Comparative genomic analyses between Asian and Caucasian prostate cancers in an 80,829 patient cohort

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Background: The Decipher 22-gene genomic classifier (GC) has been shown to predict for metastasis and survival in predominantly Caucasian and African-American men from Western cohorts. There is however little data on the clinical utility of GC in Asian prostate cancer (PCa). We investigated if GC prognosticates for metastasis-free survival (MFS) in an Asian cohort of localized PCa. Additionally, we performed comparative genomic analyses between our Asian patients and non-Asian cases from a large Decipher GRID database (Veracyte, San Francisco, CA). Methods: We used a cohort of PCa patients who were treated at a single institution from East Asia between 2006 to 2021. Patients underwent active surveillance or radical prostatectomy (RadP) and/or radiotherapy (RT) +/- hormonal therapy (HT). The GC assay (Decipher Biosciences, CA) was performed on diagnostic biopsies, following central review of the Gleason’s grade (GG) and tumor cellularity by an expert GU pathologist. MFS was the primary endpoint for survival analysis. Comparative analyses of 273 gene-signatures were performed against the full and a propensity-score matched (PSM) cohort identified from the Decipher GRID database. Adjusted p-values from Wilcoxon tests were used to select from these signatures. Results: We profiled 126 unique patient tumors, comprising of 19 (15.1%) NCCN-defined low-/favorable intermediate-, 22 (17.5%) unfavorable intermediate-, 34 (27.0%) high-, and 51 (40.5%) very high-risk groups. 24 (19.0%) patients had RadP as primary treatment, 98 (77.8%) had RT +/- HT, while 4 (3.2%) underwent active surveillance or HT alone. Using the GC, 70 (55.6%), and 56 (44.4%) were stratified as low/intermediate- (≤0.6) and high-risk ( > 0.6), respectively. GC high-risk was significantly associated with an inferior MFS than GC low/intermediate-risk ( HR 5.22 [95% CI:1.08–25.3], P = 0.04). Comparison between our Asian and the full unmatched GRID cohort (N = 80,703) revealed a lower proportion of ERG+ PCa (14% vs 41%, P < 0.001) and a higher proportion of PAM50 basal subtypes (41% vs 30%, P < 0.001), as well as a lower T-cell exclusion (median 0.080 vs 0.097; P < 0.001) and angiogenesis (-0.37 vs -0.08; P < 0.001) signature scores. These trends were also observed when comparing with the PSM-subset (N = 630; 5:1 ratio for NCCN, GG, age at diagnosis, and assay quality score). Interestingly, both high angiogenesis and T-cell exclusion signatures were associated with a worse MFS ( HR not available due to no events for low angiogenesis, P = 0.0015 by log-rank test; HR 5.12 [1.03–26.5], P = 0.046, respectively). Conclusions: We validated the Decipher 22-gene GC for prognostication of MFS in a predominantly high-risk PCa cohort. We also identified several gene expression signatures that were significantly different between Asian PCa and other cohorts. These observations may have implications for customizing treatment recommendations to an Asian population.

