OPEN ACCESS

Next-generation sequencing of adrenocortical carcinoma reveals new routes to targeted therapies

J S Ross, 1,2 K Wang,2 J V Rand,1 L Gay,2 M J Presta,1 C E Sheehan,1 S M Ali,2 J A Elvin,2 E Labrecque,2 C Hiemstra,2 J Buell,2 G A Otto,2 R Yelensky,2 D Lipson,2 D Morosini,2 J Chmielecki,2 V A Miller,2 P J Stephens2

1Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA 2Foundation Medicine, Inc., Cambridge, Massachusetts, USA

Correspondence to

Dr Jeffrey S Ross, Department of Pathology, Albany Medical College, Mail Code 81, 47 New Scotland Avenue, Albany, NY 12208, USA; rossj@mail.amc.edu

Received 23 June 2014 Revised 9 July 2014 Accepted 10 July 2014 Published Online First 30 July 2014

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To cite: Ross JS, Wang K, Rand JV, et al. J Clin Pathol 2014;67:968-973.

ABSTRACT

Aims Adrenocortical carcinoma (ACC) carries a poor prognosis and current systemic cytotoxic therapies result in only modest improvement in overall survival. In this retrospective study, we performed a comprehensive genomic profiling of 29 consecutive ACC samples to identify potential targets of therapy not currently searched for in routine clinical practice.

Methods DNA from 29 ACC was sequenced to high, uniform coverage (Illumina HiSeq) and analysed for genomic alterations (GAS).

Results At least one GA was found in 22 (76%) ACC (mean 2.6 alterations per ACC). The most frequent GAS were in TP53 (34%), NF1 (14%), CDKN2A (14%), MEN1 (14%), CTNNB1 (10%) and ATM (10%). APC, CCND2, CDK4, DAXX, DNMT3A, KDM5C, LRP1B, MSH2 and RB1 were each altered in two cases (7%) and EGFR, ERBB4, KRAS, MDM2, NRAS, PDGFRB, PIK3CA, PTEN and PTCH1 were each altered in a single case (3%). In 17 (59%) of ACC, at least one GA was associated with an available therapeutic or a mechanism-based clinical trial.

Conclusions Next-generation sequencing can discover targets of therapy for relapsed and metastatic ACC and shows promise to improve outcomes for this aggressive form of cancer.

Adrenocortical carcinoma (ACC) is a primary malignant neoplasm of the adrenal cortex that can vary widely in histologic appearance.1-3 ACC can occur at any age and has an annual incidence of 0.7-2.0 cases per million people with a peak incidence between 40 and 50 years (1-3). The disease occurs in women more often than men by a ratio of up to 1.5 to 1.1-3 ACC occurs both as an inherited form of cancer which is particularly prom- inent in some populations and also as a sporadic tumour.1-3 The most common inherited predisposition is associated with the Li-Fraumeni Syndrome (LFS) and germline TP53 mutations, but the disease has also been consistently linked to the Lynch Syndrome and germ- line alterations in DNA repair genes.46 In children, TP53 germline mutations may be present in 50-80% of ACC cases, whereas in adults, at least 95% of the tumours arise in the absence of germline TP53 altera- tions.4 5 ACC is an aggressive form of cancer and tumours that cannot be completely resected have a par- ticularly poor prognosis.7 Increased immunostaining (IHC) for the cell cycle protein Ki-67 has generally been accepted as the most reliable slide-based bio- marker of ACC prognosis.2 8 Successful surgical resec- tion for early stage disease is the only known curative procedure for ACC with a 5-year disease-free survival

for a complete resection of a Stage I-III tumour of 30%.1-3 For patients with recurrent and metastatic disease, the 5-year relative survival is poor at only 7%.1-3 The selection of medical treatment of ACC has been based on non-randomised trials or retrospective analyses.1-3 The adrenotoxic drug mitotane has been the cornerstone drug for ACC, both in adjuvant and metastatic disease settings with a recent emergence of platin-based regimens.9 10 Recently, the addition of three cytotoxic drugs, etopiside, doxorubicin and cis- platin to mitotane showed improvement in response rates and disease-free progression for metastatic ACC.11 Thus, given the poor prognosis of recurrent and meta- static ACC patients treated by chemotherapy, there has been emerging interest in studying whether comprehen- sive DNA sequencing of ACC tumours using next- generation sequencing (NGS)-based genomic profiling could detect genomic alterations (GAs) that could be used to guide targeted therapies for the personalised treatment of this challenging disease.

