Copy Number Variation Alterations Research Articles

P07.05.B DNA-METHYLATION PROFILING IS AN EFFECTIVE ASSET FOR IDENTIFICATION OF TUMORS IN SUSPECTED, YET IMMUNOHISTOCHEMICALLY UNSPECIFIABLE, NEURO-ONCOLOGICAL CASES

Abstract BACKGROUND Patients with a suspected neurooncological disease on radiographic images and no histopathological evidence of a tumor on the surgically retrieved tissue, pose a great challenge for clinicians and neuropathologists. DNA methylation-based classifications and copy number variation (CNV) analysis allow robust brain tumor classification. Here, we aim to evaluate their diagnostic properties in histopathologically unspecifiable or negative cases. MATERIAL AND METHODS We screened all neurosurgical cases, which underwent surgery at our institution between 2009 and 2021, with suspected neurooncological, but negative or unspecific histopathological diagnosis. We differentiated two groups: cases with cell-enriched, reactive tissue (+/- single tumor cells), insufficient to fully classify the lesion according to criteria of WHO for CNS tumors (group 1) and cases without histological evidence of tumor cells (group 2). In both groups, DNA methylation profiling was applied. Endpoints were diagnostic results of DNA methylation profiling (classifier Score ≥0.9) and evidence/no evidence of tumorigenic CNV alterations and eventually feasibility to make a diagnosis according to WHO 2021 criteria for brain tumors. RESULTS 23 cases with unspecifiable histopathological diagnosis were identified, out of whom 5 (21.7%) were confirmed as healthy brain tissue via DNA-methylation profiling, whereas the eventual diagnosis of tumorigenic tissue was provided in 18 (78.3%) cases. 14 of these were assigned to group 1, 4 cases to group 2. In 6 cases of group 1 (42.9%) DNA-methylation profiling resulted in a successful tumor classification (score ≥0.9) compared to 1 case (25%) in group 2. CNV indicated tumorigenic alterations in 9 (64.3%) patients in group 1 and 2 (50%) patients in group 2. Specific tumor alterations in the CNV were found in 8 (57.1%) patients in group 1 and in 1 (25%) patient in group 2. Combining CNV and DNA-methylation profiling, a final tumor diagnosis according to WHO 2021 criteria was feasible in 9 (64.3%) cases in group 1 and 3 (75%) cases in group 2. Median time from surgery to histopathological diagnosis was 6 and 7 days and 32.5 and 31 days for integrated diagnosis (group 1 vs. group 2). CONCLUSION Molecular diagnostics with DNA-methylation profiling and CNV analysis substantially increases the likelihood of a definitive diagnosis according to 2021 WHO criteria for these challenging cases.

Pediatric BCOR-Altered Tumors From Soft Tissue/Kidney Display Specific DNA Methylation Profiles

In the pediatric population, BCL6-correpresor gene (BCOR)–upregulated tumors include primitive myxoid mesenchymal tumors/undifferentiated sarcomas (PMMTI/UND), clear cell sarcomas of the kidney (CCSK), and high-grade neuroepithelial tumors (HG-NET). We investigated DNA methylation (DNAm) and copy number variation (CNV) profiling in these tumors (N = 34) using an Illumina EPIC BeadChip to better define the potential use of these tools to confirm diagnosis and predict outcomes. Twenty-seven tumors from 25 patients (age range, 0-10 years), showed molecular confirmation of genetic abnormalities as follows: BCOR internal tandem duplication in 14 PMMTI/UND, 8 CCSK, and 3 HG-NET and YWHAE fusions in 2 PMMTI/UND. The remaining 7 cases lacking informative molecular data were analyzed by immunophenotyping and were included in the study as a training cohort, clearly separated from the main study group. These were 4 PMMTI, 1 HG-NET, and 1 CCSK in which poor RNA preservation precluded the confirmation of BCOR rearrangements and 1 CCSK in which no rearrangements were found. DNAm data were compared with those of brain tumor and/or sarcoma classifier. Differentially methylated regions (DMRs) were analyzed in the 3 groups. Twenty-two cases of the 24 molecularly confirmed PMMTI/UND and CCSK and 3 of 6 of those with only immunophenotyping were classified within the methylation class “BCOR-altered sarcoma family” with optimal calibrated scores. PMMTI/UND and CCSK showed similar methylation profiles, whereas thousands of DMRs and significantly enriched pathways were evident between soft tissue/kidney tumors and HG-NET. The CNV analysis showed an overall flat profile in 19 of the 31 evaluable tumors (8/10 CCSK; 9/18 PMMTI/UND; 2/4 HG-NET). The most frequent CNVs were 1q gain and 9p and 10q loss. Follow-up time data were available for 20 patients: ≥2 CNV significantly correlated with a worse overall survival rate. In conclusion, soft tissue and kidney BCOR sarcomas matched with BCOR-altered sarcoma methylation class, whereas those from the brain matched with the central nervous system tumor classifier HG-NET BCOR, supporting the notion that DNAm profiling is an informative diagnostic tool. CNV alterations were associated with a more aggressive clinical behavior.

