Background

Once regulatory drug approval is obtained, patients and pharma would greatly benefit from identifying signals of activity in cancer subsets outside the approved indication. In the Netherlands’ precision oncology-network (www.cpct.nl), Whole Genome Sequencing (WGS) is offered to systemically treated cancer patients. This allows us to identify a spectrum of potentially actionable genetic aberrations in all types of cancer. The DRUP provides patients with such aberrations access to genetically matched treatment upon central review of the tumor profile.

Methods

Adult patients with solid tumors, glioblastoma, lymphoma or multiple myeloma, with no standard treatment options, are eligible. Patients are enrolled in multiple parallel cohorts, each defined by 1 tumor type, 1 tumor profile and 1 treatment. Efficacy is analyzed per cohort using a Simon-2-stage approach, aimed at ≥ 1 clinical benefit (CR, PR or SD ≥ 16 weeks)/8 patients in stage I, and ≥5/24 in stage II (85% power, α error rate 7.8%). A fresh tumor biopsy for biomarker research is mandatory. There are currently 23 participating hospitals and 19 study drugs, supplied by 10 pharmaceutical companies.

Results

Since study launch Sep 2016, 200 cases were submitted for review and 60 patients started treatment. Clinical benefit was observed in 37% (6% CR, 14% PR, 17% SD ≥ 16 weeks; all CRs and 2/3 of PRs were ongoing at the time of writing and awaiting ≥30 days confirmation). About 2/3 of case submissions were rejected, due to a general protocol ineligibility (18%), b current unavailability of matching study drugs (17%), c no actionable target detected (15%), d negative evidence for target-drug-match (13%), e eligible for standard treatment (12%), f eligible for competing trials (11%), g loss to follow up (10%) or h genetic tumor profile not yet assessed (4%).

Conclusions

Execution of a national multi-drug and multi-tumor precision oncology trial is feasible. By performing WGS in many different cancer types, subgroups are identified who may benefit from existing drugs outside of their registered indication. This study hereby accelerates translation of new findings to the clinic and increases the yield of existing therapies.

Clinical trial identification

NCT02925234 (release date: 26-Aug-2016) EudraCT 2015-004398-33 (release date: 01-Oct-2015).

Legal entity responsible for the study

Governance: Stichting Het Nederlands Kanker Instituut – Antoni van Leeuwenhoek Ziekenhuis, whose registered office is at Plesmanlaan 121, 1066CX, Amsterdam, lawfully represented by Prof. R. Medema, Head of the Board representing the CPCT. Coordination and running of the study: Prof. E.E. Voest, Netherlands Cancer Institute, division of Molecular Oncology, Amsterdam, the Netherlands.

Funding

Barcode for Life Foundation (BFL): funding • Dutch Cancer Society (KWF): funding • Hartwig Medical Foundation (HMF): sequencing • Pharmaceutical partners (Amgen, AstraZeneca, Bayer, Bristol-Myers Squibb, Novartis, Roche): funding and study drugs.

Disclosure

F. De Vos: Direct research support to the responsible project lead (PI): Array, AstraZeneca, BMS, GSK, Merck, Merus, Novartis, Roche/Genentech, E. Cuppen: Board of directors of Hartwig Medical Foundation (not for profit), N. Steeghs: Consulting or advisory role: Lilly Research funding: AB Science, AstraZeneca, Bayer, Boehringer Ingelheim, BristolMS. All other authors have declared no conflicts of interest.

Background

The iMYC trial is a biomarker-driven study in advanced OG cancer that prospectively screens patients for MYC amplification to assess the feasibility of ibrutinib therapy. MYC is implicated in OG cancer carcinogesis and as the acquisition of fitness enhancing mutations can drive tumour progression and treatment resistance, we present data from the screening component of the study evaluating the frequency and diversity of MYC amplification using FISH and ddPCR analysis of primary OG tumours and circulating tumour (ct)DNA.

Methods

To find potential on-chromosome (chr) 8 references for the MYC gene for the purposes of ddPCR, OG tumour sample copy number data were obtained from cBioportal using the CGDS-R package. A dual probe FISH assay to detect MYC amplification was optimised on archival OG tumour samples where centrometric probes for chr 8 and probes mapping specifically to the coding region of the MYC gene (exons 1-3) were used to distinguish between increased copies of chr 8 and extra copies of MYC.

