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1 Supplementary information! Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors Gerald Goh, Ute I. Scholl, James M. Healy, Murim Choi, Manju L. Prasad, Carol Nelson- Williams, John W. Kunstman, Reju Korah, Anna-Carinna Suttorp, Dimo Dietrich, Matthias Haase, Holger S. Willenberg, Peter Stålberg, Per Hellman, Göran Åkerström, Peyman Björklund, Tobias Carling, Richard P. Lifton

2 Contents! Supplementary Table 1: ical features of patients with cortisol-producing adrenal tumors.... 3! Supplementary Table 2: Sequencing metrics for 25 tumor-normal pairs.... 7! Supplementary Table 3: Somatic protein-altering mutations in recurrently mutated genes.... 8! Supplementary Table 4: Somatic protein-altering mutations in PRKACA-mutant tumors ! Supplementary Table 5: Expression of PKA subunit genes in normal human adrenal gland ! Supplementary Table 6: Phosphorylated CREB in PRKACA-mutant and wildtype tumors ! Supplementary Table 7: Primer sequences ! Supplementary Figure 1: Overview of copy number variants in CNV+ tumors ! Supplementary Figure 2: Significant, focal CNVs in tumors ! Supplementary Figure 3: RNA-seq of a PRKACA-mutant tumor ! Supplementary Figure 4: Increased levels of pcreb in PRKACA-mutant tumors ! Supplementary Figure 5: Histology of PRKACA-mutant tumors ! Supplementary Figure 6: Model for cortisol-producing adrenal tumor formation due to gain of function mutation in PRKACA ! References... 20!! 2

3 Supplementary Table 1: ical features of patients with cortisol-producing adrenal tumors. Patient Pathology Cohort Paired WES PRKACA GNAS CTNNB1 CNV Gender Age UFC (ug/day) (pg/ml) CUSH1 ACA Dis Yes Yes L206R WT WT CNV- F * 7* N/A CS CUSH5 ACA Dis Yes Yes L206R WT WT CNV- F * <5* N/A CS CUSH28060 ACA Dis Yes Yes L206R WT WT CNV- F * 0.4* Positive CS CUSH14 ACA Dis Yes Yes WT Q227E WT CNV- F * <5* Positive CS CUSH1045 ACA Dis Yes Yes WT R201H WT CNV- F * <5* N/A CS CUSH20 ACA Dis Yes Yes WT WT WT CNV+ F * <5* N/A CS CUSH11 ACA Dis Yes Yes WT WT WT CNV+ F * <5* Positive CS CUSH12 ACC Dis Yes Yes WT WT WT CNV+ M * <5* Positive CS CUSH1678 ACA Dis Yes Yes WT WT WT CNV+ F * <5* N/A CS CUSH1037 ACC Dis Yes Yes WT WT T41A CNV+ F * <5* N/A CS CUSH22 ACA Dis Yes Yes WT WT D32G CNV- F * <5* N/A CS CUSH15 ACA Dis Yes Yes L206R WT WT CNV- F * <5* Positive SCS ical Diagnosis Associated Signs and Symptoms Typical clinical presentation DM, osteo DM, hir, bh, str, pmw, ecch, F, hair Diagnostic Criteria,,, Size (cm) Weiss score Ki <1% 30 4 <4% # 0-2% CUSH16 ACA Dis Yes Yes L206R WT WT CNV- F 79 N/A N/A Positive SCS 2 1 2% CUSH1735 ACA Dis Yes Yes L206R WT WT CNV- F 61 elevated* N/A Positive SCS 3 0 CUSH18 ACA Dis Yes Yes WT WT WT CNV- F 59 N/A N/A Positive SCS 3 0 CUSH19 ACA Dis Yes Yes WT WT WT CNV- F * N/A Positive SCS 5 1 CUSH24 ACA Dis Yes Yes WT WT WT CNV- F * <5* N/A SCS CUSH10 ACA Dis Yes Yes WT WT WT CNV- F * 6.9* N/A SCS ! 3

