Impact Of Copy Number Alterations Research Articles

Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer.

Copy number alterations (CNAs), resulting from the gain or loss of genetic material from as little as 50 base pairs or as big as entire chromosome(s), have been associated with many congenital diseases, de novo syndromes and cancer. It is established that CNAs disturb the dosage of genomic regions including enhancers/promoters, long non-coding RNA and gene(s) among others, ultimately leading to an altered balance of key cellular functions. In cancer, CNAs have been associated with almost all steps of the disease: predisposition, initiation, development, maintenance, response to treatment, resistance, and relapse. Therefore, understanding how specific CNAs contribute to tumourigenesis may provide prognostic insight and ultimately lead to the development of new therapeutic approaches to improve patient outcomes. In this review, we provide a snapshot of what is currently known about CNAs and cancer, incorporating topics regarding their detection, clinical impact, origin, and nature, and discuss the integration of innovative genetic engineering strategies, to highlight the potential for targeting CNAs using novel, dosage-sensitive and less toxic therapies for CNA-driven cancer.

Allele-Specific Expression of Leukemia Genes Is Associated with Pathogenicity in Poor Risk AML

Introduction: An imbalance in gene expression of the different alleles of a gene (allele-specific expression or ASE) is an intriguing genome-wide and dynamic phenomenon that could have an important role in tumorigenesis. Little is known about the causes and consequences of the differential cis- and trans-regulation on resultant ASE, aside from the impact of copy number alterations (CNAs) or imprinting. Acute myeloid leukemia (AML) is an aggressive clonal hematopoietic stem cell malignancy, with a low mutational burden in comparison with other cancers, where the impact of ASE may constitute a novel mechanism of pathogenesis. Aim: Application of Whole Genome Sequencing (WGS), RNA-seq and Oxford Nanopore methylation sequencing to study the ASE landscape in a cohort of poor risk AML patients and shed light on the mechanisms triggering this phenomenon as well as its temporal dynamics. Methods: ASE landscape was explored using paired germline and tumour WGS and RNA-seq on diagnostic bone marrow or peripheral blood samples from 33 cytogenetically poor risk AML patients, and additional RNA-seq from 18 samples corresponding to follow-up timepoints (including remission, relapse and refractory samples) from eight of the patients.Heterozygous SNPs were identified in the genomic DNA, and allele frequencies in RNA-seq reads were used to quantify ASE, after filtering for CNAs in the tumor DNA. Cas9-enriched Oxford Nanopore sequencing was then performed on available patient samples at diagnosis and subsequent time points. Allele-specific methylation was determined on the Nanopore sequencing using Guppy v6.3. Results: In the diagnostic cohort, we identified 4,802 protein-coding genes exhibiting ASE in at least one sample, with a median of 169 genes per sample (range 119-468, with one outlier sample showing ASE in 1,705 genes). Overall, 283 protein-coding genes showed ASE in ≥ 20% patients across the 33 samples. These genes included known imprinted genes and the transcription factor GATA2, where ASE was previously associated with AML, validating our ASE pipeline and filtering criteria. We also identified for the first time recurrent ASE in other myeloid genes such as KMT2A (20%), the homeobox genes PBX2 (41%), PBX3 (20%), HOXA6 (20%) and HOXB cluster ( HOXB2 (31%), HOXB3 (27%), HOXB5 (40%), HOXB6 (30%)); and the myeloid differentiation genes CDKN2A (40%), PDGFRB (25%) and PRTN3 (57%). Eighteen primary AML samples from 8/33 patients had paired diagnostic, remission and relapse or refractory material, allowing us to track the dynamic ASE pattern. RNA-seq and Sanger sequencing of cDNA in these samples showed that the ASE observed at diagnosis in HOXB2, HOXB3, HOXB6, PBX3 and GATA2 was lost in the corresponding remission sample (bi-allelic expression), with ASE returning at relapse and maintained in the refractory samples. In order to explore the epigenetic mechanisms underlying these allele-specific changes in expression, Cas9-enriched Oxford Nanopore sequencing was performed in 2 patients with available DNA at diagnosis and sequential time points, to determine the pattern of allele-specific methylation of the promoter region of GATA2 (patient 1) and HOXB2 (patient 2). In patient 1 at diagnosis, 90% of CpG sites were methylated at the GATA2 promoter region on one allele versus 61% in the other allele, with the hypomethylated allele corresponding to the allele that is overexpressed in the ASE sample. However, in the remission sample, the proportion of methylated CpG sites on the two alleles was similar (83% and 73%, respectively), in agreement with the expression of both GATA2 alleles at this stage. Likewise, in the diagnostic sample of patient 2, 6% of CpG sites were methylated in the HOXB2 promoter region of one allele, corresponding to the overexpressed allele in the ASE sample, while the other promoter allele had 17% of CpG sites methylated; with no differences in CpG methylation between alleles in the remission samples (9% versus 9%), again correlating with the bi-allelic expression of HOXB2 at remission. Conclusions: Combining WGS and RNA-seq in AML primary samples, we have identified key leukemia genes showing recurrent dynamic ASE associated with disease evolution: since it is found at diagnosis, lost in remission, but recovered in relapse and persisting in refractory stages. Our results also suggest allele-specific methylation as the potential mechanism orchestrating this phenomenon.