Results

To date 96 archival tumour samples have successfully undergone FISH analysis with MYC amplification seen in 26/96 (27%). The % of cells with MYC amplification ranged widely between samples (median 57.5, range 11-94%). Intra-tumour heterogeneity was seen: 19/26 (73%) amplified samples showed a range of differing amplification ratios within the tumour specimen (bartlett test for equal variance p < 0.001) with evidence of MYC extrachromosomal amplification accounting for genetic heterogeneity. For patients displaying MYC amplification by FISH, detection of amplification by ddPCR in either tumour tissue or ctDNA was restricted to those tumours displaying a homogenous and high-level FISH amplification pattern.

Conclusions

This study represents the first attempt to screen for MYC amplification prospectively in advanced OG cancer and illustrates the utility of FISH in assessing clonal diversity and visualisation of extrachromosomal amplifications. Using a novel ddPCR assay we have detected MYC amplifications from both archival tumour and ctDNA in homogeneous and highly amplified cases however the ddPCR assay is not optimal in detecting small clonal subpopulations of amplified cells in OG cancer.

Clinical trial identification

NCT02884453.

Legal entity responsible for the study

Royal Marsden NHS Foundation Trust oundation Trust

Funding

Janssen Pharmaceuticals

Disclosure

D. Cunningham: Research funding from Roche, Amgen, Celgene, Merck, BMS, Novartis, Astra Zeneca, Bayer, Merrimack, Medimmune, Clovis, I. Chau: Advisory Board: Sanofi Oncology, Eli-Lilly, Bristol Meyers Squibb, MSD, Bayer, Roche, Five Prime Therapeutics; Research funding: Janssen-Cilag, Sanofi Oncology, Merck-Serono, Novartis Honorarium: Taiho, Pfizer, Amgen, Eli-Lilly, Gilead Science. All other authors have declared no conflicts of interest.

Background

Despite many advances in the diagnosis and treatment of gastric cancer (GC), the prognosis of patients with GC remains poor. Circular RNAs (circRNAs), a new star of the non-coding RNA network, have been identified as critical regulators in various cancers. There is increasing evidence that circRNAs represent a class of widespread and diverse endogenous RNAs that may regulate gene expression. However, the role of circRNAs in GC remains elusive. Here, we aimed to determine the circRNA expression profile and investigate the functional and prognostic significance of circRNA in GC.

Methods

In this study, we investigated the expression profile of circRNAs in three GC samples and paired adjacent normal tissues using ribo-minus RNA sequencing and a bioinformatics analysis. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to identify circRNA candidates. Molecular and cellular techniques were used to explore the biological function and mechanism of circRNA in GC cells. The prognostic significance was analyzed using the Kaplan-Meier method and the Cox proportional hazards model.

Results

We first characterized circular RNA transcripts using RNA-seq analysis of ribosomal RNA-depleted total RNA from three paired normal and cancerous gastric tissues. In all, 15623 distinct circRNA candidates were found in these tissues and at least 5500 distinct circRNAs are differently expressed in GC tissues compared with matched normal tissues. We further characterized one abundant circRNA derived from the LMTK2 gene, termed circLMTK2. The expression of circLMTK2 is often upregulated in GC tissues and the silencing of circLMTK2 significantly inhibits gastric cancer cell growth. Furthermore, the level of circLMTK2 was observed as an independent prognostic marker for overall survival and disease-free survival of patients with GC.

Conclusions

Our study revealed the circular RNA profile of GC tissues and characterized a differentially expressed circRNA derived from the LMTK2 gene. circLMTK2 may serve as a new proliferative factor and prognostic marker in gastric cancer.

Legal entity responsible for the study

Fudan University Shanghai Cancer Center

Funding

None

Disclosure

All authors have declared no conflicts of interest.

Background

Tumor-infiltrating lymphocytes (TILs) can be used to monitor the immune response, and are important in predicting treatment responses and outcomes for various types of cancer. In this study, we evaluated the prognostic significance of CD8⁺ TILs and FOXP3⁺ TILs before and after neoadjuvant chemotherapy (NAC).

Methods

Except for patients who achieved pathological complete response, 136 breast cancer patients treated with NAC were examined. CD8⁺ TILs and FOXP3⁺ TILs in biopsy specimens and residual tumors were evaluated by immunohistochemistry. CD8⁺ TILs and FOXP3⁺ TILs status was assessed, and the rates of their changes before and after NAC were calculated.

