APOBEC3 mutagenesis drives therapy resistance in breast cancer

Acquired genetic alterations commonly drive resistance to endocrine and targeted therapies in metastatic breast cancer 1-7 , however the underlying processes engendering these diverse alterations are largely uncharacterized. To identify the mutational processes operant in breast cancer and their impact on clinical outcomes, we utilized a well-annotated cohort of 3,880 patient samples with paired tumor-normal sequencing data. The mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) enzymes were highly prevalent and enriched in post-treatment compared to treatment-naïve hormone receptor-positive (HR+) cancers. APOBEC3 mutational signatures were independently associated with shorter progression-free survival on antiestrogen plus CDK4/6 inhibitor combination therapy in patients with HR+ metastatic breast cancer. Whole genome sequencing (WGS) of breast cancer models and selected paired primary-metastatic samples demonstrated that active APOBEC3 mutagenesis promoted resistance to both endocrine and targeted therapies through characteristic alterations such as RB1 loss-of-function mutations. Evidence of APOBEC3 activity in pre-treatment samples illustrated a pervasive role for this mutational process in breast cancer evolution. The study reveals APOBEC3 mutagenesis to be a frequent mediator of therapy resistance in breast cancer and highlights its potential as a biomarker and target for overcoming resistance.

Post-therapy emergence of an NBN reversion mutation in a patient with pancreatic acinar cell carcinoma

Pancreatic acinar cell carcinoma (PACC) is a rare form of pancreatic cancer that commonly harbors targetable alterations, including activating fusions in the MAPK pathway and loss-of-function (LOF) alterations in DNA damage response/homologous recombination DNA repair-related genes. Here, we describe a patient with PACC harboring both somatic biallelic LOF of NBN and an activating NTRK1 fusion. Upon disease progression following 13 months of treatment with folinic acid, fluorouracil, irinotecan, and oxaliplatin (FOLFIRINOX), genomic analysis of a metastatic liver biopsy revealed the emergence of a novel reversion mutation restoring the reading frame of NBN. To our knowledge, genomic reversion of NBN has not been previously reported as a resistance mechanism in any tumor type. The patient was treated with, but did not respond to, targeted treatment with a selective NTRK inhibitor. This case highlights the complex but highly actionable genomic landscape of PACC and underlines the value of genomic profiling of rare tumor types such as PACC.

Mesonephric and mesonephric-like adenocarcinomas of gynecologic origin: A single-center experience with molecular characterization, treatment, and oncologic outcomes

OBJECTIVES

Mesonephric (MA) and mesonephric-like (MLA) adenocarcinomas are rare cancers, and data on clinical behavior and response to therapy are limited. We sought to report molecular features, treatment, and outcomes of MA/MLA from a single institution.

METHODS

Patients with MA (cervix) or MLA (uterus, ovary, other) treated at Memorial Sloan Kettering Cancer Center (MSK) from 1/2008-12/2021 underwent pathologic re-review. For patients with initial treatment at MSK, progression-free survival (PFS1) was calculated as time from initial surgery to progression or death; second PFS (PFS2) was calculated as time from start of treatment for recurrence to subsequent progression or death. Overall survival (OS) was calculated for all patients. Images were retrospectively reviewed to determine treatment response. Somatic genetic alterations were assessed by clinical tumor-normal sequencing (MSK-Integrated Mutation Profiling of Actionable Cancer Targets [MSK-IMPACT]).

RESULTS

Of 81 patients with confirmed gynecologic MA/MLA, 36 received initial treatment at MSK. Sites of origin included cervix (n = 9, 11%), uterus (n = 42, 52%), ovary (n = 28, 35%), and other (n = 2, 2%). Of the 36 patients who received initial treatment at MSK, 20 (56%) recurred; median PFS1 was 33 months (95% CI: 17-not evaluable), median PFS2 was 8.3 months (95% CI: 6.9-14), and median OS was 87 months (95% CI: 58.2-not evaluable). Twenty-six of the 36 patients underwent MSK-IMPACT testing, and 25 (96%) harbored MAPK pathway alterations.

CONCLUSION

Most patients diagnosed with early-stage disease ultimately recurred. Somatic MAPK signaling pathway mutations appear to be highly prevalent in MA/MLA, and therapeutics that target this pathway are worthy of further study.

DNA Methylation Profiling Enables Accurate Classification of Nonductal Primary Pancreatic Neoplasms

BACKGROUND & AIMS

Cytologic and histopathologic diagnosis of non-ductal pancreatic neoplasms can be challenging in daily clinical practice, whereas it is crucial for therapy and prognosis. The cancer methylome is successfully used as a diagnostic tool in other cancer entities. Here, we investigate if methylation profiling can improve the diagnostic work-up of pancreatic neoplasms.

METHODS

DNA methylation data were obtained for 301 primary tumors spanning 6 primary pancreatic neoplasms and 20 normal pancreas controls. Neural Network, Random Forest, and extreme gradient boosting machine learning models were trained to distinguish between tumor types. Methylation data of 29 nonpancreatic neoplasms (n = 3708) were used to develop an algorithm capable of detecting neoplasms of non-pancreatic origin.

RESULTS

After benchmarking 3 state-of-the-art machine learning models, the random forest model emerged as the best classifier with 96.9% accuracy. All classifications received a probability score reflecting the confidence of the prediction. Increasing the score threshold improved the random forest classifier performance up to 100% with 87% of samples with scores surpassing the cutoff. Using a logistic regression model, detection of nonpancreatic neoplasms achieved an area under the curve of >0.99. Analysis of biopsy specimens showed concordant classification with their paired resection sample.

CONCLUSIONS

Pancreatic neoplasms can be classified with high accuracy based on DNA methylation signatures. Additionally, non-pancreatic neoplasms are identified with near perfect precision. In summary, methylation profiling can serve as a valuable adjunct in the diagnosis of pancreatic neoplasms with minimal risk for misdiagnosis, even in the pre-operative setting.

Adenoid cystic carcinoma of the Bartholin's gland is underpinned by MYB- and MYBL1- rearrangements

OBJECTIVE

Adenoid cystic carcinoma (AdCC) of the Bartholin's gland (AdCC-BG) is a very rare gynecologic vulvar malignancy. AdCC-BGs are slow-growing but locally aggressive and are associated with high recurrence rates. Here we sought to characterize the molecular underpinning of AdCC-BGs.

METHODS

AdCC-BGs (n = 6) were subjected to a combination of RNA-sequencing, targeted DNA-sequencing, reverse-transcription PCR, fluorescence in situ hybridization (FISH) and MYB immunohistochemistry (IHC). Clinicopathologic variables, somatic mutations, copy number alterations and chimeric transcripts were assessed.

RESULTS

All six AdCC-BGs were biphasic, composed of ductal and myoepithelial cells. Akin to salivary gland and breast AdCCs, three AdCC-BGs had the MYB::NFIB fusion gene with varying breakpoints, all of which were associated with MYB overexpression by IHC. Two AdCC-BGs were underpinned by MYBL1 fusion genes with different gene partners, including MYBL1::RAD51B and MYBL1::EWSR1 gene fusions, and showed MYB protein expression. Although the final AdCC-BG studied had MYB protein overexpression, no gene fusion was identified. AdCC-BGs harbored few additional somatic genetic alterations, and only few mutations in cancer-related genes were identified, including GNAQ, GNAS, KDM6A, AKT1 and BCL2, none of which were recurrent. Two AdCC-BGs, both with a MYB::NFIB fusion gene, developed metastatic disease.

CONCLUSIONS

AdCC-BGs constitute a convergent phenotype, whereby activation of MYB or MYBL1 can be driven by the MYB::NFIB fusion gene or MYBL1 rearrangements. Our observations further support the notion that AdCCs, irrespective of organ site, constitute a genotypic-phenotypic correlation. Assessment of MYB or MYBL1 rearrangements may be used as an ancillary marker for the diagnosis of AdCC-BGs.

Pathogenic germline variants in patients with endometrial cancer of diverse ancestry

BACKGROUND

Racial disparities in outcomes exist in endometrial cancer (EC). The contribution of ancestry-based variations in germline pathogenic variants (gPVs) is unknown.

METHODS

Germline assessment of ≥76 cancer predisposition genes was performed in patients with EC undergoing tumor-normal Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets sequencing from January 1, 2015 through June 30, 2021. Self-reported race/ethnicity and Ashkenazi Jewish ancestry data classified patients into groups. Genetic ancestry was inferred from Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets. Rates of gPV and genetic counseling were compared by ancestry.

RESULTS

Among 1625 patients with EC, 216 (13%) had gPVs; 15 had >1 gPV. Rates of gPV varied by self-reported ancestry (Ashkenazi Jewish, 40/202 [20%]; Asian, 15/124 [12%]; Black/African American (AA), 12/171 [7.0%]; Hispanic, 15/124 [12%]; non-Hispanic (NH) White, 129/927 [14%]; missing, 5/77 [6.5%]; p = .009], with similar findings by genetic ancestry (p < .001). We observed a lower likelihood of gPVs in patients of Black/AA (odds ratio [OR], 0.44; 95% CI, 0.22-0.81) and African (AFR) ancestry (OR, 0.42; 95% CI, 0.18-0.85) and a higher likelihood in patients of Ashkenazi Jewish genetic ancestry (OR, 1.62; 95% CI; 1.11-2.34) compared with patients of non-Hispanic White/European ancestry, even after adjustment for age and molecular subtype. Somatic landscape influenced gPVs with lower rates of microsatellite instability-high tumors in patients of Black/AA and AFR ancestry. Among those with newly identified gPVs (n = 114), 102 (89%) were seen for genetic counseling, with lowest rates among Black/AA (75%) and AFR patients (67%).

CONCLUSIONS

In those with EC, gPV and genetic counseling varied by ancestry, with lowest rates among Black/AA and AFR patients, potentially contributing to disparities in outcomes given implications for treatment and cancer prevention.

PLAIN LANGUAGE SUMMARY

Black women with endometrial cancer do worse than White women, and there are many reasons for this disparity. Certain genetic changes from birth (mutations) can increase the risk of cancer, and it is unknown if rates of these changes are different between different ancestry groups. Genetic mutations in 1625 diverse women with endometrial cancer were studied and the lowest rates of mutations and genetic counseling were found in Black and African ancestry women. This could affect their treatment options as well as their families and may make disparities worse.

Genomic and epigenomic basis of breast invasive lobular carcinomas lacking CDH1 genetic alterations

CDH1 (E-cadherin) bi-allelic inactivation is the hallmark alteration of breast invasive lobular carcinoma (ILC), resulting in its discohesive phenotype. A subset of ILCs, however, lack CDH1 genetic/epigenetic inactivation, and their genetic underpinning is unknown. Through clinical targeted sequencing data reanalysis of 364 primary ILCs, we identified 25 ILCs lacking CDH1 bi-allelic genetic alterations. CDH1 promoter methylation was frequent (63%) in these cases. Targeted sequencing reanalysis revealed 3 ILCs harboring AXIN2 deleterious fusions (n = 2) or loss-of-function mutation (n = 1). Whole-genome sequencing of 3 cases lacking bi-allelic CDH1 genetic/epigenetic inactivation confirmed the AXIN2 mutation and no other cell-cell adhesion genetic alterations but revealed a new CTNND1 (p120) deleterious fusion. AXIN2 knock-out in MCF7 cells resulted in lobular-like features, including increased cellular migration and resistance to anoikis. Taken together, ILCs lacking CDH1 genetic/epigenetic alterations are driven by inactivating alterations in other cell adhesion genes (CTNND1 or AXIN2), endorsing a convergent phenotype in ILC.

Uterine washings as a novel method for early detection of ovarian cancer: Trials and tribulations

Given the tubal origin of high-grade serous ovarian cancer (HGSC), we sought to investigate intrauterine lavage (IUL) as a novel method of biomarker detection. IUL and serum samples were collected from patients with HGSC or benign pathology. Although CA-125 and HE4 concentrations were significantly higher in IUL samples compared to serum, they were similar between IUL samples from patients with HGSC vs benign conditions. In contrast, CA-125 and HE4 serum concentrations differed between HGSC and benign pathology (P =.002 for both). IUL and tumor samples from patients with HGSC were subjected to targeted panel sequencing and droplet digital PCR (ddPCR). Tumor mutations were found in 75 % of matched IUL samples. Serum CA-125 and HE4 biomarker levels allowed for better differentiation of HGSC and benign pathology compared to IUL samples. We believe using IUL for early detection of HGSC requires optimization, and current strategies should focus on prevention until early detection strategies improve.