Abstract 2258: Germline variants associated with poorer disease prognosis in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is an endemic disease prevalent in East Asia and germline variants that confer risk for NPC have previously been identified. However, NPC patients have contrasting phenotypes at presentation that are associated with disparate risks of relapse. We hypothesize that there exist germline variants that are associated with poorer NPC disease trajectories. We performed whole exome sequencing (100x; Illumina NovaSeq) on a cohort of 795 NPC patients and probed the germline genomic landscape in a predominantly Chinese population (N=723; 90.9%). We performed univariable and multivariable - adjusting for known prognostic clinical parameters - Cox regression analyses to discover germline variants that were associated with disease-free survival (DFS). We performed joint genotyping of germline variants following GATK's best practices workflow. We next filtered out common (≥5% allele frequency in East Asian population, or ≥1% in others) and benign variants, retaining only variants classified as pathogenic (P)/likely pathogenic (LP)/variant of unknown significance (VUS) in ClinVar or are predicted to be pathogenic by Combined Annotation Dependent Depletion or Rare Exome Variant Ensemble Learner. For improved statistical power, statistical analyses (uni- and multi-variable Cox regression) were conducted at the gene level, so that contributions across all variants were aggregated for each gene. To reduce false discovery, we focused our analysis only on genes of interest: hallmark-of-cancer genes (COSMIC gene census), DNA damage and mismatch repair genes, as well as genes known to be associated with NPC risk. Genes with variants in fewer than 20 unique patients were also excluded from analysis. We observed germline variants in hallmark-of-cancer genes (FAT1 [N=133; 16.7%] and NOTCH1 [N=39; 4.9%]) and DNA repair genes (SRSF6 [N=32; 4.0%] and POLD1 [N=32; 4.0%]). Additionally, 230 (28.9%) and 180 (22.6%) patients had at least one P/LP/VUS variants in HLA-A and HLA-DRB1, consistent with known literature that variants in HLA genes confer increased NPC risk. Likewise, we observed variants in genes associated with NPC risk such as KMT2C (N=207; 26.0%), SYNE1 (N=151; 19.0%), ARID1A (N=52; 6.5%) and MST1R (N=34; 4.3%). Univariable tests of association identified variants in MMP19 (HR 2.24 with 95% confidence interval [1.30-3.87], P=0.004), MST1R (HR 2.01 [1.14-3.54], P=0.016), TGFBR2 (HR 1.85 [1.09-3.14], P=0.023), NEIL3 (HR 2.08 [1.09-3.94], P=0.025), ETV6 (HR 2.13 [1.09-4.16], P=0.028), FANCD2 (HR 2.11 [1.09-4.13], P=0.030), DDX6 (HD 2.26 [1.06-4.82], P=0.035) POLD1 (HR 1.91 [1.04-3.53], P=0.038) and RECQL4 (HR 1.92 [1.04-3.54], P=0.037) that were significantly associated with inferior DFS. Among them, MMP19, TGFBR2, FANCD2 and RECQL4 remained significant in a clinico-molecular multivariable model that comprised of age, sex, cTN-categories, EBV DNA titer and treatment (C-index = 0.71).

Citation Format: Adelene Y.L. Sim, Enya H.w. Ong, Luo Huang, Kar Perng Low, Dewi Susanti, Terence W.k. Tan, Kam Weng Fong, Yoke Lim Soong, Gek San Tan, Tony K.H. Lim, Joseph T.s. Wee, Darren W.t. Lim, N. Gopalakrishna Iyer, Jacqueline S.G. Hwang, Mohamed E. Abazeed, Jin-Xin Bei, Melvin L.k. Chua. Germline variants associated with poorer disease prognosis in nasopharyngeal carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2258.

Investigation of a 22-gene genomic classifier (GC) for risk stratification and molecular subtyping in an Asian prostate cancer (PCa) cohort

