Correlation of CCNE1 copy number levels with molecular profiles and outcomes for high grade serous ovarian and endometrial cancer (121)

Objectives: This study aimed to characterize CCNE1 copy number (CN) in relation to other molecular characteristics of tumors, along with patient outcomes, to help guide future clinical trial design and potential novel targeted therapeutics development for these aggressive molecular subtypes of high-grade serous ovarian (HGSOC) and endometrial cancers (EMCA). Methods: Tumor samples were analyzed using Next-Gen sequencing (NGS) of the DNA (NextSeq, 592 genes or NovaSeq, whole-exome sequencing) and RNA (NovaSeq, whole-transcriptome sequencing) and immunohistochemistry (IHC) (Caris Life Sciences, Phoenix, AZ). PD-L1 IHC used SP-142 (cut-off ≥1%). Microsatellite instability (MSI) was tested by fragment analysis, IHC, and NGS. Tumor mutation burden (TMB) was measured by totaling somatic mutations per tumor (high ≥10 mutations/MB). Relative abundance of immune-cell infiltrates was calculated by MCPCounter. CCNE1 amplification (CCNE1Amp) was defined as CN ≥6 and calculated by NGS/WES. Real-world overall survival (OS) was obtained from insurance claims data, and Kaplan-Meier estimates were calculated for molecularly defined patient cohorts. Statistical significance was determined using Chi-square and Wilcoxon rank-sum test, and p-values adjusted for multiple comparisons (q) to be <0.05. Results: CCNE1 was amplified in 608/6306 (9.6%) of HGSOC, 214/2098 (10.2%) of serous EMCA, 191/749 (15.3%) of uterine carcinosarcomas (UCS), and 17/2053 (0.80%) of endometrioid EMCA. TP53 mutations positively correlated with CCNE1Amp. CCNE1Amp HGSOC had fewer mutations in BRCA1/2, ARID1A, and NF1 but increased CN amplification in other genes (Table 1). PTEN mutations were negatively correlated with CCNE1Amp in UCS and endometrioid EMCA. There was no difference in immuno-oncology biomarkers (TMB, dMMR/MSI, PD-L1). However, increased CCNE1 levels were associated with decreased fibroblasts in HGSOC and serous EMCA, decreased B cells in serous EMCA, and decreased CD3+ T cells in UCS. In HGSOC, CCNE1Amp was associated with increased expression of cell-cycle checkpoint regulators, Fanconi anemia, homologous recombination, mismatch repair, and single-strand break repair pathway genes, but decreased expression of these genes in endometrioid EMCA. In tumors with >1 specimen serially submitted, there was a significant increase in CCNE1 CN over time in 29% (49/169) of HGSOC and 23% of EMCA (36/158). There was no difference in CCNE1 CN in tumors harboring BRCA reversion mutations (n=8) compared to wild-type (n=5110). CCNE1Amp correlated with mRNA expression in HGSOC and EMCA. CCNE1Amp was associated with worse OS after carboplatin-based treatment in HGSOC as well as in serous EMCA and UCS. Conclusions: CCNE1Amp in HGSOC and EMCA is less common than previously identified. Both HGSOC and endometrioid EMCAs have distinct molecular characteristics of CCNE1Amp tumors. CCNE1 CN may increase with the emergence of treatment resistance. Finally, CCNE1Amp tumors appear overall non-immunogenic. Objectives: This study aimed to characterize CCNE1 copy number (CN) in relation to other molecular characteristics of tumors, along with patient outcomes, to help guide future clinical trial design and potential novel targeted therapeutics development for these aggressive molecular subtypes of high-grade serous ovarian (HGSOC) and endometrial cancers (EMCA). Methods: Tumor samples were analyzed using Next-Gen sequencing (NGS) of the DNA (NextSeq, 592 genes or NovaSeq, whole-exome sequencing) and RNA (NovaSeq, whole-transcriptome sequencing) and immunohistochemistry (IHC) (Caris Life Sciences, Phoenix, AZ). PD-L1 IHC used SP-142 (cut-off ≥1%). Microsatellite instability (MSI) was tested by fragment analysis, IHC, and NGS. Tumor mutation burden (TMB) was measured by totaling somatic mutations per tumor (high ≥10 mutations/MB). Relative abundance of immune-cell infiltrates was calculated by MCPCounter. CCNE1 amplification (CCNE1Amp) was defined as CN ≥6 and calculated by NGS/WES. Real-world overall survival (OS) was obtained from insurance claims data, and Kaplan-Meier estimates were calculated for molecularly defined patient cohorts. Statistical significance was determined using Chi-square and Wilcoxon rank-sum test, and p-values adjusted for multiple comparisons (q) to be <0.05. Results: CCNE1 was amplified in 608/6306 (9.6%) of HGSOC, 214/2098 (10.2%) of serous EMCA, 191/749 (15.3%) of uterine carcinosarcomas (UCS), and 17/2053 (0.80%) of endometrioid EMCA. TP53 mutations positively correlated with CCNE1Amp. CCNE1Amp HGSOC had fewer mutations in BRCA1/2, ARID1A, and NF1 but increased CN amplification in other genes (Table 1). PTEN mutations were negatively correlated with CCNE1Amp in UCS and endometrioid EMCA. There was no difference in immuno-oncology biomarkers (TMB, dMMR/MSI, PD-L1). However, increased CCNE1 levels were associated with decreased fibroblasts in HGSOC and serous EMCA, decreased B cells in serous EMCA, and decreased CD3+ T cells in UCS. In HGSOC, CCNE1Amp was associated with increased expression of cell-cycle checkpoint regulators, Fanconi anemia, homologous recombination, mismatch repair, and single-strand break repair pathway genes, but decreased expression of these genes in endometrioid EMCA. In tumors with >1 specimen serially submitted, there was a significant increase in CCNE1 CN over time in 29% (49/169) of HGSOC and 23% of EMCA (36/158). There was no difference in CCNE1 CN in tumors harboring BRCA reversion mutations (n=8) compared to wild-type (n=5110). CCNE1Amp correlated with mRNA expression in HGSOC and EMCA. CCNE1Amp was associated with worse OS after carboplatin-based treatment in HGSOC as well as in serous EMCA and UCS. Conclusions: CCNE1Amp in HGSOC and EMCA is less common than previously identified. Both HGSOC and endometrioid EMCAs have distinct molecular characteristics of CCNE1Amp tumors. CCNE1 CN may increase with the emergence of treatment resistance. Finally, CCNE1Amp tumors appear overall non-immunogenic.