Abstract P2-23-03: Genomic Evaluation of Malignant Phyllodes Tumors Reveals Multiple Targetable Opportunities

Background: Malignant phyllodes tumors (MPT) are rare fibroepithelial breast tumors that disproportionately affect young women. Despite high local and distant recurrence rates, treatment is almost exclusively surgical. With no known effective chemotherapy or targeted systemic therapy options, metastatic progression portends dismal prognosis. Current national guidelines do not recommend biomarker testing in the non-metastatic setting. Management of metastatic disease follows principles of soft tissue sarcoma recommending Next-Generation Sequencing on an individual basis for patients who may qualify for clinical trials or are refractory to standard therapies. In the largest genomic profiling effort of MPT to date, we sought to describe the genomic landscape of MPTs through comprehensive genomic profiling (CGP) and immunotherapeutic biomarker analysis.

Methods: Cases of sequenced MPT were identified from a CLIA-certified, CAP-accredited laboratory database (Foundation Medicine, Cambridge, MA). Cases were categorized as localized/locally recurrent or metastatic. All cases underwent CGP by DNA extraction from FFPE samples using a hybrid capture, adaptor ligation-based next generation sequencing assay, and all classes of genomic alterations, microsatellite instability (MSI), and tumor mutational burden (TMB) were evaluated. PD-L1 expression by IHC was measured by the DAKO 22C3 assay (scored CPS) or the Ventana SP142 assay (scored as IC). Patient characteristics and results of CGP of MPT were summarized by either N (%) or median (range). Factors from MPT were compared to all cases of breast carcinoma in the lab database. Fisher’s Exact Tests were used to test for differences between groups and analysis of variance was used to test for differences for continuous variables.

Results: Of 135 MPT cases identified; 94 (69.6%) were localized/locally recurrent (breast, chest wall, soft tissue, skin, or lymph node) and 41 (30.4%) were metastatic (73% lung, followed by bone, liver, other intraabdominal). All patients were female with a median age of 54 years (range 14-86). The median TMB across samples was 2.5 mut/Mb and only 3 were TMB-high tumors (>10mut/Mb). Over 1/3 (36.8%) of samples were PD-L1+ via Ventana SP142 assay (≥1) and 21.4% were PD-L1+ via Dako 22C3 assay (CPS ≥10). All evaluable cases (N=132) were microsatellite stable. The ten most commonly altered genes included TERT-promoter (69.7%), CDKN2A (45.9%), TP53 (37.8%), NF1 (35.6%), CDKN2B (33.3%), MED12 (28.9%), MTAP (27.7%), KMT2D (22.2%), PIK3CA (20.0%), PTEN (18.5%), and RB1 (18.5%); notably distinct in frequency from the breast carcinoma cohort (Table 1). Alterations in genes affecting cell cycle regulation (i.e. CDKN2A/B and TP53) were mutually exclusive from one another (p< 0.001). Several tumors harbored genomic alterations with FDA-approved indications in other tumor types were found including: NF1, PIK3CA, EGFR Exon 19/20 insertions, and BRAF V600E mutations. There were no statistically significant differences between alterations in localized/locally recurrent versus metastatic specimens.

Conclusions: In the largest genomic evaluation of localized/locally recurrent or metastatic MPTs to date, multiple clinically actionable mutations for further exploration were found. TERT-promoter was altered in the majority of cases. PDL-1 was expressed in over 1/3 of cases suggesting that clinical investigation of immunotherapeutic strategies is warranted. Routine sequencing of metastatic MPT may provide additional information to guide treatment decisions and clinical trial enrollment.

Table 1. Frequency of Genomic Alterations identified in 135 cases of Malignant Phyllodes Tumors.

Citation Format: Laura H. Rosenberger, Richard F. Riedel, Natalie A. Danziger, Ethan Sokol, Jeffrey S. Ross, Sarah L. Sammons. Genomic Evaluation of Malignant Phyllodes Tumors Reveals Multiple Targetable Opportunities [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-03.