Esophageal Squamous Cancer from 4NQO-Induced Mice Model: CNV Alterations.

Squamous esophageal carcinoma is a common pathological type of esophageal carcinoma around the world. The prognosis of esophageal carcinoma is usually poor and diagnosed at late stages. Recently, research suggested that genomic instability occurred in esophageal cells during the development of esophageal squamous cell carcinoma (ESCC). Identifying prognostic and specific genomic characteristics, especially at the early hyperplasia stage, is critical. Mice were given 4-nitroquinoline 1-oxide (4NQO) with drinking water to induce esophageal cancer. The immortalized human esophageal epithelial cell line (NE2) was also treated with 4NQO. We performed histologic analyses, immunofluorescence, and immunohistochemical staining to detect DNA damage at different time points. Whole-exome sequencing was accomplished on the esophagus tissues at different pathological stages to detect single-nucleotide variants and copy number variation (CNV) in the genome. Our findings indicate that all mice were tumor-forming, and a series of changes from simple hyperplasia (ESSH) to intraepithelial neoplasia (IEN) to esophageal squamous cell carcinoma (ESCC) was seen at different times. The expression of γ-H2AX increased from ESSH to ESCC. In addition, mutations of the Muc4 gene were detected throughout the pathological stages. Furthermore, CNV burden appeared in the esophageal tissues from the beginning of ESSH and accumulated more in cancer with the deepening of the lesions. This study demonstrates that mutations caused by the early appearance of DNA damage may appear in the early stage of malignant tissue before the emergence of atypia. The detection of CNV and mutations of the Muc4 gene may be used as an ultra-early screening indicator for esophageal cancer.

TP53 and LRP1B Co-Wild Predicts Improved Survival for Patients with LUSC Receiving Anti-PD-L1 Immunotherapy.

Simple SummaryImmune checkpoint inhibitors (ICIs) changed the standard care of patients with lung squamous cell carcinoma (LUSC). It is an urgent need to precisely predict the population’s response to ICIs. The aim of the study was to explore novel biomarkers for LUSC immunotherapy and the potential mechanism. Five hundred and twenty-five Chinese patients with LUSC who underwent targeted sequencing were involved, and TP53 and LRP1B were the genes most frequently correlated to tumor mutational burden (TMB). Further analysis demonstrated that TP53/LRP1B co-wild was associated with improved survival of immunotherapy. Compared with those with TP53/LRP1B mutant, patients with TP53/LRP1B co-wild had lower TMB and chromosome instability, while stronger cytotoxic immune cell infiltrations, which might be the reason for the better clinical outcomes of immunotherapy. These results indicated that TP53/LRP1B co-wild might be regarded as a potential biomarker for guiding anti-PD-L1 immunotherapy in LUSC.Immunotherapy brought long-term benefits for partial patients with lung squamous cell carcinoma (LUSC). The predictor of anti-PD-L1 therapy was controversial and limited in LUSC. We aimed to explore novel biomarker for LUSC immunotherapy and the potential mechanism. Five hundred and twenty-five Chinese patients (Geneplus cohort) with LUSC underwent targeted sequencing and were involved to explore the genomic profiling. TP53 and LRP1B were the most frequently recurrent genes and correlated to higher tumor mutational burden (TMB). We observed that LUSC patients with TP53 and LRP1B co-wild (co-wild type) were associated with better survival of anti-PD-L1 therapy compared with TP53 mutant or LRP1B mutant (mutant type) in POPAR/OAK cohort. Copy-number variation (CNV) and whole genome doubling (WGD) data from TCGA LUSC cohort were obtained to assess the CNV events. There were fewer CNV alterations and lower chromosome instability in patients with TP53/LRP1B co-wild compared with those with TP53/LRP1B mutant. RNA expression data from the TCGA LUSC cohort were collected to explore the differences in RNA expression and tumor immune microenvironment (TIME) between mutant and co-wild groups. The TP53/LRP1B co-wild type had a significantly increased proportion of multiple tumor-infiltrating lymphocytes (TILs), including activated CD8 T cell, activated dendritic cell (DC), and effector memory CD8 T cell. Immune-related gene sets including checkpoint, chemokine, immunostimulatory, MHC and receptors were enriched in the co-wild type. In conclusion, TP53/LRP1B co-wild LUSC conferred an elevated response rate in anti-PD-L1 therapy and improved survival, which was associated with a chromosome-stable phenotype and an activated immune microenvironment.