Nonlobular Invasive Breast Carcinomas with Biallelic Pathogenic CDH1 Somatic Alterations: A Histologic, Immunophenotypic, and Genomic Characterization

CDH1 encodes for E-cadherin, and its loss of function is the hallmark of invasive lobular carcinoma (ILC). Albeit vanishingly rare, biallelic CDH1 alterations may be found in nonlobular breast carcinomas (NL-BCs). We sought to determine the clinicopathologic characteristics and repertoire of genetic alterations of NL-BCs harboring CDH1 biallelic genetic alterations. Analysis of 5842 breast cancers (BCs) subjected to clinical tumor-normal sequencing with an FDA-cleared multigene panel was conducted to identify BCs with biallelic CDH1 pathogenic/likely pathogenic somatic mutations lacking lobular features. The genomic profiles of NL-BCs with CDH1 biallelic genetic alterations were compared with those of ILCs and invasive ductal carcinomas (IDCs), matched by clinicopathologic characteristics. Of the 896 CDH1-altered BCs, 889 samples were excluded based on the diagnosis of invasive mixed ductal/lobular carcinoma or ILC or the detection of monoallelic CDH1 alterations. Only 7 of the 5842 (0.11%) BCs harbored biallelic CDH1 alterations and lacked lobular features. Of these, 4/7 (57%) cases were ER-positive/HER2-negative, 1/7 (14%) was ER-positive/HER2-positive, and 2/7 (29%) were ER-negative/HER2-negative. In total, 5/7 (71%) were of Nottingham grade 2, and 2/7 (29%) were of grade 3. The NL-BCs with CDH1 biallelic genetic alterations included a mucinous carcinoma (n = 1), IDCs with focal nested growth (n = 2), IDC with solid papillary (n = 1) or apocrine (n = 2) features, and an IDC of no special type (NST; n = 1). E-cadherin expression, as detected by immunohistochemistry, was absent (3/5) or aberrant (discontinuous membranous/cytoplasmic/granular; 2/5). However, NL-BCs with CDH1 biallelic genetic alterations displayed recurrent genetic alterations, including TP53, PIK3CA (57%, 4/7; each), FGFR1, and NCOR1 (28%, 2/7, each) alterations. Compared with CDH1 wild-type IDC-NSTs, NL-BCs less frequently harbored GATA3 mutations (0% vs 47%, P = .03), but no significant differences were detected when compared with matched ILCs. Therefore, NL-BCs with CDH1 biallelic genetic alterations are vanishingly rare, predominantly comprise IDCs with special histologic features, and have genomic features akin to luminal B ER-positive BCs.

Pathogenic germline variants in non-BRCA1/2 homologous recombination genes in ovarian cancer: Analysis of tumor phenotype and survival

OBJECTIVE

To define molecular features of ovarian cancer (OC) with germline pathogenic variants (PVs) in non-BRCA homologous recombination (HR) genes and analyze survival compared to BRCA1/2 and wildtype (WT) OC.

METHODS

We included patients with OC undergoing tumor-normal sequencing (MSK-IMPACT) from 07/01/2015-12/31/2020, including germline assessment of BRCA1/2 and other HR genes ATM, BARD1, BRIP1, FANCA, FANCC, NBN, PALB2, RAD50, RAD51B, RAD51C, and RAD51D. Biallelic inactivation was assessed within tumors. Progression-free (PFS) and overall survival (OS) were calculated from pathologic diagnosis using the Kaplan-Meier method with left truncation. Whole-exome sequencing (WES) was performed in a subset.

RESULTS

Of 882 patients with OC, 56 (6.3%) had germline PVs in non-BRCA HR genes; 95 (11%) had BRCA1-associated OC (58 germline, 37 somatic); and 59 (6.7%) had BRCA2-associated OC (40 germline, 19 somatic). High rates of biallelic alterations were observed among germline PVs in BRIP1 (11/13), PALB2 (3/4), RAD51B (3/4), RAD51C (3/4), and RAD51D (8/10). In cases with WES (27/35), there was higher tumor mutational burden (TMB; median 2.5 [1.1-6.0] vs. 1.2 mut/Mb [0.6-2.6]) and enrichment of HR-deficient (HRD) mutational signatures in tumors associated with germline PALB2 and RAD51B/C/D compared with BRIP1 PVs (p < 0.01). Other features of HRD, including telomeric-allelic imbalance (TAI) and large-scale state transitions (LSTs), were similar. Although there was heterogeneity in PFS/OS by gene group, only BRCA1/2-associated OC had improved survival compared to WT OC (p < 0.01).

CONCLUSIONS

OCs associated with germline PVs in non-BRCA HR genes represent a heterogenous group, with PALB2 and RAD51B/C/D associated with an HRD phenotype.

The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance

In this study, the impact of the apolipoprotein B mRNA-editing catalytic subunit-like (APOBEC) enzyme APOBEC3B (A3B) on epidermal growth factor receptor (EGFR)-driven lung cancer was assessed. A3B expression in EGFR mutant (EGFRmut) non-small-cell lung cancer (NSCLC) mouse models constrained tumorigenesis, while A3B expression in tumors treated with EGFR-targeted cancer therapy was associated with treatment resistance. Analyses of human NSCLC models treated with EGFR-targeted therapy showed upregulation of A3B and revealed therapy-induced activation of nuclear factor kappa B (NF-κB) as an inducer of A3B expression. Significantly reduced viability was observed with A3B deficiency, and A3B was required for the enrichment of APOBEC mutation signatures, in targeted therapy-treated human NSCLC preclinical models. Upregulation of A3B was confirmed in patients with NSCLC treated with EGFR-targeted therapy. This study uncovers the multifaceted roles of A3B in NSCLC and identifies A3B as a potential target for more durable responses to targeted cancer therapy.

KIT genetic alterations in breast cancer

AIMS

Activating somatic mutations or gene amplification of KIT result in constitutive activation of its receptor tyrosine kinase, which is targetable in various solid tumours. Here, we sought to investigate the presence of KIT genetic alterations in breast cancer (BC) and characterise the histological and genomic features of these tumours.

METHODS

A retrospective analysis of 5,575 BCs previously subjected to targeted sequencing using the FDA-authorised Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Targets (MSK-IMPACT) assay was performed to identify BCs with KIT alterations. A histological assessment of KIT-altered BCs was conducted, and their repertoire of genetic alterations was compared with that of BCs lacking KIT genetic alterations, matched for age, histological type, oestrogen receptor/HER2 status and sample type.

RESULTS

We identified 18 BCs (0.32%), including 9 primary and 9 metastatic BCs, with oncogenic/likely oncogenic genetic alterations affecting KIT, including activating somatic mutations (n=4) or gene amplification (n=14). All KIT-altered BCs were of high histological grade, although no distinctive histological features were observed. When compared with BCs lacking KIT genetic alterations, no distinctive genetic features were identified. In two metastatic KIT-altered BCs in which the matched primary BC had also been analysed by MSK-IMPACT, the KIT mutations were found to be restricted to the metastatic samples, suggesting that they were late events in the evolution of these cancers.

CONCLUSIONS

KIT genetic alterations are vanishingly rare in BC. KIT-altered BCs are of high grade but lack distinctive histological features. Genetic alterations in KIT might be late events in the evolution and/or progression of BC.

TERT promoter mutations and gene amplification in endometrial cancer

OBJECTIVE

To assess the clinicopathologic, molecular profiles, and survival outcomes of patients with endometrial carcinomas (ECs) harboring telomerase reverse transcriptase (TERT) hotspot mutations or gene amplification.

METHODS

ECs harboring somatic TERT promoter hotspot mutations or gene amplification (TERT-altered) were identified from 1944 ECs that underwent clinical tumor-normal sequencing from 08/2016-12/2021. Clinicopathologic variables, somatic mutation profiles, and survival outcomes of TERT-alt and TERT-wild-type EC were assessed.

RESULTS

We identified 66 TERT-altered ECs (43 TERT-mutated and 23 TERT-amplified), representing 3% of the unselected ECs across histologic subtypes. Most TERT-altered ECs were of copy number (CN)-high/TP53abn molecular subtype (n = 40, 60%), followed by microsatellite-unstable (MSI-H) or CN-low/no specific molecular profile (NSMP)(n = 13, 20% each). TERT-amplified and TERT-mutated ECs were molecularly distinct, with TERT-amplified ECs being more genomically instable and more frequently harboring TP53 and PPP2R1A alterations (q < 0.1). Compared to TERT-wild-type ECs, TERT-altered ECs were more commonly of CN-H/TP53abn molecular subtype (31% vs 57%, p = 0.001), serous histology (10% vs 26%, p = 0.004), and were significantly enriched for TP53, CDKN2A/B, and DROSHA somatic genetic alterations (q < 0.1). Median progression-free survival was 18.7 months (95% CI 11.8-not estimable [NE]) for patients with TERT-altered EC and 80.9 months (65.8-NE) for patients with TERT-wild-type EC (HR 0.33, 95% CI 0.21-0.51, p < 0.001). Similarly, median overall survival was 46.7 months (95% CI 30-NE) for TERT-altered EC patients and not reached for TERT-wild-type EC patients (HR 0.24, 95% CI 0.13-0.44, p < 0.001).

CONCLUSION

TERT-altered ECs, although rare, are enriched for CN-high/TP53abn tumors, TP53, CDKN2A/B and DROSHA somatic mutations, and independently predict worse survival outcomes.

Histologic and genomic characterization of a primary mucinous carcinoma of the skin

Aims

Primary skin mucinous carcinoma is a rare sweat gland neoplasm with a high local recurrence rate after conventional excision but a low distant-metastasis rate. The genetic underpinning of skin mucinous carcinoma is presently unknown. Here, we sought to define whether the repertoire of somatic mutations of a primary mucinous carcinoma of the skin would be similar to that of mucinous breast carcinomas, given the histologic similarities between these tumor types.

Methods and results

The tumor was situated in the dermis and partially involved the subcutaneous fat. Tumor cells were suspended in periodic acid-Schiff diastaseresistant- positive mucin lakes and expressed cytokeratin 7, synaptophysin and estrogen receptor. DNA samples extracted from microdissected tumor and matched normal tissue were subjected to massively parallel sequencing targeting 410 cancer-related genes. The skin mucinous tumor was found to have a low tumor mutation burden, but to harbor a clonal GATA3 frameshift mutation (p. T418Hfs*89) and amplification of FOXA1, genes not uncommonly altered in breast mucinous carcinomas.

Conclusions

In this primary skin mucinous carcinoma, GATA3 and FOXA1 driver genetic events were identified, consistent with a possible developmental relationship between skin and breast mucinous neoplasms.

Genomic Profiling Reveals Germline Predisposition and Homologous Recombination Deficiency in Pancreatic Acinar Cell Carcinoma

PURPOSE

To determine the genetic predisposition underlying pancreatic acinar cell carcinoma (PACC) and characterize its genomic features.

METHODS

Both somatic and germline analyses were performed using an Food and Drug Administration-authorized matched tumor/normal sequencing assay on a clinical cohort of 28,780 patients with cancer, 49 of whom were diagnosed with PACC. For a subset of PACCs, whole-genome sequencing (WGS; n = 12) and RNA sequencing (n = 6) were performed.

RESULTS

Eighteen of 49 (36.7%) PACCs harbored germline pathogenic variants in homologous recombination (HR) and DNA damage response (DDR) genes, including BRCA1 (n = 1), BRCA2 (n = 12), PALB2 (n = 2), ATM (n = 2), and CHEK2 (n = 1). Thirty-one PACCs displayed pure, and 18 PACCs harbored mixed acinar cell histology. Fifteen of 31 (48%) pure PACCs harbored a germline pathogenic variant affecting HR-/DDR-related genes. BRCA2 germline pathogenic variants (11 of 31, 35%) were significantly more frequent in pure PACCs than in pancreatic adenocarcinoma (86 of 2,739, 3.1%; P < .001), high-grade serous ovarian carcinoma (67 of 1,318, 5.1%; P < .001), prostate cancer (116 of 3,401, 3.4%; P < .001), and breast cancer (79 of 3,196, 2.5%; P < .001). Genomic features of HR deficiency (HRD) were detected in 7 of 12 PACCs undergoing WGS, including 100% (n = 6) of PACCs with germline HR-related pathogenic mutations and 1 of 6 PACCs lacking known pathogenic alterations in HR-related genes. Exploratory analyses revealed that in PACCs, the repertoire of somatic driver genetic alterations and the load of neoantigens with high binding affinity varied according to the presence of germline pathogenic alterations affecting HR-/DDR-related genes and/or HRD.

CONCLUSION

In a large pan-cancer cohort, PACC was identified as the cancer type with the highest prevalence of both BRCA2 germline pathogenic variants and genomic features of HRD, suggesting that PACC should be considered as part of the spectrum of BRCA-related malignancies.

Molecular Characterization of Endometrial Carcinomas in Black and White Patients Reveals Disparate Drivers with Therapeutic Implications

Although the incidence of endometrial carcinoma (EC) is similar in Black and White women, racial disparities are stark, with the highest mortality rates observed among Black patients. Here, analysis of 1,882 prospectively sequenced ECs using a clinical FDA-authorized tumor-normal panel revealed a significantly higher prevalence of high-risk histologic and molecular EC subtypes in self-identified Black (n = 259) compared with White (n = 1,623) patients. Clinically actionable alterations, including high tumor mutational burden/microsatellite instability, which confer benefit from immunotherapy, were less frequent in ECs from Black than from White patients. Ultramutated POLE molecular subtype ECs associated with favorable outcomes were rare in Black patients. Results were confirmed by genetic ancestry analysis. CCNE1 gene amplification, which is associated with aggressive clinical behavior, was more prevalent in carcinosarcomas occurring in Black than in White patients. ECs from Black and White patients display important differences in their histologic types, molecular subtypes, driver genetic alterations, and therapeutic targets.

SIGNIFICANCE

Our comprehensive analysis of prospectively clinically sequenced ECs revealed significant differences in their histologic and molecular composition and in the presence of therapeutic targets in Black versus White patients. These findings emphasize the importance of incorporating diverse populations into molecular studies and clinical trials to address EC disparities. This article is featured in Selected Articles from This Issue, p. 2293.

Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers

Homologous recombination (HR) deficiency is associated with DNA rearrangements and cytogenetic aberrations1. Paradoxically, the types of DNA rearrangements that are specifically associated with HR-deficient cancers only minimally affect chromosomal structure2. Here, to address this apparent contradiction, we combined genome-graph analysis of short-read whole-genome sequencing (WGS) profiles across thousands of tumours with deep linked-read WGS of 46 BRCA1- or BRCA2-mutant breast cancers. These data revealed a distinct class of HR-deficiency-enriched rearrangements called reciprocal pairs. Linked-read WGS showed that reciprocal pairs with identical rearrangement orientations gave rise to one of two distinct chromosomal outcomes, distinguishable only with long-molecule data. Whereas one (cis) outcome corresponded to the copying and pasting of a small segment to a distant site, a second (trans) outcome was a quasi-balanced translocation or multi-megabase inversion with substantial (10 kb) duplications at each junction. We propose an HR-independent replication-restart repair mechanism to explain the full spectrum of reciprocal pair outcomes. Linked-read WGS also identified single-strand annealing as a repair pathway that is specific to BRCA2 deficiency in human cancers. Integrating these features in a classifier improved discrimination between BRCA1- and BRCA2-deficient genomes. In conclusion, our data reveal classes of rearrangements that are specific to BRCA1 or BRCA2 deficiency as a source of cytogenetic aberrations in HR-deficient cells.

A Multiparameter Molecular Classifier to Predict Response to Neoadjuvant Lapatinib plus Trastuzumab without Chemotherapy in HER2+ Breast Cancer

PURPOSE

Clinical trials reported 25% to 30% pathologic complete response (pCR) rates in HER2+ patients with breast cancer treated with anti-HER2 therapies without chemotherapy. We hypothesize that a multiparameter classifier can identify patients with HER2-"addicted" tumors who may benefit from a chemotherapy-sparing strategy.

EXPERIMENTAL DESIGN

Baseline HER2+ breast cancer specimens from the TBCRC023 and PAMELA trials, which included neoadjuvant treatment with lapatinib and trastuzumab, were used. In the case of estrogen receptor-positive (ER+) tumors, endocrine therapy was also administered. HER2 protein and gene amplification (ratio), HER2-enriched (HER2-E), and PIK3CA mutation status were assessed by dual gene protein assay (GPA), research-based PAM50, and targeted DNA-sequencing. GPA cutoffs and classifier of response were constructed in TBCRC023 using a decision tree algorithm, then validated in PAMELA.

RESULTS

In TBCRC023, 72 breast cancer specimens had GPA, PAM50, and sequencing data, of which 15 had pCR. Recursive partitioning identified cutoffs of HER2 ratio ≥ 4.6 and %3+ IHC staining ≥ 97.5%. With PAM50 and sequencing data, the model added HER2-E and PIK3CA wild-type (WT). For clinical implementation, the classifier was locked as HER2 ratio ≥ 4.5, %3+ IHC staining ≥ 90%, and PIK3CA-WT and HER2-E, yielding 55% and 94% positive (PPV) and negative (NPV) predictive values, respectively. Independent validation using 44 PAMELA cases with all three biomarkers yielded 47% PPV and 82% NPV. Importantly, our classifier's high NPV signifies its strength in accurately identifying patients who may not be good candidates for treatment deescalation.

CONCLUSIONS

Our multiparameter classifier differentially identifies patients who may benefit from HER2-targeted therapy alone from those who need chemotherapy and predicts pCR to anti-HER2 therapy alone comparable with chemotherapy plus dual anti-HER2 therapy in unselected patients.

Clinicopathologic and genomic features of lobular like invasive mammary carcinoma: is it a distinct entity?

This study describes "lobular-like invasive mammary carcinomas" (LLIMCas), a group of low- to intermediate-grade invasive mammary carcinomas with discohesive, diffusely infiltrative cells showing retained circumferential membranous immunoreactivity for both E-cadherin and p120. We analyzed the clinical-pathologic features of 166 LLIMCas compared to 104 classical invasive lobular carcinomas (ILCs) and 100 grade 1 and 2 invasive ductal carcinomas (IDCs). Tumor size and pT stage of LLIMCas were intermediate between IDCs and ILCs, and yet often underestimated on imaging and showed frequent positive margins on the first resection. Despite histomorphologic similarities to classical ILC, the discohesion in LLIMCa was independent of E-cadherin/p120 immunophenotypic alteration. An exploratory, hypothesis-generating analysis of the genomic features of 14 randomly selected LLIMCas and classical ILCs (7 from each category) was performed utilizing an FDA-authorized targeted capture sequencing assay (MSK-IMPACT). None of the seven LLIMCas harbored CDH1 loss-of-function mutations, and none of the CDH1 alterations detected in two of the LLIMCas was pathogenic. In contrast, all seven ILCs harbored CDH1 loss-of-function mutations coupled with the loss of heterozygosity of the CDH1 wild-type allele. Four of the six evaluable LLIMCas were positive for CDH1 promoter methylation, which may partially explain the single-cell infiltrative morphology seen in LLIMCa. Further studies are warranted to better define the molecular basis of the discohesive cellular morphology in LLIMCa. Until more data becomes available, identifying LLIMCas and distinguishing them from typical IDCs and ILCs would be justified. In patients with LLIMCas, preoperative MRI should be entertained to guide surgical management.

NR4A3 Expression Is Consistently Absent in Acinic Cell Carcinomas of the Breast: A Potential Nosologic Shift

Acinic cell carcinoma (AciCC) is a tumor that is recognized in both the breast and salivary glands. Recently, the recurrent genomic rearrangement, t(4;9)(q13;q31) was identified in salivary AciCC that results in constitutive upregulation of the nuclear transcription factor NR4A3, which can be detected by immunohistochemistry. In this study, we sought to evaluate NR4A3 expression in breast AciCC using immunohistochemistry. Strong and diffuse nuclear staining was considered a positive result. Sixteen AciCCs were studied, including 8 pure AciCCs and 8 AciCCs admixed with other types (invasive carcinoma of no special type in 5 cases and metaplastic carcinoma in 3 cases). All 16 AciCCs showed negative results for NR4A3 expression. Four cases with available material were evaluated for rearrangements of the NR4A3 gene by fluorescence in situ hybridization and no rearrangements were observed. Whole-genome sequencing of 1 AciCC revealed a TP53 splice-site mutation, high levels of genomic instability, and genomic features of homologous recombination DNA repair defects; a structural variant analysis of this case did not reveal the presence of a t(4;9) rearrangement. We conclude that breast AciCCs consistently lack NR4A3 rearrangement or overexpression, unlike most of the salivary AciCCs, and that consistent with previous results, breast AciCCs are associated with genomic alterations more similar to those seen in triple-negative breast carcinomas than salivary gland AciCCs. These results suggest that unlike other salivary gland-like tumors that occur in the breast, the molecular underpinnings of the salivary gland and breast AciCCs are different and that the salivary gland and breast AciCCs likely represent distinct entities.

Integration of clinical sequencing and immunohistochemistry for the molecular classification of endometrial carcinoma

PURPOSE

Using next generation sequencing (NGS), The Cancer Genome Atlas (TCGA) found that endometrial carcinomas (ECs) fall under one of four molecular subtypes, and a POLE mutation status, mismatch repair (MMR) and p53 immunohistochemistry (IHC)-based surrogate has been developed. We sought to retrospectively classify and characterize a large series of unselected ECs that were prospectively subjected to clinical sequencing by utilizing clinical molecular and IHC data.

EXPERIMENTAL DESIGN

All patients with EC with clinical tumor-normal MSK-IMPACT NGS from 2014 to 2020 (n = 2115) were classified by integrating molecular data (i.e., POLE mutation, TP53 mutation, MSIsensor score) and MMR and p53 IHC results. Survival analysis was performed for primary EC patients with upfront surgery at our institution.

RESULTS

Utilizing our integrated approach, significantly more ECs were molecularly classified (1834/2115, 87%) as compared to the surrogate (1387/2115, 66%, p < 0.001), with an almost perfect agreement for classifiable cases (Kappa 0.962, 95% CI 0.949-0.975). Discrepancies were primarily due to TP53 mutations in p53-IHC-normal ECs. Of the 1834 ECs, most were of copy number (CN)-high molecular subtype (40%), followed by CN-low (32%), MSI-high (23%) and POLE (5%). Histologic and genomic variability was present amongst all molecular subtypes. Molecular classification was prognostic in early- and advanced-stage disease, including early-stage endometrioid EC.

CONCLUSIONS

The integration of clinical NGS and IHC data allows for an algorithmic approach to molecularly classifying newly diagnosed EC, while overcoming issues of IHC-based genetic alteration detection. Such integrated approach will be important moving forward given the prognostic and potentially predictive information afforded by this classification.

Comprehensive analysis of germline drivers in endometrial cancer

BACKGROUND

We sought to determine the prevalence of germline pathogenic variants (gPVs) in unselected patients with endometrial cancer (EC), define biallelic gPVs within tumors, and describe their associations with clinicopathologic features.

METHODS

Germline assessment of at least 76 cancer predisposition genes was performed in patients with EC undergoing clinical tumor-normal Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing from January 1, 2015, to June 30, 2021. In patients with gPVs, biallelic alterations in ECs were identified through analysis of loss of heterozygosity and somatic PVs. Clinicopathologic variables were compared using nonparametric tests.

RESULTS

Of 1625 patients with EC, 216 (13%) had gPVs, and 15 patients had 2 gPVs. There were 231 gPVs in 35 genes (75 [32%] high penetrance; 39 [17%] moderate penetrance; and 117 [51%] low, recessive, or uncertain penetrance). Compared with those without gPVs, patients with gPVs were younger (P = .002), more often White (P = .009), and less obese (P = .025) and had differences in distribution of tumor histology (P = .017) and molecular subtype (P < .001). Among 231 gPVs, 74 (32%) exhibited biallelic inactivation within tumors. For high-penetrance gPVs, 63% (47 of 75) of ECs had biallelic alterations, primarily affecting mismatch repair (MMR) and homologous recombination related genes, including BRCA1,BRCA2, RAD51D, and PALB2. Biallelic inactivation varied across molecular subtypes with highest rates in microsatellite instability-high (MSI-H) or copy-number (CN)-high subtypes (3 of 12 [25%] POLE, 30 of 77 [39%] MSI-H, 27 of 60 [45%] CN-high, 9 of 57 [16%] CN-low; P < .001).

CONCLUSIONS

Of unselected patients with EC, 13% had gPVs, with 63% of gPVs in high-penetrance genes (MMR and homologous recombination) exhibiting biallelic inactivation, potentially driving cancer development. This supports germline assessment in EC given implications for treatment and cancer prevention.

Detection of Biallelic Loss of DNA Repair Genes in Formalin-Fixed, Paraffin-Embedded Tumor Samples Using a Novel Tumor-Only Sequencing Panel

Patient selection for synthetic lethal-based cancer therapy may be improved by assessment of gene-specific loss of heterozygosity (LOH) and biallelic loss of function (LOF). This report describes SyNthetic lethal Interactions for Precision Diagnostics (SNiPDx), a targeted next-generation sequencing (NGS) panel for detection of LOH and biallelic LOF alterations in 26 target genes focused on DNA damage response pathways, in tumor-only formalin-fixed, paraffin-embedded (FFPE) samples. NGS was performed across all exons of these 26 genes and encompassed a total of 7632 genome-wide single-nucleotide polymorphisms on genomic DNA from 80 FFPE solid tumor samples. The Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing algorithm was optimized to assess tumor purity and copy number based on heterozygous single-nucleotide polymorphisms. SNiPDx demonstrated high sensitivity (95%) and specificity (91%) for LOH detection compared with whole genome sequencing. Positive agreement with local NGS-based testing in the detection of genetic alterations was 95%. SNiPDx detected 93% of biallelic ATM LOF mutations, 100% of ATM single-nucleotide variants and small insertions/deletions, and 100% of all ATM LOH status events identified by orthogonal NGS-based testing. SNiPDx is a novel, clinically feasible test for analysis of allelic status in FFPE tumor samples, which demonstrated high accuracy when compared with other NGS-based approaches in clinical use.

Dramatic, durable response to therapy in gBRCA2-mutated pancreas neuroendocrine carcinoma: opportunity and challenge

Poorly differentiated pancreatic neuroendocrine tumors (PDNEC), are a subtype of pancreatic cancer encompassing both small cell and large cell neuroendocrine carcinoma subtypes, and are characterized as distinct in terms of biology and prognosis compared to the more common pancreatic adenocarcinoma. Until recently, there has been a paucity of data on the genomic features of this cancer type. We describe a male patient diagnosed with PDNEC and extensive metastatic disease in the liver at diagnosis. Genomic analysis demonstrated a germline pathogenic variant in BRCA2 with somatic loss-of-heterozygosity of the BRCA2 wild-type allele. Following a favorable response to platinum-based chemotherapy (and the addition of immunotherapy), the patient received maintenance therapy with olaparib, which resulted in a further reduction on follow-up imaging (Fig. 1). After seventeen months of systemic control with olaparib, the patient developed symptomatic central nervous system metastases, which harboured a BRCA2 reversion mutation. No other sites of disease progression were observed. Herein, we report an exceptional outcome through the incorporation of a personalized management approach for a patient with a pancreatic PDNEC, guided by comprehensive genomic sequencing.

