Abstract 4346: Integrated whole genome profiling of the immune tumour interaction identifies predictive biomarkers of checkpoint inhibitor response in metastatic cancer

Immune checkpoint inhibitors are fast becoming a key therapy in the medical oncologist's toolbox across a diverse array of tumour types. The excitement surrounding the utility of these emerging agents is marred by the heterogeneous response observed among patients, highlighting the urgent need for clinically applicable predictive biomarkers. Significant progress has been made in identifying potentially relevant biomarkers including mutation burden and immune infiltration. However, it is still unclear which biomarkers are most predictive across various disease types, and how to integrate various markers of response and resistance for clinical interpretation. We hypothesized that comprehensive genomic profiling, combined with clinical data, would reveal differences in the immuno-oncologic phenotype that could be used as biomarkers for response to checkpoint inhibitor therapy. The Personalized OncoGenomics (POG) study at BC Cancer performs whole genome and transcriptome sequencing of metastatic disease across a diverse array of cancer types to comprehensively characterize cancers and inform clinical therapeutic decision-making. Here we performed in-depth genomic profiling of 64 POG patients who received immune checkpoint inhibitors encompassing multiple disease types including skin, lung, breast, pancreatic and colorectal cancers and sarcomas. Single nucleotide variants, structural variants, copy number alterations, and RNA expression derived from whole genomic and transcriptomic data were used to characterize genomic instability, neoantigen landscape, immune infiltration, and other potential biomarkers of clinical response to checkpoint inhibitors. This collection of putative immune-oncologic biomarkers were integrated into a multivariate model to stratify markers of the tumour immune response. Our analysis shows limited association between PD-L1 expression and checkpoint inhibitor response, consistent with the inadequate effectiveness of this as a universal marker, and shows stronger association between signatures of T cell infiltration based on RNA-Seq data. We also observed patients with low mutation burden that respond to checkpoint inhibitors and show high levels of immune infiltration, and cases with high mutation burden that harbour mechanisms of resistance including reduction in predicted neoantigen diversity. Additional mechanisms of therapeutic resistance observed in post treatment biopsies highlight disruption of antigen presentation and JAK1 mutations in resistant tumours. Our study helps to define which features distinguish patients most likely to respond to checkpoint inhibitors, and uses these features in selecting patients for immunotherapy treatment within the POG clinical trial.

Citation Format: Hillary Pearson, Laura Williamson, Erin Pleasance, Scott Brown, Emma Titmuss, Martin Jones, Stuart Zong, Payal Sipahimalani, Yussanne Ma, Steve Jones, Robert Holt, Marco Marra, Janessa Laskin. Integrated whole genome profiling of the immune tumour interaction identifies predictive biomarkers of checkpoint inhibitor response in metastatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4346.

Abstract LB-329: Multiple-resolution characterization of tumor heterogeneity as associated with disease progression in a mouse model of colorectal cancer

The ability to engineer models to express endogenous fluorophores has become an invaluable tool for studying tumor biology. The utility of these models is limited by the sensitivity and resolution of currently available imaging platforms. In vivo techniques enable longitudinal studies in which changes in fluorescent markers, tumors, and whole organs can be monitored over time. In vivo fluorescence suffers from poor sensitivity and resolution owing to the high absorption and scatter of light in biological tissue. While ex vivo fluorescence techniques allow for high resolution evaluation and characterization, these techniques typically only focus on a small samples of tissue instead of whole animals. Using a Cryo-Fluorescence Tomography (CFT) imaging approach, an imaging modality based on serial slicing and off-the-block fluorescence imaging, we can bridge the gap between in vivo and ex vivo resolution of the entire animal. As proof of concept, a novel mouse model expressing fluorophores was evaluated and characterized. Individual cells were labeled with either EGFP or tdTomato prior to tumor initiation. Intestinal tumors were induced through loss of Apc, the activation of PI3K, or both. Tumor heterogeneity and grade were assessed by traditional histopathology, individual-tissue CFT, and whole-animal CFT. Using CFT, serial sectioning and 3D-reconstruction of whole tissues were achieved at 10-50 µm resolution.The multi-resolution imaging approach of this model enabled visualization of molecular and histopathological information from a common in vivo resolution (1mm) to whole-tissue resolution. The CFT platform enabled a 3D data set at a resolution that was not previously available in traditional histopathology. CFT as a molecular tissue imaging technique has proven its utility as a complimentary assay in preclinical oncology studies allowing several characteristics of tumors including heterogeneity, growth, and malignant spread to be readily assessed.

Citation Format: Mohammed Farhoud, Alyssa Leystra, Dawn M. Albrecht, Mathew Brevard, Hemi Dimant, Robert Holt, Richard B. Halberg. Multiple-resolution characterization of tumor heterogeneity as associated with disease progression in a mouse model of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-329.