DNA-methylome-assisted classification of patients with poor prognostic subventricular zone associated IDH-wildtype glioblastoma

Glioblastoma (GBM) derived from the “stem cell” rich subventricular zone (SVZ) may constitute a therapy-refractory subgroup of tumors associated with poor prognosis. Risk stratification for these cases is necessary but is curtailed by error prone imaging-based evaluation. Therefore, we aimed to establish a robust DNA methylome-based classification of SVZ GBM and subsequently decipher underlying molecular characteristics. MRI assessment of SVZ association was performed in a retrospective training set of IDH-wildtype GBM patients (n = 54) uniformly treated with postoperative chemoradiotherapy. DNA isolated from FFPE samples was subject to methylome and copy number variation (CNV) analysis using Illumina Platform and cnAnalysis450k package. Deep next-generation sequencing (NGS) of a panel of 130 GBM-related genes was conducted (Agilent SureSelect/Illumina). Methylome, transcriptome, CNV, MRI, and mutational profiles of SVZ GBM were further evaluated in a confirmatory cohort of 132 patients (TCGA/TCIA). A 15 CpG SVZ methylation signature (SVZM) was discovered based on clustering and random forest analysis. One third of CpG in the SVZM were associated with MAB21L2/LRBA. There was a 14.8% (n = 8) discordance between SVZM vs. MRI classification. Re-analysis of these patients favored SVZM classification with a hazard ratio (HR) for OS of 2.48 [95% CI 1.35–4.58], p = 0.004 vs. 1.83 [1.0–3.35], p = 0.049 for MRI classification. In the validation cohort, consensus MRI based assignment was achieved in 62% of patients with an intraclass correlation (ICC) of 0.51 and non-significant HR for OS (2.03 [0.81–5.09], p = 0.133). In contrast, SVZM identified two prognostically distinct subgroups (HR 3.08 [1.24–7.66], p = 0.016). CNV alterations revealed loss of chromosome 10 in SVZM– and gains on chromosome 19 in SVZM– tumors. SVZM– tumors were also enriched for differentially mutated genes (p < 0.001). In summary, SVZM classification provides a novel means for stratifying GBM patients with poor prognosis and deciphering molecular mechanisms governing aggressive tumor phenotypes.

The PARP Inhibitor Olaparib Modulates the Transcriptional Regulatory Networks of Long Non-Coding RNAs during Vasculogenic Mimicry

In highly metastatic tumors, vasculogenic mimicry (VM) involves the acquisition by tumor cells of endothelial-like traits. Poly-(ADP-ribose) polymerase (PARP) inhibitors are currently used against tumors displaying BRCA1/2-dependent deficient homologous recombination, and they may have antimetastatic activity. Long non-coding RNAs (lncRNAs) are emerging as key species-specific regulators of cellular and disease processes. To evaluate the impact of olaparib treatment in the context of non-coding RNA, we have analyzed the expression of lncRNA after performing unbiased whole-transcriptome profiling of human uveal melanoma cells cultured to form VM. RNAseq revealed that the non-coding transcriptomic landscape differed between olaparib-treated and non-treated cells: olaparib significantly modulated the expression of 20 lncRNAs, 11 lncRNAs being upregulated, and 9 downregulated. We subjected the data to different bioinformatics tools and analysis in public databases. We found that copy-number variation alterations in some olaparib-modulated lncRNAs had a statistically significant correlation with alterations in some key tumor suppressor genes. Furthermore, the lncRNAs that were modulated by olaparib appeared to be regulated by common transcription factors: ETS1 had high-score binding sites in the promoters of all olaparib upregulated lncRNAs, while MZF1, RHOXF1 and NR2C2 had high-score binding sites in the promoters of all olaparib downregulated lncRNAs. Finally, we predicted that olaparib-modulated lncRNAs could further regulate several transcription factors and their subsequent target genes in melanoma, suggesting that olaparib may trigger a major shift in gene expression mediated by the regulation lncRNA. Globally, olaparib changed the lncRNA expression landscape during VM affecting angiogenesis-related genes.