Prognostic Impact of Copy Number Alterations' Profile and AID/RAG Signatures in Acute Lymphoblastic Leukemia (ALL) with BCR::ABL and without Recurrent Genetic Aberrations (NEG ALL) Treated with Intensive Chemotherapy.

Adult acute lymphoblastic leukemia (ALL) is associated with poor outcomes. ALL is initiated by primary aberrations, but secondary genetic lesions are necessary for overt ALL. In this study, we reassessed the value of primary and secondary aberrations in intensively treated ALL patients in relation to mutator enzyme expression. RT-PCR, genomic PCR, and sequencing were applied to evaluate primary aberrations, while qPCR was used to measure the expression of RAG and AID mutator enzymes in 166 adult ALL patients. Secondary copy number alterations (CNA) were studied in 94 cases by MLPA assay. Primary aberrations alone stratified 30% of the patients (27% high-risk, 3% low-risk cases). The remaining 70% intermediate-risk patients included BCR::ABL1pos subgroup and ALL lacking identified genetic markers (NEG ALL). We identified three CNA profiles: high-risk bad-CNA (CNAhigh/IKZF1pos), low-risk good-CNA (all other CNAs), and intermediate-risk CNAneg. Furthermore, based on RAG/AID expression, we report possible mechanisms underlying the CNA profiles associated with poor outcome: AID stratified outcome in CNAneg, which accompanied most likely a particular profile of single nucleotide variations, while RAG in CNApos increased the odds for CNAhigh/IKZF1pos development. Finally, we integrated primary genetic aberrations with CNA to propose a revised risk stratification code, which allowed us to stratify 75% of BCR::ABL1pos and NEG patients.

Adverse Prognostic Role of Copy Number Alterations and Mutations in Adults with Philadelphia Chromosome-Negative Acute Lymphoblastic Leukemia

Background: The impact of copy number alterations (CNAs) or mutations on outcomes has been broadly analyzed in pediatric acute lymphoblastic leukemia (ALL). However, the magnitude of the effect was often marginal, frequently restricted to specific genetic subtypes and rarely replicated across independent cohorts in adult ALL. Aim: We tried to analyze the prognostic relevance of genetic copy number alterations and gene mutations in patients with Ph-negative ALL who were treated with modified hyper-CVAD based chemotherapy followed by allogeneic hematopoietic cell transplantation (alllo-HCT). Methods: We investigated the role of CNAs or mutations to refine risk stratification in 128 adults with newly diagnosed Philadelphia chromosome (Ph)-negative B-cell precursor ALL treated with intensive chemotherapy followed by allo-HCT for post-remission therapy. We performed multiplex ligation-dependent probe amplification (MLPA) to detect deletions of 11 genes ( IKZF1, CDKN2A/B, EBF1, ETV6, PAX5, BTG1, JAK2, RB1, PAR1, ZFY) and high throughput sequencing (HTS) of 70 gene mutations. Results: MLPA analysis showed that IKZF1 and CDKN2A/B deletions were observed in 54 (42.2%) and 52 (40.6%) patients, respectively. The remaining gene deletions were: PAX5 in 29 (22.6%), ETV6 in 22 (17.2%), BTG1 in 15 (11.7%), EBF1 in 14 (10.9%), RB1 in 13 (10.1%), JAK2 in 8 (6.2%), and PAR1 in 4 (3.1%). By HTS, NRAS (n=21, 16.4%), KRAS (n=11, 8.6%), TP53 (n=14, 10.9%), and PTPN11 (n=12, 9.4%) mutations were frequently detected. Overall, multivariate analysis for disease-free survival (DFS) and cumulative incidence of relapse (Table 1) showed that TP53 mutations (HR 5.04, 95%CI 2.29-11.30, P<0.001) and CDKN2A/B deletions (HR 1.88, 95%CI 1.10-3.31, P=0.026) were significantly associated with a poorer DFS. Patients with TP53 mutations (HR 5.64, 95%CI 1.95-16.20, P<0.001) and IKZF1 deletions (HR 1.91, 95%CI 1.09-3.31, P=0.022) had a higher relapse risk. To better define the prognostic role of CNAs, further analyses were restricted to patients excluding 14 TP53 mutations (n=114). Here, we classified patients into 4 subgroups; (1) No deletions (n=45, 39.5%), (2) IKZF1 deletion-alone (n=11, 9.6%), (3) IKZF1plus (n=40, 35.1%), and (4) CDKN2A/B±other deletions without IKZF1 deletions (n=18, 15.8%). Patients with IKZF1plus or CDKN2A/B±other deletions had an inferior DFS ( P=0.023) and higher relapse incidence ( P=0.002) than patients having no deletions. The results were similarly reproduced in patients receiving allo-HCT in first complete remission. Conclusions: Our data showed that IKZF1 or CDKN2A/B deletions and TP53 mutations may confer a poor prognosis for adult Ph-negative B-cell precursor ALL in the setting of intensive chemotherapy and allo-HCT. The combination of genomic abnormalities and minimal residual disease response may further refine risk stratification and better select patients who could benefit from novel therapeutic approaches.