4 Patient Pathology Cohort Paired WES PRKACA GNAS CTNNB1 CNV Gender Age UFC (ug/day) (pg/ml) CUSH2 ACA Dis Yes Yes WT WT WT CNV- F * <5* N/A SCS CUSH9 ACA Dis Yes Yes WT WT WT CNV+ F * 6.8* Positive SCS ical Diagnosis Associated Signs and Symptoms CUSH95 ACC Dis Yes Yes WT WT WT CNV+ F 56 N/A N/A N/A SCS Wt, HTN Diagnostic Criteria Outpatient workup not available CUSH6 ACA Dis Yes Yes WT WT S45P CNV- M 77 N/A 11 Positive SCS, Scort 5 1 Size (cm) M Weiss score Ki67 CUSH1464 ACA Dis Yes Yes WT WT S45P CNV- F 66 elevated* N/A Positive SCS HTN, DM 6 1^ <3% CUSH1777 ACA Dis Yes Yes WT WT S45P CNV- F 44 N/A undetectable* Positive SCS HTN, emot CUSH23 ACA Dis Yes Yes WT WT S37C CNV+ F * <5* Normal SCS CUSH205 ACA Val Yes No L206R WT WT N/A F * <1.0* Positive CS CUSH104 ACA Val No No L206R WT WT N/A F * 4* N/A CS CUSH105 ACA Val No No L206R WT WT N/A F 42 elevated* <2* N/A CS CUSH106 ACA Val No No L206R WT WT N/A F * <5* N/A CS CUSH108 ACA Val No No L206R WT WT N/A F * <5* Positive CS CUSH111 ACA Val Yes No L206R WT WT N/A F 31 N/A <5* Positive CS str, mf DM, F DM, mf, pmw, amen, hair Wt, hir, mf, bh, acne Wt, hir, str, hair, F, ecch, skin, infx bh, pmw, F, emot, ecch, osteo CUSH211 ACA Val Yes No L206R WT WT N/A F * 1* N/A CS HTN, osteo CUSH203 ACA Val Yes No WT R201C WT N/A F * Positive CS CUSH206 ACA Val Yes No WT WT WT N/A F <1.0* Positive CS CUSH90854 ACA Val No No WT WT WT N/A F * <5* Positive CS DM, DM, hir, bh, str, pmw, ed Scort,, Scort,,,,, <1% ! 4

5 Patient Pathology Cohort Paired WES PRKACA GNAS CTNNB1 CNV Gender Age UFC (ug/day) (pg/ml) CUSH90856 ACC Val No No WT WT WT N/A F 18 elevated* decreased* N/A CS CUSH90873 ACA Val No No WT WT WT N/A F 54 N/A N/A N/A CS CUSH90876 ACC Val No No WT WT WT N/A M 50 N/A N/A N/A CS CUSH101 ACA Val No No WT WT WT N/A F * 3* Positive CS CUSH103 ACA Val No No WT WT WT N/A F * 2* N/A CS CUSH109 ACA Val Yes No WT WT WT N/A F * 2* Positive CS CUSH112 ACA Val Yes No WT WT WT N/A F * 2* N/A CS CUSH1654 ACC Val No Yes WT WT WT N/A F * 15 N/A CS CUSH1717 ACA Val No Yes WT WT WT N/A F * N/A N/A CS CUSH1754 ACA Val No Yes WT WT WT N/A F * undetectable* Positive CS CUSH47 ACC Val No Yes WT WT WT N/A F * <2* N/A CS CUSH58 ACC Val No Yes WT WT WT N/A F * <5* Positive CS CUSH210 ACA Val Yes No WT WT WT N/A F * <1.0* Positive CS CUSH21515 ACA Val No Yes WT WT S45Y N/A F * 2.6* Positive CS ical Diagnosis Associated Signs and Symptoms Wt, hir, str, amen, hair, acne, emot Wt, DM, hir, mf, hair Wt, DM, bh, ecch, skin DM, mf, bh, str, pmw, F hir, mf, bh, str, ed, amen, hair hir, mf, bh, pmw, F, ecch DM, hir, bh, mf, amen, skin, acne, ecchy mf, bh, emot, ecch Wt, F, emot, ecch hir, mf, bh, ecch, skin, infx hir, bh, hair, F, emot, skin pmw, F, Diagnostic Criteria loss of diurnal variation, Outpatient workup not available, Size (cm) # N/A Weiss score Ki <3% VS,,,, 6.5 0^ <3% ! 5