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Background: A 22-gene GC has been proposed to refine risk stratification of localized PCa by conventional NCCN criteria, and this may potentially influence treatment recommendations. Nonetheless, majority of studies looking at the utility of GC were conducted in White and non-White men from Western cohorts. We therefore investigated the association of GC with NCCN risk groups (RG) in an Asian PCa cohort. Additionally, we examined for inter-racial differences in molecular subtyping between Asian and White/non-White PCa. Methods: GC (Decipher Biosciences Inc., CA) was performed on diagnostic biopsies of men who were treated with radiotherapy +/- hormonal therapy at a single institution (N = 75). ISUP Gleason’s grade (GG) and tumor cellularity were reviewed by an expert GU pathologist. RNA was extracted from 2 x 2.0-mm tumor cores using Qiagen AllPrep DNA/RNA FFPE Kit (Qiagen, Germany) and gene expression was performed on Affymetrix Human Exon 1.0 ST Array (ThermoFischer, CA). PAM50 molecular subtyping was derived using the DecipherGRID database. Results: We profiled 80 tumors from 75 patients, comprising of 18 (24.0%), 9 (12.0%), 21 (28.0%), and 19 (25.3%) NCCN low-/favorable intermediate-, unfavorable intermediate-, high- and very high-RG, respectively; of note, 8 (10.7%) patients had regional/metastatic disease at diagnosis. Using the GC, 27 (33.8%), 14 (17.5%) and 39 (48.8%) were classified as low- (<0.45), intermediate- (0.45-0.6) and high-RG, respectively (>0.6). When stratified using a three-tier clinico-genomic (CG) classification system (Spratt et al. 2017), 6 of 21 (28.6%) NCCN-defined high-risk and 4 of 19 (21.1%) very high-risk patients were downgraded to CG-defined intermediate-/low-risk, while 2 of 27 (7.4%) NCCN low-/intermediate-risk patients were in fact upgraded to CG high-risk. Next, we interrogated the PAM50 basal-luminal signature in our cohort. Interestingly, when matched to White (N = 5762) and non-White (N = 155) for NCCN RG, ISUP GG and age, we observed a high proportion of basal subtype (62.7%) in Asians, which contrasted the prevalence observed in White (16.7%) and non-White (15.9%) North American patients (Chi-sq P <0.001). Conclusions: Here, we demonstrated the utility of the 22-gene GC for refining the NCCN risk stratification in a largest Asian PCa dataset to-date. An unexpectedly high proportion of PAM50 basal-subtype was observed, suggesting race-specific differences of the tumor transcriptome.

High-Dimensional Characterization of the Systemic Immune Landscape Informs on Synergism Between Radiation Therapy and Immune Checkpoint Blockade

PURPOSE

Improved antitumor responses have been observed in patients after combination radiation therapy (RT) and immune checkpoint blockade (ICB). Whether these clinical responses are linked to the host systemic immune system has not been elucidated.

METHODS AND MATERIALS

In this single-institution prospective observational study, peripheral blood was longitudinally collected from 10 patients with metastatic disease who had responded to anti-PD-1/anti-PD-L1 ICB and received RT (8-50 Gy in 1-5 fractions) upon disease progression at the following timepoints: baseline (pre-RT), 1 to 2 weeks post-RT, and post-ICB (cycle 1) on reintroduction post-RT. To thoroughly characterize the interaction between combined RT-ICB and the host immune system, we performed high-dimensional, mass cytometry-based immunophenotyping of circulating lymphocytes using a 40-marker panel addressing lineage, differentiation, activation, trafficking, cytotoxicity, and costimulatory and inhibitory functions. Phenotypic expression of circulating lymphocytes was compared across patients and time points and correlated with post-RT tumor responses.

RESULTS

Foremost, we demonstrated excellent posttreatment clinical responses, including 4 local responses with >50% reduction in radiated tumor size, 1 out-of-field response, and 4 patients who resumed ICB for >1 year. Baseline and post-RT immune states were highly heterogeneous among patients. Despite this interindividual heterogeneity in baseline immune states, we observed a systemic immune reaction to RT-ICB common across patients, histology, and radiation sites; a subset of pre-existing Ki-67+ CD8+ T cells were increased post-RT and further expanded upon reintroduction of ICB post-RT (2.3-fold increase, P = .02). Importantly, RT did not alter the phenotypic profile of these Ki-67+ CD8+ T cells, which was characterized by a distinct activated and differentiated effector phenotype.

CONCLUSIONS

Collectively, these findings point toward a sustained reinvigoration of host antitumor immunity after RT-ICB and suggest an expansion in activated Ki-67+ CD8+ T cells as a possible demonstration of this synergy, thereby providing new insights that may support the development of optimal sequencing strategies.

