Development and Validation of an Easy-to-Implement, Practical Algorithm for the Identification of Molecular Subtypes of Gastric Cancer: Prognostic and Therapeutic Implications

BACKGROUND

Gastric cancer (GC) is a heterogeneous disease, and substantial efforts have been made to develop a molecular biology-based classification system for GC. Analysis of the genomic signature is not always feasible, and thus, we aimed to (i) develop and validate a practical immunohistochemistry (IHC)- and polymerase chain reaction (PCR)-based molecular classification of GC and (ii) to assess HER2 status according to this classification.

MATERIALS AND METHODS

A total of 894 consecutive patients with GC from two individual cohorts (training, n = 507; validation, n = 387) were classified using Epstein-Barr virus (EBV) in situ hybridization, microsatellite instability (MSI) testing, and IHC for E-cadherin and p53.

RESULTS

We were able to classify patients into five groups in the training cohort: group 1 (MSI⁺), group 2 (EBV^-, MSI^-, non-epithelial-mesenchymal transition [non-EMT]-like, p53^-), group 3 (EBV⁺), group 4 (EBV^-, MSI^-, non-EMT-like, p53⁺), and group 5 (EBV^-, MSI^-, EMT-like). In the training cohort, each group showed different overall survival (OS) after gastrectomy (p < .001); group 1 had the best prognosis, and group 5 showed the worst survival outcome. The significant impact of the classification system on OS was also verified in the validation cohort (p = .004). HER2 positivity was observed in 6.5% of total population, and most of HER2-positive cases (93.1%) were included in groups 2 and 4.

CONCLUSION

We developed and validated a modified IHC- and PCR-based molecular classification system in GC, which showed significant impact on survival, irrespective of stage or other clinical variables. We also found close association between HER2 status and non-EMT phenotype in our classification system.

IMPLICATIONS FOR PRACTICE

Molecular classification of gastric cancer suggested by previous studies mostly relies on extensive genomic data analysis, which is not always available in daily practice. The authors developed a simplified immunohistochemistry- and polymerase chain reaction-based molecular classification of gastric cancer and proved the prognostic significance of this classification, as well as the close association between HER2 status and certain groups of the classification, in the largest consecutive cohort of gastric cancer. Results of this study suggest that this scheme is a cost-effective, easy-to-implement, and feasible way of classifying gastric cancer in daily clinical practice, also serving as a practical tool for aiding therapeutic decisions and predicting prognosis.

Abstract 2513: Mutational and transcriptional landscape of nodal marginal zone lymphoma

Nodal marginal zone lymphoma (NMZL) is a rare B-cell neoplasm lacking disease-defining markers. In this study, we aimed to determine the mutational profile of Asian NMZLs and report novel genetic features of this disease. We performed WES on FFPE samples of eight Korean NMZLs and two matched non-neoplastic tissue samples. For unmatched cases, additional variant filtering was performed to minimize germline contamination. RNAseq was performed on six NMZL FFPE samples with acceptable samples quality. A total of 394 non-synonymous variants in 370 genes were found with the mean number of variants per case of 49.3 (range 14 – 98). We selected 93 candidate NMZL genes (CNGs) based on the following criteria: (i) genes with mutations in ≥ 2 patients; (ii) genes with mutations in either of two cases with matched control; (iii) genes with mutations in at least one case and reported to have biological roles in B-cell lymphomas. Mutations in genes involved in chromatin remodeling including KMT2D (25%), HIST1H1E (25%), and HIST1H1B (13%) were observed, which was consistent with previous studies. Genes encoding key components of B-cell receptor (BCR) signaling and related pathways were also affected, including CD79B (25%), CARD11 (13%) and BCL6 (13%). Of note, NFKBIE (c.759_762delTTAC) frameshift mutation was found in one patient; this mutation was proven to be loss-of-function in nature, resulting in deregulation of NF-κB signaling. Identical mutation was reported in Hodgkin lymphoma and primary mediastinal B-cell lymphoma, however, this is the first report of this mutation in NMZL. Genes involved in immune response including MYD88 (13%), PIM1 (13%), CD70 (13%) and TNFRSF14 (13%) were also mutated, suggesting the linkage between immune dysregulation and NMZL pathogenesis. At the transcriptome level, three samples were consistently clustered together. This group of patients was characterized by higher Ki-67 proliferation index compared to the others, and was associated with older age, higher serum LDH level and higher IPI score. Gene set analysis (GSA) based on lymphoma-specific gene sets from SignatureDB (https://lymphochip.nih.gov/signaturedb/) showed significant association between XBP1 target