6 Patient Pathology Cohort Paired WES PRKACA GNAS CTNNB1 CNV Gender Age UFC (ug/day) (pg/ml) CUSH116 ACA Val Yes No WT WT S45P N/A F 49 elevated* decreased* Positive CS CUSH201 ACA Val Yes No WT WT WT N/A F 71 N/A 4* Positive SCS ical Diagnosis Associated Signs and Symptoms F, ecch, infx Diagnostic Criteria, CUSH202 ACA Val Yes No WT WT WT N/A F Positive SCS Wt, HTN CUSH204 ACA Val Yes No WT WT WT N/A F 68 N/A 4.6* Positive SCS CUSH207 ACA Val Yes No WT WT WT N/A F * N/A SCS pmw 2 0 Size (cm) # 4 0 N/A 1 Weiss score Ki67 CUSH209 ACA Val Yes No WT WT WT N/A F N/A Positive SCS Wt CUSH107 ACA Val No No WT WT WT N/A F * N/A N/A SCS DM CUSH113 ACA Val Yes No WT WT WT N/A F 55 N/A N/A N/A SCS Wt, HTN CUSH114 ACA Val Yes No WT WT WT N/A F 45 50* 2* N/A SCS CUSH115 ACA Val Yes No WT WT WT N/A F 58 elevated* 3* Positive SCS Wt, HTN CUSH117 ACA Val Yes No WT WT WT N/A M 44 N/A <2* N/A SCS HTN, emot VS Outpatient workup not available Scort, <1% # <1% CUSH119 ACA Val Yes No WT WT WT N/A M * 62 N/A SCS UFC <1% CUSH208 ACA Val Yes No WT WT S45P N/A F * <1.0* Normal SCS Wt, HTN CUSH1605 ACA Val No Yes WT WT S45P N/A M * 10 Normal SCS Wt UFC Scort, 3 0 WES, whole-exome sequencing; urinary free cortisol; ACA, adenoma; ACC, carcinoma; adrenocorticotropic hormone; Dis, discovery cohort; Val, validation cohort; WT, wildtype; N/A, not available; CS, Cushing Syndrome; SCS, Subclinical Cushing Syndrome; asterisks (*) represent test values outside the laboratory-specific normal range; represents 9 tumors with incomplete documentation in available medical records Associated signs and symptoms: Wt, recent weight gain; HTN, hypertension; DM, diabetes mellitus; hir, hirsutism; mf, moon facies, facial plethora; bh, buffalo hump; str, striae; pmw, proximal muscle weakness; ed, peripheral edema; amen, amenorrhea or menstrual abnormalities; hair, thinning of hair or alopecia; acne, increased acne; F, fatigue or weakness; emot, emotional lability or depression; ecch, Ecchymosis or easy bruisability; skin, thin skin; osteo, osteoporosis or osteopenia; infx, recurrent or difficult-to-treat infections.! 6

7 : Dexamethasone suppression test. Positive denotes failure to suppress serum cortisol following administration of dexamethasone. Patients were administered between a dexamethasone dose of 1 8 mg in the evening followed by AM measurement of serum cortisol; cortisol levels > 2.5ug/dL were considered pathologic ( positive ) 1. Diagnostic criteria: UFC denotes elevated urinary free cortisol; denotes suppressed ; Scort denotes elevated serum cortisol;, denotes positive dexamethasone suppression test; VS, adrenal venous sampling;, documented clinical symptoms suggestive of Cushing syndrome. Weiss score: # denotes a tumor with a preponderance of oncocytic cells. For these tumors, an alternative score based on Lin-Weiss-Bisceglia criteria 2, was used; ^ denotes uncertain malignant potential; M, metastatic.! 7

8 Supplementary Table 2: Sequencing metrics for 25 tumor-normal pairs. Normal Tumor Mean number of reads per sample (M) Median coverage (X) Mean coverage (X) % of reads that map to genome 91.4% 91.7% % of reads that map to target 66.0% 66.4% % of targeted bases with > 8 reads 95.0% 95.2% % of targeted bases with > 20 reads 89.0% 89.6% Mean error rate 0.7% 0.8% % PCR duplicates 5.4% 7.6%! 8

