Utility of Multimodality Molecular Profiling for Pediatric Patients with Central Nervous System Tumors

Background

As our molecular understanding of pediatric central nervous system (CNS) tumors evolves, so too do diagnostic criteria, prognostic biomarkers, and clinical management decision-making algorithms. Here, we explore the clinical utility of wide-breadth assays including whole-exome sequencing (WES), RNA sequencing (RNAseq), and methylation array profiling as an addition to more conventional diagnostic tools for pediatric CNS tumors.

Methods

This study comprises an observational, prospective cohort followed at a single academic medical center over three years. Paired tumor and normal control specimens from 53 enrolled pediatric patients with CNS tumors underwent WES. A subset of cases also underwent RNAseq (n=28) and/or methylation array analysis (n=27).

Results

RNAseq identified driver and/or targetable fusions in 7/28 cases, including potentially targetable NTRK fusions, and uncovered possible rationalized treatment options based on outlier gene expression in 23/28 cases. Methylation profiling added diagnostic confidence (8/27 cases) or diagnostic subclassification endorsed by the WHO (10/27 cases). WES detected clinically pertinent Tier 1 or Tier 2 variants in 36/53 patients. Of these, 16/17 SNVs/indels and 10/19 copy number alterations would have been detected by current in-house conventional tests including targeted sequencing panels.

Conclusions

Over a heterogeneous set of pediatric tumors, RNAseq and methylation profiling frequently yielded clinically relevant information orthogonal to conventional methods while WES demonstrated clinically-relevant added-value primarily via copy number assessment. Longitudinal cohorts comparing targeted molecular pathology workup versus broader genomic approaches including therapeutic selection based on RNA-expression data will be necessary to further evaluate the clinical benefits of these modalities in practice.

Molecular alterations in prostate cancer and association with MRI features

BACKGROUND

Multiparametric magnetic resonance imaging (mpMRI) has been increasingly used for prostate cancer (PCa). Recent studies identified distinct molecular subclasses of PCa with recurrent genomic alterations. However, the associations between molecular alterations in PCa and characteristics on mpMRI are unknown. Therefore, the objective of this study was to investigate recurrent molecular alterations in PCa and their associations with mpMRI features.

METHODS

Sixty-two PCa nodules >0.5 cm had a preoperative mpMRI. Nodules were evaluated for ERG rearrangement, PTEN deletion, SPINK1 overexpression, SPOP mutation and CHD1 deletion. Each PCa focus was matched to the corresponding location on mpMRI. Lesions were scored by single observer according to the PI-RADSv2 scale.

RESULTS

Of the 62 nodules, 22 (35.5%) were ERG positive, 6 (9.7%) had SPINK1 overexpression, 6 (9.7%) had SPOP mutations, 4 (6.5%) had CHD1 deletions and 1 (1.6%) had PTEN deletion. All of the nodules with CHD1 deletions were not visible on mpMRI (P=0.037). All of the nodules with SPINK1 overexpression were visible on mpMRI, although the association was not statistically significant (P=0.06). There were no significant associations between any molecular alteration with the severity of the PI-RADS scores (all P>0.05).

CONCLUSIONS

This investigation represents the first description of an association between recurrent molecular alterations and the characterization of PCa nodules on mpMRI. This study can be considered hypothesis-generating for future studies to rigorously evaluate the association of specific PCa molecular subclasses with imaging features and potentially define specific subsets of PCa for which the utility of MRI is higher or lower.

Molecular characterization of neuroendocrine prostate cancer (NEPC) and identification of new drug targets

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Background: NEPC is an aggressive variant of prostate cancer that can arise de novo or from existing prostate adenocarcinoma (PCA). We sought to better understand the molecular transformation of NEPC and identify new drug targets.

Methods: We used Next Generation RNA sequencing and oligonucleotide arrays to profile 7 NEPC, 30 PCA, 5 benign prostate (BEN), and validated findings on tumors from a large cohort of patients (30 NEPC, 118 PCA, 30 BEN) using IHC and FISH. Functional studies were performed using NCI-H660 (NEPC), VCaP and LnCaP (PCA), RWPE (BEN).