genes and these high Ki-67 group (P = 0.024). In summary, this study showed high prevalence of mutations in chromatin remodeling and BCR signaling pathway, readdressing the importance of these pathways in NMZL. Several novel genetic alterations in NMZL were found including NFKBIE c.759_762delTTAC, warranting further validation to clarify the significance of these alterations. We also found that NMZLs with high Ki-67 index were associated with specific gene expression profile, providing clue to the explanation for the heterogeneity of NMZLs.

Citation Format: Jiwon Koh, Seongmin Choi, Insoon Jang, Sehui Kim, Cheol Lee, Jin Ho Paik, Kwangsoo Kim, Yoon Kyung Jeon. Mutational and transcriptional landscape of nodal marginal zone lymphoma [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 2513.

A subset of diffuse-type gastric cancer is susceptible to mTOR inhibitors and checkpoint inhibitors

Background

Mechanistic target of rapamycin (mTOR) pathway is essential for the growth of gastric cancer (GC), but mTOR inhibitor everolimus was not effective for the treatment of GCs. The Cancer Genome Atlas (TCGA) researchers reported that most diffuse-type GCs were genomically stable (GS). Pathological analysis suggested that some diffuse-type GCs developed from intestinal-type GCs.

Methods

We established patient-derived xenograft (PDX) lines from diffuse-type GCs, and searched for drugs that suppressed their growth. Diffuse-type GCs were classified into subtypes by their gene expression profiles.

Results

mTOR inhibitor temsirolimus strongly suppressed the growth of PDX-derived diffuse-type GC-initiating cells, which was regulated via Wnt-mTOR axis. These cells were microsatellite unstable (MSI) or chromosomally unstable (CIN), inconsistent with TCGA report. Diffuse-type GCs in TCGA cohort could be classified into two clusters, and GS subtype was major in cluster I while CIN and MSI subtypes were predominant in cluster II where PDX-derived diffuse-type GC cells were included. We estimated that about 9 and 55% of the diffuse-type GCs in cluster II were responders to mTOR inhibitors and checkpoint inhibitors, respectively, by identifying PIK3CA mutations and MSI condition in TCGA cohort. These ratios were far greater than those of diffuse-type GCs in cluster I or intestinal-type GCs. Further analysis suggested that diffuse-type GCs in cluster II developed from intestinal-type GCs while those in cluster I from normal gastric epithelial cells.

Conclusion

mTOR inhibitors and checkpoint inhibitors might be useful for the treatment of a subset of diffuse-type GCs which may develop from intestinal-type GCs.

Electronic supplementary material

The online version of this article (10.1186/s13046-019-1121-3) contains supplementary material, which is available to authorized users.

Primary Malignant Melanoma of the Breast: A Report of Two Cases

Primary malignant melanoma of the breast (PMMB) is a rare tumor with only a few case reports available in the literature. We report two cases of PMMB, one derived from the breast parenchyma and the other from the breast skin. The first case consisted of atypical epithelioid cells without overt melanocytic differentiation like melanin pigments. The tumor cells showed diffuse positivity for S100 protein, tyrosinase, and BRAF V600E. However, the tumor cells were negative for cytokeratin, epithelial membrane antigen, and HMB-45. The second case showed atypical melanocytic proliferation with heavy melanin pigmentation. The tumor cells were positive for S100 protein, HMB-45, tyrosinase, and BRAF V600E. These two cases represent two distinct presentations of PMMB in terms of skin involvement, melanin pigmentation, and HMB-45 positivity. Although PMMB is very rare, the possibility of this entity should be considered in malignant epithelioid neoplasms in the breast parenchyma.