Whole-genome sequencing reveals distinct genetic bases for insulinomas and non-functional pancreatic neuroendocrine tumours: leading to a new classification system

ObjectiveInsulinomas and non-functional pancreatic neuroendocrine tumours (NF-PanNETs) have distinctive clinical presentations but share similar pathological features. Their genetic bases have not been comprehensively compared. Herein, we used whole-genome/whole-exome sequencing (WGS/WES)...

High false-positive non-invasive prenatal screening results for sex chromosome abnormalities: Are maternal factors the culprit?

To explore the impact of maternal sex chromosome aneuploidies (SCAs) and copy number variation (CNV) on false-positive results of non-invasive prenatal screening (NIPS) for predicting foetal SCAs. In total, 22 844 pregnant women were recruited to undergo NIPS. Pregnant women with high-risk of SCAs underwent prenatal diagnosis and maternal copy number variation sequencing (CNV-seq). Among 117 women with high-risk of SCAs, 72 accepted prenatal diagnosis, 86 accepted maternal CNV-seq, and 21 had maternal sex chromosome abnormalities. The abnormality rate was significantly higher than women at low-risk of SCAs (24.42% vs 3.51%). Using a novel parameter cffDNA (ChrX)/cffDNA, when the ratio was greater than 2, all foetuses had normal karyotype, and 75.0% (6/8) had abnormal maternal chromosome X. If the ratio was less than or equal to 2, only 10% (4/40) of the mothers had chromosome X CNV alterations, while 33.3% (13/40) of their foetuses had sex chromosomes CNV abnormalities. Approximately 25% of pregnant women with SCAs predicted by NIPS had sex chromosome abnormalities as determined by CNV-seq. The ratio of cffDNA (ChrX)/cffDNA can tentatively distinguish the maternal or foetal origin of abnormal cell-free DNA. In a reanalysis of previous NIPS data, false-positive results caused by maternal CNV might be elucidated.

BSCI-26. COMPARATIVE METHYLATION PROFILING OF EGFR MUTANT LUNG ADENOCARCINOMA AND PAIRED BRAIN METASTASIS

BACKGROUND: Adenocarcinomas (ADC) are the most common lung tumours and EGFR-mutant lesions have a higher risk of brain metastasis development, which confers poorer survival. Genetic and epigenetic signatures of brain metastasis have not been comprehensively identified. The aim of this study is to compare the methylome of EGFR-mutant primary lung tumor and matched brain metastasis to identify mechanisms of brain metastasis and new treatment targets. METHOD: Seven matched primary to brain metastasis tumours were profiled using the Illumina Infinium MethylationEPIC BeadChip array. Hierarchical clustering and principal component analyses (PCA) were performed using most variable CpG sites. Supervised analyses were performed between lung and brain tumour samples. Copy number variation (CNV) plots identified alterations between pairs along with Leukocytes unmethylation for purity (LUMP) score and prediction lymphocyte proportion analyses to measure immune infiltration. RESULTS: Unsupervised clustering showed that the fourteen tumours clustered according to patient with similar methylation profiles between each of seven matched pairs. On the supervised analysis using 83K significant CpG sites, the fourteen samples clustered into two groups based on tumour site being lung or brain. Of these 83K CpG sites, 2.4K were either hypermethylated or hypomethylated in all lung samples. One quarter of these 2.4K CpG sites were located in promoter regions. CNV analyses showed losses of FGFR1, C19MC, CDKN2A, PTCH1, and MYCN genes with higher deep deletions in brain versus lung primary samples. Immune infiltration measures were similar between lung and brain metastasis pairs (LUMP-score=0.64) consistent with high immune cell infiltration. CONCLUSION: In this EGFR-mutant lung adenocarcinomas and matched brain metastases, differentially methylated CpG sites and CNV alterations are identified that distinguish lung from brain samples. Further work with additional matched samples may further elucidate signatures specific to brain metastasis and aid in our understanding of the mechanisms of brain metastasis.