Abstract P2-23-09: Ultra-high Tumor Mutation Burden in Metastatic/Clinically Advanced Breast Cancer (MBC)

Background: High (HTMB) tumor mutation burden (TMB) defined as ≥10 mutations/megabase (Mb) identifies breast cancer patients who could benefit from pembrolizumab. The higher the TMB the greater the likelihood of benefit. The goal of this analysis was to determine the frequency and genomic landscape of MBC with ultra-high TMB (UHTMB) defined as a TMB > 20 mutations/Mb. Design 2,049 MBC patients (pts) underwent hybrid capture based comprehensive genomic profiling for genomic alterations (GA) in at least 324 genes including determination of TMB to guide therapy decisions using the FoundationOne®CDx assay. ER, PR and HER2 expression were abstracted from submitted pathology reports. Results: 165 of 2049 MBC (8.1%) had HTMB > 10 mutations/Mb, among these 45 (2.2% of all cases) had UHTMB. When compared with the 2,004 non-UHTMB MBC pts with TMB < 20 mutations/Mb, the 45 UHTMB pts were older (mean 64.6 yrs vs 58.2 yrs; p<.0001), more often had lobular histology (40.00% vs 14.5%; p<.0001) and ER+ disease (86.6% vs 70.0%), had higher average driver GA/tumor (9.84 vs 5.7; p<.0001), and less often had TNBC (13.3% vs 27.0%; p=.041) compared to non-UHTMB high cancers. There were no significant differences in ancestry. Mutation signature analysis revealed that APOBEC was predominant in UHTMB samples (82.5%) with a minor portion with an MMR signature (10%), however, MSI-H status was significantly higher in UHTMB high cases (11.6% vs 0.40%; p<.0001). GA more frequently identified in UHTMB cases included CDH1 (45.50% vs 14.32%; p<.0001), PIK3CA (81.80% vs 37.86%; p<.0001), CDKN2A (11.40% vs 3.19%; p=.017), ARID1A (25.00% vs 5.01%; p<.0001) and NF1 (20.50% vs 5.94%; p=.0014). PD-L1 (CD274) gene amplification (2.3% vs 1.3%) or protein expression by the Ventana SP142 assay (57.14% vs 51.10%) were not significantly different. Conclusions: UHTMB MBC is a rare but clinically important subset in breast cancer that could have high response rates to single agent pembrolizumab. This phenotype is driven by APOBEC mutagenesis, more often seen in ER+ lobular cancers, and have higher frequencies of MSI-high status and mutations in CDH1 and PIK3CA.

Citation Format: Kristina Fanucci, maryam lustberg, Neal Fischbach, Maureen Pelletier, Abirami Sivapiragasam, Prashanth Ashok Kumar, Mansi Kallem, Natalie A. Danziger, Ethan Sokol, Smruthy Sivakumar, Dean Pavlick, Jeffrey S. Ross, Lajos Pusztai. Ultra-high Tumor Mutation Burden in Metastatic/Clinically Advanced Breast Cancer (MBC) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-09.

Molecular analysis of endometrial serous carcinoma reveals distinct clinicopathologic and genomic subgroups

OBJECTIVES

Endometrial serous carcinoma (EMSC) is an aggressive variant of uterine cancer with limited therapeutic options. We sought to define distinct clinicopathologic and genomic EMSC subgroups.

METHODS

We retrospectively analyzed 2159 EMSC and 2346 endometrioid-type endometrial carcinomas (EEC) tissue specimens that had undergone comprehensive genomic profiling (CGP) via the FoundationOne CDx assay during routine clinical care. High tumor mutational burden (TMB) was defined as ≥10mut/Mb using the FDA-approved CDx cutoff for pembrolizumab. Microsatellite instability (MSI) was determined on 95 loci. Evidence of homologous recombination deficiency (HRD) was determined via genomic loss of heterozygosity (gLOH), a validated HRD detection method for predicting PARP inhibitor effectiveness in ovarian carcinoma. High gLOH was defined as ≥16%.

RESULTS

A genomic analysis of 2159 EMSCs revealed a predominance of TP53 mutations, microsatellite stability, low tumor mutational burden (TMB), and recurrent alterations of PIK3CA, PPP2R1A, ERBB2, CCNE1, FBXW7 and MYC. Evidence of HRD via high gLOH was identified in 22% of EMSCs. BRCA1 and BRCA2 alterations, as well as unique SET (solid, pseudo-endometrioid, and transitional cell-like) variant morphology, were enriched in HRD-EMSC. There was an increased frequency of CCNE1 amplification, a lower prevalence of PIK3CA and PPP2R1A alterations, and no differences in HRD, MSI or TMB biomarker frequencies in patients of predicted African ancestry. EMSC exhibited distinct gene mutation frequencies and MSI, TMB and gLOH biomarker signatures compared to a cohort 2346 EEC.

CONCLUSIONS

Molecularly defined subgroups provide a framework to test the susceptibility of EMSC to targeted therapies in specific genetic settings (e.g. HRD, PIK3CA, PPP2R1A, ERBB2, MYC, CCNE1).