Results: ERG rearrangement was present in 47% of NEPC, but ERG protein expression was absent and corresponded directly with lack of AR expression. 936/25932 genes were differentially expressed in NEPC versus PCA (P<0.001). Aurora kinases (AURKA, AURKB) and N-myc (MYCN) were overexpressed in NEPC (P<0.001) and AURKA and MYCN amplified. Using IHC and FISH, we validated these findings on a large cohort and found majority (>80%) of NEPC showed Aurora overexpression, 35% had AURKA and MYCN amplification. A small subset of PCA (5%) and no BEN were positive. Transfection of MYCN induced AURKA expression and kinase activity in vitro, and MYCN or AURKA could induce expression of neuroendocrine (NE) markers (SYP, NSE). After validating NCI-H660 as model of NEPC, we observed dramatic and enhanced in vitro and in vivo sensitivity to the Aurora kinase inhibitor PHA-739358 in NCI-H660 compared to minimal to no effect in LnCaP and VCaP. Phospho-H3 expression, a downstream marker of Aurora kinase activity, was inhibited in the treated NCI-H660 and not in PCA. Notably, NE marker expression was also suppressed in the treated NCI-H660 xenografts, again supporting a role of Aurora kinase in modulating the NE phenotype.

Conclusions: There is likely clonal origin of NEPC from PCA (with ERG fusion positivity seen in both), but ERG expression is limited to PCA and driven by AR signaling. We discovered significant overexpression and gene amplification of Aurora kinases and N-myc in NEPC and a small subset of PCA, and evidence that that they cooperate and induce a NE phenotype in prostate cells. In vitro and in vivo data confirms that these are novel drug targets for NEPC.

No significant financial relationships to disclose.

Analysis of user-satisfaction with the use of a teleconsultation system in oncology

There is an increasing interest in assessing telemedicine as alternative method of delivering high quality cancer treatment to patients living in rural areas. In the Province of Trento (north-east Italy) a tele-oncology system was implemented to provide non-surgical oncological consultation to district general hospitals. The aim of this study was to explore user-satisfaction with the system after 6 months of experimentation. During the on-field validation two questionnaires with open and closed-response questions were distributed to 80 physicians and nurses 6 months apart to investigate the users' expected benefits vs. perceived ones. The two questionnaires were compared to assess how perceived benefits differed from expected ones. Significant differences were found regarding improvements in: the standardization of diagnostic-therapeutic procedures using the Electronic Patient Record (EPR)]; information sharing; data updating; consultation speed; and the possibility to diminish patients' travels through the use of teleconsultation (TC). Physicians' responses showed a significant difference regarding the EPR's effects on relationship with patient, the nurses' responses with regards to its effects on care quality. Physicians felt that both modalities of teleconsultation were useful in enhancing communication with colleagues (86% for the synchronous TC, 80% for the asynchronous TC). Responses indicated that the major difficulties encountered were in the introduction of the system into the daily routine. Despite this, user expectations for its future use in clinical field were considerably high.

UbcH10 expression may be a useful tool in the prognosis of ovarian carcinomas

The UbcH10 gene codes for a protein that belongs to the ubiquitin-conjugating enzyme family. Previous studies of our group suggest UbcH10 expression as a valid indicator of the proliferative and aggressive status of thyroid carcinomas. Therefore, to better understand the process of ovarian carcinogenesis, and to look for possible tools to be used as prognostic markers in these neoplasias, we decided to extend the analysis of the UbcH10 expression to the ovarian neoplastic disease. We found that the UbcH10 gene was upregulated in some ovarian carcinoma cell lines analysed. Then, immunohistochemical studies demonstrate that UbcH10 expression significantly correlates with the tumor grade and the undifferentiated histotype of the ovarian carcinomas. Furthermore, a significant relationship between UbcH10 expression and overall survival was observed. Finally, the block of UbcH10 protein synthesis by RNA interference inhibited the growth of ovarian carcinoma cell lines, suggesting a role of UbcH10 overexpression in ovarian carcinogenesis. Therefore, all these data taken together suggest the possibility to use UbcH10 detection as a marker for the diagnosis and prognosis of these neoplastic diseases and open the perspective of a therapy of some ovarian carcinomas based on the suppression of the UbcH10 synthesis and/or function.

An evaluation of the use of and user satisfaction with a teleconsultation system in oncology practice

A three-year oncology teleconsulting project was concluded in November 2000. During a six-month study period, 38 clinical physicians and 47 nurses used the system. A total of 617 electronic patient records were created in the oncology department, 297 in dermatology and 24 in gynaecology. There were 45 synchronous teleconsultations involving various participants, lasting a total of 708 min. We conducted surveys of the attitudes of users to the teleconsulting system both before and after its implementation. There were no significant differences between the two surveys and the results showed that users had a positive reaction to the system and high expectations of its future utilization.

Design and initial implementation of a regional tele-oncology project

Two tele-oncology projects have been in progress since 1997 in the Province of Trento in north-east Italy. The common aim of the projects concerns the design and the implementation of a non-surgical tele-oncology system intended to provide a flexible computing environment for the joint management of oncology patients in a wide-area network. The two projects involve both hospital specialists and general practitioners treating oncological patients. The first phase of the project involves the design and implementation of the oncology teleconsultation service.