Programmed Death-Ligand 1 Copy Number Alteration as an Adjunct Biomarker of Response to Immunotherapy in Advanced NSCLC

IntroductionThis study aimed to evaluate the value of programmed death-ligand 1 (PD-L1) copy number (CN) alteration as an additional biomarker to standard immunohistochemistry (IHC) in predicting response to immune checkpoint inhibitor (ICI) therapy in advanced NSCLC. MethodsBefore ICI monotherapy, tumor PD-L1 CN alteration (gain, neutral, or loss) was called using whole-exome sequencing data and compared with IHC results (tumor proportion score ≥50, 1–49, or 0). Progression-free survival (PFS) and overall survival were correlated with both biomarkers. In addition, the impact of CN alteration was further evaluated in two independent cohorts using next-generation sequencing panel. ResultsA total of 291 patients with advanced-stage NSCLC met the study inclusion criteria. Although the IHC classification distinguished the best responsive group (tumor proportion score ≥ 50), the CN-based classification distinguished the worst responsive group (CN loss) from the others (PFS, p = 0.020; overall survival, p = 0.004). After adjusting for IHC results, CN loss was an independent risk factor for progression (adjusted hazard ratio = 1.32, 95% confidence interval: 1.00–1.73, p = 0.049) and death (adjusted hazard ratio = 1.39, 95% confidence interval: 1.05–1.85, p = 0.022). A risk classification system was developed on the basis of IHC and CN profiles, which outperformed the conventional IHC system. In the validation cohorts, CN loss determined by next-generation sequencing panel was independently associated with worse PFS after ICI treatment, revealing its practical value. ConclusionsThis is the first study to directly compare CN alterations with IHC results and survival outcomes after anti–PD-(L)1 therapy. Tumor PD-L1 CN loss can serve as an adjunct biomarker to predict the lack of response. Prospective studies are required to further validate this biomarker.

Clinical and Prognostic Impact of Copy Number Alterations and Associated Risk Profiles in a Cohort of Pediatric B-cell Precursor Acute Lymphoblastic Leukemia Cases Treated Under ICiCLe Protocol.

Copy number alteration (CNA) status and CNA risk profiles of IKZF1plus, UK-ALL CNA risk groups and MRplus scores, were evaluated for clinical and prognostic impact in a cohort of 493 B-cell acute lymphoblastic leukemia cases diagnosed and treated under the Indian Collaborative Childhood Leukemia group (ICiCLe) protocol trial. Overall CNA frequency was 59% with 60% of cases showing 2-loci deletion. CDKN2A/B deletion was most common CNA (36.3%), while IKZF1 deletion and IKZF1plus profile were noted in 19.5% and 13.4% of cases, respectively. IKZF1 deletions and other CNA risk profiles were significantly associated with poor (PR)/high risk (HR) clinical and genetic profile parameters (P < 0.001). In addition, the 3-year OS, event-free survival (EFS) was significantly poor with high relapse rate (RR) of 38.6%, 46.5%, and 35.2% for IKZF1 deletions, IKZF1plus profiles, and UK-ALL CNA-intermediate risk (IR)+PR risk groups, respectively (P < 0.001). Integrated evaluation of UK-ALL CNA risk profile with ICiCLe trial risk stratification groups revealed a worse overall survival, EFS, and RR of 63.3%, 43.2%, and 35.2% for CNA-IR+PR profile compared to CNA-good risk profile (81.3%, 65.0%, and 21.0%; P < 0.001). Hence, routine CNA testing in our setting is must to identify standard risk and IR cases likely to benefit from HR treatment.