Clinical significance of APOB inactivation in hepatocellular carcinoma

Recent findings from The Cancer Genome Atlas project have provided a comprehensive map of genomic alterations that occur in hepatocellular carcinoma (HCC), including unexpected mutations in apolipoprotein B (APOB). We aimed to determine the clinical significance of this non-oncogenetic mutation in HCC. An Apob gene signature was derived from genes that differed between control mice and mice treated with siRNA specific for Apob (1.5-fold difference; P < 0.005). Human gene expression data were collected from four independent HCC cohorts (n = 941). A prediction model was constructed using Bayesian compound covariate prediction, and the robustness of the APOB gene signature was validated in HCC cohorts. The correlation of the APOB signature with previously validated gene signatures was performed, and network analysis was conducted using ingenuity pathway analysis. APOB inactivation was associated with poor prognosis when the APOB gene signature was applied in all human HCC cohorts. Poor prognosis with APOB inactivation was consistently observed through cross-validation with previously reported gene signatures (NCIP A, HS, high-recurrence SNUR, and high RS subtypes). Knowledge-based gene network analysis using genes that differed between low-APOB and high-APOB groups in all four cohorts revealed that low-APOB activity was associated with upregulation of oncogenic and metastatic regulators, such as HGF, MTIF, ERBB2, FOXM1, and CD44, and inhibition of tumor suppressors, such as TP53 and PTEN. In conclusion, APOB inactivation is associated with poor outcome in patients with HCC, and APOB may play a role in regulating multiple genes involved in HCC development.

Somatic mutational profiles of stage II and III gastric cancer according to tumor microenvironment immune type

We aimed to determine somatic mutational profiles of stage II/III gastric cancers (GCs) according to their tumor microenvironment immune types (TMITs), which classify cancer based on co-assessment of PD-L1 expression and CD8⁺ tumor infiltrating lymphocytes. Eighty patients with stage II/III GC were classified as follows: TMIT I (PD-L1⁺ /CD8^High ), TMIT II (PD-L1^- /CD8^Low ), TMIT III (PD-L1⁺ /CD8^Low ), and TMIT IV (PD-L1^- /CD8^High ). Deep targeted sequencing using a panel of 170 cancer-related genes was performed on an Illumina HiSeq-2500 system. Most frequently mutated genes included GNAQ (41.3%), TP53 (38.8%), CREBBP (35.0%), and MAP3K1 (35.0%). PIK3CA mutations were observed more frequently in TMIT I (45.8%) and III (66.7%), than in II (12.0%) and IV (8.0%). Other genes with enriched mutations within TMIT I included ATM (33.3%), BRCA2 (33.3%), MAP3K4 (29.2%), and FLT4 (25.0%). FGFR3, MAP3K1, and RUNX1 mutations were more frequently found in TMIT II. TMIT III had a unique somatic mutation profile harboring enriched mutations of histone modifiers including CREBBP and KMT2A, and we found FGFR2 amplification exclusively within TMIT IV. Fuzzy clustering analysis based on somatic mutation frequencies identified a hypermutated group (cluster 1) and a hypomutated group (cluster 2). Cluster 1 had significant associations with TMIT I, EBV⁺ GCs, and MSI-H GCs (P = .023, .014, and .004), and had better overall survival (P = .057) than Cluster 2. TMIT I, EBV⁺ , and MSI-H GCs were estimated to have greater tumor mutational burden (P = .023, .003, and .015). By analyzing somatic mutation profiles according to TMIT classification, we identified TMIT-specific genetic alterations that provide clues for biological linkage between GC genetics and microenvironment.

Cytologic Diagnosis of Metastatic Alveolar Rhabdomyosarcoma in Cerebrospinal Fluid: A Case Report

Rhabdomyosarcoma is a malignant soft tissue tumor which shows skeletal muscle differentiation. Leptomeningeal metastasis can occur as a late complication, but currently there are no reports that have documented the cytologic features in cerebrospinal fluid (CSF). We report a case of metastatic alveolar rhabdomyosarcoma diagnosed in the CSF of a 28-year-old male who was originally diagnosed with rhabdomyosarcoma on the neck, and that went through systemic therapy. The tumor was positive for anaplastic lymphoma kinase, but progressed despite additional therapy with crizotinib. The CSF specimen revealed small round cells, large atypical cells with abundant cytoplasm and eccentric nuclei, and cells with horseshoe-shaped nuclei. These cytologic findings were in agreement with previous literature and well-correlated with histopathology. This is the first report to document the cytologic feature of rhabdomyosarcoma in CSF. In many cases it is difficult to perform ancillary tests in a CSF specimen and cytopathologists should be aware of the cytomorphologic characteristics to avoid misdiagnosis.

