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1 Supplementary Appendix This appendix has been provided by the authors to give readers additional information about their work. Supplement to: Cheng MH, Fan U, Grewal N, et al. Acquired autoimmune polyglandular syndrome, thymoma, and an AIRE defect. N Engl J Med 2010;362:764-6.

2 Supplemental information Supplemental Figure 1 Panel A illustrates the evolution of autoimmune disease culminating in the discovery of the thymoma. Diagnostic milestones ( ) in the diagram are correlated with significant laboratory test results ( ) detailed in the corresponding table below. Abnormal values are indicated in boldface. The patient was admitted in January 2005 for severe hypocalcemia. Her past medical history, family history, and physical exam were unremarkable. Hypoparathyroidism was diagnosed by low serum calcium, elevated phosphate, and inappropriately low intact parathyroid hormone (PTH) levels, as evident on admission in January 2005 and on follow-up in the clinic (September 2005 and May 2006). Assessment of vitamin D levels, urine calcium and bone density was unremarkable (not shown). Testing for adrenal insufficiency in May of 2006 and March of indicated normal adrenal response based on post-stimulation serum cortisol levels. Mineralocorticoid deficiency was suspected based on a trend of mild hyponatremia evident from September of 2006 onward. Formal testing in March of was diagnostic for hypoaldosteronism with a low aldosterone level and markedly elevated renin level. Repeat testing in May of after initiation of fludrocortisone therapy indicated a good response with rise of serum sodium and normalization of renin levels despite persistently depressed aldosterone. Withdrawal from fludrocortisone in June of to determine the etiology of hypoaldosteronism recapitulated the abnormal renin and aldosterone levels but revealed no defect in aldosterone synthesis based on a normal 18-OH corticosterone level. However, markedly elevated 21-OH autoantibodies drawn at this time were diagnostic for adrenal autoimmunity. Following the diagnosis of thymoma, testing for myasthenia gravis was done with negative acetylcholine receptor antibodies. ( Serum cortisol values and the reference ranges given refer to values at baseline (pre) and 45 minutes following (post) a standard 250 mcg cosyntropin stimulation test for adrenal function. *Reference ranges for plasma renin activity and aldosterone levels here assume a normal sodium diet and upright position.) Panel B summarizes the results of AIRE genotyping of the patient and the thymic tumor tissue. AIRE exons are diagrammed showing wild-type (WT, light blue boxes) and polymorphic exons (SNP, dark blue boxes) from our analysis. DNA sequencing of the patient s endogenous AIRE locus revealed no mutations and identified three single nucleotide polymorphisms (SNPs) in exons 1, 5, and 10, respectively. The table notes the position of the SNPs; nucleotide changes refer to base pair position in the fulllength AIRE cdna (NM_ ), and corresponding amino acid position is also listed. Each SNP was synonymous, resulting in no change in amino acid sequence, and were found in

3 heterozygosity as indicated by the presence of only one allele of the listed sequence (far right column). Sequencing of total DNA isolated from thymoma tissue sections did not reveal any mutations in the AIRE coding sequence, though the same SNPs were also identified in heterozygosity. Panel C shows a section of the patient s thymoma, illustrating sheets of neoplastic thymic stromal cells (arrows) filled with lymphocytic cells of various stages (arrowheads). Panel D shows flow cytometry analysis of lymphocytic cells from the thymic tumor. Staining for CD4 and CD8 markers reveals both single and double positive lymphocytes in a distribution typical of normal developing thymocytes. Percentages of CD4 +, CD8 + and CD4 + CD8 + populations are indicated by each gate and are characteristic of those found in normal thymus. In Panel E, matched sections from a normal control thymus (left panels) and the patient s thymoma (right panels) are shown. Positive DAB immunohistochemistry appears as brown staining, and hematoxylin counterstaining highlights cell morphology. The panels show staining for the following thymic epithelial markers: cytokeratin 8 (K8, top), MHC Class II (MHC, middle), and Claudin 4 (Cld, bottom). Note the thymoma was also positive for these other markers characteristic of normal mtecs (K8, MHC, Cld). Scale bars in the lower left of each image represent 100 μm.

4 A Clinical Course Summary Diagnoses Hypoparathyroidism Hypoaldosteronism Thymoma Jan 2005 May 2005 Sep 2005 Jan 2006 May 2006 Sep 2006 Jan May Sep Jan 2008 Jan 2005 Sep 2005 May 2006 Mar May Jun Date of test Test Normal range Ca mg/dl hormone pg/ml 10 9 <2.5 Albumin g/dl PO mg/dl Na mmol/l K mmol/l BUN 8-23 mg/dl Cr mg/dl ACTH 6-58 pg/ml 24 Cortisol (pre) mcg/dl 11.8 Cortisol (post) > mcg/dl Plasma renin activity* ng/ml/hour Aldosterone* ng/dl 2.8 < OH Abs U/mL OH corticosterone 9-58 ng/dl 11 Acetylcholine receptor Abs negative nmol/l, positive 0.5 nmol/l Feb B SNP WT AIRE Exons Supplemental Table. AIRE Genotyping SN P s ide nt ifi e d Exon SNP Am ino A cid Po si tion Allele Frequency T -> C A C -> T S T -> C A399 1 C D 9.5% 75.3% 5.1% CD4 CD8

5 E Control Thymoma K8 K8 MHC MHC Cld Cld

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