9 Supplementary Table 3: Somatic protein-altering mutations in recurrently mutated genes. Gene Patient Genome change (hg18) Tumor sample Normal sample Protein MutSig MutSig Ref. Non-ref. % Non-ref. Ref. Non-ref change p-value q-value allele allele allele allele allele PRKACA CUSH15 g.chr19: a>c p.l206r % E E-04 CUSH16 g.chr19: a>c p.l206r % 34 0 CUSH1 g.chr19: a>c p.l206r % 25 0 CUSH28060 g.chr19: a>c p.l206r % CUSH5 g.chr19: a>c p.l206r % 49 0 CUSH1735 g.chr19: a>c p.l206r % 68 0 CTNNB1 CUSH6 g.chr3: t>c p.s45p % E E+00 CUSH1464 g.chr3: t>c p.s45p % 61 0 CUSH1777 g.chr3: t>c p.s45p % 63 0 CUSH22 g.chr3: a>g p.d32g % 65 0 CUSH23* g.chr3: c>g p.s37c % 60 0 CUSH1037* g.chr3: a>g p.t41a % TP53 CUSH20* g.chr17: c>a p.r196l % E E+00 CUSH9* g.chr17: t>c p.m246v % 93 0 CUSH23* g.chr17: _ deltgagg p.p295fs % 98 0 RB1 CUSH9* g.chr13: g>a p.v654m % E E+00 CUSH1037* g.chr13: t>g p.l665r % USP6NL CUSH12* g.chr10: g>a p.a20v % E E+00 CUSH9* g.chr10: c>t p.r421k % 46 0 CUL2 CUSH20* g.chr10: g>a p.a121v % E E+00 CUSH9* g.chr10: c>t p.r165q % GNAS CUSH1045 g.chr20: g>a p.r201h % E E+00 CUSH14 g.chr20: c>g p.q227e % *, CNV+ tumor! 9

10 Supplementary Table 4: Somatic protein-altering mutations in PRKACA-mutant tumors. Patient CUSH15 CUSH16 CUSH1 CUSH28060 CUSH5 CUSH1735 Gene Genome change (hg18) Protein change Ref. allele Tumor sample Non-ref. allele % Non-ref. allele Normal sample Ref. allele PRKACA g.chr19: a>c p.l206r % 41 0 DMBT1 g.chr10: t>c p.s338p % FAM193B g.chr5: a>c p.v744g % HSD17B12 g.chr11: a>c p.t207_splice % PRKACA g.chr19: a>c p.l206r % 34 0 GLP2R g.chr17: c>a p.p91t % GLP2R g.chr17: t>c p.s92p % CHAF1B g.chr21: t>g p.v95g % 59 1 NEO1 g.chr15: c>g p.p979a % 75 0 PRKACA g.chr19: a>c p.l206r % 25 0 HYDIN g.chr16: a>c p.v2150g % PRKACA g.chr19: a>c p.l206r % MAP3K4 g.chr6: g>a p.r1007h % MUC16 g.chr19: g>c p.t13896r % ACER3 g.chr11: a>g p.t238a % APPL1 g.chr3: a>g p.q117r % BBS7 g.chr4: a>c p.f379v % CDH13 g.chr16: a>g p.i38v % EIF3B g.chr7: t>g p.s465a % ITSN2 g.chr2: c>a p.a1578s % Non-ref allele NHS g.chrx: g>t p.v350f % NINL g.chr20: g>c p.l1308v % STAT6 g.chr12: a>c p.l93r % THOC2 g.chrx: a>g p.i93t % PRKACA g.chr19: a>c p.l206r % 49 0 C10orf90 g.chr10: a>t p.l339i % 37 0 DCLRE1C g.chr10: t>c p.n448d % 98 0 LAMC1 g.chr1: t>c p.s272p % MTRF1 g.chr13: g>a p.q24* % 77 1 PRKACA g.chr19: a>c p.l206r % 68 0 CTTNBP2 g.chr7: g>a p.h1657y % MMS22L g.chr6: c>g p.g900r % PROKR2 g.chr20: g>a p.r248w % 59 0! 10

11 Supplementary Table 5: Expression of PKA subunit genes in normal human adrenal gland. Gene Subunit FPKM PRKACA Cα PRKACB Cβ 7.27 PRKACG Cγ PRKAR1A R1α PRKAR1B R1β PRKAR2A R2α 4.79 PRKAR2B R2β 2.36 FPKM, fragments per kilobase of exon per million reads! 11

12 Supplementary Table 6: Phosphorylated CREB in PRKACA-mutant and wildtype tumors. PRKACA-mutant Wildtype Number of tumors assessed 8 5 % of nuclei positive for phosphorylated CREB Median Mean S.D Wildtype, tumors without mutations in PRKACA, CTNNB1 or GNAS.! 12