Prognostic impact of copy number alterations and tumor mutational burden in carcinoma of unknown primary.

Chromosomal aberrations are known to drive metastatic spread, but their profile is still elusive in carcinoma of unknown primary (CUP). Therefore, the aim of this study was to characterize the chromosomal aberration pattern in CUP depending on histological and clinical features and to assess its prognostic impact together with chromothripsis, tumor mutational burden (TMB), microsatellite instability (MSI), and mutational profiles as potential prognostic biomarkers. Chromosomal aberrations and chromothripsis were detected by methylation-based copy number variation (CNV) analysis, whereas TMB and MSI were calculated based on large next-generation sequencing (NGS) panels. Putative primaries were assigned by consensus between two independent oncologists. CNV losses varied depending on putative primaries and were more abundant in patients harboring TP53 mutations and/or deletions 17p. CNV loss was prognostically adverse in localized CUP treated with surgery and/or radiotherapy, but not in disseminated poor-risk CUP treated with palliative chemotherapy. CNV loss also worsened the prognosis in squamous cell CUP. Chromothripsis was detected in 18/59 (30.5%) patients without prognostic effect. TMB was highest in cases with MSI, squamous cell histology, and with lung, anal or cervical putative primaries. Overall, CNV, chromothripsis, TMB, and MSI profiles in CUP are reminiscent of biological characteristics known from other cancer entities without a unifying CUP-specific signature. Markedly, high-level CNV loss is an adverse predictive biomarker in localized but not disseminated chemotherapy-treated CUP. This implies that chromosomal losses drive CUP progression, but also increase susceptibility to chemotherapy, with both effects apparently leveling out in disseminated CUP.

Abstract P3-09-13: Androgen receptor loss is associated with genomic instability characterized by copy number alterations and mirna deregulation in triple-negative breast cancer

Abstract Background: Triple-negative breast cancer (TNBC) comprises 10%-20% of invasive breast carcinoma cases. Patients with TNBC exhibit poorer 5-year survival and higher rates of metastasis and recurrence than patients with other breast cancer subtypes. TNBC is further divided based on gene expression profiling into androgen receptor (AR)-positive (AR+) TNBC and AR-negative TNBC (or quadruple-negative breast cancer [QNBC]). While AR is an emerging therapeutic target for AR+ TNBC, there are no treatment options for QNBC. AR expression is associated with favorable disease-free, overall, and recurrence-free survival in patients with TNBC, suggesting that AR loss in TNBC tumors confers an aggressive disease course. Genomic instability has been recognized as one of the drivers of tumorigenesis and can be evidenced by the presence of chromosomal instability, such as DNA copy number alterations (CNAs). Although there are many studies characterizing the genomic profiles of TNBCs, little is known about the tumor biology and genetic makeup of QNBCs. In this study, we explored the impact of CNAs on microRNA (miRNA) expression and, subsequently, on signaling pathways associated with QNBC aggressiveness and clinical outcomes. Methods: AR expression was immunohistochemically assessed in tissues of 53 patients with TNBC from the Histopathology and Tissue Shared Resources of Georgetown University. AR positivity was defined as AR expression in &amp;gt;1% of cells. Genome-wide copy number profiling of formalin-fixed paraffin-embedded samples was performed using the Agilent SurePrint G3 Human CGH Microarray, and miRNA expression analysis was conducted using NanoString nCounter Human v3a miRNA Expression Assay. Differentially expressed miRNAs between TNBC and. QNBC samples were integrated with array CGH data from the same tissue sample to identify common gene targets that may be affected by both CNAs and miRNA deregulation. Functional enrichment analysis was performed to identify cancer pathways deregulated in QNBC. The expression levels of Centrosome Amplification 20 (CA20) and Chromosome Instability 25 (CIN 25) gene signatures were evaluated in 524 primary invasive breast cancers from The Cancer Genome Atlas (TCGA) database. Results: We observed that 64% of TNBC samples lacked AR expression and that QNBCs exhibited a significantly higher CNA level (p&amp;lt;0.05) and frequency (p&amp;lt;0.0001) compared with TNBCs. Gains at 1q21-q44, 6p25.3-p12.1, 8q11.1-q24.3, 9p24.3-p13.1, 10p15.3-p11.1, and 12p13.33-p11.1 were common CNAs observed in &amp;gt;50% of QNBCs. Additionally, CNAs affecting genes of the CIN25 signature were significantly higher in QNBC than in TNBC; however, CNAs in CA20 signature genes were similar in QNBC and TNBC samples. Notably, the expression levels of CA20 and CIN25 genes were significantly higher in QNBC than in TNBC. Moreover, we identified 184 differentially expressed miRNAs between QNBC and TNBC samples (p&amp;lt;0.05, FDR&amp;lt;0.25). Among these miRNAs, 15 were mapped at cytobands with CNAs, and eight (miR-23c, miR-548ai, miR-567, miR-613, miR-943, miR-1204, miR-1265, and miR-1267) presented concordance between their expression levels and CNAs. The target genes of these eight miRNAs were associated with genomic instability, cell cycle, and DNA damage response. Importantly, the combined expression levels of these eight miRNAs robustly discriminated between TNBCs and QNBCs with an area under the curve of 0.946. Conclusions: Our study highlights that loss of AR expression in TNBC is associated with profound genomic instability as evidenced by CNAs and deregulation of miRNA expression, which leads to upregulation of signaling pathways associated with cancer aggressiveness. Citation Format: Shristi Bhattarai, Bruna M. Sugita, Luciane Cavalli, Ritu Aneja. Androgen receptor loss is associated with genomic instability characterized by copy number alterations and mirna deregulation in triple-negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-09-13.

Comprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancers

BackgroundAlterations in genes encoding chromatin regulatory proteins are prevalent in cancers and may confer oncogenic properties and molecular changes linked to therapy resistance. However, the impact of copy number alterations (CNAs) of the SWItch/Sucrose NonFermentable (SWI/SNF) complex on the oncogenic and immunologic properties has not been systematically explored across human cancer types.MethodsWe comprehensively analyzed the genomic, transcriptomic and clinical data of The Cancer Genome Atlas (TCGA) dataset across 33 solid cancers.ResultsCNAs of the SWI/SNF components were identified in more than 25% of all queried cancers, and tumors harboring SWI/SNF CNAs demonstrated a worse overall survival (OS) than others in several cancer types. Mechanistically, the SCNA events in the SWI/SNF complex are correlated with dysregulated genomic features and oncogenic pathways, including the cell cycle, DNA damage and repair. Notably, the SWI/SNF CNAs were associated with homologous recombination deficiency (HRD) and improved clinical outcomes of platinum-treated ovarian cancer. Furthermore, we observed distinct immune infiltrating patterns and immunophenotypes associated with SWI/SNF CNAs in different cancer types.ConclusionThe CNA events of the SWI/SNF components are a key process linked to oncogenesis, immune infiltration and therapeutic responsiveness across human cancers.

HPV-associated penile cancer: Impact of copy number alterations in miRNA/mRNA interactions and potential druggable targets.

Penile cancer (PeCa) is a rare disease, but its incidence has increased worldwide, mostly in HPV+ patients. Nevertheless, there is still no targeted treatment for this carcinoma. To predict the main signaling pathways involved in penile tumorigenesis and its potential drug targets. Genome-wide copy number profiling was performed in 28 PeCa. Integration analysis of CNAs and miRNAs and mRNA targets was performed by DIANA-TarBase v.8. The potential impact of the miRNAs/target genes on biological pathways was assessed by DIANA-miRPath v.3.0. For each miRNA, KEGG pathways were generated based on the tarbase and microT-CDS algorithms. Pharmaco-miR was used to identify associations between miRNAs and their target genes to predict druggable targets. 269 miRNAs and 2,395 genes were mapped in cytobands with CNAs. The comparison of the miRNAs mapped at these cytobands and the miRNAs that were predicted to regulate the genes also mapped in these regions, resulted in a set of common 35 miRNAs and 292 genes. Enrichment pathway revealed their involvement in five top signaling pathways. EGFR and COX2 were identified as potential druggable targets. Our data indicate the potential use of EGFR and COX2 inhibitors as a target treatment for PeCa patients.

Set-Wise Differential Interaction Between Copy Number Alterations and Gene Expressions of Lower-Grade Glioma Reveals Prognosis-Associated Pathways.