Abstract 4284: Enhancing subclonal reconstruction algorithm for resolving complex tumor phylogenies from multi-sample tumor DNA sequencing

Cancer is characterized by the ongoing accumulation of somatic mutations, providing selective advantages that may lead to dysregulated cellular proliferation. While the cancer genome at diagnosis has been extensively studied, many cancer types still lack strong prognostic biomarkers. The continuous acquisition and selection for driver mutations in a population of cancer cells acts as a Darwinian process, resulting in clonal expansions of progressively more aberrant and fit phenotypes. Reconstructing tumor evolution allows us to understand key events that drive cancer progression and patterns of mutation co-occurrence within clones. These evolutionary features guide our understanding of fundamental mechanisms that lead to disease lethality. Inferring tumor evolution from DNA sequencing data is becoming part of routine analysis in cancer research. As sequencing costs drop, sequencing multiple tumor samples from a patient becomes routine. These multiple samples can represent different spatial regions of a tumor, longitudinal samples from a single region or a combination of both. This provides an opportunity to study tumor evolution in much greater detail and accuracy than was previously feasible through single-sample datasets. The most widely used methods to reconstruct the subclonal evolution of a tumor utilize stochastic-search algorithms. These approaches iterate through a parameter space to select phylogenetic solutions that maximize the likelihood of observed sequencing data. They are optimized for low complexity cases, where the size and number or subclones are relatively limited. As tumor subclonal structure increases in complexity, the parameter space grows exponentially, and stochastic-search algorithms become computationally intractable. For instance, recent benchmarking studies have revealed that many methods fail to reconstruct clone trees for data with as few as ten subclones. To circumvent current computational limitations, we developed a deterministic algorithm for subclonal reconstruction that leverages fundamental principles of cancer biology to encode heuristics that reduce the solution space to biologically plausible phylogenies. When applied to samples (4-36 tumors; median 16) from 12 patients with metastatic breast cancer, our method reduced the average runtime ten-fold. We were able to delineate the evolutionary history of up to 57 distinct subclones per patient, which is infeasible with most current methods. Benchmarking using methods developed for the SMCHet DREAM challenge on real and simulated datasets further quantifies the accuracy, resolution, and scalability. We have thus presented a novel method for rapid and optimized reconstruction of tumor evolutionary histories.

Citation Format: Helena Winata, Daniel Knight, Juber A. Patel, Nicholas K. Wang, Pier Selenica, Stefan E. Eng, Caroline Kostrzewa, Jaron Arbet, Yingjie Zhu, Ronglai Shen, Jorge Reis-Filho, Pedram Razafi, Paul C. Boutros. Enhancing subclonal reconstruction algorithm for resolving complex tumor phylogenies from multi-sample tumor DNA sequencing. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4284.

Abstract 3375: Ultrasensitive ctDNA minimal residual disease monitoring in early NSCLC with PhasED-Seq

Background: Circulating tumor DNA (ctDNA) minimal residual disease (MRD) detection is a promising approach for personalization of adjuvant therapy in non-small cell lung cancer (NSCLC). First generation ctDNA MRD assays that employ tumor-informed approaches to track single nucleotide variants (SNVs) have limits of detection (LOD95) of ~1E-4 and have high positive predictive values for recurrence. However, they have suboptimal clinical sensitivity, with false negative results at the completion of therapy in most patients who will ultimately recur. PhasED-Seq is a novel ctDNA MRD method that tracks multiple “phased” variants (PVs) within individual DNA fragments with a LOD95 ~100-fold better than first generation assays. Here we report PhasED-Seq ctDNA MRD results for the first prospective cohort of early stage NSCLC patients.

Methods: Tumor tissues (n=46), PBMCs (n=46) and plasma samples (n=169) from 46 Stage I-III NSCLC patients treated with curative intent were prospectively collected at Memorial Sloan Kettering Cancer Center. All patients underwent resection and received neoadjuvant +/- adjuvant therapy (n=14), adjuvant therapy only (n=17), or neither (n=15). Samples were analyzed in Foresight Diagnostics' CLIA laboratory (Aurora, CO) using personalized PhasED-Seq. Briefly, PVs were identified via whole genome sequencing of tumors and matched blood germline DNA. Custom capture panels targeting PVs were synthesized and used to assess MRD status in pre-, on- and post-treatment plasma samples. Detection of ctDNA MRD was assessed at a post-treatment landmark, defined as the first post-therapy sample or when not available the last post-surgical sample taken during therapy. To enable comparisons, the same plasma samples were analyzed using an SNV-based ctDNA MRD approach.

Results: PVs were identified in tumor tissue from all 46 patients. Across all plasma samples PhasED-Seq achieved a median LOD95 of 1.3E-6 and as low as 2.5E-7. Of 74 plasma samples with detectable ctDNA, 38 (51%) contained concentrations below 1E-4 and the lowest level of ctDNA MRD detected was 1.7E-7. For post-treatment landmark samples (n=45), the median time from end of therapy was 2 months. Cancer recurred in all patients (n=10) with detectable MRD at the landmark. Furthermore, PhasED-Seq better stratified freedom from recurrence (log-rank p=3E-8, Cox HR=10.8) than the SNV-based approach (log-rank p=0.08, Cox HR=2.5) and detected MRD at the landmark in more patients who ultimately recurred (56% vs 28%). PhasED-Seq also achieved longer lead times, including detecting MRD in 66% of samples collected 12 to 24 months prior to recurrence versus only 33% using SNV-based monitoring.

Conclusion: PhasED-Seq achieves ctDNA detection below 1 part per million and appears to be significantly more sensitive than SNV-based MRD monitoring. These results suggest that PhasED-Seq is a promising approach for use in risk adapted trials in early stage NSCLC.

Citation Format: James M. Isbell, Bob T. Li, Pedram Razavi, Jorge Reis-Filo, Si-Yang Liu, Pier Selenica, Prasad Adusumilli, Matthew Bott, David R. Jones, Valerie W. Rusch, Smita Sihag, Darren J. Buonocore, Justin Jee, Emily Lebow, Daniel Gomez, Andreas Rimner, Fernando C. Santini, Charles M. Rudin, Jordan E. Eichholz, Andres Martinez, Daphne Alerte, Gregory J. Hogan, Andre Schultz, Ronald P. Schuyler, Alanna Roff, Dustin Hite, Jacob J. Chabon, David M. Kurtz, Ash A. Alizadeh, Maximilian Diehn. Ultrasensitive ctDNA minimal residual disease monitoring in early NSCLC with PhasED-Seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3375.

Molecular Biomarkers of Disease Outcomes and Mechanisms of Acquired Resistance to First-Line Osimertinib in Advanced EGFR-Mutant Lung Cancers

INTRODUCTION

Preferred first-line treatment for patients with metastatic EGFR-mutant lung cancer is osimertinib, yet it is not known whether patient outcomes may be improved by identifying and intervening on molecular markers associated with therapeutic resistance.

METHODS

All patients with metastatic EGFR-mutant lung cancer treated with first-line osimertinib at the Memorial Sloan Kettering Cancer Center (n = 327) were identified. Available pretreatment and postprogression tumor samples underwent targeted gene panel sequencing and mutational signature analysis using SigMA algorithm. Progression-free survival (PFS) and overall survival were estimated using the Kaplan-Meier method.

RESULTS

Using multivariate analysis, baseline atypical EGFR (median PFS = 5.8 mo, p < 0.001) and concurrent TP53/RB1 alterations (median PFS = 10.5 mo, p = 0.015) were associated with shorter PFS on first-line osimertinib. Of 95 patients with postprogression biopsies, acquired resistance mechanisms were identified in 52% (off-target, n = 24; histologic transformation, n = 14; on-target, n = 12), with MET amplification (n = 9), small cell lung transformation (n = 7), and acquired EGFR amplification (n = 7), the most frequently identified mechanisms. Although there was no difference in postprogression survival on the basis of identified resistance (p = 0.07), patients with subsequent second-line therapy tailored to postprogression biopsy results had improved postprogression survival (hazard ratio = 0.09, p = 0.006). The paired postprogression tumors had higher tumor mutational burden (p = 0.008) and further dominant APOBEC mutational signatures (p = 0.07) compared with the pretreatment samples.

CONCLUSIONS

Patients with EGFR-mutant lung cancer treated with first-line osimertinib have improved survival with treatment adaptation on the basis of identified mechanisms of resistance at time of progression using tissue-based genomic analysis. Further survival gains may be achieved using risk-based treatment adaptation of pretreatment genomic alterations.

Direct prediction of Homologous Recombination Deficiency from routine histology in ten different tumor types with attention-based Multiple Instance Learning: a development and validation study

Background

Homologous Recombination Deficiency (HRD) is a pan-cancer predictive biomarker that identifies patients who benefit from therapy with PARP inhibitors (PARPi). However, testing for HRD is highly complex. Here, we investigated whether Deep Learning can predict HRD status solely based on routine Hematoxylin & Eosin (H&E) histology images in ten cancer types.

Methods

We developed a fully automated deep learning pipeline with attention-weighted multiple instance learning (attMIL) to predict HRD status from histology images. A combined genomic scar HRD score, which integrated loss of heterozygosity (LOH), telomeric allelic imbalance (TAI) and large-scale state transitions (LST) was calculated from whole genome sequencing data for n=4,565 patients from two independent cohorts. The primary statistical endpoint was the Area Under the Receiver Operating Characteristic curve (AUROC) for the prediction of genomic scar HRD with a clinically used cutoff value.

Results

We found that HRD status is predictable in tumors of the endometrium, pancreas and lung, reaching cross-validated AUROCs of 0.79, 0.58 and 0.66. Predictions generalized well to an external cohort with AUROCs of 0.93, 0.81 and 0.73 respectively. Additionally, an HRD classifier trained on breast cancer yielded an AUROC of 0.78 in internal validation and was able to predict HRD in endometrial, prostate and pancreatic cancer with AUROCs of 0.87, 0.84 and 0.67 indicating a shared HRD-like phenotype is across tumor entities.

Conclusion

In this study, we show that HRD is directly predictable from H&E slides using attMIL within and across ten different tumor types.

Abstract P2-23-15: Histologic, immunohistochemical and genomic comparison between classic Invasive lobular carcinomas and lobular-like invasive ductal carcinomas

Background: Invasive lobular carcinomas (ILCs) are the most frequent special histologic subtype of breast cancer, accounting for up to 15% of all breast cancer cases. ILCs are characterized by a distinctive discohesive growth pattern, with cells arranged in single cell infiltrative file and dispersed throughout the stroma, which stems from the loss of E-cadherin expression due to bi-allelic inactivation of the CDH1 gene. A subset of breast cancers display a similar single cell infiltrative growth pattern but, in contrast to classic ILC, display diffuse strong membranous E-cadherin reactivity and membranous p120 expression. We refer to such cases as “lobular-like invasive ductal carcinoma” (LLIDC), but it is unclear if this terminology is appropriate and if such cases show biallelic inactivation of CDH1, similarly to ILCs. Here, we sought to define whether LLIDCs would harbor bi-allelic alterations of CDH1 and to perform an exploratory, hypothesis generating analysis of the repertoire of somatic genetic alterations of LLIDCs and classic ILCs. Materials and methods: Representative H&Es, as well as sections subjected to E-cadherin and p120 immunohistochemistry from seven classic ILCs and seven bona fide “lobular-like invasive ductal carcinomas” were retrieved and independently reviewed by two pathologists with experience and expertise in breast pathology. DNA samples were extracted from representative sections from tumor and normal breast tissue from each patient and subjected to an FDA-approved targeted sequencing assay comprising the coding regions and selected regulatory elements of 515 genes. Somatic single nucleotide variants (SNVs) were detected with MuTect, indels with Strelka, Varscan2, Scalpel and Lancet. All mutations were manually inspected using the Integrative Genomics Viewer (IGV). The cancer cell fraction (CCF) of each mutation was inferred, as well as clonal probability, using ABSOLUTE. Copy number alterations and loss of heterozygosity were determined using FACETS. Mutational signatures were inferred using SigMA based on all synonymous and nonsynonymous somatic mutations. Results: Based on the histopathologic evaluation, of the 14 cases analyzed, seven were classified as ILC, and the other seven were classified as LLIDC. Sequencing analysis revealed that the classic ILCs harbored 16q LOH and CDH1 mutations (7/7), of which five were frameshift indel and two were splice site mutations consistently coupled with loss-of-heterozygosity (LOH) of the wild-type allele. Conversely, five of the seven LLIDCs did not harbor CDH1 mutations or genomic rearrangements. CDH1 mutations were identified in 2 LLIDCs: one harbored a subclonal CDH1 in-frame indel mutation coupled with LOH. This case displayed membranous E-cadherin and p120 expression with areas of aberrant expression. The other CDH1-mutated LLIDC harbored a complex in-frame indel with subclonal LOH. This case displayed membranous E-cadherin and p120 expression. The comparative analysis of the repertoire of somatic genetic alterations and mutational signatures present in LLIDCs and classic ILCs did not reveal any significant differences. Conclusion: Despite the histologic similarities, LLIDCs differ from classic lobular carcinomas based on the lack of CDH1 bi-allelic inactivation and the patterns of expression of E-cadherin and p120 catenin. Further whole-genome sequencing analyses are warranted to define the molecular basis of the discohesive cancer cells of LLIDC display.

Citation Format: Edaise M. da Silva, Thais Basili, Jing Yu, Juan Blanco-Heredia, Pier Selenica, Qiqi Ye, Arnaud da Cruz Paula, Higinio Dopeso, Antonio Marra, Steffi Oesterreich, Jorge Reis-Filho, Rohit Bhargava. Histologic, immunohistochemical and genomic comparison between classic Invasive lobular carcinomas and lobular-like invasive ductal carcinomas [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 P2-23-15.

