The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets

Metastatic and locally-advanced neuroendocrine neoplasms (aNEN) form clinically and genetically heterogeneous malignancies, characterized by distinct prognoses based upon primary tumor localization, functionality, grade, proliferation index and diverse outcomes to treatment. Here, we report the mutational landscape of 85 whole-genome sequenced aNEN. This landscape reveals distinct genomic subpopulations of aNEN based on primary localization and differentiation grade; we observe relatively high tumor mutational burdens (TMB) in neuroendocrine carcinoma (average 5.45 somatic mutations per megabase) with TP53, KRAS, RB1, CSMD3, APC, CSMD1, LRATD2, TRRAP and MYC as major drivers versus an overall low TMB in neuroendocrine tumors (1.09). Furthermore, we observe distinct drivers which are enriched in somatic aberrations in pancreatic (MEN1, ATRX, DAXX, DMD and CREBBP) and midgut-derived neuroendocrine tumors (CDKN1B). Finally, 49% of aNEN patients reveal potential therapeutic targets based upon actionable (and responsive) somatic aberrations within their genome; potentially directing improvements in aNEN treatment strategies.

Driver mutations occur frequently in metastases of well-differentiated small intestine neuroendocrine tumours

AIMS

To investigate the clinicopathological significance of driver mutations in metastatic well-differentiated small intestine neuroendocrine tumours (SI-NETs).

METHODS AND RESULTS

Whole genome sequencing (WGS) of 35 metastatic SI-NETs and next-generation sequencing (NGS) of eight metastatic SI-NETs were performed. Biopsies were obtained between 2015 and 2019. Tumours were classified according to the 2019 World Health Organization classification. WGS included assessment of somatic mutations in all cancer-related driver genes, the tumour mutational burden (TMB), and microsatellite status. NGS entailed a cancer hotspot panel of 58 genes. Our cohort consisted of 21% grade 1, 60% grade 2 and 19% grade 3 SI-NETs. Driver mutations were identified in ~50% of SI-NETs. In total, 27 driver mutations were identified, of which 74% were in tumour suppressor genes (e.g. TP53, RB1, and CDKN1B) and 22% were in proto-oncogenes (e.g. KRAS, NRAS, and MET). Allelic loss of chromosome 18 (63%), complete loss of CDKN2A and CDKN1B (both 6%) and CDKN1B mutations (9%) were most common. Potential targetable genetic alterations were detected in 21% of metastasised SI-NETs. All tumours were microsatellite-stable and showed low TMBs (median 1.10; interquartile range 0.87-1.35). The Ki67 proliferation index was significantly associated with the presence of driver mutations (P = 0.015).

CONCLUSION

Driver mutations occur in 50% of metastasised SI-NETs, and their presence is associated with a high Ki67 proliferation index. The identification of targetable mutations make these patients potentially eligible for targeted therapy.

Abstract 5673: In-depth analysis of the genomic landscape of 91 metastatic neuroendocrine tumors reveals subtype-heterogeneity and potential therapeutic targets

Background: Metastatic neuroendocrine tumors (mNET) form a clinically and genetically heterogeneous malignancy, characterized by distinct prognosis based upon primary tumor localization, functionality, grade and proliferation index, and a wide variation in treatment outcome. To get a better insight into this heterogeneity in prognosis and outcome, and also to reveal putative novel treatment targets, we here analyzed the mutational landscape of 91 metastatic mNET biopsies derived from whole-genome sequencing (WGS).

Material and Methods: Between May 2016 and July 2018, 91 mNET patients from 14 Dutch hospitals were included in the study protocol (NCT01855477) of the Center for Personalized Cancer Treatment (CPCT). Patients with mNET were categorized by primary location into midgut (N = 44), pancreas (N = 26), lung (N = 5), unknown (N = 12) and other (N = 4). The WGS of matched peripheral blood and tumor tissues was performed on a HiSeq X Ten system to sequencing depths of 38x and 105x, respectively, and subsequently aligned to the human reference genome (GRCh37) and analyzed for somatic mutations, mutational signatures, copy-number alterations and structural variants with the GRIDSS, PURPLE, LINX suite, GISTIC2 and in-house algorithms.