METHODS

Genomic profiling was performed in a CLIA-certified, CAP-accredited reference laboratory (Foundation Medicine). DNA extracted from clin- ical formalin-fixed paraffin-embedded tumour samples of 29 consecutively submitted ACC samples was analysed by hybridisation capture of 3320 exons from 236 cancer-related genes and 47 introns of 19 genes commonly rearranged in cancer. At least 50 ng of DNA per specimen was isolated and sequenced to high, uniform coverage (mean 734X) on the Illumina HiSeq2500 instru- ment, as previously described.12 GAs (base substitu- tions, short insertions and deletions, focal gene amplifications, homozygous deletions and select rearrangements) were determined and then reported for each patient sample. To maximise mutation detection sensitivity in heterogeneous ACC biopsies and resections, the test was validated to detect base substitutions at ≥10% mutant allele frequency with ≥99% sensitivity and indels at ≥20% mutant allele frequency with ≥95% sensitivity, with a false discovery rate of <1%.12 Actionable alterations are defined as those whose effect is targetable using anticancer drugs currently on the market or in registered clinical trials. Local site permissions to use clinical samples were obtained for this study.

Patient characteristics are shown in table 1. All 29 (100%) patients had developed locally advanced and/or metastatic ACC refractory to their last line

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Table 1 Clinicopathologic features of the 29 cases of adrenocortical carcinoma
CaseGenderAge (years)Tissue used for NGSTumour gradeTumour typeTumour stage at the time of NGS
1F50Adrenal4OncocyticpT3pNxpMx
2M33Lung3OncocyticpT3pNxpM1 (lung)
3M42Adrenal4PleomorphicpT3pNxpM1
4M67Liver3OncocyticpT3pNxpM1
5M51Lung4PleomorphicpT3pNxpM1 (lung)
6F46Lung3Clear cellpT3pNxpM1 (lung)
7M60Adrenal3OncocyticpT3pNxpMx
8M31Bone4PleomorphicpT3pNxpM1 (bone)
9F55Adrenal3OncocyticpT2pNxpMx
10F53Lung3OncocyticpT3pNxpM1 (lung)
11M21Adrenal3Clear cellpT3pNxpMx
12F60Liver3Clear cellpT3pNxpM1 (liver)
13M48Adrenal4PleomorphicpT3pN1pM1 (liver)
14M51Liver4Clear cellpT4pN1pM1 (liver)
15F64Liver4PleomorphicpT3pN0pM1 (liver)
16M54Lung4PleomorphicpT3pNxpM1 (lung)
17M68Adrenal4PleomorphicpT3pN1pM1 (lung)
18F50Liver4PleomorphicpT3pNxpM1 (liver)
19FNARetroperitoneum4PleomorphicpT3pNxpMx
20F37Retroperitoneum4PleomorphicpT3pNxpM1
21M66Adrenal4OncocyticpT2pNxpMx
22F55Kidney4PleomorphicpT3pNxpM1
23F63Adrenal4OncocyticpT3pNxpM1 (neck)
24F47Adrenal4OncocyticpT3pNxpM1 (lung)
25F74Kidney4OncocyticpT4pN1pM1 (kidney)
26F46Lung3OncocyticpT3pNxpM1 (lung)
27F33Lung4PleomorphicpT3pNxpM1 (lung)
28M51Adrenal3OncocyticpT3pNxpM1 (oesophagus)
29M61Peritoneum3Clear cellpT3pNxpM1 (peritoneum)

NGS, next-generation sequencing.

of cytotoxic chemotherapy. The median age of the ACC patients at the time of sequencing was 50 years (range 21-74 years). There were 12 (41%) ACC with predominantly oncocytic tumour cell cytoplasm, 12 (41%) ACC with markedly pleo- morphic nuclei and 5 (17%) ACC with predominantly clear cell cytoplasm. There were 11 (40%) Grade 3 and 18 (60%) Grade 4 tumours using the Fuhrman grading system (table 1). Two ACC were Stage II, 4 were Stage III and 23 were Stage IV at the time of profiling. Sequencing was performed on the original primary ACC in 11(38%) and on a metastasis or recurrence biopsy or resection in 18 (62%) ACC (table 1).