Abstract HER2-07: HER2-07 Genomic Characterization of Primary and Metastatic HER2-low Breast Cancers

Background: Varying levels of HER2 expression without ERBB2 gene amplification can be detected by immunohistochemistry (IHC) in approximately 60% of all invasive breast cancers (BCs). HER2-low-expressing BCs have recently been shown to respond to novel anti-HER2 antibody drug conjugates. Several studies have demonstrated that HER2-low BCs do not seem to constitute a distinct clinical and transcriptomic subtype as compared to HER2-0 BCs. Here we sought to define the clinicopathologic features and repertoire of somatic genetic alterations in HER2-low BCs. Methods: We retrieved clinical, pathological, and genomic data of BCs that were subjected to targeted sequencing using the FDA-cleared MSK-IMPACT assay from April 2014 to December 2021. After removing cases where any available biopsy had HER2 3+ and/or positive ERBB2 fluorescence in situ hybridization (FISH), 3608 samples (primary=1347; post-treatment/metastatic=2261) were included. Tumors were classified as HER2-low if they had an HER2 IHC score of 1+ or 2+ with a non-amplified FISH assay and HER2-0 if they had an HER2 IHC score of 0. Somatic mutations and DNA copy number alterations from MSK-IMPACT were analyzed. Multiple testing correction using the Benjamini-Hochberg method was applied to control for the false discovery rate (q). Q values &lt; 0.1 were considered significant. Results: Among 3608 HER2- BCs, 1460 (40%) and 2148 (60%) were HER2-0 and HER2-low, respectively. Hormone receptor (HR) expression was significantly higher in HER2-low than HER2-0 tumors in both primary (781 [68.3%] vs 362 [31.7%]; p&lt; 0.001) and metastatic (1031 [60.5%] vs 673 [39.5%]; p&lt; 0.001) samples. A higher proportion of HER2-low tumors was found in metastatic than primary samples (59% vs 41%; p&lt; 0.001) in this cohort. No difference in histology subtype, tumor grade, disease stage (among primary tumors), mutational signatures, and tumor mutational burden was found overall and when cases were stratified by HR expression. In HR-positive BCs, HER2-0 BCs harbored higher frequency of TP53 (33% vs 25%; odds ratio [OR] 1.49, 95% confidence interval [CI] 1.25-1.78, q&lt; 0.001) and CDKN1A (1% vs 0%; OR 17.47, 95% CI 2.48-756.37, q=0.02) alterations than HER2-low BCs. Similar findings were observed in metastatic but not in primary HR-positive BCs. No differences were detected in HR-negative BCs stratified into HER2-low and HER2-0. Given the potential misclassification that exists between IHC HER2-0 and HER2-1+, we then conducted an exploratory analysis splitting the HER2-low group into HER2 1+ and 2+. TP53 alterations remained significantly enriched in HER2-0 compared to HER2-1+ HR-positive tumors (33% vs 24%; OR 1.55, 95% CI 1.28-1.87, q&lt; 0.001). In HR-positive BCs, HER2-2+ displayed a higher frequency of genetic alterations in genes encoding for transcription factors, such as MYC (14.2% vs 7.3%; OR 2.09, 95% CI 1.44-3.04, q=0.02) and YAP1 (2% vs 0.3%; OR 6.86, 95% CI 1.7-39.57, q=0.1), and DNA damage response, such as FAM175A (1.6% vs 0%; OR 18.23, 95% CI 2.43-807.73, q=0.03) and BRCA2 (4% vs 1%; OR 3.09, 95% CI 1.49-6.55, q=0.1), than HER2-0 tumors. In HR-negative HER2-2+ tumors, a higher frequency of PIK3CA mutations was observed in comparison to HER2-0 (36.9% vs 19.5%; OR 2.41, 1.4-4.1, q=0.1), overall and in the metastatic setting. Conclusions: HER2-low BCs seem not to represent a distinct pathologic subtype. At the genomic level, however, some differences were identified and these became more conspicuous upon subclassification of HER2 IHC expression into 1+ and 2+. Further investigation into methods that more accurately detect and quantify low levels of HER2 expression in BC samples as well as better characterize the biology behind the HER2-low/ultralow expression is warranted.

Citation Format: Antonio Marra, Anton Safonov, Joshua Drago, Emanuela Ferraro, Pier Selenica, Andrea Gazzo, Giuseppe Curigliano, Shanu Modi, Pedram Razavi, Jorge Reis-Filho, Sarat Chandarlapaty. HER2-07 Genomic Characterization of Primary and Metastatic HER2-low Breast Cancers [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 HER2-07.

Abstract P1-13-17: Hyperactivation of the EGFR pathway is associated with resistance to tucatinib in HER2-positive breast cancer models

Background: The HER2-specific tyrosine kinase inhibitor (TKI) tucatinib (Tuca) recently approved for advanced HER2+ breast cancer is making a move towards the early setting. Given its growing use, resistance is inevitable, as observed in the HER2CLIMB study, where only one patient with brain metastasis remained progression free after 2 years on Tuca. Driven by the prevailing lack of knowledge about the mechanisms of resistance, in this study, we sought to define these mechanisms and identify treatment strategies to overcome them. We previously reported (SABCS 2021) that our BT474 TucaR models acquired EGFR amplification and showed elevated levels of phosphorylated (p) and total (t) EGFR, pHER2, pHER3, and downstream pAKT and pS6. Since the HER pathway is activated by ligands, here we aim to assess if hyperactivation of EGFR via high levels of its ligands is an alternative mechanism of Tuca resistance. Materials and Methods: Our recently developed HER2+ BT474 (ATCC and AZ) cell models with acquired resistance to Tuca (TucaR) developed through long-term exposure to gradually increasing doses of Tuca and their naïve parental (P) were used. Genomic (DNA-seq), transcriptomic (RNA-seq), and proteomic (western blot) characterization were performed. Changes in cell growth and migration were assessed by methylene blue and Incucyte wound healing assays, respectively. Results: RNA-seq analysis demonstrated that the levels of TGFα was significantly higher in our BT474 TucaR models compared to P cells. Our results now demonstrate that exogenous supplementation of EGF to BT474-P cells rescues the Tuca-mediated inhibition of pEGFR, pHER2, and the downstream pAKT, pERK, and pS6 levels. Exogenous EGF was also found to reduce the levels of apoptosis, as assessed by cleaved PARP, mitigating the Tuca-induced cell death. Exogenous EGF or TGFα rendered naïve BT474 and SKBR3 cells resistant to Tuca while neratinib, a pan-HER TKI, effectively inhibited this ligand-driven cell growth. We previously showed that the HER signaling reactivation observed in our EGFR-amplified TucaR cells was inhibited by the EGFR-specific TKI gefitinib (Gef) (SABCS 2021) and that the TucaR cells displayed enhanced migratory capabilities (AACR 2022). Here, we demonstrate that in addition to curbing the growth of TucaR cells, Gef, either alone or together with Tuca, also markedly reverts the migration of the TucaR cells. Knockdown (KD) of EGFR but not HER2 selectively and substantially inhibited the migration of the TucaR cells. KD of EGFR also had a marked cell killing effect on only the TucaR cells, whereas HER2 KD inhibited the growth of P but not TucaR cells. Our findings are consistent with the notion that while the P cells are functionally dependent on HER2, in TucaR cells the survival dependence could be rewired to rely primarily on the hyperactive EGFR signaling. Genomic analysis further revealed that in addition to EGFR amplification, the AZ TucaR cells also acquired a gain of YES1, a src family receptor tyrosine kinase implicated in cancer cell growth, invasion, and metastasis. Functional studies using 2 siRNAs, however, showed that YES1 KD had no effect on the growth of TucaR cells, and the migration of both TucaR and P cells was equally affected by YES1 KD, precluding the potential role of YES1 in driving the resistant and enhanced migratory phenotypes. Conclusions: Hyperactivation of the EGFR pathway via amplification of EGFR or increased expression of its ligands confers resistance to Tuca, which may be overcome using dual/pan-HER TKIs or the combination of potent EGFR and HER2 inhibitors. Given the rapidly evolving treatment landscape of HER2+ breast cancer and biomarkers of resistance, our novel findings have potentially crucial therapeutic implications and suggest that rationally sequencing the currently available TKIs may be clinically important.

Citation Format: Fu-Tien Liao, Tia Gordon, Chia Chia Liu, Pier Selenica, Yingjie Zhu, Juber Patel, Sarmistha Nanda, Lanfang Qin, Xiaoyong Fu, Andrea Gazzo, Antonio Marra, Juan Blanco-Heredia, Britta Weigelt, Jorge Reis-Filho, C. Kent Osborne, Mothaffar Rimawi, Rachel Schiff, Jamunarani Veeraraghavan. Hyperactivation of the EGFR pathway is associated with resistance to tucatinib in HER2-positive breast cancer models [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 P1-13-17.

Abstract P4-08-12: Clinical and Genomic Landscape of Breast Cancers Carrying CCNE1 Amplification

Background: Cyclin E1 (CCNE1) plays a critical role in cell cycle regulation. CCNE1 overexpression and/or gene amplification (amp) have been associated with poor outcome in several tumors, including breast cancer (BC). CCNE1 amp has recently been identified as a potential therapeutic target for novel synthetic lethality-based therapies. Here we sought to define the clinical and genomic features of BCs carrying CCNE1 amp. Methods: Genomic and clinical data from all consecutive BCs, which had been subjected to targeted sequencing using the FDA-authorized MSK-IMPACT assay from April 2014 to December 2021, were retrieved. Allele-specific copy number and fraction genome altered (FGA) were assessed using FACETS. Whole genome doubling (WGD) status was inferred from MSK-IMPACT sequencing data. Samples were categorized as CCNE1 amp or non-amp based on copy number profile assessed by FACETS. Mutual exclusivity and co-occurrence analyses between CCNE1 amp and other genetic alterations were performed using CoMEt. Multiple testing correction using the Benjamini–Hochberg procedure was applied to control for the false discovery rate. Progression-free survival (PFS) was assessed by Kaplan Meier method and Cox proportional-hazards models. Survival analyses were restricted to only patients with available pre-treatment samples. Results: Of 3,753 BCs with full clinical and genomic data, 125 (3.3%) harbored CCNE1 amp. A significant difference in the proportion of CCNE1 amp between treatment-naïve and post-treatment/metastatic samples was observed (2.4% vs 4%, p=0.007). CCNE1 amp was significantly less frequently detected in hormone receptor (HR)+/HER2- BCs than in HR-/HER2+ and HR-/HER2- subtypes (2% vs 7.6% and 7.2%, respectively, p&lt; 0.001), and was particularly rare in invasive lobular BCs (1/452 cases). BCs with CCNE1 amp displayed a higher frequency of WGD (p&lt; 0.001) and higher median FGA (p&lt; 0.001) than non-amp tumors, overall and in different subtypes, suggesting increased genomic instability. No difference in tumor mutational burden (TMB) between CCNE1 amp and non-amp was found. In primary BC (n=1,385), a higher proportion of TP53 alterations was found in cases with CCNE1 amp (odds ratio [OR] 6.0, 95% confidence interval [CI] 2.5-16.6, q&lt; 0.001). Conversely, CCNE1 amp was mutually exclusive with CDH1 alterations (q&lt; 0.001). Comparable results were found in the analysis of post-treatment/metastatic samples (n=2,368). A subset analysis on HR+/HER2- BCs confirmed that TP53 (OR 4.2, 95%CI 2.28-8.11, q&lt; 0.001) and CDH1 (OR 0.09, 95%CI 0.002-0.57, q&lt; 0.1) alterations co-occurred and were mutually exclusive, respectively, with CCNE1 amp. ARID2 alterations were also enriched in HR+/HER2- tumors harboring CCNE1 amp (OR 10.6, 95%CI 2.54-33.93, q&lt; 0.1). CCNE1 amp was significantly associated with reduced median PFS (8.8 vs 15.2 months in CCNE1 amp [n=9] vs CCNE1 non-amp [n=402]; hazard ratio [HR] 2.82, 95% CI 1.38-5.75, p=0.004) on first line treatment with CDK4/6 inhibitor plus endocrine therapy (ET) in HR+/HER2- metastatic BCs, regardless of the ET partner, FGA and TMB. CCNE1 amp was also associated with numerically inferior median PFS (7.3 vs 20.8 months in CCNE1 amp [n=5] vs CCNE1 non-amp [n=106]; HR 3.1, 95% CI 1.24-7.87, p=0.01) on first line trastuzumab/pertuzumab/taxane treatment in HER2+ metastatic BCs, with a trend toward significance after adjusting for FGA and TMB (p=0.09). Conclusions: CCNE1 amp is associated with specific clinicopathological and genomic features in BCs and linked to an increased genomic instability. CCNE1 amp defines a subset of metastatic BCs with marked poor clinical response to available standard-of-care treatments. Further studies testing novel therapeutic approaches, including synthetic lethality-based strategies targeting CCNE1 amp and CDK2-selective inhibition, are warranted.

Citation Format: Antonio Marra, Pier Selenica, Yingjie Zhu, Pedram Razavi, Anton Safonov, Emanuela Ferraro, Sarat Chandarlapaty, Jorge Reis-Filho. Clinical and Genomic Landscape of Breast Cancers Carrying CCNE1 Amplification [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 P4-08-12.

High-Sensitivity Mutation Analysis of Cell-Free DNA for Disease Monitoring in Endometrial Cancer

PURPOSE

We sought to determine whether sequencing analysis of circulating cell-free DNA (cfDNA) in patients with prospectively accrued endometrial cancer captures the mutational repertoire of the primary lesion and allows for disease monitoring.

EXPERIMENTAL DESIGN

Peripheral blood was prospectively collected from 44 newly diagnosed patients with endometrial cancer over a 24-month period (i.e., baseline, postsurgery, every 6 months after). DNA from the primary endometrial cancers was subjected to targeted next-generation sequencing (NGS) of 468 cancer-related genes, and cfDNA to a high-depth NGS assay of 129 genes with molecular barcoding. Sequencing data were analyzed using validated bioinformatics methods.

