNA, anti-Ro, anti-La, anti-Sm, anti-RNP, anti-Jo-1, anti-Scl70
      Specific antibodies (dsDNA, anti-Sm) highly suggestive of SLE
      Interpret carefully; consult rheumatology if unsure
    

      Complement proteins (C3, C4)
      Part of immune system complement cascade
      Not useful in isolation
      Low C3/C4 + positive autoantibodies → support SLE
    

      Rheumatoid factor (RF)
      Autoantibody in RA, SLE, Sjögren; also positive in some infections
      Variable sensitivity (60–90%); low specificity
      20–30% of SLE patients may be RF positive; not diagnostic alone
    

      Anti-cyclic citrullinated peptide (anti-CCP)
      Specific autoantibody in RA
      High specificity for RA
      Positive → increases probability of RA vs SLE
    

      ESR
      Indirect inflammation marker
      High false positives/negatives
      Interpret with other findings; normal does not rule out disease
    

      CRP
      Direct inflammation marker
      More sensitive than ESR for acute inflammation
      Elevated → supports inflammation; normal → does not rule out disease
    

      Liver function tests
      AST, ALT, GGT, ALP, albumin, bilirubin, INR/PTT
      Variable
      Elevations may indicate lupus hepatitis; warrants further workup
    

      eGFR
      Kidney function
      Equation-based accuracy (e.g., CKD-EPI)
      Reduced → consider lupus nephritis, vasculitis
    

      Urine ACR
      Proteinuria assessment
      Higher sensitivity/specificity than urinalysis
      Elevated → kidney involvement; consider lupus nephritis
    

      Urine routine & microscopy (R&M)
      Screen for kidney damage
      High sensitivity; lower specificity
      RBC casts, proteinuria → glomerulonephritis / lupus nephritis
    

      CBC
      Screen for anemia, leukopenia, thrombocytopenia
      Variable
      Normal counts do not rule out autoimmune disease
    

      Serum protein electrophoresis (SPEP)
      Detects hypergammaglobulinemia
      Not definitive for SLE
      Elevated gamma globulins → autoimmune activity; watch for M-spike
    

      TSH
      Screen for autoimmune thyroid disease
      High sensitivity
      TSH >10 → hypothyroid; TSH <0.1 → hyperthyroid
    



  

For a more detailed table breakdown, check out this document.

Bottom Line

Order labs based on pre-test probability: Do you suspect SLE? RA? A seronegative arthritis? Multi-organ involvement?
Interpret within the context of the patient: disease prevalence, history, physical exam, and other results matter more than any single test.
When in doubt, consult a specialist: rheumatology or internal medicine.
Red flags for autoimmune testing: if a patient presents with multi-organ symptoms such as arthritis, myositis, pleuritis, proteinuria, hematologic abnormalities (e.g. hemolytic anemia, thrombotic features), seizures, psychosis, etc.

A practical rule of thumb: consider inflammatory markers and autoimmune testing in patients with at least two of the following unexplained findings:

Malar or discoid rash
Inflammatory arthritis
Myositis
Oral ulcers
Pleurisy or pericarditis (pleuritic chest pain)
Proteinuria or active urinary sediment
Sicca symptoms (dry eyes/dry mouth)
Cytopenias (anemia, thrombocytopenia, neutropenia, or lymphopenia)
Seizures
Psychosis
Raynaud’s phenomenon
Scleroderma skin changes (thickening, tightness)
Scarring alopecia

In our patient, who presents with multi-organ concerns (chest pain, renal involvement, hypertension), a broader laboratory workup is appropriate. This may include: ANA, RF, anti-CCP, C3/C4, ESR, CRP, eGFR, urine ACR, urinalysis (R&M), liver enzymes, CBC, SPEP, and TSH.

That said, these tests should not be ordered indiscriminately in patients with minimal or nonspecific symptoms suggestive of autoimmune disease.

Let’s review our results and see how our probability of disease changes:

ANA: 1:320 (high)
Reflex ENA testing completed: ds-DNA: positive, anti-smith: positive (high specificity for SLE)
C3, C4: low (with elevated ANA, positive ds-DNA and anti-smith, higher likelihood of SLE)
RF, CRP normal
ESR mild elevation
Urine R&M: 10 rbc/hpr, RBC casts (kidney involvement – lupus nephritis?)
eGFR: 90 (stable)
Urine ACR: 30 (elevated – kidney involvement – lupus nephritis)
CBC: hgb 110g/L (11 g/dL)) (low), wbc 3.0 (low), platelets 400 (normal)
SPEP: normal
TSH: normal
Other testing to consider - repeat ECG and chest x-ray: normal

Most likely diagnosis: systemic lupus erythematosus – time to refer to urgent rheumatology + nephrology given her multi-organ involvement and disease activity.

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References

Petri M, Orbai AM, Alarcón GS, Gordon C, Merrill JT, Fortin PR, et al. Derivation and validation of the Systemic Lupus International Collaborating Clinics classification criteria for systemic lupus erythematosus. Arthritis Rheum. 2012;64(8):2677–2686.
Petriw L, Gupta A, Leung M, Kung T, Joneja M. Rheumatology cases. Apple Books; 2017. Available from: https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewBook?id=1265645368
NP Reasoning. ESR and CRP [Internet]. 2024 [cited 2026 Feb 19]. Available from: https://www.npreasoning.com/lab-test-interpretation/esr-and-crp
NP Reasoning. Thyroid lab tests: conundrums & controversies [Internet]. 2024 [cited 2026 Feb 19]. Available from: https://www.npreasoning.com/lab-test-interpretation/thyroid-labs
BC Guidelines. Antinuclear antibody (ANA) testing [Internet]. 2024 [cited 2026 Feb 19]. Available from: https://www2.gov.bc.ca/gov/content/health/practitioner-professional-resources/bc-guidelines/ana-testing
Wallace DJ, Gladman DD. Systemic lupus erythematosus in adults: clinical manifestations and diagnosis [Internet]. In: Pisetsky DS, editor. UpToDate. 2025 [cited 2026 Feb 19]. Available from: https://www.uptodate.com/contents/systemic-lupus-erythematosus-in-adults-clinical-manifestations-and-diagnosis
Aringer M, Costenbader K, Daikh D, Brinks R, Mosca M, Ramsey-Goldman R, et al. 2019 European League Against Rheumatism/American College of Rheumatology classification criteria for systemic lupus erythematosus. Arthritis Rheumatol. 2019;71(9):1400–1412. doi:10.1002/art.40930.

Victoria Sanderson