New variant and expression studies provide further insight into the genotype-phenotype correlation in YAP1-related developmental eye disorders

YAP1, which encodes the Yes-associated protein 1, is part of the Hippo pathway involved in development, growth, repair and homeostasis. Nonsense YAP1 mutations have been shown to co-segregate with autosomal dominantly inherited coloboma. Therefore, we screened YAP1 for variants in a cohort of 258 undiagnosed UK patients with developmental eye disorders, including anophthalmia, microphthalmia and coloboma. We identified a novel 1 bp deletion in YAP1 in a boy with bilateral microphthalmia and bilateral chorioretinal coloboma. This variant is located in the coding region of all nine YAP1 spliceforms, and results in a frameshift and subsequent premature termination codon in each. The variant is predicted to result in the loss of part of the transactivation domain of YAP1, and sequencing of cDNA from the patient shows it does not result in nonsense mediated decay. To investigate the role of YAP1 in human eye development, we performed in situ hybridisation utilising human embryonic tissue, and observed expression in the developing eye, neural tube, brain and kidney. These findings help confirm the role of YAP1 and the Hippo developmental pathway in human eye development and its associated anomalies and demonstrate its expression during development in affected organ systems.

Identification and functional characterisation of genetic variants in OLFM2 in children with developmental eye disorders

Anophthalmia, microphthalmia, and coloboma are a genetically heterogeneous spectrum of developmental eye disorders and affect around 30 per 100,000 live births. OLFM2 encodes a secreted glycoprotein belonging to the noelin family of olfactomedin domain-containing proteins that modulate the timing of neuronal differentiation during development. OLFM2 SNPs have been associated with open angle glaucoma in a case-control study, and knockdown of Olfm2 in zebrafish results in reduced eye size. From a cohort of 258 individuals with developmental eye anomalies, we identified two with heterozygous variants in OLFM2: an individual with bilateral microphthalmia carrying a de novo 19p13.2 microdeletion involving OLFM2 and a second individual with unilateral microphthalmia and contralateral coloboma who had a novel single base change in the 5' untranslated region. Dual luciferase assays demonstrated that the latter variant causes a significant decrease in expression of OLFM2. Furthermore, RNA in situ hybridisation experiments using human developmental tissue revealed expression in relevant structures, including the lens vesicle and optic cup. Our study indicates that OLFM2 is likely to be important in mammalian eye development and disease and should be considered as a gene for human ocular anomalies.

Abstract 5226: Genomic analysis of pancreatic ductal adenocarcinoma in a patient with MUTYH-associated polyposis

Biallelic pathogenic germline variants in the DNA repair glycosylase, MUTYH, cause MUTYH-associated polyposis, characterised by an increased susceptibility to colorectal adenomas and carcinomas secondary to defective base excision repair. We report a patient diagnosed with Stage IIB distal pancreatic ductal adenocarcinoma (PDAC) at the age of 45 years. Prior colonoscopy and gastroscopy noted three colonic tubular adenomas and a gastric fundic gland polyp. The patient was consented to whole genome and transcriptome sequencing of the PDAC and matched normal blood DNA through the British Columbia Personalized Onco-Genomics (POG) program. Analysis of germline and somatic variants including single nucleotide variants, copy number determination, loss of heterozygosity detection and mutational signatures was undertaken. Expression fold-changes were calculated against Illumina BodyMap pancreatic tissue averages and compared against The Cancer Genome Atlas PDAC cases. Germline analysis revealed biallelic mutations in the MUTYH gene. In light of this patient's personal and family history of adenomatous colon polyps, clinic-initiated panel testing of 14 cancer susceptibility genes, including MUTYH, via Illumina sequencing with reflex Sanger confirmation revealed the same biallelic MUTYH changes. Analysis of the patient's PDAC revealed a base excision repair pathway signature, demonstrated by an increased frequency of C:G>A:T transversions, consistent with deficient MUTYH activity. This is the first association of germline MUTYH biallelic pathogenic variants with PDAC and provides evidence of the contribution of aberrant MUTYH function to the genomic landscape of a PDAC. Detection of the base excision repair mutational signature may be a sensitive way to screen tumors for aberrant MUTYH function that can reveal potential germline MUTYH-related cancer susceptibility, and allow inference of pathogenicity of detected MUTYH variants, which may have cancer prevention and therapeutic implications.

Citation Format: Kasmintan A. Schrader, Carolyn Chu’ng, Eric Zhao, Hui-li Wong, Yaoqing Shen, Martin Jones, Tom Thomson, Howard Lim, Sean Young, Carol Cremin, Robert Holt, Peter Eirew, Joanna Karasinska, Jacquie Schein, Yongjun Zhao, Andy Mungall, Richard Moore, Yussanne Ma, Alexandra Fok, Robyn Roscoe, Stephen Yip, Gillian Mitchell, Aly Karsan, Steven Jones, David Schaeffer, Janessa Laskin, Marco Marra, Daniel Renouf. Genomic analysis of pancreatic ductal adenocarcinoma in a patient with MUTYH-associated polyposis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5226.

Morning stiffness response with delayed-release prednisone after ineffective course of immediate-release prednisone

Objective: To assess morning stiffness in rheumatoid arthritis (RA) patients switched from immediate-release (IR) to delayed-release (DR) prednisone.