Abstract 3404: Clinical significance of APOB inactivation in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the seventh most common cancer and second the most lethal cancer globally. 5-year OS rates in US are only 11%. Sequencing of HCC genome revealed unexpected frequent mutations in serum proteins such as albumin (ALB) and apolipoprotein B (APOB), which are not frequently mutated in other cancers. However, clinical significance and underlying biology of loss of these serum proteins in HCC are currently unknown. Here we show that loss of APOB, major carrier of lipid in blood, in HCC is significantly associated with poor survival of HCC patients by applying comparative genomics approach that integrate genomic data from mouse models and human HCC tumors. We further show that loss of APOB leads to shifting balance of lipid metabolisms favoring for tumor growth. For development of genomic signature reflecting hepatic APOB activity and test and validation of its association with prognosis, we used unsupervised approach combined with supervised prediction models. First, gene expression signature were generated from Apob-silenced mouse livers and hepatic Apob-specific signature was identified by applying statistical analysis (P &lt; 0.005 and 1.5-fold difference between Apob-silenced vs. Apob-Wt). Second, by applying unsupervised hierarchical clustering of mouse hepatic Apob signature in human HCC tumors first and constructing Bayesian prediction models later, HCC tumors with low APOB activity were identified. When HCC patients were stratified into APOB-high and APOB-low subgroups, overall survival (OS) rate and recurrence free survival (RFS) rate of patients in APOB-low group is significantly lower than those in APOB-high (P &lt; 0.001), indicating that APOB activity in HCC is significantly associated with prognosis of patients. This association was validated in 4 independent cohorts of HCC patients (n=88, 240, 242, and 371 in total of 941 patients). Since APOB is one of major carrier proteins for lipid, loss of APOB in HCC would lead to accumulation of intracellular fatty acid. Many studies showed that fatty acid are necessary for proliferation of cancer cells as essential for cell membranes and de novo biogenesis rate of fatty acid is well associated with prognosis of cancer patients. APOB expression is negatively correlated with methylation of APOB promoter. Our study suggested potential novel strategy of cancer cells to increase supply of fatty acids for fast proliferation. HCC cells increase supply of intracellular fatty acids by inhibiting export of fatty acids through inactivation of APOB. Further analysis of multiple genomic data revealed oncogenic YAP1 are highly active in APOB-low subgroup as evidenced by expression of downstream targets such as FOXM1 and TEAD4, suggesting that alteration in lipid metabolism could lead to activation of YAP1. For the first time, we showed that APOB inactivation has a clinical impact in HCC patients with significant alteration in regulators associated with tumorigenesis.

Citation Format: Gena Lee, Min Jun Kwak, Do Won Kim, Jiwon Koh, Eun Wook Joo, Susie Kah, Yeong-Eun Sim, Sun Young Yim, Ju-Seog Lee. Clinical significance of APOB inactivation in hepatocellular carcinoma [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 3404.

Clinicopathologic implications of immune classification by PD-L1 expression and CD8-positive tumor-infiltrating lymphocytes in stage II and III gastric cancer patients

We co-assessed PD-L1 expression and CD8⁺ tumor-infiltrating lymphocytes in gastric cancer (GC), and categorized into 4 microenvironment immune types. Immunohistochemistry (PD-L1, CD8, Foxp3, E-cadherin, and p53), PD-L1 mRNA in situ hybridization (ISH), microsatellite instability (MSI), and EBV ISH were performed in 392 stage II/III GCs treated with curative surgery and fluoropyrimidine-based adjuvant chemotherapy, and two public genome databases were analyzed for validation. PD-L1⁺ was found in 98/392 GCs (25.0%). The proportions of immune types are as follows: PD-L1⁺/CD8^High, 22.7%; PD-L1⁻/CD8^Low, 22.7%; PD-L1⁺/CD8^Low, 2.3%; PD-L1⁻/CD8^High, 52.3%. PD-L1⁺/CD8^High type accounted for majority of EBV⁺ and MSI-high (MSI-H) GCs (92.0% and 66.7%, respectively), and genome analysis from public datasets demonstrated similar pattern. PD-L1⁻/CD8^High showed the best overall survival (OS) and PD-L1⁻/CD8^Low the worst (P < 0.001). PD-L1 expression alone was not associated with OS, however, PD-L1⁻/CD8^High type compared to PD-L1⁺/CD8^High was independent favorable prognostic factor of OS by multivariate analysis (P = 0.042). Adaptation of recent molecular classification based on EBV, MSI, E-cadherin, and p53 showed no significant survival differences. These findings support the close relationship between PD-L1/CD8 status based immune types and EBV⁺, MSI-H GCs, and their prognostic significance in stage II/III GCs.