Rapid Phenotypic and Genomic Change in Response to Therapeutic Pressure in Prostate Cancer Inferred by High Content Analysis of Single Circulating Tumor Cells

Timely characterization of a cancer's evolution is required to predict treatment efficacy and to detect resistance early. High content analysis of single Circulating Tumor Cells (CTCs) enables sequential characterization of genotypic, morphometric and protein expression alterations in real time over the course of cancer treatment. This concept was investigated in a patient with castrate-resistant prostate cancer progressing through both chemotherapy and targeted therapy. In this case study, we integrate across four timepoints 41 genome-wide copy number variation (CNV) profiles plus morphometric parameters and androgen receptor (AR) protein levels. Remarkably, little change was observed in response to standard chemotherapy, evidenced by the fact that a unique clone (A), exhibiting highly rearranged CNV profiles and AR+ phenotype was found circulating before and after treatment. However, clinical response and subsequent progression after targeted therapy was associated with the drastic depletion of clone A, followed by the sequential emergence of two distinct CTC sub-populations that differed in both AR genotype and expression phenotype. While AR- cells with flat or pseudo-diploid CNV profiles (clone B) were identified at the time of response, a new tumor lineage of AR+ cells (clone C) with CNV altered profiles was detected during relapse. We showed that clone C, despite phylogenetically related to clone A, possessed a unique set of somatic CNV alterations, including MYC amplification, an event linked to hormone escape. Interesting, we showed that both clones acquired AR gene amplification by deploying different evolutionary paths. Overall, these data demonstrate the timeframe of tumor evolution in response to therapy and provide a framework for the multi-scale analysis of fluid biopsies to quantify and monitor disease evolution in individual patients.

Abstract 4599: Sequential monitoring of single-cell copy number variation in metastatic prostate cancer.

Abstract The high-definition circulating tumor cell (HD-CTC) assay provides for an enrichment-free approach to CTC identification. Here, we utilized the HD-CTC approach to study androgen receptor (AR) expression combined with single-nucleus sequencing for genome-wide analysis of copy number variation (CNV) in sequential CTCs samples obtained from a patient with metastatic prostate cancer treated with abiraterone acetate (an androgen synthesis inhibitor). At baseline, before initiation of abiraterone treatment, we observed a balanced proportion of AR-negative and AR-positive CTCs. During a brief period of clinical response (marked with a decreased serum PSA and decreased pain) the proportion of AR-positive CTCs declined followed by a rapid increase associated with clinical progression (increased PSA and pain). CNV analysis of single CTCs revealed multiple genomic rearrangements, such as AR amplification along with the chromosomal gains and losses typical of prostate cancer, in multiple cells at baseline. During treatment response, the frequency of CNV alterations significantly declined, followed by a reemergence to a pattern of multiple, complex alterations associated with clinical progression. Detailed analysis of the CNV profiles revealed that many abnormalities were commonly shared between the CTC populations, but a number were unique to the AR+ resistant/hormone refractory CTC population including increased MYC amplification alteration and the AR amplicon that include additional adjacent genes. Remarkably, the reconstruction of tumor lineage history based on the CTC genomic profiles enables us to trace and identify the precise treatment time point where the putative therapy-resistant CTC clone emerges, under therapeutic pressure, until it eventually expanded to become the AR+ resistant CTC population at the point of therapeutic relapse. Overall, our results demonstrated that the integration of the HD-CTC enumeration technology with protein expression and single cell genomic analyses could successfully be applied to real time monitoring of ADT therapy emergent change in a prostate cancer patient, and may provide a direct roadmap for personalized cancer medicine in the near future. Citation Format: Peter Kuhn, Angel E. Dago, Asya Stepansky, Anders Carlsson, Natalie Felch, Madelyn Luttgen, Anand Kolatkar, James Hicks, Mitchell E. Gross. Sequential monitoring of single-cell copy number variation in metastatic prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4599. doi:10.1158/1538-7445.AM2013-4599