Results: The overall mutational landscape of mNET is hallmarked by a relative stable diploid tumor genome and low median tumor mutational burden (TMB) of 1.32 (IQR: 0.91 - 2.1) mutations per genomic Mb. Differences in median TMB relating to primary location were observed; ranging from 1.1 (midgut), 1.49 (pancreas), 2.87 (lung) to 4.18 (unknown); six mNET had high tumor mutational burden (TMB ≥ 10), but without microsatellite-instability signatures. In addition, we observed striking evidence of somatic aberrations due to alkylating agents (sig. 11), combined with the highest cohort-wide TMB (39.6) for a single patient treated with streptozocin prior to biopsy. Three mNETs revealed MUTYH-related alterations (sig. 18) and furthermore, we detected chromothripsis (n = 6) and APOBEC-related regional hypermutation (kataegis; n = 11). Midgut-derived mNET (n = 44) predominantly harbored somatic alterations in CDKN1B (n = 11) and CDKN2A/B (n = 7). Strikingly, no somatic driver mutation was seen in almost half of these midgut-derived mNET (n = 21). Pancreatic mNET (n = 26) predominantly harbored alterations in MEN1 (n = 8), TP53 (n = 8), ATRX (n = 6), CDKN2A/B (n = 6) and DAXX (n = 5). In total, 39 mNET (43%) showed clinically-actionable somatic alterations for current on- and off-label NET therapies.

Conclusion: This study comprises the largest WGS repository of mNET to date, and demonstrates the genetic heterogeneity of mNET linked to primary localization. Several potential therapeutic targets were identified which are worthwhile to explore for their clinical value in the treatment of mNET patients.

Citation Format: Job van Riet, Harmen J. van de Werken, Edwin Cuppen, Ferry A. L. M. Eskens, Margot E. Tesselaar, Linde M. van Veenendaal, Heinz-Josef Klümpen, Wouter Dercksen, Gerlof D. Valk, Martijn P. J. K. Lolkema, Stefan Sleijfer, Bianca Mostert. In-depth analysis of the genomic landscape of 91 metastatic neuroendocrine tumors reveals subtype-heterogeneity and potential therapeutic targets [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5673.

The Clinical Utility of Neuron-Specific Enolase (NSE) Serum Levels as a Biomarker for Merkel Cell Carcinoma (MCC)

BACKGROUND

No adequate biomarker for Merkel cell carcinoma (MCC) has been identified. Serum neuron-specific enolase (NSE) has been tested and is commonly used as a biomarker for several other small cell malignancies. However, the role of NSE in MCC is still unclear. The purpose of this study was to investigate the role of NSE as a biomarker in MCC.

METHODS

A prospective cohort of MCC patients was analyzed using Kaplan-Meier curves with log-rank test, ROC curves, Cox regression, and mixed models. A separate evaluation was performed for patients treated with immunotherapy.

RESULTS

Eighty-four patients were included [47 males, median age 71 years, stages I & II, III, and IV MCC in respectively 39 (46%), 42 (50%), and 4 (3%) patients at time of diagnosis] with 565 NSE samples (median 15; interquartile range 12.6-22 ng/ml). Baseline NSE had no association with prognosis. NSE correlated with extent of disease (P = 0.01) and increased with 15 ng/ml per class (no tumor load, localized MCC, regional or distant metastases, respectively). NSE was able to detect progression (AUC 0.89). A NSE of 18.2 ng/ml was considered the most optimal level for clinical use (sensitivity 91%, specificity 78%, PPV 48%, NPV 98%). During immunotherapy (N = 23; 248 NSE values), all complete responders (N = 10) had a normalized NSE (< 18.2 ng/ml), all partial responders (N = 5) had a decreasing NSE. In nonresponders (N = 8), all NSE levels remained elevated.

CONCLUSIONS

NSE could be a valuable biomarker in MCC. NSE correlates with extent of disease; it is able to rule out progression and distinguishes responders from nonresponders during immunotherapy.