Germline Polymorphisms and Length of Survival of Nasopharyngeal Carcinoma: An Exome-Wide Association Study in Multiple Cohorts

Germline polymorphisms are linked with differential survival outcomes in cancers but are not well studied in nasopharyngeal carcinoma (NPC). Here, a two-phase association study is conducted to discover germline polymorphisms that are associated with the prognosis of NPC. The discovery phase includes two consecutive hospital cohorts of patients with NPC from Southern China. Exome-wide genotypes at 246 173 single nucleotide polymorphisms (SNPs) are determined, followed by survival analysis for each SNP under Cox proportional hazard regression model. Candidate SNP is replicated in another two independent cohorts from Southern China and Singapore. Meta-analysis of all samples (n = 5553) confirms that the presence of rs1131636-T, located in the 3'-UTR of RPA1, confers an inferior overall survival (HR = 1.33, 95% CI = 1.20-1.47, P = 6.31 × 10-8). Bioinformatics and biological assays show that rs1131636 has regulatory effects on upstream RPA1. Functional studies further demonstrate that RPA1 promotes the growth, invasion, migration, and radioresistance of NPC cells. Additionally, miR-1253 is identified as a suppressor for RPA1 expression, likely through regulation of its binding affinity to rs1131636 locus. Collectively, these findings provide a promising biomarker aiding in stratifying patients with poor survival, as well as a potential drug target for NPC.

Immune dysregulation underpins radioresistance in nasopharyngeal carcinoma (NPC)

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Background: Radiotherapy (RT) is a primary modality in the treatment of NPC. However, 30% of patients present with disease recurrence following RT of this radiosensitive tumor. Here, we investigated the molecular and immune profiles associated with radioresistant (RR) NPC. Additionally, we investigated for aberrant molecular pathways in paired recurrences of patients to uncover new drivers underpinning radioresistance. Methods: We prospectively recruited a cohort of 100 NPC patients who completed definitive RT/chemoRT; including 30 cases who were recruited at recurrence. Whole exome sequencing (WES) at 200x was performed to identify low frequencies ( < 1%) of true somatic nucleotide variants (SNVs) and copy number alterations (CNAs). Transcriptomic profiles from RNAseq were interrogated using supervised and unsupervised statistical approaches to determine aberrant pathways that were significantly associated with RR. Results: Genomic instabilityas characterized by percentage genome alteration (PGA) was comparable in our cohort. Additionally, we did not observe any common or exclusive CNAs between RR- and nr-NPC cases. Based on a constellation of immune-related signatures, we observed an “immune-cold” profile that is associated with RR-NPC compared to nr-NPC controls, which is characterized by low expression of CD8+ T cell infiltration and interferon-γ response. Expectedly, pathways relating to angiogenesis, hypoxia and NOTCH signaling were upregulated in the RR-NPC cohort. Interestingly, we observed a reversal of the immune phenotype from “cold” to an enrichment of effector T cell infiltration in the paired recurrences. Conclusions: Here, we present a comprehensive mutational landscape of RR-NPC, which revealed the potential role of the immune environment in modulating RR. The longitudinal immune dysregulation of the tumor microenvironment between the de novo tumors and recurrences could be a driver or passenger event during the onset of recurrence.

A novel computational OMICS and non-OMICS approach for identifying true pathogenic risk variants for Asian prostate cancer

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Background: Large-scale genome-wide association studies have established germline polygenic risk loci that underpin the susceptibility to prostate cancer (PCa). However, most trials conducted are in men of European ancestry with data missing for Asian male PCa. Here, we report on an in-house multidimensional bioinformatics pipeline that integrates OMICS and non-OMICS approaches in identifying true germline risk-variants for PCa in Asian men. Methods: We utilized a prospective cohort study of Asian men who were newly diagnosed with PCa. Whole exome sequencing (Illumina Hiseq, CA) of blood (100X) was performed. The OMICS-based approach entailed a stepwise screen for hallmarks of cancer-specific pathways. A genome-proteome network was then developed to filter for known pathogenic variants; this was followed by comparison against a large artificial database of aggregated germline variants (N = 95,000) with reported linkage to PCa susceptibility. Finally, mutations were filtered through a non-OMICS pipeline that entailed data synchronization with population-level statistics and clinical outcomes (recurrence and survival). Results: Preliminary analyses were based on 277 PCa cases; of which 50 were M1 cases. Screening using a non-combined unbiased approach yielded 36,157 germline variants. This contrast against our OMICS-based approach, which reduced the variant calls to 6,144 significantly associated mutations. Next, by focusing on pathway-specific genes related to hormonal regulation and known cancer hotspot mutations, we could further tighten our variant calls to 3,562 hormone-related variants (rs9269958 on HLA-DRB1) and 2,125 variants in known cancer genes, notably (rs8176320 on BRCA1/2, rs2555691 on LILRA2, rs8036934 on TP53BP1). Conclusions: Here, we show that application of an OMICS approach that combines pathway-driven analyses and an artificial dataset, along with population-level statistics and clinical relevance resulted in more robust annotation of germline variants that were associated with PCa.