The integrative analysis of copy number alteration (CNA) and gene expression (GE) is an essential part of cancer research considering the impact of CNAs on cancer progression and prognosis. In this research, an integrative analysis was performed with generalized differentially coexpressed gene sets (gdCoxS), which is a modification of dCoxS. In gdCoxS, set-wise interaction is measured using the correlation of sample-wise distances with Renyi’s relative entropy, which requires an estimation of sample density based on omics profiles. To capture correlations between the variables, multivariate density estimation with covariance was applied. In the simulation study, the power of gdCoxS outperformed dCoxS that did not use the correlations in the density estimation explicitly. In the analysis of the lower-grade glioma of the cancer genome atlas program (TCGA-LGG) data, the gdCoxS identified 577 pathway CNAs and GEs pairs that showed significant changes of interaction between the survival and non-survival group, while other benchmark methods detected lower numbers of such pathways. The biological implications of the significant pathways were well consistent with previous reports of the TCGA-LGG. Taken together, the gdCoxS is a useful method for an integrative analysis of CNAs and GEs.

Distribution differences in prognostic copy number alteration profiles in IDH-wild-type glioblastoma cause survival discrepancies across cohorts

The diagnosis and prognostication of glioblastoma (GBM) remain to be solely dependent on histopathological findings and few molecular markers, despite the clinical heterogeneity in this entity. To address this issue, we investigated the prognostic impact of copy number alterations (CNAs) using two population-based IDH-wild-type GBM cohorts: an original Japanese cohort and a dataset from The Cancer Genome Atlas (TCGA). The molecular disproportions between these cohorts were dissected in light of cohort differences in GBM. The Japanese cohort was collected from cases registered in Kansai Molecular Diagnosis Network for CNS tumors (KNBTG). The somatic landscape around CNAs was analyzed for 212 KNBTG cases and 359 TCGA cases. Next, the clinical impacts of CNA profiles were investigated for 140 KNBTG cases and 152 TCGA cases treated by standard adjuvant therapy using temozolomide-based chemoradiation. The comparative profiling indicated unequal distribution of specific CNAs such as EGFR, CDKN2A, and PTEN among the two cohorts. Especially, the triple overlap CNAs in these loci (triple CNA) were much higher in frequency in TCGA (70.5%) than KNBTG (24.3%), and its prognostic impact was independently validated in both cohorts. The KNBTG cohort significantly showed better prognosis than the TCGA cohort (median overall survival 19.3 vs 15.6 months). This survival difference between the two cohorts completely resolved after subclassifying all cases according to the triple CNA status. The prognostic significance of triple CNA was identified in IDH-wild-type GBM. Distribution difference in prognostic CNA profiles potentially could cause survival differences across cohorts in clinical studies.

Abstract P1-05-18: Genomic copy number alterations (CNA) associated with pCR in HER2-positive (HER2+) early-stage breast cancer (BrCa) patients receiving neoadjuvant trastuzumab (T)

Abstract Introduction: Genetic alterations such as amplifications and deletions frequently contribute to tumorigenesis. These alterations can change gene expression which alters the normal cell growth and survival regulatory mechanisms. Characterisation of DNA copy number alterations (CNA) is important to understand cancer progression and response to therapy. The aim of this study is to determine patterns of CNAs in HER2+ early-stage BrCa patients achieving pathological complete response (pCR) to neoadjuvant T therapy. Methods: Retrospective analysis of our database of 95 HER2+ BrCa (stages I-III) who received T neoadjuvantly revealed 46 % (44/95) achieved pCR compared with 53 % (51/95) who did not respond (NR). DNA from pre-treatment tumour biopsy specimens from neoadjuvant T therapy patients was extracted, and array-based comparative genomic hybridization (aCGH, n = 8; 6 pCR:2 NR) was used to identify CNAs, which correlated with pCR. Pathway analysis was then used to identify functionally relevant genes in aberrant regions. Results: aCGH analysis of DNA from pCR and NR identified distinct patterns of CNAs. HER2 amplicon was confirmed by IHC and aCGH in all samples. Although there was no significant difference in the average CNAs between groups (20±17 vs 17±2), there was greater variation in the range of CNAs in pCR (8-56 CNA) compared to NR (15-19 CNA). More gains and amplifications were observed in pCR patients with more deletions in the NR group. The most common chromosomal amplification region included chr8q12.1-q24 with 87.5% of all cases displaying gains. Of the 6 patients who achieved pCR, 50% displayed a deletion in chr9 spanning p24.3-p21.3, consistent with a deletion of tumour suppressor CDKN2A. No aberrations in chr9 were observed in NR cohort. The deleted genomic region contained 65 common protein-coding genes, with the interferon biological pathway as the most significant (p=1.03E-36). Conclusions: Distinct genomic CNAs were observed between patients achieving pCR compared to NR. However, of the 8 pts characterised here, none have relapsed. Follow-up data revealed a relapse rate of 6.8 % (3/44) vs 11.8 % (6/51) in the pCR and NR groups, respectively. To further elucidate the immunological response, we will present CNA data patterns on relapse and response and compare the impact of CNAs, immune-related proteins and pCR as surrogate predictors for outcome. Citation Format: Walsh N, Gullo G, Maguire A, O'Donovan N, Quinn C, Crown J. Genomic copy number alterations (CNA) associated with pCR in HER2-positive (HER2+) early-stage breast cancer (BrCa) patients receiving neoadjuvant trastuzumab (T) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-18.