RESULTS

cfDNA levels correlated with surgical stage in endometrial cancers, with higher levels of cfDNA being present in advanced-stage disease. Mutations in cfDNA at baseline were detected preoperatively in 8 of 36 (22%) patients with sequencing data, all of whom were diagnosed with advanced-stage disease, high tumor volume, and/or aggressive histologic type. Of the 38 somatic mutations identified in the primary tumors also present in the cfDNA assay, 35 (92%) and 38 (100%) were detected at baseline and follow-up, respectively. In 6 patients with recurrent disease, changes in circulating tumor DNA (ctDNA) fraction/variant allele fractions in cfDNA during follow-up closely mirrored disease progression and therapy response, with a lead time over clinically detected recurrence in two cases. The presence of ctDNA at baseline (P < 0.001) or postsurgery (P = 0.014) was significantly associated with reduced progression-free survival.

CONCLUSIONS

cfDNA sequencing analysis in patients with endometrial cancer at diagnosis has prognostic value, and serial postsurgery cfDNA analysis enables disease and treatment response monitoring. See related commentary by Grant et al., p. 305.

Expanded genetic testing of GIST patients identifies high proportion of non-syndromic patients with germline alterations

Traditional genetic testing for patients with gastrointestinal stromal tumors (GISTs) focus on those with syndromic features. To assess whether expanded genetic testing of GIST patients could identify hereditary cancer predisposition, we analyzed matched tumor-germline sequencing results from 103 patients with GISTs over a 6-year period. Germline pathogenic/likely pathogenic (P/LP) variants in GIST-associated genes (SDHA, SDHB, SDHC, NF1, KIT) were identified in 69% of patients with KIT/PDGFRA-wildtype GISTs, 63% of whom did not have any personal or family history of syndromic features. To evaluate the frequency of somatic versus germline variants identified in tumor-only sequencing of GISTs, we analyzed 499 de-identified tumor-normal pairs. P/LP variants in certain genes (e.g., BRCA1/2, SDHB) identified in tumor-only sequencing of GISTs were almost exclusively germline in origin. Our results provide guidance for genetic testing of GIST patients and indicate that germline testing should be offered to all patients with KIT/PDGFRA-wildtype GISTs regardless of their history of syndromic features.

Comprehensive Genomic Profiling of Cell-Free Circulating Tumor DNA Detects Response to Ribociclib Plus Letrozole in a Patient with Metastatic Breast Cancer

Analysis of cell-free circulating tumor DNA obtained by liquid biopsy is a non-invasive approach that may provide clinically actionable information when conventional tissue biopsy is inaccessible or infeasible. Here, we followed a patient with hormone receptor-positive and human epidermal growth factor receptor (HER) 2-negative breast cancer who developed bone metastases seven years after mastectomy. We analyzed circulating cell-free DNA (cfDNA) extracted from plasma using high-depth massively parallel sequencing targeting 468 cancer-associated genes, and we identified a clonal hotspot missense mutation in the PIK3CA gene (3:178952085, A > G, H1047R) and amplification of the CCND1 gene. Whole-exome sequencing revealed that both alterations were present in the primary tumor. After treatment with ribociclib plus letrozole, the genetic abnormalities were no longer detected in cfDNA. These results underscore the clinical utility of combining liquid biopsy and comprehensive genomic profiling to monitor treatment response in patients with metastasized breast cancer.

APOBEC mutagenesis, kataegis, chromothripsis in EGFR-mutant osimertinib-resistant lung adenocarcinomas

BACKGROUND

Studies of targeted therapy resistance in lung cancer have primarily focused on single-gene alterations. Based on prior work implicating apolipoprotein b mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) mutagenesis in histological transformation of epidermal growth factor receptor (EGFR)-mutant lung cancers, we hypothesized that mutational signature analysis may help elucidate acquired resistance to targeted therapies.

PATIENTS AND METHODS

APOBEC mutational signatures derived from an Food and Drug Administration-cleared multigene panel [Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)] using the Signature Multivariate Analysis (SigMA) algorithm were validated against the gold standard of mutational signatures derived from whole-exome sequencing. Mutational signatures were decomposed in 3276 unique lung adenocarcinomas (LUADs), including 93 paired osimertinib-naïve and -resistant EGFR-mutant tumors. Associations between APOBEC and mechanisms of resistance to osimertinib were investigated. Whole-genome sequencing was carried out on available EGFR-mutant lung cancer samples (10 paired, 17 unpaired) to investigate large-scale genomic alterations potentially contributing to osimertinib resistance.

RESULTS

APOBEC mutational signatures were more frequent in receptor tyrosine kinase (RTK)-driven lung cancers (EGFR, ALK, RET, and ROS1; 25%) compared to LUADs at large (20%, P < 0.001); across all subtypes, APOBEC mutational signatures were enriched in subclonal mutations (P < 0.001). In EGFR-mutant lung cancers, osimertinib-resistant samples more frequently displayed an APOBEC-dominant mutational signature compared to osimertinib-naïve samples (28% versus 14%, P = 0.03). Specifically, mutations detected in osimertinib-resistant tumors but not in pre-treatment samples significantly more frequently displayed an APOBEC-dominant mutational signature (44% versus 23%, P < 0.001). EGFR-mutant samples with APOBEC-dominant signatures had enrichment of large-scale genomic rearrangements (P = 0.01) and kataegis (P = 0.03) in areas of APOBEC mutagenesis.

CONCLUSIONS

APOBEC mutational signatures are frequent in RTK-driven LUADs and increase under the selective pressure of osimertinib in EGFR-mutant lung cancer. APOBEC mutational signature enrichment in subclonal mutations, private mutations acquired after osimertinib treatment, and areas of large-scale genomic rearrangements highlights a potentially fundamental role for APOBEC mutagenesis in the development of resistance to targeted therapies, which may be potentially exploited to overcome such resistance.

Microsatellite Instability-High Endometrial Cancers with MLH1 Promoter Hypermethylation Have Distinct Molecular and Clinical Profiles

PURPOSE

Microsatellite instability-high (MSI-H) endometrial carcinomas are underpinned by distinct mechanisms of DNA mismatch repair deficiency (MMR-D). We sought to characterize the clinical and genetic features of MSI-H endometrial cancers harboring germline or somatic mutations in MMR genes or MLH1 promoter hypermethylation (MLH1ph).

EXPERIMENTAL DESIGN

Of > 1,100 patients with endometrial cancer that underwent clinical tumor-normal sequencing, 184 had MSI-H endometrial cancers due to somatic MMR mutations or MLH1ph, or harbored pathogenic germline MMR mutations. Clinicopathologic features, mutational landscape, and tumor-infiltrating lymphocyte (TIL) scores were compared among MMR-D groups using nonparametric tests. Log-rank tests were used for categorical associations; Kaplan-Meier method and Wald test based on Cox proportional hazards models were employed for continuous variables and survival analyses.

RESULTS

Compared with patients with germline (n = 25) and somatic (n = 39) mutations, patients with MLH1ph endometrial cancers (n = 120) were older (P < 0.001), more obese (P = 0.001) and had more advanced disease at diagnosis (P = 0.025). MLH1ph endometrial cancers were enriched for JAK1 somatic mutations as opposed to germline MMR-D endometrial cancers which showed enrichment for pathogenic ERBB2 mutations. MLH1ph endometrial cancers exhibited lower tumor mutational burden and TIL scores compared with endometrial cancers harboring germline or somatic MMR mutations (P < 0.01). MLH1ph endometrial cancer patients had shorter progression-free survival (PFS) on univariate analysis, but in multivariable models, stage at diagnosis remained the only predictor of survival. For stage I/II endometrial cancer, two-year PFS was inferior for patients with MLH1ph endometrial cancers compared with germline and somatic MMR groups (70% vs. 100%, respectively).

CONCLUSIONS

MLH1ph endometrial cancers likely constitute a distinct clinicopathologic entity compared with germline and somatic MMR-D ECs with potential treatment implications.

Recurrent WWTR1 S89W mutations and Hippo pathway deregulation in clear cell carcinomas of the cervix

Clear cell carcinoma (CCC) of the cervix (cCCC) is a rare and aggressive type of human papillomavirus (HPV)-negative cervical cancer with limited effective treatment options for recurrent or metastatic disease. Historically, CCCs of the lower genital tract were associated with in utero diethylstilbestrol exposure; however, the genetic landscape of sporadic cCCCs remains unknown. Here we sought to define the molecular underpinning of cCCCs. Using a combination of whole-exome, targeted capture, and RNA-sequencing, we identified pathogenic genetic alterations in the Hippo signaling pathway in 50% (10/20) of cCCCs, including recurrent WWTR1 S89W somatic mutations in 40% (4/10) of the cases harboring mutations in the Hippo pathway. Irrespective of the presence or absence of Hippo pathway genetic alterations, however, all primary cCCCs analyzed in this study (n = 20) harbored features of Hippo pathway deregulation at the transcriptomic and protein levels. In vitro functional analysis revealed that expression of the WWTR1 S89W mutation leads to reduced binding of TAZ to 14-3-3, promoting constitutive nuclear translocation of TAZ and Hippo pathway repression. WWTR1 S89W expression was found to lead to acquisition of oncogenic behavior, including increased proliferation, migration, and colony formation in vitro as well as increased tumorigenesis in vivo, which could be reversed by targeted inhibition of the TAZ/YAP1 complex with verteporfin. Finally, xenografts expressing WWTR1 S89W displayed a shift in tumor phenotype, becoming more infiltrative as well as less differentiated, and were found to be composed of cells with conspicuous cytoplasmic clearing as compared to controls. Our results demonstrate that Hippo pathway alterations are likely drivers of cCCCs and likely contribute to the clear cell phenotype. Therapies targeting this pathway may constitute a new class of treatment for these rare, aggressive tumors. © 2022 The Pathological Society of Great Britain and Ireland.

ESR1 hotspot mutations in endometrial stromal sarcoma with high-grade transformation and endocrine treatment

High-grade endometrial stromal sarcomas (HGESSs) are more aggressive and have higher rates of resistance to endocrine therapy than low-grade endometrial stromal sarcomas (LGESSs). The pathogenesis of hormonal resistance in these lesions has yet to be defined. Here we sought to histologically and genetically characterize 3 LGESSs and their recurrences that underwent histologic high-grade transformation following endocrine therapy. For this, DNA from primary tumors and select subsequent recurrences were subject to massively parallel sequencing targeting 468 cancer-related genes. Somatic mutation analyses were performed using validated bioinformatics methods. In addition, RNA from each case was evaluated for the presence of gene fusions using targeted RNA-sequencing. All patients initially presented with LGESS, developed HGESS recurrences, and received at least 2 lines of hormonal suppressive therapy. Gene fusions classically described as associated with LGESS were identified in all 3 cases, including JAZF1-PHF1, EPC1-PHF1 and JAZF1-SUZ12 fusions for Cases 1, 2 and 3, respectively. Targeted sequencing analysis revealed that none of the primary LGESS, however the HGESS recurrences of Cases 1 and 3, and the LGESS and HGESS recurrences of Case 2 post endocrine treatment harbored ESR1 p.Y537S hotspot mutations. These ESR1 ligand-binding domain mutations have been found as a mechanism of acquired endocrine resistance in breast cancer. Also, a reduction in estrogen receptor (ER) expression was observed in recurrences. Our findings suggest that the ESR1 p.Y537S hotspot mutation in LGESS with histologic high-grade transformation may be associated with endocrine resistance in these lesions. Furthermore, our data suggest that genetic analyses may be performed in recurrent LGESS following hormonal therapy, development of high-grade morphology, and/or altered/diminished ER expression.

Abstract 1692: Single-cell DNA sequencing from frozen endometrial tumors to address clonal evolution of somatic mutations

Background: Single-cell DNA sequencing with droplet microfluidics has enabled the characterization of genetic heterogeneity in hematologic malignancies and fresh solid tumors through the direct DNA sequencing of thousands of single cells from individual samples without the need of whole-genome amplification. The application of this technology in banked solid tumor samples has been rather limited to date, however. Here, we describe and validate a method to characterize clonal evolution of somatic mutations from frozen tumor specimens, utilizing endometrial carcinomas (ECs) as an example.

Methods: Tissue cores were obtained from frozen ECs and the extracellular matrix was enzymatically digested. A subset of extracted nuclei were used for bulk DNA extraction and targeted sequencing. The remaining nuclei were encapsulated with cell lysis buffer, and the DNA was primed and barcoded with hydrogel beads containing 317 cancer gene amplicons using a Tapestri instrument (Mission Bio). Following droplet PCR, Illumina libraries were generated and sequenced on a NovaSeq6000. Sequencing reads were trimmed and mapped to the reference genome. Barcode sequences were error-corrected and cells were detected from barcodes based on number of reads assigned to each barcode and amplicon read completeness. Genotyping was performed using GATK and the allele drop-out (ADO) rate was calculated. Non-neoplastic cells were defined by the absence of somatic mutations. Allele-specific copy number (ASCN) profiles for each tumor cell were estimated by normalizing mean reads per cell per amplicon to reads of non-neoplastic cells.