RESULTS

A total of 76 alterations were identified (25 base substitutions and short indels, 14 gene amplifications, 7 gene homozygous deletions and 30 gene truncations) in 43 genes, with 22 cases (76%) harbouring at least one alteration, for a mean of 2.6 alterations per tumour (table 2, figure 1). No gene fusions were identified. The most common biologically relevant alterations that cannot currently be linked to a targeted treatment option were found in TP53 (34%), MEN1 (14%) CTNNB1 (10%), APC (7%), DAXX (7%), KDM5C (7%), LRP1B (7%), MSH2 (7%) and RB1 (7%). At least one clinically meaningful alteration that could potentially guide decisions for targeted treatment was found in 59% (17/29) of the ACC cases. The most common potentially actionable alterations involved NF1 (14%), CDKN2A (14%), ATM (10%), CCND2 (7%), CDK4 (7%),

DNMT3A (7%) with EGFR, ERBB4, KRAS, MDM2, NRAS, PDGFRB, PIK3CA, PTEN, PTCH1 and STK11, each altered in a single case. There were no observable differences in the pattern of GAs of the ACC where the primary tumour was sequenced compared with ACC where a metastasis sample was used.

DISCUSSION

The genetic background and pathogenesis of ACC have been widely studied using a variety of methodologies.13-16 Recent molecular analysis of ACC has predominantly studied DNA copy number alterations by comparative genomic hybridisation, mRNA levels by gene expression profiling and epigenetic altera- tions by PCR-based methods.13-22 TP53 mutations have been reported in ACC at frequencies ranging from 10% to 70% and have been associated with decreased disease-free survival and poor outcomes.23-26 Germline TP53 mutations have also been linked with the development of ACC, particularly in paediatric patients with a family history of LFS and Li-Fraumeni-like Syndrome.26 In this study, the mean age of the patients with ACC with and without TP53 mutation was 59.4 years versus 50.2 years, respectively, and no TP53-mutated ACC was identi- fied in a patient younger than 46 years. Patient-matched normal specimens required to definitively determine the germline status of TP53 mutation were not available for this study.

Given the limited success of systemic cytotoxic chemotherapy in the treatment of relapsed and metastatic ACC, investigators have queried whether genomic profiling could uncover potential

Table 2 Genomic alterations (GAs) identified in 29 cases of adrenocortical carcinoma (ACC)
CaseMedian coverage depthTotal GASActionable GASGAs present in each ACC
135820RB1 (S414fs*10); TP53 (C124fs*25)
249132CCND2 (amp); CDK4 (amp); PDRM1 (R921*)
361131EP300 (P925T)
469900
5112210TP53 (R282W)
666641DNMT3A (splice); LRP1B (splice); RB1 (loss); TP53 (C176F)
773611PDGFRB (amp)
865700
986100
10125911CDKN2A (loss)
1192110CTNNB1 (E15*)
1247911NF1 (F1708fs*2)
13110843CDK4 (amp); CUL4A (V275M); MDM2 (amp); TP53 (S241Y)
14113800
1567141DAXX (A47fs*92); EGFR (P848 L); KDM5C (V833fs*21);TP53 (F134C)
16103511ATM (R337H)
1771063EPHB1 (P167 L); ERBB4 (amp); KEAP1 (V369 L); NRAS (G13 V); STK11 (D194Y); TP53 (C135W)
1885633ATM (R3008C); BAP1 (E54*); NF1 (C509fs*1)
1957120CTNNB1 (S45P); MEN1 (V58fs*60)
2065800
21633125APC (R1171H); ATRX (T1582fs*24); GATA1 (T402fs*14+); MEN1 (R521fs*43); NF1 (E2029*, G849fs*29); PIK3CA (H1047R); PTCH1 (S1203fs*52); PTEN (N323fs*2); SPRN (P3317fs*83); TP53 (R273H)
2255273CCND1 (amp); CDKN2A (loss); CTNNB1 (S37C); ETV6 (truncation); FGF23 (amp); KRAS (amp); MEN1 (F43fs*74)
2355873AURKB (R123H); CDKN2A (loss); FGF3 (H122N); MCL1 (amp); MYC (amp); TP53 (V173 L & K132N)
2472210SETD2 (T1652fs*14)
2586200
2648661APC (S1465fs*3); ATM (R189 K); DAXX (H620fs*37); KDM5C (L1305fs*5); MSH2 (splice site 1760-2A>G); TP53 (R213*)
2766000
2869133AKT2 (amp); CCNE1 (amp); DNMT3A (loss)
2952931CDKN2A (I49 T); LRP1B (loss); TP53 (M237I)
Figure 1 Tile plot of genomic alterations identified in 29 adrenocortical carcinoma cases.