Abstract 527: High-dimensional profiling of the systemic immune response informs on optimal sequencing of radiotherapy (RT) and immune checkpoint blockade (ICB)

Background: Combinatorial RT-ICB potentiates anti-tumour reactivity by modulating the immune response. We therefore performed in-depth phenotypic profiling of the systemic T cell compartment following treatment with RT-ICB.

Methods: We recruited 20 patients with biopsy-proven metastatic renal cell and non-small cell lung carcinoma, who were treated with a sandwich regime of ICB-RT-ICB under a prospective observational study protocol, and compared against a RT alone-treated cohort (N=10). All patients received ablative RT (8-50Gy/1-5fr) for oligoprogression and/ or local palliation. Blood samples were longitudinally collected at pre-RT, 14 d post-RT and cycle 2 ICB post-RT. Deep T cell profiling was performed by mass cytometry using a customised 41 parameter panel, together with high dimensional analysis tools.

Results: Median follow-up of the overall cohort was 18mo; median duration of ICB received in the ICB-RT-ICB arm was 15mo. We observed significant diversity of the systemic T cell repertoire between patients at baseline, and this corresponded to significant interpatient heterogeneity in T cell responses specific to the central/ effector memory, EMRA and Treg subsets post-RT. Dramatic local response (complete response at 1 mo post-RT) was significantly higher in the ICB-RT-ICB cohort compared to the RT alone cohort (12/20 vs 1/10, P&lt;0.01). This clinical phenomenon corresponded to an increased %Ki67high CD8 and CD4 T cells post-RT exclusively in the combinatorial treated cohort, which was further enhanced upon resumption of ICB (mean = 10% vs 3% [CD8]; 13% vs 2% [CD4]; P&lt;0.01). Deeper immunophenotyping of the Ki67high subsets revealed associated high expression of GranzymeB and Eomes.

Conclusions: Here, we observed changes in the T cell phenotypes that varied remarkably across all patients following RT. We further highlight a RT-dependent T cell proliferation amongst all RT-ICB-treated patients that was further enhanced by ICB in prior responders. This immune phenomenon may account for the dramatic responses to combinatorial treatment, and informs on optimal sequencing strategies for combining RT and ICB.

Citation Format: Kevin L. Chua, Michael Fehlings, Pek Lim Chu, Xiao-Tian Lin, Eugenia Yeo, Kar Perng Low, Dennis Poon, Enya Ong, Wai Yee Woo, Joseph Wee, Alessandra Nardin, Gopalakrishna Iyer, Daniel S. Tan, Kee Chee Soo, Evan Newell, Melvin Chua. High-dimensional profiling of the systemic immune response informs on optimal sequencing of radiotherapy (RT) and immune checkpoint blockade (ICB) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 527.