Method: Circadian Administration of Prednisone in Rheumatoid Arthritis-1 (CAPRA-1) is a 12-week, randomized, multicentre, active-controlled study of morning stiffness that consisted of a double-blind phase and a 9-month open-label extension. Patients receiving IR prednisone with no significant improvement after the double-blind study were switched to DR prednisone. Morning stiffness duration and median absolute and relative changes in pain and global assessment were evaluated (3, 6, and 9 months).

Results: In patients switched from IR to DR prednisone (n = 110), statistically significant reductions in morning stiffness occurred over 3 months and were sustained for 9 months. Absolute reduction of morning stiffness was ~50 min with > 40% relative reduction at each visit. Interleukin (IL)-6 levels were reduced by the same amount. Statistically significant and clinically meaningful mean reductions in morning stiffness were maintained at > 67 min at each visit along with significant improvements in pain and patient global assessment. There was no evidence of tachyphylaxis seen over the 9-month study.

Conclusions: Patients receiving disease-modifying anti-rheumatic drugs (DMARDs) and IR prednisone who had not had significant reductions in morning stiffness demonstrated statistically significant and clinically meaningful improvements when switched to DR prednisone.

Developmental white matter microstructure in autism phenotype and corresponding endophenotype during adolescence

During adolescence, white matter microstructure undergoes an important stage of development. It is hypothesized that the alterations of brain connectivity that have a key role in autism spectrum conditions (ASCs) may interact with the development of white matter microstructure. This interaction may be present beyond the phenotype of autism in siblings of individuals with ASC, who are 10 to 20 times more likely to develop certain forms of ASC. We use diffusion tensor imaging to examine how white matter microstructure measurements correlate with age in typically developing individuals, and how this correlation differs in n=43 adolescents with ASC and their n=38 siblings. Correlations observed in n=40 typically developing individuals match developmental changes noted in previous longitudinal studies. In comparison, individuals with ASC display weaker negative correlation between age and mean diffusivity in a broad area centred in the right superior longitudinal fasciculus. These differences may be caused either by increased heterogeneity in ASC or by temporal alterations in the group's developmental pattern. Siblings of individuals with ASC also show diminished negative correlation between age and one component of mean diffusivity-second diffusion eigenvalue-in the right superior longitudinal fasciculus. As the observed differences match for location and correlation directionality in our comparison of typically developing individuals to those with ASC and their siblings, we propose that these alterations constitute a part of the endophenotype of autism.

A prospective observational study to investigate the association between abnormal hand movements and delirium in hospitalised older people

OBJECTIVE

to examine the relationship between carphology (aimlessly picking at bedclothes), floccillation (plucking at the air) and delirium in older patients admitted to specialist elderly care wards.

DESIGN

daily observation for behaviours of carphology and floccillation embedded within a 'before' and 'after' study.

SETTING

three specialist elderly care wards in a general hospital.

SUBJECTS

older people admitted to hospital as emergencies.

METHODS

patients recruited into a delirium prevention study were observed daily for delirium using the confusion assessment method (CAM). Occurrences of carphology and/or floccillation were also recorded. Sensitivity, specificity and positive and negative predictive values for carphology/floccillation for the diagnosis of delirium were calculated. Inpatient mortality rates were compared for patients who did, and did not exhibit features of carphology and/or floccillation.

RESULTS

four hundred and thirty-seven patients were recruited into the study. One hundred and ten participants experienced an episode of delirium, 21 exhibited behaviours of carphology and/or floccillation. The sensitivity and specificity of carphology and/or floccillation for the diagnosis of delirium were 14 and 98%, respectively; positive likelihood ratio 6.8. Carphology and floccillation were associated with both hyper- and hypo-active delirium subtypes, and occurred early during incident delirium (67% within 2 days of delirium onset). The inpatient mortality rate in patients with carphology/floccillation was double the rate in patients without the behaviours (23.8 versus 11.2%, Fisher's exact test P = 0.16).

CONCLUSIONS

carphology and floccillation are uncommon physical signs, but their presence is highly suggestive of delirium. The behaviours are unrelated to delirium subtype making their presence particularly useful in the diagnosis of hypo-active delirium.

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-β signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy.

Metagenomic and metabolomic characterization of rabies encephalitis: new insights into the treatment of an ancient disease

Rabies virus (RV) infection is a fatal nervous system disorder. We describe a patient who died of rabies despite a neuroprotective intervention. Neuropathology showed neuronal loss with abundant RV antigen, genome, and Negri bodies, accompanied by intense neuroinflammation, including by CD8(+) T lymphocyte infiltrates. Deep sequencing and real-time reverse-transcription polymerase chain reaction revealed RNA encoding a bat RV strain together with inflammatory gene induction. RV-infected brain demonstrated reduced neuronal metabolites with an anaerobic metabolic profile by nuclear magnetic resonance (NMR) spectroscopy. These multiplatform studies highlight the extent of ongoing viral replication coupled with inflammation in treated rabies, indicative of a neurological immune reconstitution inflammatory syndrome.