Results: We performed single-cell genotyping and ASCN profiling on two ECs with matched bulk sequencing data. For EC1, 5,004 tumor and 132 non-neoplastic cells were sequenced, for a 97% tumor purity. For EC2, 2,981 tumor and 165 non-neoplastic cells were obtained, for a 95% tumor purity. The average number of reads per amplicon per cell for EC1 and EC2 was 116 and 146 with an ADO rate of 6% and 8%, respectively. The data obtained from single-cell analysis were concordant with the matched bulk sequencing data in terms of clonal and subclonal mutations, and their respective cancer cell fraction. Single-cell sequencing further revealed the presence of loss of heterozygosity and emergence of minor subclones as late events in tumor evolution, which could not be inferred by bulk sequencing. In EC2, branch mutations displayed a spectrum consistent with microsatellite instability (MSI), reflecting its acquired MSI phenotype.

Conclusions: Here we describe a robust method to perform single-cell targeted DNA sequencing with droplet microfluidics of individual nuclei isolated from frozen tissue samples, providing the opportunity to determine the repertoire of somatic mutations at single cell resolution and to infer cancer clonal architecture and dynamics utilizing banked solid cancer tissue samples.

Citation Format: Arnaud Da Cruz Paula, Yingjie Zhu, Shirin Issa Bhaloo, Fresia Pareja, Timothy Hoang, Pier Selenica, Etta Hanlon, Thais Basili, Higinio Dopeso, Nadeem Abu-Rustum, Jorge Sergio Reis-Filho, Britta Weigelt. Single-cell DNA sequencing from frozen endometrial tumors to address clonal evolution of somatic mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1692.

Abstract LB517A: The role of EGFR in resistance to tucatinib and its therapeutic implications

Tucatinib (Tuc) was recently approved for metastatic disease and is moving towards the early setting in HER2+ breast cancer (BC). Given the increasing clinical use of Tuc, resistance will likely soon emerge as a challenge. Here, we explore the yet unknown mechanisms of resistance to Tuc and identify treatment strategies to overcome it. Our recently developed models of BT474 (AZ and ATCC) with acquired resistance to Tuc (TucR) and their sensitive parental (P) were used. DNA-seq, RNA-seq, and RPPA/western blot were performed. Knockdown studies were performed using EGFR siRNA. Drug efficacy studies involved cell growth assays by imaging-based or methylene blue assays. We recently reported (SABCS 2021) that our BT474 TucR models acquired EGFR amplification. The TucR cells displayed elevated levels of phosphorylated (p) and total (t) EGFR, pHER2, pHER3, and downstream pAKT and pS6, which were substantially suppressed by the EGFR-specific tyrosine kinase inhibitor (TKI) gefitinib (Gef) or even further when combined with Tuc. Our new results demonstrate that EGFR knockdown selectively inhibits the growth and pHER2 levels in TucR vs P cells, supporting our hypothesis that heterodimerization of amplified EGFR with HER2 leads to higher pHER2 levels in TucR cells. We have recently also shown that TucR models were hypersensitive to Gef and this inhibition was further enhanced with Gef+Tuc, implying their survival dependence on EGFR. Here, we demonstrate that the TucR cells made resistant to 200nM Tuc maintain their resistant growth and elevated EGFR-dependent signaling even when exposed to 500nM, and can begrown as xenografts in the presence of clinically relevant dose of Tuc, emphasizing their true resistance via amplified EGFR. Importantly, both TucR models vs P cells were cross-resistant to trastuzumab but maintain partial sensitivity to TDM1. While the EGFR-specific antibody cetuximab (Cet) was partially effective as a single agent only in the ATCC model, it potently inhibited growth and induced cell killing in combination with Tuc in both models. A significantly greater inhibition in cell growth and survival was also observed when trastuzumab or TDM1 was combined with either Gef or Cet. Taken together, our results suggest that the activation of HER2 and the resistant growth and survival in the TucR models is completely dependent on the amplified EGFR, which we are currently further corroborating by additional mechanistic and xenograft studies. Whilst we have previously reported that resistance to lapatinib and neratinib confer cross-resistance to Tuc, our recent findings show that resistance to Tuc may be overcome using dual/pan-HER TKIs or the combination of potent EGFR and HER2 inhibitors. Overall, our novel findings hold crucial implications in light of the current treatment landscape of HER2+ BC and biomarkers of resistance, and places a particular emphasis on considerations to sequence currently available TKIs.

Citation Format: Jamunarani Veeraraghavan, Fu-Tien Liao, Tia Gordon, Pier Selenica, Sarmistha Nanda, Lanfang Qin, Yingjie Zhu, Juber A. Patel, Andrea Gazzo, Fabio Stossi, Michael A. Mancini, Carolina Gutierrez, Britta Weigelt, Jorge S. Reis-Filho, C. Kent Osborne, Mothaffar F. Rimawi, Rachel Schiff. The role of EGFR in resistance to tucatinib and its therapeutic implications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB517A.

Genomic Determinants of Early Recurrences in Low-Stage, Low-Grade Endometrioid Endometrial Carcinoma

Low-stage, low-grade endometrioid endometrial carcinoma (EEC), the most common histologic type of endometrial cancer, typically has a favorable prognosis. A subset of these cancers, however, displays an aggressive clinical course with early recurrences, including distant relapses. All statistical tests were 2-sided. Using a combination of whole-exome and targeted capture sequencing of 65 FIGO stage IA and IB grade 1 EECs treated with surgery alone, we demonstrate that chromosome 1q gain (odds ratio [OR] = 8.09, 95% confidence interval [CI] = 1.59 to 54.6; P = .02), PIK3CA mutation (OR = 9.16, 95% CI = 1.95 to 61.8; P = .01), and DNA mismatch repair-deficient molecular subtype (OR = 7.92, 95% CI = 1.44 to 87.6; P = .02) are independent predictors of early recurrences within 3 years in this patient population. Chromosome 1q gain was validated in an independent dataset of stage I grade 1 EECs subjected to whole-exome sequencing. Our findings expand on the repertoire of genomic parameters that should be considered in the evaluation of patients with low-stage, low-grade EEC.

Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer

Patients with high-grade serous ovarian cancer suffer poor prognosis and variable response to treatment. Known prognostic factors for this disease include homologous recombination deficiency status, age, pathological stage and residual disease status after debulking surgery. Recent work has highlighted important prognostic information captured in computed tomography and histopathological specimens, which can be exploited through machine learning. However, little is known about the capacity of combining features from these disparate sources to improve prediction of treatment response. Here, we assembled a multimodal dataset of 444 patients with primarily late-stage high-grade serous ovarian cancer and discovered quantitative features, such as tumor nuclear size on staining with hematoxylin and eosin and omental texture on contrast-enhanced computed tomography, associated with prognosis. We found that these features contributed complementary prognostic information relative to one another and clinicogenomic features. By fusing histopathological, radiologic and clinicogenomic machine-learning models, we demonstrate a promising path toward improved risk stratification of patients with cancer through multimodal data integration.

Allelic dosage of RB1 drives CDK4/6 inhibitor treatment resistance in metastatic breast cancer

1010

Background: We recently reported inferior outcomes to CDK4/6 inhibitors and endocrine therapy (CDK4/6i-ET) associated with germline BRCA2 (g BRCA2) in a cohort of estrogen receptor (ER) positive breast cancers. Co-occurrence of gBRCA2 with loss of heterozygosity (LOH) of neighboring RB1 was found to portend particularly poor outcomes. Here, we sought to define the effects of pre-treatment RB1 allelic copy number status on outcomes of CDK4/6i-ET and the likelihood of developing RB1 loss-of-function (LOF) mutations on CDK4/6i through the analysis of an expanded cohort of metastatic ER+ breast cancer patients. Methods: Patients who underwent sequencing on MSK-IMPACT from April 2014 to May 2021 were included. For every sample preceding CDK4/6i-ET, we performed FACETS to infer RB1 allele specific copy number, ploidy, tumor purity and fraction genome altered (FGA). Patients were categorized based on RB1 allelic status: HetLoss (total of one allelic copy), copy neutral LOH (CNLOH), other allelic imbalance including all other aneuploidy states, and diploid. Progression free survival (PFS) was assessed using univariate and multivariate Cox proportional hazard models adjusted for ET partner and FGA. Firth penalized logistic regression was used to study association of pre-treatment RB1 status with acquired RB1 LOF variants in paired post-CDK4/6i samples. Results: Of 2,630 potentially eligible patients, 279 patients had genomic sequencing performed prior to 1st line CDK4/6i-ET. Of these, 75 (26.8%) exhibited RB1 HetLoss, 39 (14.0%) had CNLOH of RB1, 111 (39.7%) exhibited diploid RB1 state, while 54 (19.4%) had other patterns of RB1 allelic imbalance. All non-diploid RB1 states were associated with significantly shortened PFS relative to diploid (univariate HetLoss HR: 2.05, 95% CI: 1.42, 2.97; CNLOH HR: 2.08, 95% CI: 1.32, 3.25; other imbalance HR: 1.70, 95% CI: 1.11, 2.58). Only HetLoss remained significant when adjusted for FGA (HR 1.61, 95% CI: 1.09, 2.38, p = 0.017). RB1 LOF was rare in pre-CDK4/6i tumors (< 1%); excluding these cases did not change our results. Of the 176 patients with paired pre- and post-CDK4/6i samples, only RB1 HetLoss in pre-CDK4/6i sample was significantly associated with development of RB1 LOF mutations in post-CDK4/6i sample (18.4%) as compared to diploid (4.2%, OR 4.25, 95% CI 1.02, 17.7, p = 0.047). These results indicate that tumors with one functional copy of RB1 are more likely to acquire RB1 LOF on CDK4/6i to achieve biallelic RB1 loss as a mechanism of CDK4/6i resistance. Conclusions: We demonstrate that LOH and allelic imbalance of RB1 are associated with shorter PFS on CDK4/6-ET. We postulate this may occur partly as a result of more frequent acquired RB1 LOF mutations under selective pressure of CDK4/6i. These data supports the implementation of more refined allele-specific copy number methods and identifies a high-risk population for escalated monitoring and treatment approaches.

Abstract GS4-08: Comprehensive genomic profiling of patients with breast cancer identifies germline-somatic interactions mediating therapy resistance

Background: Germline genetic alterations are established mediators of breast carcinogenesis, often giving rise to specific forms of genomic instability. BRCA1/2 pathogenic variants (PVs) are emblematic of this phenomenon through their induction of homologous recombination deficiency. While specific patterns of genomic instability may sensitize cancers to therapies such as PARP inhibitors (PARPi) or platinum chemotherapy, their implications for lineage-directed therapies such as endocrine therapy (ET) or CDK4/6 inhibitors (CDK4/6i) are unknown. Herein, we systematically investigated the patterns of association of germline alterations with specific somatic alterations and explored the resulting effect on clinical outcomes. Methods: Patients who underwent germline and matched tumor tissue sequencing utilizing MSK-IMPACT from April 2014 to May 2021 and had available germline analysis results were included. The final analysis presented at SABCS will include 6000 tumors from 5,150 patients, anonymized according to established institutional IRB guidelines to allow for germline analysis on the full cohort. We analyzed genomic data to inform the full spectrum of somatic and germline mutations, ploidy, and allele-specific copy number to determine loss of heterozygosity (LOH). We performed gene- and pathway-level enrichment analyses between somatic variants and germline PVs. Univariable and multivariable Cox proportional hazards models were constructed to assess the association of therapy-specific progression-free survival (PFS) with select germline PVs and germline-somatic interactions. Results: The preliminary analysis includes 2,798 tumors from 2,242 patients with germline and somatic sequencing results. The most frequent germline PVs were: BRCA2 (n = 81), BRCA1 (n = 67), CHEK2 (n = 57), ATM (n = 32), PALB2 (n = 19). The cohort robustly confirmed previously established relationships such as mutual exclusivity of gATM and TP53 variants (OR 0.10, 95% CI 0.032 - 0.33, q = 0.005). Alterations of TP53 were seen in 83% (56/67) of gBRCA1 patients; however, this did not achieve significance when adjusted for receptor subtype (OR 3.90, 95% CI 1.34-11.38, q = 0.15). The size of the cohort allowed discovery of several novel relationships. For instance, gBRCA2 loss was associated with alterations in TGF-B pathway components (OR 3.58, 95% CI 1.70 - 7.56, q = 0.002), potentially relevant to metastatic disease progression. PIK3CA mutations were significantly less prevalent in both gBRCA2 (OR 0.52, 95% CI 0.31 - 0.87, q = 0.063) and gBRCA1 PVs (OR 0.21, 95% CI 0.085 - 0.51, q = 0.014). Our analysis uncovered a strong association between gBRCA2 and somatic RB1 pathogenic alterations (OR 3.58, 95% CI 1.70 - 7.56, q = 0.011), with most variants (80%) encountered in metastatic gBRCA2 tumors. Given the essential role of RB1 in CDK4/6i response, we investigated the effect of BRCA2 status on clinical efficacy of CDK4/6i-ET. Strikingly, gBRCA2 PVs were significantly associated with inferior PFS (HR 2.17, 95% CI 1.46-3.22, p &lt; 0.001) on first line treatment with CDK4/6i-ET. We posited the enrichment of somatic RB1 loss as a potential mechanism of resistance to CDK4/6i. Given the proximity of RB1 to BRCA2 on chromosome 13, we hypothesized that co-LOH of BRCA2 and RB1 predisposes the cancer cells to bi-allelic loss under therapeutic pressure of CDK4/6i. Indeed, 18/26 gBRCA2 (69.2%) tumors evaluable for allele-specific copy number had evidence of RB1 LOH. Discussion: Analysis of germline-somatic interactions yielded novel associations relevant to breast cancer progression and treatment resistance. Among these, we demonstrated BRCA2 carriers to have inferior outcomes to first line CDK4/6i-ET with potential implications for optimal first line therapy and sequencing of CDK4/6i vs PARPi in this patient population.