The role of high-dimensional profiling of the systemic immune response on optimal sequencing of radiotherapy (RT) and immune checkpoint blockade (ICB)

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Background: Combinatorial RT-ICB potentiates anti-tumour reactivity by modulating the immune response. We therefore performed in-depth phenotypic profiling of the systemic T cell compartment following treatment with RT-ICB. Methods: We recruited 20 patients with biopsy-proven metastatic renal cell and non-small cell lung carcinoma, who were treated with a sandwich regime of ICB-RT-ICB under a prospective observational study protocol, and compared against a RT alone-treated cohort (N = 10). All patients received ablative RT (8-50 Gy/1-5 fr) for oligoprogression and/or local palliation. Blood samples were longitudinally collected at pre-RT, 14 d post-RT and cycle 2 ICB post-RT. Deep T cell profiling was performed by mass cytometry using a customised 41 parameter panel, together with high dimensional analysis tools. Results: Median follow-up of the overall cohort was 18 mo; median duration of ICB received in the ICB-RT-ICB arm was 15 mo. We observed significant diversity of the systemic T cell repertoire between patients at baseline, and this corresponded to significant interpatient heterogeneity in T cell responses specific to the central/effector memory, EMRA and Treg subsets post-RT. Dramatic local response (complete response at 1 mo post-RT) was significantly higher in the ICB-RT-ICB cohort compared to the RT alone cohort (12/20 vs 1/10, P <0.01). This clinical phenomenon corresponded to an increased % Ki67highCD8 and CD4 T cells post-RT exclusively in the combinatorial treated cohort, which was further enhanced upon resumption of ICB (mean = 10% vs 3% [CD8]; 13% vs 2% [CD4]; P <0.01). Deeper immunophenotyping of the Ki67high subsets revealed associated high expression of GranzymeB and Eomes. Conclusions: Here, we observed changes in the T cell phenotypes that varied remarkably across all patients following RT. We further highlight a RT-dependent T cell proliferation amongst all RT-ICB-treated patients that was further enhanced by ICB in prior responders. This immune phenomenon may account for the dramatic responses to combinatorial treatment, and informs on optimal sequencing strategies for combining RT and ICB.

Physical supports from liver cancer cells are essential for differentiation and remodeling of endothelial cells in a HepG2-HUVEC co-culture model

Blood vessel remodeling is crucial in tumor growth. Growth factors released by tumor cells and endothelium-extracellular matrix interactions are highlighted in tumor angiogenesis, however the physical tumor-endothelium interactions are highly neglected. Here, we report that the physical supports from hepatocellular carcinoma, HepG2 cells, are essential for the differentiation and remodeling of endothelial cells. In a HepG2-HUVEC co-culture model, endothelial cells in direct contact with HepG2 cells could differentiate and form tubular structures similar to those plated on matrigel. By employing HepG2 cell sheet as a supportive layer, endothelial cells formed protrusions and sprouts above it. In separate experiments, fixed HepG2 cells could stimulate endothelial cells differentiation while the conditioned media could not, indicating that physical interactions between tumor and endothelial cells were indispensable. To further investigate the endothelium-remodeling mechanisms, the co-culture model was treated with inhibitors targeting different angiogenic signaling pathways. Inhibitors targeting focal adhesions effectively inhibited the differentiation of endothelial cells, while the growth factor receptor inhibitor displayed little effect. In conclusion, the co-culture model has provided evidences of the essential role of cancer cells in the differentiation and remodeling of endothelial cells, and is a potential platform for the discovery of new anti-angiogenic agents for liver cancer therapy.

Prevalence of eye diseases and visual impairment in urban population - a study from university of malaya medical centre

One thousand one hundred and sixty-nine (1169) patients were examined in the Eye Clinic of University of Malaya Medical Centre over a period of three weeks to determine the prevalence of eye diseases and visual impairment. Age, gender, race, visual acuity and diagnosis of patients were noted from the case records. Cataract (385, 32.9%) was the most common eye disease seen in our study followed by glaucoma (274, 23.4%). Refractive errors were seen in 126 (10.8%) while diabetic retinopathy was noted in 113 (9.7%) patients. One hundred and fifteen (9.6%) patients had visual impairment and 11 (0.9%) had blindness in our study according to WHO classification of visual impairment. Refractive errors are the most common causes of visual impairment in children, while cataract, glaucoma and diabetic retinopathy account for visual impairment in elderly people. All these eye diseases are treatable and the severe eye conditions may be potentially preventable with early diagnosis.