Clinical significance of overexpression of NRG1 and its receptors, HER3 and HER4, in gastric cancer patients

BACKGROUND

Neuregulin 1 (NRG1), a ligand for human epidermal growth factor (HER) 3 and HER4, can activates cell signaling pathways to promote carcinogenesis and metastasis.

METHODS

To investigate the clinicopathologic significance of NRG1 and its receptors, immunohistochemistry was performed for NRG1, HER3, and HER4 in 502 consecutive gastric cancers (GCs). Furthermore, HER2, microsatellite instability (MSI), and Epstein-Barr virus (EBV) status were investigated. NRG1 gene copy number (GCN) was determined by dual-color fluorescence in situ hybridization (FISH) in 388 available GCs.

RESULTS

NRG1 overexpression was observed in 141 (28.1%) GCs and closely correlated with HER3 (P = 0.034) and HER4 (P < 0.001) expression. NRG1 overexpression was significantly associated with aggressive features, including infiltrative tumor growth, lymphovascular, and neural invasion, high pathologic stage, and poor prognosis (all P < 0.05), but not associated with EBV, MSI, or HER2 status. Multivariate analysis identified NRG1 overexpression as an independent prognostic factor for survival (P = 0.040). HER3 and HER4 expressions were observed in 157 (31.3%) and 277 (55.2%), respectively. In contrast to NRG1, expression of these proteins was not associated with survival. NRG1 GCN gain (GCN ≥ 2.5) was detected in 14.7% patients, including two cases of amplification, and was moderately correlated with NRG1 overexpression (κ, 0.459; P < 0.001).

CONCLUSIONS

Although our results indicate a lack of prognostic significance of HER3 and HER4 overexpression in GC, overexpression of their ligand, NRG1, was associated with aggressive clinical features and represented an independent unfavorable prognostic factor. Therefore, NRG1 is a potential prognostic and therapeutic biomarker in GC patients.

Correlation between tumor infiltrating immune cells and peripheral regulatory T cell determined by methylation analyses and its prognostic significance in gastric cancer

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Background: Peripheral regulatory T cells (pTregs) might involve in tumor immune microenvironment. We aim to evaluate the correlation between pTregs and tumor immune microenvironment. Methods: pTregs status was determined from assessment of the pTreg/total T cell ratio (ratio of Foxp3 Treg-specific demethylated region (TSDR) to CD3G/CD3D demethylation) through epigenetic pattern of bisulfite pyrosequencing in long-term stored peripheral blood of 442 gastric cancer patients who received curative surgery. Immunohistochemical staining of multiple immune-related markers including CD3, CD4, CD8, Foxp3, 1-selectin arginase, ADAM metallopeptidase domain 17, CD163 and CD45RO within tumor microenvironment were performed in resected gastric tumor specimen. Results: The median value of FoxP3-TSDR and CD3G/CD3D demethylation was 5.8% and 32.3%, respectively. When pTreg/total T cell ratio was divided into eight equal groups from the lowest to the highest value, the extreme pTreg/total T cell ratio of the upper eighth and the lower eighth was significantly associated with lower CD45RO expressed cell counts within tumor microenvironment. In terms of arginase and CD163, inverse results were observed. Patients with extreme pTreg/total T cell ratio had significantly shorter disease-free survival (DFS) and overall survival (OS) compared to the patients with non-extreme pTreg/total T cell ratio. Multivariate analysis which included age, stage, lymphatic invasion, vascular invasion, and perineural invasion as covariates demonstrated that the extreme pTreg/total T cell ratio was an independent predictor for shorter DFS (HR 1.740, 95% CI 1.128 – 2.682; p = 0.012) and OS (HR 1.900, 95% CI 1.175 – 3.070; p = 0.003). Conclusions: Our results suggest that the pTreg/total T cell ratio determined by epigenetic methylation analysis is correlated with specific immune cell infiltration within tumor microenvironment in resected gastric tumors, and gives prognostic information in gastric cancer patients. pTreg/total T cell ratio could be an easy-obtained potential biomarker for prognosis and future immunotherapeutic treatment strategies.