13 Supplementary Table 7: Primer sequences. Primer name CTNNB1_S45_F CTNNB1_S45_R GNAS_R201_F GNAS_R201_R GNAS_Q227_F GNAS_Q227_R PRKACA_L205_R PRKACA_L205_R! Primer sequence 5'-GCTGATTTGATGGAGTTGGAC-3' 5'-CAGGACTTGGGAGGTATCCA-3' 5'-ACTATGTGCCGAGCGATCA-3' 5'-CAGTTGGCTTACTGGAAGTTGA-3' 5'-ACCCCAGTCCCTCTGGAATA-3' 5'-CCAAAGAGAGCAAAGCCAAG-3' 5'-TTGTAGCCCTGGAGCAAGAT-3' 5'-GCCCACAGGTGACAGACTTC-3'! 13

14 Supplementary Figure 1: Overview of copy number variants in CNV-positive tumors. Frequency of gains (red) and losses (blue) plotted across genome.! 14

15 Supplementary Figure 2: Significant, focal CNVs in tumors. Left, deletions in blue. Right, amplifications in red. The green line signifies the threshold for significance, q = 0.25.! 15

16 Supplementary Figure 3: RNA-seq of a PRKACA-mutant tumor. Both wild-type (A) and mutant (C) alleles are detected in the tumor, as shown in the position highlighted.! 16

17 Supplementary Figure 4: Increased levels of phosphorylated CREB in PRKACAmutant tumors. Representative images of PRKACA-mutant tumor and wildtype tumor (no mutation in PRKACA, CTNNB1 or GNAS) stained for CREB phosphorylated at Ser133. Intense nuclear-specific staining is observed in majority of the nuclei in (a) the mutant tumor, but not in (b) the wildtype tumor. Scale bars represent 60 µm.!! 17

Supplementary Figure 5: Histology of PRKACA-mutant tumors.!! All tumors reviewed with PRKACA (n = 6) mutations were well-defined, solitary adrenal cortical nodules with well-differentiated morphology.

18 Supplementary Figure 5: Histology of PRKACA-mutant tumors.!! All tumors reviewed with PRKACA (n = 6) mutations were well-defined, solitary adrenal cortical nodules with well-differentiated morphology. The majority of these tumors had low-grade nuclei (5/6), and none of the tumors showed fibrosis, necrosis, mitosis and hemorrhage, consistent with benign adenomas. (a) 2.6-cm cortisol secreting adrenal cortical adenoma showing a bright yellow and brown cut surface that corresponds to its cellular composition as shown in b. The ruler is in centimeters and millimeters. (b) The tumor is comprised of lipid-rich clear cells (filled arrow) and oncocytic cells (open arrow) with granular eosinophilic cytoplasm. The scale bar represents 60 µm.! 18

19 Supplementary Figure 6: Model for cortisol-producing adrenal tumor formation due to gain-of-function mutation in PRKACA.! (a) In quiescent adrenal fasciculata cells, protein kinase A exists as an inactive tetramer, with the catalytic subunits bound to a dimer of regulatory subunits. (b) binds to its receptor, melanocortin receptor 2, which stimulates adenylyl cyclase via Gα s, leading to an increase in intracellular camp levels. camp binds to the regulatory subunits, causing the release of the catalytic subunits and downstream signaling, which leads to cell proliferation and cortisol production. (c) The mutant catalytic subunits are not bound by the regulatory subunit, and are thus constitutively active in the absence of external stimuli. The resulting uncontrolled cell proliferation and cortisol production lead to the formation of a cortisol-producing adrenal tumor. MC 2, melanocortin receptor 2; AC, adenylyl cyclase; R, regulatory subunit; C, catalytic subunit.!! 19

20 References 1. Nieman, L.K. et al. The diagnosis of Cushing's syndrome: an Endocrine Society ical Practice Guideline. J Endocrinol Metab 93, (2008). 2. Duregon, E. et al. Oncocytic adrenocortical tumors: diagnostic algorithm and mitochondrial DNA profile in 27 cases. Am J Surg Pathol 35, (2011).!! 20

The Adrenal Glands. I. Normal adrenal gland A. Gross & microscopic B. Hormone synthesis, regulation & measurement. II.

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