TP53

NF1

MEN1

CDKN2A

LRPIB

CTNNB1

ATM

RB1

MSH2

KDM5C

DNMT3.A

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APC

STK11

SPEN

SETD2

PTEN

PTCHI

PIK3CA

PDGFRB

PBRMI

NRAS

MYC

MDM2

MCL1

KRAS

KEAP1

GATA1

FGF6

FGF3

FGF23

ETV6

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CUL4.A

CCNE1

BAP1

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16

12

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Gene amplification

Gene deletion

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Figure 2 Case 13. A pleomorphic adrenocortical carcinoma liver metastasis derived from a 48-year-old man harboured CDK4 and MDM2 amplifications, CUL4A (V275M) and TP53 (S241Y) mutations.

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targets of therapy not routinely searched for in the management of this disease.27 28 In one previous NGS-based study of ACC interrogating fewer genes and using a method that does not detect all classes of GAS, a few obvious genomic-derived thera- peutic targets emerged.29 In the current study, interrogating an expanded series of cancer-related genes with an assay capable of detecting all classes of GAS, half of the ACC harboured poten- tially clinically meaningful GAs.12

For example in Case 13, a pleomorphic ACC derived from a 48-year-old man that had metastasized to the liver, amplifications of CDK4 and MDM2 were identified (figure 2). CDK4 encodes cyclin-dependent kinase 4, which, along with functional homo- logue CDK6 and family member CDK2, regulates cell cycle G1 phase progression and the G1/S transition.3º Amplification of

CDK4 has been identified in multiple cancer types and in a small number of adrenal carcinomas.31 A number of drugs that target CDK4 are under investigation in phase I clinical trials.32 Similarly, therapies targeting MDM2 are under study in clinical trials.33 In another case (Case 7), a locally advanced oncocytic ACC derived from a 60-year-old man, a single alteration was identified, amplifi- cation of PDGFRB (figure 3). GAs, including amplification of PDGFRB, have not been reported in ACC in the literature until now. PDGFRB amplification has been associated with PDGFRB protein overexpression and increased kinase activity in a variety of other tumours.34 Although there are no PDGFRB inhibitors cur- rently approved for use in ACC, several drugs that inhibit PDGFRB, including dasatinib, imatinib, sorafenib and sunitinib, have been food and drug administration (FDA) approved for use

Figure 3 Case 7. A Stage III Fuhrman Grade 3 adrenocortical carcinoma with extensive tumour necrosis derived from a 60-year-old man harboured PDGFRB amplification.

PDGFRB Amplification

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Table 3 Significant targetable genomic alterations (GAs) discovered by NGS assessment of 29 cases of adrenocortical carcinoma (ACC)
Gene (frequency in ACC)GASTotal cases with targetable GASPotential targeted therapeutic
Loss (homozygous deletion)Base substitutionTruncationAmplification
NF1 (17%)54 (1 case with 2 NF1 GAs)Everolimus Temsirolimus
CDKN2A/B (14%)314CDK 4/6 inhibitors
ATM (10%)33Everolimus
Temsirolimus
CDK4 (7%)22CDK 4/6 inhibitors
EGFR (3%)11Erlotinib
Gefitinib
PDGFRB (3%)11Dasatinib Imatinib
Sorafenib Sunitinib
PTCH1 (3%)11Vismodegib
PIK3CA (3%)11Everolimus
Temsirolimus
NGS, next-generation sequencing.