Citation Format: Anton Safonov, Chai Bandlamudi, Paulino Tallón de Lara, Emanuela Ferraro, Fatemeh Derakhshan, Marie Will, Mark Donoghue, Pier Selenica, Joshua Drago, Ezra Rosen, Carlos dos Anjos, Elaine Walsh, Elizabeth A Comen, Mehnaj Ahmed, Barbara Acevedo, Ahmet Zehir, Michael F Berger, David Solit, Larry Norton, Ronglai Shen, Zsofia Stadler, Simon Powell, Jorge S Reis-Filho, Sarat Chandarlapaty, Mark Robson, Pedram Razavi. Comprehensive genomic profiling of patients with breast cancer identifies germline-somatic interactions mediating therapy resistance [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 GS4-08.

Abstract PD8-06: Acquired resistance to tucatinib is associated with EGFR amplification in HER2+ breast cancer (BC) models and can be overcome by a more complete blockade of HER receptor layer

Background: With recent approval of the irreversible pan-HER tyrosine kinase inhibitor (TKI) neratinib (N) and the HER2-specific TKI tucatinib (T) in the advanced setting and their edging towards the early setting in HER2+ BC, resistance will likely emerge as a challenge, as illustrated by the HER2CLIMB study, where only one patient with brain metastasis remained progression free after 2 years on T. We set out to define the mechanisms of resistance to T and treatment strategies to overcome it. Materials and Methods: Our previously characterized HER2+ BT474 models with acquired resistance to lapatinib (L; LapR) or N (NrbR) (SABCS20-PD3-09), and our recently developed models of BT474 and SKBR3 with acquired resistance to T (TucaR) developed through long-term exposure to increasing doses of T (up to 200nM) and their naïve parental (P) were used. Genomic (DNA-seq), transcriptomic (RNA-seq), and proteomic (RPPA, western blot) characterization were performed. Drug efficacy studies involved cell growth assays by the imaging-based IncuCyte system. Results: We recently reported that while LapR is associated with acquisition of HER2 L755S mutation, which partially reactivates the HER pathway, NrbR is associated with the additional co-acquisition of a pathogenic PIK3CA mutation. Preliminary analysis of 2 BT474 TucaR models (ATCC and AZ) showed highly elevated levels of phosphorylated (p) and total (t) EGFR, suggesting EGFR signaling activation. Levels of pHER2, pHER3, and downstream pAKT and pS6 were also markedly higher in the TucaR models compared to P or short-term T. The TucaR but not LapR or NrbR models exhibited EGFR amplification, explaining the higher EGFR levels and signaling. Further, the elevated pEGFR, pHER2, pHER3, pAKT, and pS6 levels in TucaR models were substantially suppressed by the EGFR-specific TKI gefitinib (G) (50, 500nM) or even further when combined with T (500 nM G+200nM T). These results suggest that the higher pHER2 levels in TucaR models is probably due to heterodimerization of the amplified EGFR with HER2 and subsequent HER2 phosphorylation. In contrast to the P cells where the apoptotic marker cleaved (c)-PARP was not induced with G alone (50, 500nM), but with T (200nM) or 500nM G+T, in the TucaR model, 500nM G alone was enough to induce c-PARP, which was further enhanced when combined with T, implying the survival dependence of TucaR cells on EGFR signaling. The TucaR models were hypersensitive to G compared to P cells, and this growth inhibition was further enhanced with G+T. Whilst we previously reported that the LapR and NrbR cells were cross-resistant to T, the TucaR cells remained highly sensitive to the pan-HER TKIs N, poziotinib, and pyrotinib. Finally, in a second HER2+ model SKBR3, at 200nM TucaR, we observed elevated pEGFR, pHER2, pHER3, and pAKT levels, the underlying mechanism of which is under investigation by genomic and molecular analysis. In-depth characterization of our TucaR models to determine the differential gene expression and signatures is ongoing to gain additional mechanistic insights. Conclusions: Our findings suggest that whilst complete blockade of the HER layer using N is evaded by acquisition of HER and PIK3CA mutations, resistance to the HER2 TKI T is associated with EGFR amplification, a finding that underscores the HER signaling pathway redundancy and cross-talk between HER receptors to compensate for partial blockade of the pathway. Further, while resistance to L and N confers cross-resistance to T, resistance to T may be overcome using pan-HER TKIs or the combination of potent EGFR and HER2 inhibitors. Together, our findings hold crucial implications in light of the current treatment landscape of HER2+ BC, with a particular emphasis on the considerations to strategize the treatment sequence of currently available TKIs.

Citation Format: Jamunarani Veeraraghavan, Sreyashree Bose, Ragini Mistry, Pier Selenica, Sarmistha Nanda, Lanfang Qin, Andrea Gazzo, Yingjie Zhu, Michael A Mancini, Fabio Stossi, Britta Weigelt, Jorge S Reis-Filho, C. Kent Osborne, Mothaffar F Rimawi, Rachel Schiff. Acquired resistance to tucatinib is associated with EGFR amplification in HER2+ breast cancer (BC) models and can be overcome by a more complete blockade of HER receptor layer [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 PD8-06.

Abstract P4-01-01: Resistance to next generation tyrosine kinase inhibitors (TKIs) in HER2-positive breast cancer (BC): Role of HER and PIK3CA mutations and development of new treatment strategies and study models

Background: We recently reported that acquired resistance to the dual HER1/2 TKI lapatinib (Lap) was mediated by HER2 L755S, while resistance to the pan-HER TKI neratinib (Nrb) was associated with co-acquisition of an additional pathogenic PIK3CA mutation. Though the role of HER2 mutations is gaining attention in HER2-positive (+) BC, less is known about their role and clinical implications in next generation TKI resistance, particularly when co-occurring with PIK3CA mutations in HER2+ BC. Investigating optimal treatment combinations and the development of new clinically relevant 3D models are warranted.Materials and Methods: HER2+ BT474 parental (P) cells and models with acquired resistance to Lap (LapR) and Nrb (NrbR) (SABCS20-PD3-09) were used. Xenografts established in mice using P, LapR, and NrbR cells and 3D organoids derived from these xenografts using the Hans Clevers (HC, PMID 29224780) or Mark Burkard (MB, PMID 31175091) method were characterized by qRT-PCR and western blot. Drug efficacy was assessed by growth changes in 2D and 3D models using the IncuCyte system or by microscopy-based analysis. Results: We previously showed that Lap and Nrb resistance confers cross-resistance to tucatinib (Tuca) and trastuzumab, and that targeting the HER and downstream PI3K pathway, especially using small molecule agents that are key for treatment of CNS lesions, is effective only in combination with Nrb or poziotinib (Pozio), but not Tuca. Our new studies revealed that the MEK inhibitor (i) AZD6244 (selumetinib; Sel), mTORi everolimus (Eve), and selective estrogen receptor degrader fulvestrant (Ful) were not effective as single agents in inhibiting the growth of either LapR or NrbR models. Whilst the LapR cells were highly sensitive to the irreversible HER1/2 TKI afatinib (Afa) and the irreversible dual/pan-HER TKI pyrotinib (Pyro) as single agents, the NrbR models were cross-resistant to both TKIs, highlighting the importance of the co-occurring PIK3CA mutation in resistance. Interestingly, Afa and Pyro were only partly effective when combined with Eve+Ful, Sel+Eve, or Sel+the PIK3CAi alpelisib in inhibiting NrbR growth. Consistent with our previously reported findings for Nrb and Pozio, Pyro was highly effective with TDM1. As opposed to the P xenografts, the LapR and NrbR tumors grew in the presence of the respective TKI, confirming their resistant phenotype in vivo. P and resistant xenograft-derived organoids (XDOs) were successfully established using the HC but not MB method, but the HC-derived XDOs were subsequently grown in MB condition and used for molecular and functional studies. Preliminary characterization showed that the LapR tumors and XDOs harbor HER2 L755S, whereas the NrbR tumors and XDOs also have a concomitant PIK3CA E542V mutation, findings that are in line with our 2D results, suggesting that the xenografts and XDOs retain and recapitulate the molecular profile of their 2D or tumor counterparts. Early drug efficacy studies indicate that, akin to the 2D models, the LapR XDOs are highly sensitive to Nrb, whereas both the LapR and NrbR XDOs exhibit cross-resistance to Tuca but remain sensitive to Pozio.Conclusions: Our data suggest that the potency of next generation irreversible HER TKIs in HER2+ BC may be challenged by the emergence of mutations in HER2, together with other co-occurring downstream mutations, such as PIK3CA. Our findings present a clear roadmap for the development of combinatorial therapies that should be individualized for patients with HER2+ BC. Our newly developed XDO strategy may offer a new platform to confirm and prioritize optimal drug combinations to overcome this resistance and may facilitate the near future development of patient-derived organoids for precision medicine of resistant HER2+ BC.

Citation Format: Sreyashree Bose, Ragini Mistry, Chia Chia Liu, Sarmistha Nanda, Lanfang Qin, Pier Selenica, Andrea Gazzo, Yingjie Zhu, Michael A. Mancini, Fabio Stossi, Irmina Diala, Lisa D. Eli, Britta Weigelt, Jorge S. Reis-Filho, Mothaffar F. Rimawi, C. Kent Osborne, Rachel Schiff, Jamunarani Veeraraghavan. Resistance to next generation tyrosine kinase inhibitors (TKIs) in HER2-positive breast cancer (BC): Role of HER and PIK3CA mutations and development of new treatment strategies and study models [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 P4-01-01.

Abstract PD1-06: Apobec mutagenesis is a pervasive feature of poor prognosis breast cancer associating with ESR1 wild type, endocrine resistant disease

Background: Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) enzymes drive genomic instability in breast cancer (BC) characterized by specific single base substitution mutation signatures (COSMIC S2 and S13). Computational algorithms have the potential to derive signatures from targeted sequencing assays with relatively small genomic footprints. We sought to develop a computational approach to identify APOBEC mutagenesis in samples subjected to targeted sequencing and to characterize the genomic and clinical features of APOBEC-positive BC. Methods: We retrieved clinical and genomic data from 4,595 consecutive BCs that had been subjected to targeted sequencing using the FDA-approved MSK-IMPACT assay. Additional whole exome sequencing (WES) data were retrieved from publicly available datasets, including TCGA (primary BC, n=1019) and Bertucci et al. cohorts (metastatic BC, n=617). APOBEC-related mutational signatures were computed by using the SigMA algorithm (Gulhan, Nat Genet 2019) for MSK-IMPACT samples with at least 5 single nucleotide variants (SNV) (n=2,983). Survival analyses were performed by using Kaplan Meier method with log-rank test and Cox proportional-hazards models. Results: A significant positive correlation between APOBEC exposure calculated by SigMA vs other computational tools (e.g., DeconstructSig, SigProfiler, MutationalPatterns) was found (r=0.99). After down-sampling the WES data from the TCGA BC dataset to the genomic footprint of MSK-IMPACT, SigMA showed high concordance in determining APOBEC exposures (r=0.78). BCs with high APOBEC exposure were enriched for pathogenic somatic mutations affecting several genes, including PIK3CA, CDH1 and GATA3 (q&lt;0.05), as compared to tumors with no/low APOBEC. In the MSK-IMPACT cohort, median APOBEC mutational exposure was significantly higher in metastatic than primary samples (0.27 vs 0.19, p&lt;0.001) and was the dominant mutational signature in 26% of primary and 34% of metastatic BC. A significant enrichment for APOBEC exposure in the metastatic setting was observed in both hormone receptor-positive (HR+) (p&lt;0.001) and triple-negative (TN) (p&lt;0.001) subtypes. Invasive lobular BCs displayed a higher proportion of cases with high APOBEC mutagenesis when compared to invasive ductal BCs in both primary and metastatic setting (p&lt;0.001). Enrichment of APOBEC in metastatic samples could be due to signature acquisition or enrichment in poor prognosis tumors, to address this, we assessed the presence of APOBEC mutational exposure in patients with paired samples, which included 352 primary/metastasis (P/M) cases and 514 metastasis/metastasis (M/M) cases. Strikingly, no statistically significant increment of APOBEC exposure was found in the P/M nor in the M/M cohort (Wilcoxon signed-rank test p&gt;0.05), overall and in different BC subtypes. We also assessed the association between APOBEC and response to endocrine therapy (ET). Patients with metastatic HR+ BC and APOBEC as dominant signature had a statistically significant lower progression-free survival (PFS) on first-line single-agent ET (aromatase inhibitors or SERDs; median PFS of 9.7 versus 14.7 months, p&lt;0.001). This difference was more pronounced in patients treated with SERD with a median PFS of 4.7 and 14.3 months for APOBEC-dominant and APOBEC non-dominant tumors (p&lt;0.001), respectively. Conclusions: Evidence for APOBEC mutagenesis is present in &gt;30% of metastatic breast cancers and associated with resistance to ET. Unlike ESR1 mutations, which are acquired as a late event in metastatic HR+ BCs, APOBEC mutagenesis is commonly present in paired primary and metastatic BCs, indicating its relatively early onset and potential role in driving the poor prognosis of these cancers.

Citation Format: Antonio Marra, Andrea Gazzo, Pier Selenica, Xin Pei, Avantika Gupta, Fresia Pareja, Giuseppe Curigliano, Reuben Harris, Nadeem Riaz, Jorge S. Reis-Filho, Sarat Chandarlapaty. Apobec mutagenesis is a pervasive feature of poor prognosis breast cancer associating with ESR1 wild type, endocrine resistant disease [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 PD1-06.