Abstract B091: Vulvar squamous cell carcinoma: Comprehensive genomic profiling of HPV(+) versus HPV(–) forms reveals a different set of potentially actionable biomarkers

Introduction: One major form of vulvar squamous cell carcinoma (vSCC) is associated with detectable high-risk strains of human papillomavirus (hrHPV) and is often accompanied by usual-type vulvar intraepithelial neoplasia (VIN). The second major form of vSCC is often associated with chronic dystrophic or inflammatory lesions in postmenopausal women, does not harbor detectable HPV infection, and is often preceded by p53-mutant differentiated VIN. While studies have examined the two subtypes, no large-scale genomic study has been performed to our knowledge. We sought to assess the genomics of a large cohort of aggressive vSCCs, with an aim to identify distinct mutational signatures based on the presence or absence of hrHPV genome reads. Methods: 280 vSCC were tested by hybridization capture of up to 406 cancer-related genes evaluated for base substitutions, small indels, amplification (amp), and rearrangements. HPV genome sequences were detected by de novo assembly of non-human sequencing reads and BLASTn comparison against all viral nucleotide sequences in the NCBI RefSeq database. Tumor mutational burden (TMB, mutations/Mb) was determined on ~1.1 Mbp of sequenced DNA. PD-L1 status was determined by IHC (Dako 22C3), with ≥50% tumor proportion score defined as high positive. Results: 102/280 vSCCs contained hrHPV sequences. Of these, 90 were HPV-16, 7 HPV-18, 1 HPV-31, 3 HPV-33, 1 HPV-58, and 1 HPV-67. Patients were significantly younger in the HPV(+) group (median 59 v. 64 years, p=0.001). Compared with the HPV(–) cohort, HPV(+) cases showed significantly more pathogenic genomic alterations (GA) in PIK3CA (31% vs. 17%, p=0.004), PTEN (14% vs. 2%, p<0.0001), EP300 (14% vs. 1%, p<0.0001), STK11 (14% vs. 1%, p<0.0001), AR (5% vs. 0%, p=0.006), and FBXW7 (10% vs. 3%, p=0.03). In contrast, HPV(–) cases showed significantly more alterations in TP53 (82% vs. 3%, p<0.0001), TERTp (71% vs. 8%, p<0.0001), CDKN2A (55% vs. 2%, p<0.0001), CCND1 (23% vs. 2%, p<0.0001), FAT1 (25% vs. 4%, p<0.0001), NOTCH1 (19% vs. 6%, p=0.002), and EGFR (amp: 12% vs. 0%, p<0.0001), as well as a higher rate of 9p24.1 (PDL1/PDL2) amp (7% vs. 1%) and PD-L1 IHC high-positive tumor staining (33% vs. 9%, p=0.04). Differences in alterations were observed between known primary and metastatic sites in cases with similar HPV status but did not reach significance (table). HPV(+)HPV(–) PrimaryMetastasisPrimaryMetastasis # of cases504112442 Age (range)58 (36-81)60 (29-83)64 (25-89)63 (45-89) Median TMB (range)5.2 (0-18.3)6.1 (0-47.8)3.5 (0-90.5)5.0 (0-13) PIK3CA GA26%37%17%17% PTEN GA18%10%2%2% STK11 GA10%22%1%2% FBXW7 GA10%10%5%0% TP53 GA0%5%82%81% TERTp GA6%10%73%64% CDKN2A GA0%5%55%52% CCND1 GA2%2%20%29% EGFR amp0%0%12%14% CD274(PD-L1) amp*0%0%6%10% PD-L1 IHC high*8%11%30%33% TMB >10*6%24%3%19%

Conclusions: vSCCs show significant differences in molecular profile based on HPV status. 63% of metastatic HPV(+) cases (54% overall) have a potentially actionable alteration in the PI3K/mTOR pathway, and 42% of metastatic HPV(–) cases (39% overall) have at least one potential predictive biomarker* for response to immunotherapy. Our findings provide compelling rationale for tandem comprehensive genomic profiling and HPV assessment of advanced vulvar SCCs to more fully inform therapeutic options and stratification in clinical trials.

Citation Format: Erik A Williams, Adrienne J Werth, Meagan Montesion, Ethan S Sokol, Dean C Pavlick, Nikunj A Shah, Jo-Anne Vergilio, Natalie A Danziger, Jonathan K Killian, Douglas A Lin, Vincent A Miller, Jeffrey S Ross, Julia A Elvin. Vulvar squamous cell carcinoma: Comprehensive genomic profiling of HPV(+) versus HPV(–) forms reveals a different set of potentially actionable biomarkers [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B091. doi:10.1158/1535-7163.TARG-19-B091