in other tumour types. Although an initial study indicated signifi- cant efficacy of sorafenib in the treatment of metastatic ACC, more recent phase II trial was unable to duplicate that result.35 36 The vascular endothelial growth factor (VEGF) inhibitor axitinib has also shown limited impact on the outcome of this disease.37

The poor prognosis of patients with locally advanced and metastatic ACC has increased interest in identifying targeted therapies for patients with ACC.38-40 The GAs identified linked to targeted therapies in this study involved multiple genes and pathways, including the receptor tyrosine kinase, retrovirus asso- ciated sarcoma (RAS) signalling, molecular targets of rapamycin (MTOR) and Hedgehog pathways. These alterations are thus candidates for referral of patients to a broad series of mechanism-driven registered clinical trials using targeted therap- ies such as MTOR inhibitors, epidermal growth factor receptor (EGFR) inhibitors, Hedgehog pathway inhibitors and cyclin dependent kinase (CDK) inhibitors.

A recent study further classified ACC based on genomic signa- tures into indolent and aggressive subtypes.41 This study reported many, but not all of the alterations found in the current study which was restricted to aggressive ACC which had

Take home messages

A sensitive/validated next-generation sequencing (NGS) assay can readily be performed on formalin-fixed paraffin-embedded biopsies of patients diagnosed with adrenocortical carcinoma (ACC).

In 22 (76%) ACC, at least one genomic alteration (GA) was identified (mean 2.6 alterations per ACC).

The most frequent GAs in ACC were in TP53 (34%), NF1 (14%), CDKN2A (14%), MEN1 (14%), CTNNB1 (10%) and ATM (10%). APC, CCND2, CDK4, DAXX, DNMT3A, KDM5C, LRP1B, MSH2 and RB1 were each altered in two cases (7%) and EGFR, ERBB4, KRAS, MDM2, NRAS, PDGFRB, PIK3CA, PTEN and PTCH1 were each altered in a single case (3%).

In 17 (59%) ACC, at least one GA was associated with an available therapeutic or a mechanism-based clinical trial.

NGS can discover targets of therapy for relapsed and metastatic ACC and shows promise to improve outcomes for this aggressive form of cancer.

relapsed locally or spread to regional or distant sites. In this study, clinically meaningful GAs that could potentially guide tar- geted treatment options were identified in 58% of patients sequenced (table 3). However, the complexity of the alterations identified presents challenges to the NGS platform used to test patients with relapsed ACC resistant to conventional therapies. The use of NGS to discover novel targets of therapy not rou- tinely searched for in the current management of ACC shows promise and warrants further study and the development of new mechanism-driven clinical trials designed to improve out- comes for this aggressive form of cancer.

Contributors The following authors contributed to the development and submission of this manuscript. Substantial contributions to the conception or design of the work; or the acquisition, analysis or interpretation of data for the work: JSR, KW, JVR, MJP, CES, SA, JAE, EL, CH, JB, GAO, RY, DL, DM, JC, VAM, PJS. Drafting the work or revising it critically for important intellectual content: JSR, KW, JVR, MJP, CEES, SMA, JAE, ELB, CH, JB, GAO, RY, DL, DM, J, VAM, PJS. Final approval of the version to be published: JSR, KW, JVR, MJP, CES, SMA, JE, ELB, CH, JB, GAO, RY, DL, DM, JC, VAM, PJS. Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved: JSR, KW , JR, MJP, CES, SMA, JAE, ELB, CH, JB, GAO, RY , DL, DM, JC, VAM, PJS.

Competing interests None.

Ethics approval Local site permissions were used that included signed authorisations from submitting institutions.

Provenance and peer review Not commissioned; externally peer reviewed.

Data sharing statement All relevant data from this study are included in the submission. A supplementary file, including genomic variants of undetermined significance not reported in patient records, can be prepared and sent to reviewers if required. This file would then be made available to the readership.

Open Access This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/ licenses/by-nc/4.0/

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