High-Resolution Whole-Genome Copy Number Profiling Identifies High-Risk and Low-Risk Patients with Mantle Cell Lymphoma, a Result of the Lyma-Genomic Project Conducted on Behalf the Lysa Group

Abstract Introduction: Prognosis markers available at diagnosis are needed to discriminate high-risk (HR) from low-risk (LR) mantle cell lymphoma (MCL) patients (Delfau-Larue et al. Blood 2005; Balasubramanian et al. ASH 2014 abstract 78). In the present work, we report a whole-genome copy number analysis performed with a new technical approach. Samples from ninety-six young MCL patients treated in the phase III LyMa trial (Le Gouill et al. ASH 2014) have been investigated. Methods: Samples were selected according to material availability and patient's outcome. The cohort included 9 HR patients with primary refractory disease or relapse within one year post-diagnosis and 87 patients still in response one year after diagnosis, including 64 LR patients who were still in complete remission more than 30 months after diagnosis. Lymph node biopsies collected at diagnosis, formalin-fixed and paraffin-embedded were used to extract DNA, even when highly degraded. Both whole-genome copy number profiling and the most frequent somatic mutations of TP53 were analyzed with 50 ng of genomic DNA using the OncoScan® FFPE Assay, a new robust and validated single nucleotide polymorphism (SNP) array (Foster et al. BMC Med Genomics 2015). This assay uses the Molecular Inversion Probe technology (MIP) optimized for highly degraded FFPE samples. The ~200000 probes allowed for the detection of genome-wide copy number alterations (CNAs) with a higher concentration in cancer-related genes. The frequency and prognosis impact of CNAs were evaluated. Results and discussion: Overall, 68 recurrently altered regions were observed in 98% of patients. Deletions were more frequent than amplifications, at 9 vs 3 by patient respectively. Recurrent CNAs included losses at 1p21 (43%), 11q22 (ATM) (40%), 13q14 (24%), 9q22-31 (CDKN2A/CDKN2B) (25%), 13q33-34 (RB1) (21%), 8p11 (18%), 17p13 (TP53) (17%) and gains at 3q26-27 (35%), 3q21 (27%), 10q11 (13%) 15q11 (13%), 11q13 (CCND1) (12%), 13q31 (mir-17-92) (11%), 7p22 (CARD11) (10%), 10p12 (BMI1) (9%), 8q24 (MYC) (8%) and 12q13 (CDK4) (7%). TP53 mutations were detected in 5 patients including two with 17p13 deletion and showed a trend to be more frequent in the HR group vs LR (22% vs 3%; p=0.07). Deletions of TP53 (44% vs 14%; p=0.04), CDKN2A (67% vs 29%; p=0.054) and 8p11 (89% vs 24%; p=0.0002) were more frequent in the HR. The CDK4 (33% vs 6%; p=0.03) and mir-17-92 (44% vs 9%; p=0.01) loci were more frequently amplified in HR patients. Amplification of the miR-17-92 locus could explain why miR-17-92 overexpression, a PI3K/AKT pathway regulator, was associated with a worse prognosis in MCL (Roisman et al. Genes Chromosomes Cancer 2016). In contrast, amplification of the CARD11 locus was associated with LR (16% vs 0%; p=0.03). Conclusion: This study confirms the poor prognostic impact of TP53 alterations and reveals new CNAs associated with HR MCL such as 8p11 deletion and mir-17-92 locus amplification. Conversely CARD11 amplification appears to be associated with LR and absent from HR patients. These findings provide important clues for future theranostic-driven therapies in MCL. Disclosures Hermine: Alexion: Research Funding; Novartis: Research Funding; Celgene: Research Funding; AB science: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Patents &amp; Royalties, Research Funding, Speakers Bureau.

Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach.