The clinical utility of neuron-specific enolase serum levels as a biomarker for Merkel cell carcinoma

9570

Background: To date no adequate biomarker for Merkel Cell carcinoma (MCC) has been identified. The introduction of immunotherapy (IT) for metastatic MCC increases the need for a biomarker. Serum Neuron-specific enolase (NSE) has already been tested and is commonly used as a biomarker for several small cell malignancies. However, the role of NSE in MCC is still unclear. Aim: To investigate the role of NSE as a biomarker in MCC. Methods: A prospective cohort of MCC patients treated from 2016 to July 2018 was analyzed. Kaplan Meier curves with log rank test, Cox regression and mixed models were used to analyze NSE. A separate evaluation was performed for patients treated with IT. Results: A total of 78 patients (42 males, median age 71 years, stage I&II, III and IV MCC in 37(47%), 39(50%) and 2(3%) patients at time of diagnosis with 474 NSE levels (median 15 ; IQR 12,6-22 ng/ml were included. Baseline NSE (n=36) had no influence on survival or progression. During follow-up (FU) NSE levels correlated with tumorload (p=0,01) with increase of 15 ng/ml per class (no tumorload, localized MCC, nodal and distant metastases, respectively). NSE level during FU was able to detect progression (AUC 0,89). Several cut off values were evaluated. A NSE of 18,2 ng/ml was considered the most optimal level for clinical use (sensitivity 91%, specificity 78%, PPV 48%, NPV 98% to detect progression). During IT (n=16; 195 NSE values) all complete responders (n=7) had a normalized NSE (<18,2 ng/ml), all partial responders (n=3) had a decreasing NSE. In non-responders (n=6) all NSE levels remained elevated, one patient responded after switching to different IT with normalizing NSE values. Conclusions: NSE seems to be a valuable biomarker in MCC. NSE correlates with tumorload; is able to rule out progression and distinguishes responders from non-responders during IT.

Recommendations for radioembolisation after liver surgery using yttrium-90 resin microspheres based on a survey of an international expert panel

INTRODUCTION

Guidelines on how to adjust activity in patients with a history of liver surgery who are undergoing yttrium-90 radioembolisation (90Y-RE) are lacking. The aim was to study the variability in activity prescription in these patients, between centres with extensive experience using resin microspheres 90Y-RE, and to draw recommendations on activity prescription based on an expert consensus.

METHODS

The variability in activity prescription between centres was investigated by a survey of international experts in the field of 90Y-RE. Six representative post-surgical patients (i.e. comparable activity prescription, different outcome) were selected. Information on patients' disease characteristics and data needed for activity calculation was presented to the expert panel. Reported was the used method for activity prescription and whether, how and why activity reduction was found indicated.

RESULTS

Ten experts took part in the survey. Recommendations on activity reduction were highly variable between the expert panel. The median intra-patient range was 44 Gy (range 18-55 Gy). Reductions in prescribed activity were recommended in 68% of the cases. In consensus, a maximum DTarget of 50 Gy was recommended.

CONCLUSION

With a current lack of guidelines, large variability in activity prescription in post-surgical patients undergoing 90Y-RE exists. In consensus, DTarget ≤50 Gy is recommended.

KEY POINTS

• BSA method does not account for a decreased remnant liver volume after surgery. • In post-surgical patients, a volume-based activity determination method is recommended. • In post-surgical patients, a mean D Target of ≤ 50Gy should be aimed for.

A painful finger as first sign of a malignancy

INTRODUCTION

Bone metastases are frequently seen in patients with malignancies, but only 0.007% to 0.3% of these metastases are located in the hand or foot. In 16%, the metastasis is the first manifestation of a malignancy. These acrometastases have a poor prognoses with a median survival of 6 months. Treatment is usually palliative and consists of radiation or amputation.

CASE DESCRIPTION

An 83-year-old woman was seen with pain and swelling of the right middle finger since 3 months. A radiograph of this finger showed a lytic lesion of the proximal phalanx. A metastasis, primary bone tumor, or osteomyelitis was considered. Because of a radically resected colon carcinoma in patient's medical history, the carcinoembryonic antigen level was analyzed and proved to be elevated. Computed tomography scan of thorax and abdomen showed 2 (primary) pulmonary tumors with mesenteric metastases. Patient refrained from further analysis and treatment of these lung tumors. However, because of persistent pain the right middle finger was amputated. Pathological examination of the finger confirmed the diagnosis of an adenocarcinoma most likely to be a metastasis of lung cancer. Lung cancer is in most cases responsible for metastases in the hand.

CONCLUSION

Acrometastasis may be the first manifestation of malignancy. Given the poor prognosis, early diagnosis is important to offer adequate treatment. Delay of appropriate treatment can adversely affect the quality of life in these often preterminal patients. This case report could contribute to a (more) rapid recognition of acrometastases as patients with acrometastases are often presented to specialists who do not frequently deal with cancer.