Results

All patients with high rates of changes in the CD8⁺ TILs or low rates of changes in the FOXP3⁺ TILs or high rates of changes in the CD8/FOXP3 ratio (CFR) had significantly better recurrence-free survival (RFS) (P = 0.006, P = 0.044, P < 0.001, respectively) and overall survival (OS) (P = 0.037, P = 0.025, P < 0.001, respectively). In multivariate analysis, rates of changes in the CD8⁺ TILs and rates of changes in the CFR were an independent predictor for RFS (hazard ratio (HR) = 2.304, 95% confidence interval (CI) 1.052-5.776, P = 0.036; HR = 4.663, 95% CI 2.133-11.68, P < 0.001, respectively). Pathological response was also significantly correlated with RFS (HR = 5.260, 95% CI 2.373-11.14, P < 0.001). Of the 39 patients with triple-negative breast cancer, rates of changes in the CFR were independent predictor for RFS (HR = 13.02, 95% CI 2.241-258.1, P = 0.002). Of the 78 patients with hormone receptor-positive breast cancer, rates of changes in the CFR were significantly correlated with RFS too (HR = 4.377, 95% CI 1.641-13.71, P = 0.003).

Conclusions

Improvement in immune microenvironment following NAC has a relationship with good outcome. In particular, rates of changes in the CFR may be a useful biomarker to predict prognosis of patients treated with NAC in all breast cancer subtypes.

Legal entity responsible for the study

Shinichiro Kashiwagi

Funding

None

Disclosure

All authors have declared no conflicts of interest.

Background

Somatic mutations are attractive therapeutic targets for “individuvalized neoantigen vaccines” because of lack of host central tolerance and reduced risk of autoimmunity. Here, we perform large-scale –omic analyses to assess the neoantigen landscape of colorectal cancer, a cancer largely refractory to immune-checkpoint inhibition.

Methods

We performed whole genome sequencing (WGS) (60x tumor, 30x normal) and deep whole transcriptomic sequencing (RNA-Seq) (∼200x10e⁶ reads per tumor) on 158 Colorectal cancers including 32 patients with microsatellite instability (MSI), 126 microsatellite stable (MSS). Whole Exome Sequencing (200x tumor,100x normal) was also performed on 120 tumours. HLA typing, somatic mutations, gene expression & neoepitope predictions were computationally evaluated. Inferred HLA-A alleles were orthogonally validated with Pacbio long-read sequencing.

Results

The most common HLAs were, by allele count: A*11:01: 56; A*33:03: 38; B*58:01: 33; B*46:01: 29; B*40:01: 26; C*01:02: 41; C*07:02: 33. Inferred HLA-A alleles from WGS data was largely concordant with Pacbio long-read sequencing. There were a median of 2,850 (1229-6909) [MSI] & 213 (27-13,835) [MSS] coding variants, from which 10,487 (4,307-27,365) [MSI] & 726.5 (50-59,096) [MSS] possible neoepitopes were derived, after accounting for epitope processing, the normal proteome and general population variome based on dbSNP, Of these, 5,707 (2,608-15,218) [MSI] & 320 (14-25,243) [MSS] neoepitopes are expressed (based on RNA-Seq). Epitope prediction algorithms revealed a median of 423 (17-1,056) [MSI] & 26 (0-1,102) [MSS] bound & expressed neoepitopes. 5 MSS tumors did not have any predicted bound nor expressed neoepitopes, 112 of 126 (89%) of MSS tumors had at least 5 predicted bound, expressed neoepitopes.

Conclusions

There is substantial variability in the neoantigen landscape amongst MSI & MSS Colorectal cancers. MSI contains multiple-fold higher neo-antigens. Amongst MSS tumors, 89% of patients have at least 5 predicted bound and expressed neo-epitopes that could be targeted in neoantigen-based vaccines for personalized immunotherapy.

Legal entity responsible for the study

National Cancer Centre Singapore

Funding

NMRC Clinician Scientist Award (Iain Tan), A*STAR Core Funding, NantOmics LLC

Disclosure

A. Nguyen, S. Benz, S. Rabizadeh: Employee of NantOmics LLC

All other authors have declared no conflicts of interest.