Copy number alterations (CNAs) are thought to account for 85% of the variation in gene expression observed among breast tumours. The expression of cis-associated genes is impacted by CNAs occurring at proximal loci of these genes, whereas the expression of trans-associated genes is impacted by CNAs occurring at distal loci. While a majority of these CNA-driven genes responsible for breast tumourigenesis are cis-associated, trans-associated genes are thought to further abet the development of cancer and influence disease outcomes in patients. Here we present a network-based approach that integrates copy-number and expression profiles to identify putative cis- and trans-associated genes in breast cancer pathogenesis. We validate these cis- and trans-associated genes by employing them to subtype a large cohort of breast tumours obtained from the METABRIC consortium, and demonstrate that these genes accurately reconstruct the ten subtypes of breast cancer. We observe that individual breast cancer subtypes are driven by distinct sets of cis- and trans-associated genes. Among the cis-associated genes, we recover several known drivers of breast cancer (e.g. CCND1, ERRB2, MDM2 and ZNF703) and some novel putative drivers (e.g. BRF2 and SF3B3). siRNA-mediated knockdown of BRF2 across a panel of breast cancer cell lines showed significant reduction in cell viability for ER-/HER2+ (MDA-MB-453) cells, but not in normal (MCF10A) cells thereby indicating that BRF2 could be a viable therapeutic target for estrogen receptor-negative/HER2-enriched (ER-/HER2+) cancers. Among the trans-associated genes, we identify modules of immune response (CD2, CD19, CD38 and CD79B), mitotic/cell-cycle kinases (e.g. AURKB, MELK, PLK1 and TTK), and DNA-damage response genes (e.g. RFC4 and FEN1). siRNA-mediated knockdown of RFC4 significantly reduced cell proliferation in ER-negative normal breast and cancer lines, thereby indicating that RFC4 is essential for both normal and cancer cell survival but could be a useful biomarker for aggressive (ER-negative) breast tumours. under NetStrat.

Abstract SY44-01: Proteogenomic analysis of human colon and rectal cancer

Abstract SY44-01: Proteogenomic analysis of human colon and rectal cancer

ICan: an integrated co-alteration network to identify ovarian cancer-related genes.

BackgroundOver the last decade, an increasing number of integrative studies on cancer-related genes have been published. Integrative analyses aim to overcome the limitation of a single data type, and provide a more complete view of carcinogenesis. The vast majority of these studies used sample-matched data of gene expression and copy number to investigate the impact of copy number alteration on gene expression, and to predict and prioritize candidate oncogenes and tumor suppressor genes. However, correlations between genes were neglected in these studies. Our work aimed to evaluate the co-alteration of copy number, methylation and expression, allowing us to identify cancer-related genes and essential functional modules in cancer.ResultsWe built the Integrated Co-alteration network (ICan) based on multi-omics data, and analyzed the network to uncover cancer-related genes. After comparison with random networks, we identified 155 ovarian cancer-related genes, including well-known (TP53, BRCA1, RB1 and PTEN) and also novel cancer-related genes, such as PDPN and EphA2. We compared the results with a conventional method: CNAmet, and obtained a significantly better area under the curve value (ICan: 0.8179, CNAmet: 0.5183).ConclusionIn this paper, we describe a framework to find cancer-related genes based on an Integrated Co-alteration network. Our results proved that ICan could precisely identify candidate cancer genes and provide increased mechanistic understanding of carcinogenesis. This work suggested a new research direction for biological network analyses involving multi-omics data.

Amplified and Homozygously Deleted Genes in Glioblastoma: Impact on Gene Expression Levels

BackgroundGlioblastoma multiforme (GBM) displays multiple amplicons and homozygous deletions that involve relevant pathogenic genes and other genes whose role remains unknown.MethodologySingle-nucleotide polymorphism (SNP)-arrays were used to determine the frequency of recurrent amplicons and homozygous deletions in GBM (n = 46), and to evaluate the impact of copy number alterations (CNA) on mRNA levels of the genes involved.Principal FindingsRecurrent amplicons were detected for chromosomes 7 (50%), 12 (22%), 1 (11%), 4 (9%), 11 (4%), and 17 (4%), whereas homozygous deletions involved chromosomes 9p21 (52%) and 10q (22%). Most genes that displayed a high correlation between DNA CNA and mRNA levels were coded in the amplified chromosomes. For some amplicons the impact of DNA CNA on mRNA expression was restricted to a single gene (e.g., EGFR at 7p11.2), while for others it involved multiple genes (e.g., 11 and 5 genes at 12q14.1–q15 and 4q12, respectively). Despite homozygous del(9p21) and del(10q23.31) included multiple genes, association between these DNA CNA and RNA expression was restricted to the MTAP gene.ConclusionsOverall, our results showed a high frequency of amplicons and homozygous deletions in GBM with variable impact on the expression of the genes involved, and they contributed to the identification of other potentially relevant genes.